Thursday, August 20, 2020

20th August,2020 Daily Global Regional Local Rice Digital Edition

Virus Hit Economy Reviving Fast Under PM Leadership: Economist

3 hours ago Thu 20th August 2020 | 03:06 PM

Description: Virus hit economy reviving fast under PM leadership: Economist

Description: Somalia values its ties with Pakistan: Khadija Al-Makhzumi

Description: APP - Associated Press Of Pakistan

Pakistan is already exporting world famous textile brands, rice and soccer footballs. We have also started manufacturing imports substitutes locally to save millions of Dollars.

How eating too much rice raises global mortality

By Chukwuma Muanya

20 August 2020 | 4:13 am

Description: https://guardian.ng/wp-content/uploads/2020/08/Rice-1062x598.jpg

*Fried rice CREDIT: Nigerian Food TV

*Low levels of arsenic in grains can increase risk of dying from heart disease, cancer, liver disease, study warns

Scientists have found that eating a lot of rice increases the risk of dying from heart disease due to the naturally occurring arsenic in the crop.

Rice is the most widely consumed staple food source for a large part of the world’s population. It has now been confirmed that rice can contribute to prolonged low-level arsenic exposure leading to thousands of avoidable premature deaths per year.

Arsenic is well known acute poison, but it can also contribute to health problems, including cancers and cardiovascular diseases, if consumed at even relatively low concentrations over an extended period of time.

Compared to other staple foods, rice tends to concentrate inorganic arsenic. Across the globe, over three billion people consume rice as their major staple and the inorganic arsenic in that some to give rise to over 50,000 avoidable premature deaths per year has estimated rice.

Meanwhile, a study found Britons in the top 25 per cent of rice consumption are at six per cent increased risk of dying from cardiovascular disease than the bottom quarter.

The chemical gathers naturally in the crop and has repeatedly been linked to illness, dietary-related cancers and liver disease. In serious cases, it can result in death.

A collaborating group of cross-Manchester researchers from The University of Manchester and The University of Salford have published new research exploring the relationship, in England and Wales, between the consumption of rice and cardiovascular diseases caused by arsenic exposure.

Their findings, published in the journal Science of the Total Environment, showed that once corrected for the major factors known to contribute to cardiovascular disease (for example obesity, smoking, age, lack of income, lack of education) there is a significant association between elevated cardiovascular mortality, recorded at a local authority level, and the consumption of inorganic arsenic bearing rice.

Prof. David Polya from The University of Manchester said: “The type of study undertaken, an ecological study, has many limitations, but is a relatively inexpensive way of determining if there is plausible link between increased consumption of inorganic arsenic bearing rice and increased risk of cardiovascular disease.

“The modelled increased risk is around six per cent (with a confidence interval for this figure of two per cent to 11 per cent). The increased risk modelled might also reflect in part a combination of the susceptibility, behaviours and treatment of those communities in England and Wales with relatively high rice diets.”

While more robust types of study are required to confirm the result, given many of the beneficial effects otherwise of eating rice due to its high fibre content, the research team suggest that rather than avoid eating rice, people could consume rice varieties, such as basmati, and different types like polished rice (rather whole grain rice) which are known to typically have lower inorganic arsenic contents. Other positive behaviours would be to eat a balanced variety of staples, not just predominately rice.

Arsenic occurs naturally in the soil and is increased in locations that have used arsenic-based herbicides or water laced with the toxin for irrigation purposes.

Rice is grown under flooded conditions and this draws arsenic out of the soil and into the water, ahead of eventual absorption by the plants.

Rice is particularly vulnerable because arsenic mimics other chemicals the plant absorbed via its root system, allowing the toxin to bypass the plant’s defences.

Rising temperatures caused by global warming could cause the amount of arsenic in rice to triple by the end of the century, a new study warns.

Scientists at the University of Washington in the US grew rice and replicated various temperatures to mimic growing conditions under various global warming projections.

Trials were done at the current normal temperature of 77°F (25°C) as well as 82°F (28°C), 87°F (30.5°C), and 91°F (33°C) to mimic potential climates by 2100. Plants grown in warmer conditions were found to have higher levels of arsenic throughout the plant – including the grains.

MEANWHILE, rice is about the commonest, cheapest and easiest staple food prepared not only by Nigerian households but in most parts of the world as well.

Indeed, statistics from the United Nations Food and Agricultural Organisation (FAO) indicate that half the world’s population eats rice every day, making the staple a major source of nutrition for billions of people.

But recent studies have associated the much-loved staple with rise in chronic and degenerative diseases such as cancer, diabetes, gastrointestinal problems, depression, developmental problems in children, heart disease and nervous system damage.

Most worrisome are lung and bladder cancers.While researchers have found traces of arsenic from old industrial pesticides on rice grains sold globally, a study reported in the journal PLoS ONE, showed rice has 10 times more inorganic arsenic than other foods and the European Food Standards Authority has reported that people who eat a lot of it are exposed to troubling concentrations.

According to the study, the levels of arsenic in rice vary by type, country of production and growing conditions.Generally, brown rice has higher levels because the arsenic is found in the outer coating or bran, which is removed in the milling process to produce white rice.

The study noted that in the short term, the regular consumption of rice could cause gastrointestinal problems, muscle cramping and lesions on the hands and feet.

The researchers observed that the risk of arsenic poisoning is greatest for people who eat rice several times a day, and for infants, whose first solid meals are often rice-based baby food.

In July 2014, the World Health Organisation (WHO) set worldwide guidelines for what it considers to be safe levels of arsenic in rice, suggesting a maximum of 200 microgrammes per kilogramme for white rice and 400 μg kg−1 for brown rice.

Also, scientists have identified rice as one of the staple diets that are genetically modified (GMOs). Others include corn, soy, cotton, papaya (pawpaw), tomatoes, rapeseed, dairy products, potatoes, and peas.

GMOs are accused of causing cancer, destroying the environment and storing up devastating health risks for children. Controversies surround genetically modified organisms on several levels, including ethics, environmental impact, food safety, product labeling, and role in meeting world food requirements, intellectual property and role in industrial agriculture.

An online journal, China Daily, reported potential serious public health and environment problems with genetically modified rice considering its tendency to cause allergic reactions with the concurrent possibility of gene transfers.

Scientists including the American Academy of Environmental Medicine (AAEM) have warned that GMOs pose a serious threat to health, and it is no accident that there can be a correlation between it and adverse health effects.

In fact, the AAEM has advised doctors to tell their patients to avoid GMOs as the introduction of GMOs into the current food supply has correlated with an alarming rise in chronic diseases and food allergies.

It has been shown that eating a diet of white bread and rice could increase the risk of depression in older women, but whole grain foods, roughage and vegetables could reduce it.

According to a study published in The American Journal of Clinical Nutrition, refined foods cause blood sugar levels to spike rapidly – prompting the body to pump out the hormone insulin, which helps break down the sugar. But this process can cause symptoms of depression. The findings could pave the way for depression being treated and prevented using nutrition.

In a study that included data from more than 70,000 post-menopausal women, scientists found a link between refined carbohydrate consumption and depression.

Britain’s leading expert on rice and contamination, Andy Meharg, a professor of plant and soil sciences at Queens University in Belfast, prevented his own children from eating some rice products because of the arsenic levels.

Meharg said the current method for cooking rice, essentially boiling it in a pan until it soaks up all the liquid, binds into place any arsenic contained in the rice and the cooking water.

By contrast, cooking it in a coffee percolator allows the steaming hot water to drip through the rice, washing away contaminants. There was a 57per cent reduction in arsenic with a ratio of 12 parts of water to one of rice and in some cases as much as 85per cent.

Meharg said: “Rice both white and brown are of good nutritional value. Brown rice especially contains E and B vitamins and minerals such as iron, calcium, magnesium, phosphorus, potassium, sodium and zinc.

“White rice is not that good. More so the processed one that is genetically modified has higher levels of toxins.

“Firstly when you cook rice, rinse properly when it is warm before full boiling, and drain out the fluid. This will get rid of some of the toxins.”

Study author Dr. James Gangwisch, of Columbia University, United States, said: “This suggests that dietary interventions could serve as treatments and preventive measures for depression.

“Further study is needed to examine the potential of this novel option for treatment and prevention, and to see if similar results are found in the broader population.”

White refined foods, known as ‘bad carbs’, have also been said to contribute to obesity, low energy levels and insomnia. Different from their healthier counterparts, white carbs start with flour that has been ground and refined by stripping off the outer layer where fibre is found.

This missing fibre could do wonders for the body, helping reduce the risk of type 2 diabetes, lower blood cholesterol and help people feel fuller for longer. Generally, the more refined the grain-based food, the lower the fibre count. By purchasing organic rice, limiting one’s rice intake and eating a balanced diet, however, experts suggest that health issues associated with long-term arsenic consumption can be avoided.

https://guardian.ng/features/health/how-eating-too-much-rice-raises-global-mortality/

Daybreak: Ross pitches Biden at DNC

08/19/20 12:23 PM By Brad Hooker

KEYWORDS CDFA SECRETARY KAREN ROSS DEMOCRATIC NATIONAL CONVENTION FRESNO STATE FRIANT-KERN CANAL JOE BIDEN JOINT POWERS AUTHORITY KAMALA HARRIS SB 559

Friant bill returns from the dead * Rice farmers look to Iraq

Focus on Japan

08.19.2020

By Chris Lyddon

Japan is a small-scale producer of grain, with a relatively large population, making it an important import customer. Rice remains the most important part of the national diet.

Japan’s grains production is too small to figure in the International Grains Council’s (IGC) forecasts. The IGC does put the country’s total grains imports in 2020-21 at 24.2 million tonnes, up from 23.9 million in 2019-20. The 2020-21 figure includes an unchanged 5.8 million tonnes of wheat and 16.5 million of maize, up from 16.3 million in 2019-20. Imports of barley are put at 1.2 million tonnes, the same level as in the previous year.

The country is also set to import 600,000 tonnes of sorghum in 2020-21, up from 500,000 the year before, and 45,000 tonnes of oats, up from 40,000. The IGC forecasts Japanese imports of rye in 2020-21 at 22,000 tonnes, up from 15,000 the previous year.

The IGC forecasts Japanese rice production at an unchanged 7.4 million tonnes in 2021, with imports at 700,000 and exports at 100,000 tonnes, both figures also unchanged. Imports of rapeseed in 2020-21 are forecast at 2.3 million tonnes, again the same as in the previous year, with soybean imports at 3.4 million, up from 3.3 million in 2018-19.

In an annual report on the sector dated March 19, the attaché put Japan’s total maize production at some 2,000 tonnes in 2020-21, on an area of less than 1,000 hectares.

“Roughly 4.5 million tonnes of whole crop silage corn is produced on 95,000 hectares each year,” the attaché said.

The Foreign Agricultural Service in Tokyo expects maize consumption to remain stable in 2020-21 at 16 million tonnes, with 12.3 million used for food and feed and 3.7 million for seed and industrial purposes. The attaché expects maize imports at an unchanged 16 million tonnes.

“The United States is the primary supplier of corn to Japan, but imports from Brazil spiked during Japan’s winter months,” the report said. “A large, high-quality crop coupled with a weak Brazilian Real paved the way for a short-term increase of imports from Brazil between October 2019 and January 2020, expanding Brazil’s share of the Japanese corn market to over 70%.”

The attaché forecasts an 870,000-tonne wheat crop in 2020-21, well down on the previous year’s record 1.1 million, bolstered by favorable weather, despite an unchanged area.

“This stability is attributable to wheat’s popularity as a rotation crop or a second crop after rice and MAFF’s support payments,” the attaché said, referring to the Japanese farm ministry. “Similar to barley, to incentivize the conversion of table rice production to wheat production, MAFF provides support payments of 35,000 yen (approximately $335 USD) per 0.1 hectare based on the planted area of wheat in rice paddies.”

The report forecasts food, seed and industrial use of wheat at 5.65 million tonnes in 2020-21, unchanged from the previous year.

“Japan’s population has been decreasing at an average rate of 0.16% over the last eight years and people over 70 now account for more than 20% of the population,” the report said. “Consumers are eating more protein and fat and fewer carbohydrates, although to date most of the shift away from carbohydrates has been at the expense of rice.

“Despite these changes, Japanese wheat consumption had been relatively stable, in part due to increasing numbers of visitors to Japan, which has welcomed a surge of inbound visitors, steadily increasing each year from 8.4 million people in 2012 to 31.8 million in 2019, helping to stabilize wheat consumption.”

Source: US Department of Agriculture

However, industry sources believe that the Japanese wheat flour market has plateaued and consumption, driven by demographic changes, is now in decline, the attaché added.

The report explained the stable forecast by saying that “a projected recovery in inbound visitors will be nullified by Japan’s continued population decline and changes in dietary preferences.”

“Most food wheat is imported from the United States, Canada and Australia within the WTO quota and through the MAFF operated state-trading system,” the attaché said.

In addition to the WTO quota, Japan established quotas with reduced markups under the Comprehensive and Progressive Agreement for Trans-Pacific Partnership (CPTPP), the Japan-EU EPA (Economic Partnership Agreement), and the United States Japan Trade Agreement (USJTA).

“These quotas are not expected to influence total imports as demand is projected to be flat,” the attaché said. “However, industry sources are concerned about the wheat supply from Australia due to the ongoing drought and indicated they may have to seek alternative suppliers for semi-soft wheat.”

Japanese exports of wheat products, predominantly wheat flour, have been stable, the attaché said, putting the 2020-21 level at 280,000 tonnes.

According to information supplied to World Grain by Takanobu Urata of the 22 member Japan Flour Milling Association, the country had 74 millers in 2018, compared with 90 in 2013. They produced 4,834,000 tonnes of flour at a capacity usage rate of 73.6% in 2018, compared with 4,868,000 tonnes at 70.4% utilization in 2013. The share of the big four millers is 73.6%, while the big 13 have 90%.

Rice trends

The attaché forecasts a 600,000-tonne fall in rice consumption in 2020-21, to 8.25 million tonnes, “as the steady decline of table rice consumption in Japan continues.”

“According to MAFF, the decrease in table rice consumption has accelerated since MY 2016-17 and is declining at annual rate of 91,000 tonnes,” the report said. “The accelerated pace of decline is attributed to population decline, reduced carbohydrate intake, and a year-on-year increase of table rice prices since MY 2015-16.”

High table rice prices adversely effect rice consumption in the foodservice and processing industries as serving portions are decreased to maintain low prices, it said.

“While total rice consumption continues to decline, some consumption has shifted from rice cooked at home to ready-to-eat rice,” the report said.

It also noted that “production of frozen rice has also grown 80% over the last decade, reaching a total of 178,000 tonnes (product volumes) in 2019.”

Oilseeds output rises

In an annual report, dated April 1, on the oilseeds sector, the attaché forecast total soybean production in 2020-21 at 235,000 tonnes, compared to 212,000 the year before, while the rapeseed crop is seen at an unchanged 4,000 tonnes.

“Driven by the decline in soybean prices, Japanese farmers, particularly in Hokkaido, have a marginal preference for planting adzuki beans and other legume rotation crops, over soybeans,” the attaché said. “Soybeans are Japan’s most heavily consumed oilseed.

“Three large oil crushers (Nisshin Oillio, J-Oil Mills, Showa Sangyo) produce over 80% of Japan’s edible vegetable oil.”

Biotech and biofuels

Japan remains one of the world’s largest per-capita importers of food and feed produced using modern biotechnologies, the attaché said in a March 30 report.

“In 2019, Japan imported 16 million tonnes of corn, 3.2 million tonnes of soybeans, and 2.4 million tonnes of canola, products that are predominately genetically engineered,” the report noted.

Japan’s annual biofuel target of 500 million liters (crude oil equivalent) for the transport sector was reached on time in 2017 and continues unchanged this year, the attaché said in a report dated Nov. 6, 2019.

“Following a 2018 revision of environmental standards for bioethanol, Japan began importing ETBE made from US corn ethanol for the first time in July 2019, but its ethanol blend rate remains among the lowest of countries with a fuel ethanol program,” the report said.

https://www.world-grain.com/articles/14120-focus-on-japan

Iranian customs bans rice imports as of August Economy

August 19, 2020 - 14:19

TEHRAN - The Islamic Republic of Iran Customs Administration (IRICA) has banned any registration for imports of rice as of the beginning of the next Iranian calendar month of Shahrivar (August 22) until further notice.

According to Orounaqi, nearly 800,000 tons of rice was imported into the country and was cleared from various customs in the previous Iranian calendar year (ended on March 19).

The official noted that rice imports have decreased by about 20 percent in the current year, saying: “About 390,000 tons of rice has been cleared through customs, while some cargoes are still stored in customs.”

According to the Secretary of Iran Rice Association Jamil Alizadeh Shayeq, Iranian farmers managed to produce 2.6 million tons of rice during the past Iranian calendar year 1398.

The country’s rice production stood between 2.2 and 2.3 million tons in the preceding year 1397 (March 2018-March 2019) and the increase in the production consequently decreased the imports of the commodity.

Iran’s annual rice consumption stands at about three million tons. That means nearly 400,000 tons of the product is required to be imported into the country, according to Shayeq.

However, customs data show that nearly 700,000 tons of rice was imported into the country in the first quarter of the previous year (March 21-June 21, 2019).

More than 90 percent of Iran’s rice is produced in the northern provinces of Gilan and Mazandaran, and less than 10 percent of the commodity is produced in the provinces of Isfahan, Ilam, Kurdistan, Khouzestan and so on.

Based on official statistics, over 620,000 hectares of the country’s agricultural lands are under rice cultivation, of which 520,000 hectares are in Mazandaran, Gilan and Golestan provinces.

EF/MA

https://www.tehrantimes.com/news/451440/Iranian-customs-bans-rice-imports-as-of-August-22

Minister calls on farmers to plant rice

Filipe NaikasoSenior Multimedia Journalist Westfnaikaso@fbc.com.fj | @fnaikaso

AUGUST 20, 2020 4:40 PM

Description: https://www.fbcnews.com.fj/wp-content/uploads/2020/08/Rice-2.jpg

CANE FARMERS ARE BEING URGED TO PLANT RICE SINCE 83% OF LOCALLY CONSUMED RICE IS IMPORTED.

Cane farmers are being urged to plant rice since 83% of locally consumed rice is imported.

Speaking during the Rice Field Day in Nawaicoba, Nadi Agriculture Minister Dr Mahendra Reddy says on average Fiji spends $42.6m on rice imports.

“Fiji was 66% self-sufficient in rice now 17% so we have gone down substantially from 66% to 17%, we want to go back up. I want to go back to 80% or 90% and we can do it.”

Dr Reddy says cane farmers can greatly assist the rice industry in achieving self-sufficiency and at the same time earn extra cash.

He suggests small portions of cane land can be used to plant rice.

There are at least eight rice farms in Nawaicoba.

https://www.fbcnews.com.fj/news/minister-calls-on-farmers-to-plant-rice/

Southeast to Highlight Rice Variety Development, Furrow Irrigation at Virtual Missouri Rice Field Day

ome»Science, Technology, Engineering and Mathematics»Agriculture»Southeast to Highlight Rice Variety Development, Furrow Irrigation at Virtual Missouri Rice Field Day

ON AUGUST 19, 2020

The latest developments in rice variety development, weed management and furrow irrigation will be highlighted by Southeast Missouri State University and University of Missouri faculty at the Missouri Rice Research and Merchandising Council’s (MRC) annual Rice Field Day Aug. 20.

This year’s event will take place virtually due to the COVID-19 pandemic, and researchers have prepared a series of online presentations that focus on research being conducted across southeastern Missouri.

Rice Field Day, which will be hosted on missouririce.com, is a chance for the rice producers of Missouri and their colleagues in Arkansas, Mississippi, Louisiana and Texas to collaborate using science and technology to provide new rice varieties, said Dr. Michael Aide, Southeast soil scientist.

It is also a chance for rice producers to improve technologies that maintain an abundant supply of low-cost and high nutritious rice for American consumers and foreign markets, he said.

“Emerging technologies include real-time crop monitoring using unmanned aerial vehicles to rapidly detect plant stress, water management, weed management, soil fertility and market conditions,” Aide said. “Missouri rice is a $250 million investment in the most southern portion of Missouri which, in turn, supports our local schools, roads and other infrastructures.”

Topics to be addressed during the virtual field day are row rice and remote sensing, rice variety development and potential long grain lines at the first stage of multi-location field testing, furrow irrigated bed widths, nitrogen fertilization for furrow irrigated rice, and complete residual grass control in rice.

Aide will discuss the benefits and potential issues associated with furrow irrigated rice, or row rice, which is an increasing practice among producers of Missouri and Arkansas. There are several advantages to row rice including reduce water pumping and field preparation costs, reduced labor, and reduced energy usage, he said.

“Row rice shows great promise; many producers are very happy with it,” Aide said.

Southeast rice breeder Dr. Christian De Guzman will discuss rice variety development and the potential long grain lines at the first stage of multi-location field testing trials which are being conducted in the Missouri communities of Fisk, Morehouse, Campbell and Neelyville.

De Guzman’s presentation will also include information about rice breeding for abiotic stress tolerance — specifically heat, aerobic germination and seedling flood tolerance.

After extreme heat caused Missouri rice yields to decline several years ago, De Guzman began developing a heat-tolerant variety capable of producing significant yield that will be available soon. In all the lines tested, De Guzman said the effects of heat reduce yields, or spikelet fertility, by about 20%.

Anaerobic germination and seedling flood tolerance trials are being tested now in Southeast’s greenhouse, De Guzman said, in response to the problems breeders encounter when newly planted lines see too much rain right away.

Field trials will begin once researchers have collected enough data from these tests, he said.

Along with Aide and De Guzman in Southeast’s Department of Agriculture, Rice Field Day speakers will include Johanna Nelson, research specialist with the University of Missouri; Dr. Gene Stevens, agronomy extension professor with the University of Missouri Fisher Delta Research Center; Dr. David Reinbott, agriculture business program with the University of Missouri Extension, Southeast Region; and Dr. James Heiser, senior research associate with the University of Missouri Fisher Delta Research Center. Videos from the Aug. 20 event will be available at missouririce.com.

The Missouri Rice Council hosts the annual Missouri Rice Field Day with support from Southeast Missouri State University and the University of Missouri Fisher Delta Research Center. In 2021, organizers plan to resume Rice Field Day in a face-to-face format to showcase the latest technologies and get feedback from rice producers in person, Aide said.

https://news.semo.edu/southeast-to-highlight-rice-variety-development-furrow-irrigation-at-virtual-missouri-rice-field-day/

Need ordinance to ensure farmers get MSP

The way these ordinances have been pushed through in haste, bypassing full deliberations in Parliament, when we are battling the pandemic and the economic slowdown, is disquieting. Instead of nudging the states through a model draft or consultations, the Centre has taken the ordinance route on the subject of agriculture, thus eroding the federal system of the country.

SHARE ARTICLEPosted: Aug 20, 2020 06:39 AM (IST)

Fair play: Any person found purchasing agricultural produce at below the MSP should be made liable for criminal prosecution.

Bhupinder Singh Hooda

Former Haryana CM

The three ordinances promulgated by the Union government in June and touted as structural reforms for transforming the agricultural sector have triggered a maelstrom of protests by the farmers of Punjab, Haryana and other parts of the country. Myriad farmers’ organisations and unions have strongly opposed these ordinances, even though the purported aim of these reforms is to help the farmer get a more remunerative price for crops by unshackling the agricultural markets through barrier-free inter-state and intra-state agri-trade; by giving the farmers and the traders the freedom of choice in the sale and purchase of agricultural produce outside the market premises or mandis; and, by a more informed decision through the digital platform of e-markets and global markets.

The attractive package and media hype around these ordinances have failed to hide the insidious anti-farmer bias. The grim reality is that through these ordinances, the Union government has sought to facilitate the corporate sector — exporters, aggregators, processors, wholesalers, large retailers and suppliers in the value addition chain — all persons with deep pockets. A centralised ‘one nation, one market’ is sought to be created in the country, which will divest the farmer of a level playing field by eroding the safety net of MSP (minimum support price) and other checks and balances.

The common thread running through the Farmers’ (Empowerment and Protection) Agreement on Price Assurance and Farm Services Ordinance, and the Farmers’ Produce Trade and Commerce (Promotion and Facilitation) Ordinance is that these two seek to deregulate the agricultural markets in the country by diluting the provisions of the Agricultural Produce Marketing Committees Act (APMCA), removing inter-state barriers on the sale of crops as also the intra-state stipulation of sale of crops within the marketing yards or mandis designated under the APMCA. Both ordinances exempt agricultural transactions in the trade area outside the purview of the APMCA from market fee, cess or any charge levied under this Act or any other state law.

The dispute redressal mechanism under the two ordinances provides for a conciliation process, the local SDM being the first port of call to resolve the dispute and revisional/appellate jurisdiction vesting with the senior officers of the government. It has been envisioned to do away with the system of intermediaries called arhtiyas or commission agents. This will pave the way for withering away of marketing yards or mandis set up under APMCA, as in traditional mandis; market fee and cess would continue to be charged whereas all transactions in the trade area under these ordinances would be exempt from market fee or cess, thus creating a huge asymmetry between the two. The traditional mandi system has stood the test of time, and its crumbling is likely to hurt states like Punjab and Haryana more, as these have a sound mandi/procurement network. In 2006, Bihar did away with the APMCA. Once the traditional marketing yards or mandis were out of the picture, unscrupulous traders started fleecing farmers by procuring crops at rates much below the MSP, wrongly charging the market fee from farmers and pocketing the same. This is also manifest in the rice millers’ scam in Haryana, where according to media reports, wrong stocks of paddy were shown, fake invoices were generated by rice millers, keeping the leeway for making good the short stocks by sourcing an equivalent produce from Bihar and other states at rates much below the MSP.

The arhtiya-kisan relationship is symbiotic, the former financing the latter for farm operations, family functions and other emergent needs. The commission agent makes logistics arrangements to act as a bridge between the farmer and the procuring agencies. Dismantling this institution without a better alternative is problematic. The dispute redressal mechanism provided for under the ordinances does not inspire confidence as it is silent on recourse to the courts of law. The latter of the two ordinances is an enabling legislation for facilitating contract farming. Surprisingly, benchmarking for price discovery under this ordinance has been linked to the APMCA prices, whereas the contract farmers supply seed to seed companies at rates higher than the MSP. The case of Pepsico suing contract farmers of Gujarat for compensation for hefty sums should be kept in mind in this context.

The Essential Commodities (Amendment) Ordinance amends Section 3 of the Essential Commodities Act in order to do away with the stock limits on cereals, pulses, potato, onions, edible oilseeds and oils except in situations of war, natural calamity or extraordinary price rise. In India, we have been witnessing a regularly recurring phenomenon of prices of agricultural produce dipping at the time of arrival of crops in the marketing yard and then shooting up in the off-season. As cereals, pulses, potato and onions will be stocked by exporters, processors and suppliers in the value addition chain without proper regulation, their rates are likely to fluctuate, hurting the poor consumer the most as these are part of staple diet.

The way these ordinances have been pushed through in haste, bypassing full deliberations in Parliament, when we are battling the Covid-19 pandemic and the economic slowdown, is disquieting. Instead of nudging the states through a model draft or consultations, the Centre has taken the ordinance route on the subject of agriculture, thus eroding the federal system of the country. These ordinances will weaken the state finances already challenged due to GST. The government should remove anomalies in these ordinances and bring in a fourth ordinance guaranteeing the farmer that the crop would be procured not below the MSP, calculated on the C-2 formula (covering labour, operational, capital, storage, transport and other incidental charges) in the Swaminathan Commission recommendations. Any person found purchasing the agricultural produce at below the MSP should be made liable for criminal prosecution in the proposed fourth ordinance.

https://www.tribuneindia.com/news/comment/need-ordinance-to-ensure-farmers-get-msp-128637

USA Rice Delivers Expert Testimony to Dietary Committee

By Cameron Jacobs

WASHINGTON, DC -- Last week, USA Rice spokesperson and nutrition expert Dr. Julie Miller Jones testified on the recently released Dietary Guidelines Advisory Committee Scientific Report which will serve as the foundation for the 2020-2025 Dietary Guidelines for Americans (DGA).

Dr. Jones, distinguished scholar and professor emerita of foods and nutrition at St. Catherine University, spoke via video conference, and focused on three components of the report: the recommendations for grains (whole, enriched, and refined), the significance of fortification, and the importance of respecting cultural-based preferences in the guidelines.

Dr. Jones applauded the Committee's conclusion that whole grains are an integral part of a healthy diet. She noted that enriched grains provide important nutrients such as folic acid, and asked that the final DGA clarify the role of refined grains as a staple food for many cultures that provide some nutritional benefits.

Her testimony also focused on the role that rice, and rice products, play in increasing the consumption of certain under-consumed nutrients, and advocated that iron-fortified rice cereal can help children under two-years-old meet the new recommendation of consuming foods rich in iron and zinc during the second six months of life among breastfed infants.

Finally, Dr. Jones talked about the importance of respecting cultural-based preferences by reminding the Committee that rice provides nutritional benefits as a staple food for many cultures across the U.S. and the world that also is affordable and easily accessible.

"The DGA report recommendations are largely positive for rice, and having an expert like Dr. Julie Miller Jones testify "in-person" on behalf of the U.S. rice industry is powerful," said Michael Klein, USA Rice vice president of domestic promotion. "Dr. Jones is a well-respected voice within the scientific community and her support gives enormous credibility to the USA Rice recommendations."

Publication of the final version of the 2020-2025 Dietary Guidelines for Americans is expected later this year or in early 2021.

Rice farmers hope cash infusion spurs Iraqi imports

08/18/20 3:45 PM By Bill Tomson

KEYWORDS EXIM EXPORTS FOOD AID IRAQ RICE USDA

American rice farmers are counting on a recent $450 million loan from the U.S. Export-Import bank to Iraq to restart the country’s rice imports.

https://www.agri-pulse.com/articles/14295-rice-farmers-hope-cash-infusion-spurs-iraqi-imports

Punjab tightens noose around pesticide dealers

In the fresh orders to District Agriculture Officers of the state on Tuesday, Secretary Agriculture, Kahan Singh Pannu has stated that if after testing Basmati grains are found to contain the residues of nine pesticides banned recently, an inquiry will be ordered.

Written by Kanchan Vasdev | Chandigarh | Published: August 18, 2020 11:33:49 pm

Description: agri experts, Montek panel report, Jalandhar news, Punjab news, Indian express news

Prof Gian Singh, former Economics Professor at Punjabi University, Patiala, and an expert on farm issues, said that this committee was promoting Centre’s controversial farm ordinances. (Representational)

Months after Basmati grains from Punjab failed the Maximum Residual Limit (MRL) test for several pesticides, the government has now threatened the agro-chemical dealers of the state with strong action following an inquiry, if the produce is found in the residues in this Basmati season.

In the fresh orders to District Agriculture Officers of the state on Tuesday, Secretary Agriculture, Kahan Singh Pannu has stated that if after testing Basmati grains are found to contain the residues of nine pesticides banned recently, an inquiry will be ordered and if any pesticide dealer is found to have sold the banned pesticide to farmers, then action under the Insecticides Act, 1968 will be taken. The Act provides for cancellation of licence, and launching of prosecution against the errant dealer which entails a punishment of three years and a fine of Rs 75,000.

The orders also direct the AOs to not even allow stocking of the banned pesticides and sensitise farmers that the orders were in their favour so that their produce gets good price in the international market.

The latest orders come days after Chief Minister Amarinder Singh ordered the ban on Acephate, Triazophos, Thiamethoxam, Carbendazim, Tricyclazole, Buprofezin, Carbofuron, Propiconazole and Thiophinate Methyl.

Pannu said, “We want to make sure that Basmati does not get even the minimum residue of these banned pesticides and the produce gets a good price in the international market and the produce also finds favour with the European Union (EU) that had stopped importing Basmati from India owing to the residue of these pesticides. Now, we will go to the last man to find out who has sold these pesticides to farmers even though the PAU recommends safer pesticides.”

He said that the government had been making efforts that there were no residues of these chemicals but last year despite these efforts the residues were found in the samples of the produce. Punjab Government Food Safety Laboratory, Kharar indicated that out of 51 samples, nine samples of rice contained the residue of these chemicals above the MRL (Maximum Residue Limit) value.

Similarly, Punjab Biotechnology Incubator Agri and Food Testing Laboratory, Sahibzada Ajit Singh Nagar, Punjab; NABL accredited laboratory of government of Punjab, in its report submitted that seven number of samples were found to contain pesticide residue in rice above MRL value.

The EU, having 28 countries in the union, had started rejecting consignments of Indian Basmati a few years ago after bringing the MRL for all these agro-chemicals, from 0.03 mg to 0.01 mg per kg except Triazophos for which the MRL is 0.02 mg. This has cost the Basmati growers dear as India’s four lakh tonnes Basmati export to the EU earlier had come down to 1.85 lakh tonnes.

The Centre had made a certification of inspection from Export Inspection Council (EIC) mandatory for Basmati. Many samples had failed the test last year. This had led to a fall in price of Basmati from Rs 3,700 per quintal in 2018 to Rs 2,700 per quintal in 2019.

Punjab Rice Millers and Exporters Association had also reported that many samples got tested by them contained the residue value of these pesticides much above the MRL values in Basmati Rice. The Association requested for ban of these agrochemicals to save the heritage Basmati produce of Punjab, and to ensure hassle free export of rice to other countries. Following this, the government has taken strong steps.

https://indianexpress.com/article/cities/chandigarh/to-ensure-basmati-finds-takers-in-eu-punjab-tightens-noose-around-pesticide-dealers-6560327/

Basmati export picks up amid pandemic

Exporters have also received big orders for the coming months.

· Written by Anju Agnihotri Chaba | Jalandhar | Published: August 18, 2020 11:49:01 am

Description: Basmati export picks up amid pandemic

Fetches `34k cr in 2019-20 — highest in 3 years.

Not withstanding the Covid-19 pandemic, Basmati rice export from India, mainly Punjab and Haryana, has seen the highest export in the past three years, in the financial year of 2019-20. The country has earned Rs 34,000 crore from this cash crop.

April and May of 2020 have recorded export worth Rs 6,488 crore because export orders of March of the 2019-20 were extended to April and May due to the nationwide lockdown announced on March 23.

Exporters have also received big orders for the coming months.

According to data provided by the Punjab Rice Millers Export Association (PRMEA), the total export of Basmati in 2017-18 was 4 million tonnes (40 lakh tonnes) worth Rs 26,870 crore while in 2018-19 the total export was 4.41 million tonnes worth Rs 32,800 crore. This year 4.45 million tonnes Basmati was exported, fetching around Rs 34,000 crore — an increase of Rs 12,00 crore were witnessed.

“During the pandemic, essential food items, especially rice export, have registered good growth. Basmati export has almost touched Rs 34,000 crore for the 2019-20 financial year against Rs 32,800 crore in 2018-19,” said Ashok Sethi, a leading exporter of Basmati rice and director of PRMEA, adding that exporters had orders for over 10 lakh tonnes to be delivered in February and March, but due to lockdown, March orders were not completed and extended to April, while Ramadan brought in extra cheer with Middle East countries ordering more supplies.

“The lockdown had a big impact on shipments as container movement was halted but exporters managed to ship several consignments to break the impasse,” said a senior member of the exporters Association.

Exporters said that 60% of the Basmati export had taken place with three countries including Saudi Arabia, Iraq and Iran also got Indian Basmati through the indirect way in April and May months.

“The growth would have been even better as Iran being a major importer of Basmati rice, used to import around 14 lakh tonnes rice from India annually, but due to the US sanctions, export to Iran got hit,” said an exporter, adding that though indirectly Iran imported some amount of Indian Basmati via other Middle East countries.

India’s Basmati export is around 3.75 lakh tonnes monthly but in April and May month the export 8.67 lakh tonnes (4.33 lakh tonnes monthly) export was recorded against 7.85 lakh tonnes last year in these two months which is a growth of around 10%, said an exporter.

Exporters said that the Indian government should have a dialogue with the Iran government over Basmati rice export keeping the oil issue aside as under US pressure, India stopped buying oil from Iran which impacted the Basmati rice export to Iran since last one year.

“The Punjab Basmati rice industry has been in the forefront in exports since 1981, and now this premium food item is being exported to more than 100 countries. Punjab and neighboring Haryana have accounted for around 80 per cent of the total export,” said Sethi.

As Pusa Basmati 1121, which is among the high yield varieties of Basmati, covers major areas in Punjab and Haryana,as it gives 18 to 20 quintals yield per acre.

“1121 saw phenomenal growth and markets around the world, mainly in Arab countries, and has also made the route to European, American and Canadian markets,” said exporter and president of All India Rice Export Association, Nathi Ram Gupta.

Due to the rejection of some consignments of Indian Basmati by the European Union a couple of years ago, now exporters and Punjab agriculture department officials have become quite serious about keeping harmful pesticides away from this crop, which has a great demand worldwide.

“We are happy that pesticides including Tricyclazole and Buprofezin, which are widely used by farmers on the crop, are being banned in India very soon,” said Sethi, adding that the pandemic has given the industry some break to define new strategies and push hard for controlled use of harmful pesticides which will boost Basmati export further.

https://indianexpress.com/article/cities/chandigarh/basmati-export-picks-up-amid-pandemic-6559431/

Iranian customs bans rice imports as of August 22

As Mehr News Agency reported, IRICA Deputy Head Mehrdad Jamal Orounaqi told a local radio program that the plan for the seasonal ban on rice imports, which aims at supporting the domestic farmers, should have been implemented in the beginning of the current Iranian calendar month (July 22) but was postponed to the next month. According to Orounaqi, nearly 800,000 tons of rice was imported into the country and was cleared from various customs in the previous Iranian calendar year (ended on March 19). The official noted that rice imports have decreased by about 20 percent in the current year, saying: “About 390,000 tons of rice has been cleared through customs, while some cargoes are still stored in customs.” According to the Secretary of Iran Rice Association Jamil Alizadeh Shayeq, Iranian farmers managed to produce 2.6 million tons of rice during the past Iranian calendar year 1398. The country’s rice production stood between 2.2 and 2.3 million tons in the preceding year 1397 (March 2018-March 2019) and the increase in the production consequently decreased the imports of the commodity. Iran’s annual rice consumption stands at about three million tons. That means nearly 400,000 tons of the product is required to be imported into the country, according to Shayeq. However, customs data show that nearly 700,000 tons of rice was imported into the country in the first quarter of the previous year (March 21-June 21, 2019). More than 90 percent of Iran’s rice is produced in the northern provinces of Gilan and Mazandaran, and less than 10 percent of the commodity is produced in the provinces of Isfahan, Ilam, Kurdistan, Khouzestan and so on. Based on official statistics, over 620,000 hectares of the country’s agricultural lands are under rice cultivation, of which 520,000 hectares are in Mazandaran, Gilan and Golestan provinces.

Author Name: https://www.tehrantimes.com/news/451440/Iranian-customs-bans-rice-imports-as-of-August-22

Early rice production in China expands 3.9 percent

The National Bureau of Statistics (NBS) said on Wednesday that the early rice production in China saw an expansion of 3.9 percent in 2020 following seven years in a row of declines. The production came in at 27.29 million tons, rising 1.03 million tons compared to 2019. The stable rise in the early rice output was mostly over an expansion in the cultivation area, even though strong floods in parts of southern China resulted in a decline in per unit area yield, according to Li Suoqiang, an NBS official. A bumper summer harvest along with a rise in early rice output gave a solid foundation for stable grain output of the year, the official said.

https://menafn.com/1100660555/Early-rice-production-in-China-expands-39-percent

Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing

Arnaud Comlan Gouda,
Marie Noelle Ndjiondjop,
Gustave L. Djedatin,
Marilyn L. Warburton,
Alphonse Goungoulou,
Sèdjro Bienvenu Kpeki,
Amidou N’Diaye &
Kassa Semagn

Scientific Reports volume 10, Article number: 13995 (2020) Cite this article

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Abstract

To minimize the cost of sample preparation and genotyping, most genebank genomics studies in self-pollinating species are conducted on a single individual to represent an accession, which may be heterogeneous with larger than expected intra-accession genetic variation. Here, we compared various population genetics parameters among six DNA (leaf) sampling methods on 90 accessions representing a wild species (O. barthii), cultivated and landraces (O. glaberrima, O. sativa), and improved varieties derived through interspecific hybridizations. A total of 1,527 DNA samples were genotyped with 46,818 polymorphic single nucleotide polymorphisms (SNPs) using DArTseq. Various statistical analyses were performed on eleven datasets corresponding to 5 plants per accession individually and in a bulk (two sets), 10 plants individually and in a bulk (two sets), all 15 plants individually (one set), and a randomly sampled individual repeated six times (six sets). Overall, we arrived at broadly similar conclusions across 11 datasets in terms of SNP polymorphism, heterozygosity/heterogeneity, diversity indices, concordance among genetic dissimilarity matrices, population structure, and genetic differentiation; there were, however, a few discrepancies between some pairs of datasets. Detailed results of each sampling method, the concordance in their outputs, and the technical and cost implications of each method were discussed.

Introduction

The levels and distributions of intra-accession (within-accession) genetic diversity in genebank collections provide invaluable information for diverse purposes, including (a) deciding the number of seeds (plants) per panicle (ear) and the number of panicles per accession (or variety) that should be sampled and conserved to capture given attributes; and (b) serving as baseline data for germplasm management and distribution as well as monitoring genetic variation and integrity during conservation and regeneration1^,2^,3^,4. Using limited numbers of accessions and/or agro-morphological traits and markers in different species, previous studies assessed intra-accession genetic diversity using morphological and isozymes5, amplified fragment length polymorphisms (AFLP)3^,4^,6, random amplified polymorphic DNA (RAPD)7, inter simple sequence repeat (ISSR)8^,9, and simple sequence repeats (SSR) markers10. RAPD, AFLP, and ISSR markers are currently becoming obsolete for germplasm characterization for multiple reasons, including dominant inheritance, low reproducibility, low throughput for genotyping thousands of collections conserved at most genebanks, low marker density (genome coverage), poor resolution associated with the size-based fragment analysis system, and difficulty in merging multiple datasets generated by different collaborators or labs11. SSR markers are codominant and more reproducible, with better genome coverage than AFLP, RAPD and ISSRs; however, they are not well suited for large-sale characterization of genebank collections, primarily due to lower throughput, high genotyping cost, and difficulty in merging genotypic data generated by multiple collaborators or labs due to their ability in detecting multiple alleles, stuttering, and addition or omission of a nucleotide during polymerase chain reaction (± A) that causes ambiguity in automated fragment analysis systems using capillary DNA sequencers12^,13^,14.

The availability of low-cost next-generation sequencing (NGS) technologies that generate high-density genome-wide SNPs is providing genetic resource scientists tremendous opportunities to enhance the quality, efficiency, and cost-effectiveness of genebank operations15^,16. These include germplasm curation17; generation of high-density reference genotypic data18 and molecular passport data19; gene discovery using genomewide association studies and selective sweep analysis18^,19^,20^,21^,22; understanding the genetic profiles of the entire collection19^,23; identifying redundant collections and creating subsets of genetically unique accessions for genetic and breeding studies19^,24^,25; and correcting mislabeled, taxonomically misclassified and/or misidentified collections26^,27. Using GBS, for example, nearly 33% of the 22,626 barley accessions at the Leibniz Institute of Plant Genetics and Crop Plant Research’s (Gatersleben, Germany)19 and 50% of the 1,143 accessions of a wild relative of wheat (Aegilops tauschii)17 were found to be potential duplicates.

Recently, our team at the AfricaRice center implemented a pilot study to characterize 4,115 rice accessions representing Oryza barthii A. Chev., O. glaberrima Steud. (African rice) and O. sativa L. (Asian rice) using DArTseq technology28. The DArTseq-based SNPs were highly useful for a wide range of purposes, including (1) understanding the genetic diversity, population structure, and genetic differentiation among African rice (Oryza glaberrima Steud.) collections, and developing core and minicore sets25; (2) developing species- and subspecies-diagnostic SNP markers to minimize misclassification, misidentification and mislabeling errors during germplasm acquisition and routine genebank operations26; (3) identifying candidate genes using selective sweep analysis21; and (4) comparing the extent of genetic variation and relatedness among various landraces and improved intraspecific and interspecific rice varieties developed by AfricaRice breeders with those developed by other institutions29. Based on the pilot study, we aim to genotype the entire rice collection conserved at AfricaRice using DArTseq and use the data to improve our germplasm curation. We will create subsets of the most genetically diverse accessions for further field evaluation, gene discovery, trait donor selection, and pre-breeding, which will ultimately promote the use of the collections in rice improvement. To reduce genotyping costs per accession, most molecular characterization studies in self-pollinating species are conducted by randomly sampling a single plant to represent an accession. This has been the case in our previous studies and other studies in rice25^,30^,31, barley19, and wild relatives of wheat17. Single plant samples have provided invaluable data for assessing inter-accession genetic diversity, relatedness and population structure in self-pollinating species, but are not suitable for measuring intra-accession diversity, which forms one of the bases of the current study. Furthermore, a single plant genotype data may be misleading when the extent of intra-accession diversity is greater than expected for different reasons, including a higher level of outcrossing32^,33, phenotypic heterogeneity, seed admixture, pollen contamination and off-types, which is another basis for this study. For example, sorghum landraces and wild rice showed an outcrossing rates that varied from 5 to 40%32 and from 4 to 25%33, respectively. As a result, there is concern among the genetic resources scientists that results based on a single individual genotype may not be comparable with multiple plants per accession, genotyped either individually or in bulks17.

Bulk segregant analysis34^,35 refers to the genotyping of bulks of individuals using either plant tissue bulking or DNA pooling36. In outcrossing species, the bulking method has been commonly used for quick and economic genotyping of inbred lines, populations, and open-pollinated varieties for different purposes37^,38^,39. In selfing species, however, bulk segregant analysis has been used primarily for mapping genes and quantitative trait loci (QTL) associated with target traits of importance in breeding34^,40^,41^,42^,43^,44. Some researchers have recommended bulking (pooling) method for characterizing multiple individuals per accession as the basis for evaluating genetic identity and diversity within accession in self-pollinating species15^,17, but this method also has its limitations, including knowing the minimum number of individuals required in the bulk15, and the sensitivity of the genotyping platforms in detecting rare alleles due to allele dilution problems38^,45. The alternative method of genotyping multiple plants per accession individually may be ideal for capturing rare alleles and estimating intra-accession genetic diversity but will increase the genotyping costs per accession multi-fold. The objectives of this study were, therefore, to: (1) assess intra-accession and inter-accession genetic diversity in 90 rice accessions, each represented by six leaf sampling methods (a randomly selected single plant, 5 plants, 10 plants and 15 plants, bulks of 5 plants and bulks of 10 plants); (2) compare the concordance among the different sampling methods with respect to species (O. barthii, O. glaberrima, and O. sativa) and genetic backgrounds of the germplasm (wild vs. landraces vs. improved); and (3) compare the outputs of the different datasets and assess if there were cases where one method provided obvious advantages over the others as well as the cost and technical implications of each method for large-scale germplasm curation and characterization in selfing species.

Methods

Plant materials and genotyping

This study was conducted using a total of 1,527 DNA samples from 90 accessions and varieties (all referred here as accessions) that represented a wild O. barthii (18), landraces of cultivated species of O. glaberrima (21), O. sativa subsp. indica (19), O. sativa subsp. japonica (18), and improved interspecific varieties/genotypes derived from crosses between O. glaberrima and O. sativa (14) (Supplementary Table S1). The 90 accessions were part of the rice germplasm used in our previous studies for the development of species- and subspecies-diagnostic SNP markers26 and for comparing diversity indices and selective sweeps21. Each accession was represented by 17 DNA samples (Fig. 1) comprised of 15 single plants, a bulk of 5 plants (plants numbered 1–5), and another bulk of 10 plants (plants numbered 6–15). The detailed procedures for genomic DNA extraction and SNP genotyping using DArTseq have been described in our previous study25. Each DNA sample was genotyped with 67,728 SNPs by the DArT Pty Ltd, Australia (https://www.diversityarrays.com). Three DNA samples had over 70% missing data points and were excluded from the dataset. The genotype data of the remaining 1,527 samples were imputed using Random Forest46, which is implemented as “randomForest” in the R package47.

Figure 1

Outline of the DNA (leaf) sampling methods used in each of the 90 accessions. Each accession was originally represented by 15 individuals (plant numbered from 1 to 15), a bulk of 5 plants (plant #1–5), and another bulk of 10 plants (plant #6–15).

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Statistical analyses

To evaluate the accuracy of the imputed SNPs in genetic diversity and population structure analyses, we first computed identity-by-state (IBS)-based genetic distance matrices from the 67,728 SNPs before and after imputation and compared the two distance matrices using the Mantel test48 implemented in NTSYSpc v2.149. Because genotyping errors may account for about 1% of observed differences26^,50^,51, it is often difficult to consider SNPs with minor allele frequency < 0.01 as polymorphic sites. For that reason, we filtered the imputed genotype data using a minor allele frequency (MAF) of 0.01 and maximum heterozygosity of 0.50, which formed dataset Set-1 that consisted of 15 individual samples and two bulks. In this study, we used heterozygosity for simplicity to refer both to heterozygosity in the individuals (single plants) and heterogeneity in the bulks. Eleven additional subsets of data were created from Set-1 corresponding to all 15 plants individually (Set-2), a bulk of 5 plants (Set 3), another bulk of 10 plants (Set-4), and randomly selected individuals from Set-2 repeated 6-times (Set-5 to Set-10), 5 plants individually (Set 11) and 10 plants individually (Set 12).

Most of the statistical analyses were performed as described in previous studies20^,25. Briefly, heterozygosity, IBS-based genetic distance matrices, and principal component analysis (PCA) were computed using TASSEL v.5.2.5852. The first two principal components (PCs) from the PCA were plotted for visual examination in XLSTAT 2012 (Addinsof, New York, USA; www.xlstat.com) using species/subspecies and predicted group memberships from phylogenetic and population structure analyses as categorical variables. The correlation between pairs of genetic distance matrices was computed using the Mantel test48 implemented in NTSYSpc v2.149. The HapMap format of each dataset was exported to PHYLIP interleaved format using TASSEL v.5.2.57, which was then converted to MEGA X53, STRUCTURE v.2.3.454 and ARLEQUIN v.3.5.2.255 formats using PGDSpider v.2.1.1.356. We used Molecular Evolutionary Genetics Analysis (MEGA) X to compute the pairwise maximum composite likelihood (MCL)-based genetic distance between DNA samples and accessions, for constructing phylogenetic trees using the neighbor-joining method, and for computing number of segregating sites (S), the proportion of polymorphic sites (Ps), Theta (θ), and nucleotide diversity (π). A site (SNP) was considered segregating if it had two or more nucleotides at that site; π refers to the average number of pairwise nucleotide differences between two sequences (samples), while θ was used as another estimator of diversity parameters based on the number of segregating sites in the samples. Phylo.io57 was used for comparing pairs of phylogenetic trees side-by-side as well as for computing Robinson-Foulds (RF) distance58 and number of subtree prune-and-regraft (SPR) distances59^,60 between pairs of phylogenetic trees. For such purposes, Newick files were generated for each dataset using MEGA X and used as inputs into Phylo.io.

Population structure was analyzed using the model-based method implemented in the software package STRUCTURE v.2.3.454 as described in the previous studies20^,25^,61. DNA samples and accessions with membership probabilities > 60% were assigned to the same clusters (group), while those with probabilities < 60% in any group were assigned to a “mixed” group. Analysis of molecular variance (AMOVA)62 and F_ST-based pairwise genetic distance matrices63 were computed among and within groups using ARLEQUIN v.3.5.2.255. Accessions were assigned into 3–5 groups (populations) based on their species/subspecies, ecologies or group membership predicted from the phylogenetic and population structure analyses.

Results

Intra-accession diversity

Of the 67,728 SNPs used for genotyping the 1,527 DNA samples (Supplementary Table S2), the proportion of missing data per SNP and sample before imputation varied from 0 to 64.1% for single plants and from 4.2 to 61.1% for bulks, with an overall average of 20.8%. In the initial genotyping data set, 69.1% of the markers (46,818 SNPs) were polymorphic across the 1,527 samples (Set-1), each with a minor allele frequency varying from 0.01 to 0.050 (Supplementary Table S3). Pearson correlation coefficients between minor allele frequency and heterozygosity estimated before and after imputation were high, at 0.983 and 0.998, respectively. The Mantel test performed on genetic distance matrices computed from all SNPs before and after imputation also revealed a very high positive correlation (r = 0.987). Hence, detailed results are presented only for the imputed version of the 46,818 polymorphic SNPs.

We assessed intra-accession diversity from Set-2, Set-11, and Set-12 that consisted of genotypic data of 15, 5, and 10 individuals, respectively. The percentage of SNP polymorphism, allele frequencies, heterozygosity, θ, π, and genetic distance between pairs of individuals belonging to the same accession are used as indicators of intra-accession genetic diversity. The level of SNP polymorphism across the 90 accessions was highly similar across the different datasets (Fig. 2), which was 99.5–99.7% for single plants, 98.8–99.9% in the 5–15 individual plants, 98.9–99.2% in the bulks (Table 1, Supplementary Table S2). Observed heterozygosity per accession computed from 5, 10 and 15 DNA samples ranged from 0.5 to 25.7, from 0.2 to 12.3% and from 0.2 to 25.7%, respectively (Supplementary Table S1, Fig. S1). Only 11 accessions had observed heterozygosity exceeding 6% for at least one individual (three accessions in all Set-2, Set-11, and Set-12; four accessions in both Set-2 and Set-11; four accessions in both Set-2 and Set-12), which is the expected average outcrossing rate reported in cultivated rice30^,64. The average heterozygosity per accession estimated from all sets of 5, 10 and 15 individuals ranged from 0.5 to 5.6%, from 0.5 to 4.0% and from 0.5 to 3.8%, respectively (Supplementary Table S1).

Figure 2

Summary of the percentages of polymorphic SNPs used for statistical analyses of all accessions (N = 90), O. barthii (18), O. glaberrima (21), O. sativa subsp. indica (19), O. sativa subsp. japonica (18), improved interspecific genotypes (14), lowland O. sativa (30), and upland O. sativa (21). See Supplementary Table S1 for germplasm summary and Table S2 for details on the number of polymorphic SNPs for all datasets.

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Table 1 Summary of polymorphic SNPs selected for statistical analyses of 90 accessions in all datasets.

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As summarized in Fig. 3 and Supplementary Table S4, θ and π computed within every accession ranged from 0.017 to 0.205 based on 5 plants per accession; from 0.019 to 0.149 based on 10 plants, and 0.019–0.140 based on 15 plants, which is an indication of a relatively low intra-accession diversity and more homogenous seed lot within most accessions. Values for θ and π estimated from Set-2, Set-11 and Set-12 within 90 accessions were highly correlated (0.967 ≤ r ≤ 0.996) and very low, with 81 of the 90 accessions showing < 0.06 θ and π values (Supplementary Fig. S2, Supplementary Table S4). However, nine O. sativa accessions adapted to the lowland (WAB0009756, WAB0023634, and WAB0032222) and upland (WAB0007857, WAB0010251, WAB0013330, WAB0021280, WAB0029923, WABTMP106) ecologies had θ and/or π values ranging from 0.061 to 0.205 in at least one of the three datasets, which may be due to broader intra-accession diversity or to errors that might have occurred during genotyping and/or sample preparation (e.g., seed mix up during planting, labeling error, contamination during leaf sampling or DNA extraction). To determine the cause of such unexpectedly large intra-accession diversity within these accessions, we compared pairwise IBS-based genetic distance for the 15 individuals in Set-2. Figure 4 and Supplementary Table S1 summarizes the minimum, maximum, and average genetic distance between pairs of individuals within each accession. Pairs of individuals belonging to the same accession differed between 1.6 and 41.2% of the scored alleles, of which 48 accessions differed by ≤ 6% of the alleles of the 46,818 SNPs. The remaining 42 accessions showed at least a pair of individuals that differed by > 6% of the scored alleles, which is due to either greater intra-accession diversity or due to the presence of outliers. Figure 5 and Supplementary Fig. S3 demonstrates intra-accession diversity of some accessions with and without potential outliers.

Figure 3

Summary of nucleotide diversity (π) computed as measures of intra-accession genetic diversity in O. barthii (18), O. glaberrima (21), lowland O. sativa (30) and upland O. sativa (21). Each accession was represented by 15 single plant DNA samples genotyped with 48,818 SNPs. See Supplementary Table S1 for germplasm summary and Table S4 for molecular diversity indices of each accession.

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Figure 4

Comparisons of minimum, maximum, and average genetic distance values computed between pairs of 15 individuals sampled per accession in Set-2, each genotyped with 48,818 SNPs. See Supplementary Table S8 for details.

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Figure 5

A plot of identity-by-state-based genetic distance values computed within 4 accessions, each represented by 15 single plant DNA samples genotyped with 48,818 SNPs. Genetic distances between pairs of individuals within WAB0029281 and WAB0029923 were within the expected range for self-pollinated species, while WAB0023634 and WAB0021280 have outlier individuals. See Supplementary Figure S3 for 10 more accessions that had larger than expected intra-accession diversity.

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Figure 6 shows a neighbor-joining phylogenetic tree and a principal component analysis plot of the 1,347 individuals in Set-2. In the phylogenetic tree, all individuals from 61 of the 90 accessions (67.8%) tend to be more similar to each other and clustered together as expected, while 25 accessions (27.8%) had 1–4 individuals that clustered with other accessions belonging to either the same or a different species/subspecies. Overall, 47 of the 1,347 individuals (3.5%) from 25 accessions were suspected outliers, which included O. barthii (2), O. glaberrima (12), O. sativa (29); the latter includes indica (2), japonica (15) and interspecific genotypes (12). The 15 individuals from each of 4 other accessions were divided into two distinct but genetically similar sub-clusters.

Figure 6

(a) Neighbor-joining tree constructed using Molecular Evolutionary Genetics Analysis (MEGA) X (https://www.megasoftware.net/), and (b) plots of PC1 and PC2 from principal component analyses of 1,347 single plant DNA samples in Set-2 based on 46,818 SNPs. In both figures, samples belonging to the same group have the same font color: O. glaberrima (red), O. barthii (blue), O. sativa adapted to the upland ecology (pink) and lowland ecology (black). See Supplementary Table S1 for group membership and Supplementary Table S8 for genetic distance matrices.

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We observed nine accessions (WAB0023634, WAB0029281, WAB0032222, WAB0010251, WAB0013330, WAB0018251, WAB0021280, WAB0029923, and WABTMP106) that differed by at least 5% of the scored alleles based on π, θ and IBS-based genetic distance between pairs of individuals from within the accession; all these accessions except WAB0029281 each had 1–3 samples that did not cluster together with the other individuals originating from the same accession in the phylogenetic tree. The first five principal components from PCA performed in Set-2 accounted for 70.6% of the variation observed across the 1,347 individuals (Supplementary Table S5). A plot of PC1 (51.3%) and PC2 (12.1%) revealed a similar grouping pattern as the neighbor-joining analysis (Fig. 6). However, all individual samples originating from O. barthii and O. glaberrima appeared nearly identical in the PCA plot because only 40% of the 46,818 SNPs were polymorphic within these two species as compared to 65% of the SNPs that were polymorphic among the O. sativa accessions.

Inter-accession diversity in multiple datasets

Using genotypic data of all accessions, we compared SNP polymorphisms, heterozygosity, θ, π, and genetic dissimilarity across the twelve datasets. Of the 48,818 SNPs that were polymorphic across the 1,527 single plants and bulked DNA samples in Set-1, 98.8 to 99.9% of the SNPs were polymorphic in the datasets represented by a randomly selected single plant, 5–15 single plants, and bulks of either 5 or 10 plants. Marker polymorphisms computed among accessions belonging to the four different species and eco-geographical groups demonstrated highly similar patterns of polymorphism irrespective of the DNA sampling methods and genetic background of the germplasm (Fig. 2). For example, the lowest (19.7–20.6%) marker polymorphism was observed within O. glaberrima, which was very consistent whether each accession was represented by a randomly selected individual, multiple individuals ranging from 5 to 15, or bulks. Pearson correlation coefficients between minor allele frequencies ranged from 0.993 to 1.00 (mean of 0.996) and heterozygosity estimated per SNP ranged from 0.902 to 1.00 (mean of 0.965) across all datasets (Supplementary Table S6). Observed heterozygosity per accession computed across all datasets ranged from 0.2 to 25.7% (Supplementary Table S1), with an overall average of 1.1%. Fourteen of the 90 accessions (15.6%) had an observed heterozygosity > 6.0% in one or more datasets (Supplementary Fig. S4), of which WAB0007857 and WAB0029923 were the most heterozygous accessions represented by 5 and 8 DNA samples with > 6.0% heterozygosity, respectively. Overall, approximately 84% of the 90 accessions had consistently < 6% heterozygosity across all datasets irrespective of the DNA sampling methods (Supplementary Fig. S4, Supplementary Table S1).

We examined the overall genetic diversity indices across all datasets by assigning accessions into groups (Fig. 7, Supplementary Table S7). When all 90 accessions were used for analyses, Ps, θ and π estimated across all datasets varied from 0.976 to 0.995, from 0.128 to 0.195 and from 0.257 to 0.268, respectively, and each parameter was highly similar across datasets except relatively smaller values for θ when genotyping was done on 5–15 individuals in Set-2, Set-11, and Set-12. When we repeated the analyses using groups, Ps and θ values computed from Set-3 to Set-10 as well as π values estimated from all datasets showed similar patterns irrespective of the genetic background. On the other hand, Ps was larger and Θ was smaller when computed from the 5–15 individuals in Set-2, Set-11, and Set-12 compared to all other datasets. Overall, observed nucleotide diversity within O. glaberrima across all datasets, as measured by π, accounted for 40.9–50.1%, 33.4–51.9% and 28.5–35.9% of those of the wild O. barthii, the two O. sativa subspecies and the improved interspecific genotypes, respectively (Fig. 7, Supplementary Table S7).

Figure 7

Summary of the proportion of polymorphic sites (Ps), θ and π across all datasets based on 48,818 SNPs. This figure was constructed using Microsoft Excel. See Supplementary Table S7 for details. Interspecific refers to improved genotypes derived from crosses between O. glaberrima and O. sativa.

Full size image

Genetic distance and population structure

The genetic distance matrices computed between pair of the 90 accessions across all datasets are summarized in Fig. 8 and Supplementary Fig. S5. Overall, the minimum, maximum, and average pairwise genetic distances of the 90 accessions were highly similar irrespective of the DNA sampling methods. For example, the mean genetic distance between all pairs of the 90 accessions computed from the 5–15 single plants per accession as well as the bulk of five and ten plants varied from 0.019 to 0.697, from 0.021 to 0.732, and from 0.013 to 0.725, respectively. Mantel tests revealed a very high positive correlation among distance matrices between pairs of accessions (Supplementary Table S8) computed from all datasets, which ranged from 0.925 to 0.998 in all accessions (Supplementary Fig. S6). To determine if the genetic background of the germplasm influenced the correlations, we compared genetic distance matrices between pairs of accessions belonging to (a) O. glaberrima, O. barthii, O. sativa spp. indica, O. sativa spp. japonica and interspecific improved genotypes, and (b) the three groups predicted based on cluster analyses, PCA and the model-based population structure analyses (see below). Mantel correlations between datasets varied from 0.270 to 0.991 in O. glaberrima, from 0.878 to 0.999 in O. barthii, from 0.786 to 0.999 in indica, from 0.741 to 0.995 in japonica, and from 0.906 to 0.999 in interspecific improved genotypes. The lowest Mantel correlation coefficients were, therefore, observed within O. glaberrima, which is also evident from relatively inconsistent frequency distributions of the genetic distance matrices. When groups predicted based on the multivariate methods were considered, Mantel correlation coefficients among the distance matrices computed from all datasets were higher in the O. glaberrima/O. barthii group (0.945 ≤ r ≤ 1.000), followed by O. sativa adapted to the lowland (0.878 ≤ r ≤ 0.999) and upland (0.749 ≤ r ≤ 0.990) ecologies (Supplementary Table S9).

Figure 8

Frequency distribution categories of pairwise genetic distance between pairs of accessions computed from 11 datasets, each with 46,818 SNPs. See Supplementary Table S8 for details.

Full size image

We examined the neighbor-joining tree constructed from the genetic distance matrix of all 1,527 samples in Set-1 to assess if the bulks of 5 and bulk of 10 plants consistently clustered with the 15 individual samples, which was observed among the 85 and 87 of the 90 accessions, respectively. About 96.4% of 1,527 single plants and bulked DNA samples originating from the same accession were clustered together as expected, while 3.5% of the individual and bulked samples from 26 accessions appeared to be potential outliers (Supplementary Fig. S7). DNA samples that were found to be potential outliers or mis-clustered are likely errors for different reasons, including admixture, contamination, and mislabeling during sampling, DNA extraction, and genotyping. We then assessed population structure among the 90 accessions to determine how they tended to cluster into groups across all datasets. Overall, the neighbor-joining tree constructed from the genetic distance matrix computed from Set-2 showed three major groups (Fig. 6). Accessions belonging to O. glaberrima and O. barthii formed the first group. In contrast to both O. glaberrima and O. barthii accessions that did not show any population structure by their ecology of origin, O. sativa accessions formed two separate groups that were consistent with their adaptation ecologies. All O. sativa accessions and interspecific genotypes that are adapted to the lowland (primarily indica) and the upland (primarily japonica) ecologies were assigned into the second and third groups, respectively. The phylogenetic trees constructed from the other datasets revealed similar grouping patterns and are summarized in Supplementary Fig. S7. Overall, accessions belonging to each species and/or subspecies consistently clustered together across all datasets irrespective of the leaf (DNA) sampling methods with two exceptions. In Set-2, Set-6, Set-7, Set-10, Set-11, and Set-12, an O. barthii accession (WAB0028942) clustered together with O. glaberrima accessions, while another O. barthii accession (WAB0038213) clustered with O. glaberrima in Set-2, Set-11, and Set-12. Robinson-Foulds (RF) and SPR distances computed as measures of differences (disagreements) between pairs of the neighbor-joining phylogenies constructed from all datasets varied from 0.15 to 0.76 (RF) and from 7 to 37 (SPR) (Supplementary Table S10). The highest agreement (with the lowest RF value of 0.15 and SPR value of 7) was observed between phylogenies constructed from the 15 individuals in Set-2 and 10 individuals in Set-12.

The model-based population structure analyses revealed three distinct groups, similar to the phylogenetic analysis, with an O. barthii/O. glaberrima group, and two O. sativa groups adapted to the lowland and upland ecologies (Supplementary Table S1). The first five principal components from PCA performed across all datasets accounted for 70.6 to 72.3% of the molecular variation (Supplementary Table S5). A plot of PC1 and PC2 from all datasets also showed three distinct groups similar to the model-based population structure and the neighbor-joining analyses (Fig. 6, Supplementary Fig. S8). The DNA samples that we considered as potential outliers in the phylogenetic trees were also evident in the PCA plots.

Genetic differentiation

The partitioning of the molecular variances of the various datasets into three, four, and five groups using AMOVA revealed that differences in groups accounted from 70.8 to 73.0%, from 69.7 to 71.9%, and from 66.8 to 68.4%, of the total variation, respectively. From 27.0 to 33.2% of the genetic variation resided within accessions irrespective of the dataset (sampling methods) and the number of groups used in the analyses (Supplementary Fig. S9, Table S11). F_ST estimated between pairs of the three, four and five groups computed from all datasets showed either great (0.150–0.250) or very great (> 0.250) genetic differentiation65, which varied from 0.154 to 0.819 between pairs of the 5 groups, from 0.261 to 0.827 between pairs of the four groups and from 0.453 to 0.785 between pairs of the three groups (Supplementary Table S12). The extent of molecular variance partitioned within and among groups as well as the extent of genetic differentiation between pairs of groups was consistently similar irrespective of the sampling methods and datasets

Discussion

Genetic diversity within and between accessions

In most genomics studies of self-pollinating species held in genebank collections, each accession is often represented by genotype data taken from a single randomly sampled individual19^,25^,66; this is usually done before or after one or more generations of seed purification using single seed descent under field or screen-house conditions67. Accessions conserved at a given genebank may have been originally collected as populations, which are often heterogeneous with a larger plant to plant variation. Most genebanks minimize such high levels of intra-accession variation by purifying seed lots to make them acceptable for genetic and pre-breeding studies68. In a recent example, our group at the AfricaRice genotyped 3,245 accessions belonging to O. barthii (115), O. sativa (772) and O. glaberrima (2,358) with 26,073 physically mapped SNPs21, with each accession represented by a single plant after seed purification25. There are, however, concerns regarding the development of purified seed lots and/or use of a single individual to represent a genebank collection, especially in landraces and wild accessions. First, seed purification of thousands of accessions conserved at a given genebank incurs additional financial resources, personnel, time, and space. Since each accession can be then split into two or more new seed lots after purification, these additional resources are needed not only for purification but also for managing/maintaining the purified seed lots68. Second, most genebanks do not have clear strategies to manage the purified germplasm sets (seed lots). Third, the genotypic data generated from a single individual per accession with or without seed purification may not capture the genetic variation available within a given collection. Finally, genotyping of bulks of multiple individuals per accession for genomic studies in selfing species has been suggested17 but is not yet commonly used in inbreeding species, although is it commonly used for similar purposes in cross-pollinating species37^,38^,61^,69^,70. To the best of our knowledge, therefore, this is the first extensive and systematic study to generate well-designed empirical data for assessing the level and distribution of intra- and inter-accession genetic diversity across different leaf/DNA sampling methods in three rice species and different genetic backgrounds using genome-wide SNPs.

Overall, the various types of univariate and multivariate analyses performed in the present study revealed relatively consistent patterns of marker polymorphisms, heterozygosity, intra-accession, and inter-accession diversity indices, genetic dissimilarity, population structure, and genetic differentiation irrespective of the sampling methods. Of the 1,527 DNA samples used in the present study, (1) 96.5% of the single plant DNA samples originating from the same accession clustered together as expected and only 3.5% of the individuals clustered with other accessions; (2) the two bulks of 5 and 10 plants within an accession consistently clustered with the 15 single plant samples in 95.6% of the 90 accessions; (3) θ and π computed as measures of genetic diversity within each accession were smaller than 0.06 in 81 of the 90 accessions, which suggests greater than expected intra-accession diversity within 10% of the accessions; (4) there were highly comparable patterns of polymorphisms (98.8–99.9%) among all datasets irrespective of the sampling methods (Supplementary Table S2); and (5) there were high to very high correlations among distance matrices computed from the different datasets generated for all 90 accessions, except for O. glaberrima (see below) when analyses were done on a priori known groups.

Although our genotypic data for the 5–15 individuals per accession did not provide strong justification for compensating the 4–14-fold increase in sample preparation and genotyping costs compared to using a single plant, we observed some level of disagreement between datasets within some accessions, which included O. glaberrima (1 accession), O. barthii (2 accessions), and O. sativa adapted to the lowland (6 accessions) and upland (7 accessions) ecologies. Pairwise differences among the multiple individuals of these accessions have been summarized in Figs. 3, 4 and 5 and Supplementary Figs. S1-S2, which demonstrated a relatively larger intra-accession genetic diversity due to a few individuals that are equivalent to inter-accession diversity; this has also been seen in other studies of self-pollinated genebank material5^,19. In a genomic study of barley genebank accessions using GBS, there were 32 accessions represented by 10 individuals each that revealed varying degrees of intra-accession diversity. About 34% of the 32 barley accessions showed very little intra-accession diversity, while 16% showed an intra-accession divergence that was equivalent to inter-accession diversity19. Using morphological and isozyme markers, intra-accessions genetic diversity has also been reported in another study of barley landraces conserved in genebanks for 10–72 years5. In most accessions, our results obtained from the two datasets corresponding to the 5 and 10 single plants were highly similar to those of the 15 individuals.

To capture the larger intra-accession diversity observed within some of the accessions, we recommend a single bulk of either 5 or 10 individuals instead of genotyping 5–15 plants individually per accession; this is evident from the very high positive correlations (0.871 ≤ r ≤ 0.995) between distance matrices computed from Set-2, Set-3, Set-4, Set-11 and Set-12 (Supplementary Table S9). The genotyping cost of a bulk (of 5 or 10 plants) would be the same as a single individual and 4–14-fold cheaper than genotyping 5–15 plants individually (see below for details), but bulks should help capture more intra-accession diversity than a single plant. We recommend, however, that the bulks be made by pooling approximately equal leaf tissue from every individual and only use up to 15 plants per bulk in order not to dilute rare alleles when more plants are bulked per accession38^,45. O. glaberrima was the only exception that showed lower correlations between distance matrices computed from the 5–15 individuals in Set-2, Set-11 and Set-12 vs. the bulks of 5 and 10 plants in Set-3 and Set-4 (0.477 ≤ r ≤ 0.690), which may either be due to the genetic background of this species and/or an ascertainment bias in the SNPs. Although ascertainment bias is minimal with genotyping by sequencing technologies, it may arise when marker data is not obtained from a random sample of the polymorphisms71, which could occur in the current study due to the use of the O. sativa spp. japonica (cv. Nipponbare) reference genome for aligning marker sequences. Some level of ascertainment bias may have also been introduced by the Random Forest46 imputation method used in this study, as has been reported in another study in wheat72.

Genetic relationship and population structure

Overall, the different DNA sampling methods revealed very consistent patterns of genetic relationships, population structures, and genetic differentiation irrespective of species, genetic background, and predicted group memberships (Fig. 6, Supplementary Fig. S7, Fig. S8, Table S11, Table S12). However, there were some exceptions, including 3.5% of the individual samples that clustered together with other accessions of either the same or a different species and two O. barthii accessions that showed an inconsistent pattern of clustering across datasets in the phylogenetic trees (Fig. 6, Supplementary Fig. S7). The mis-clustered samples are likely outliers due to errors during seed handling, sample preparation and/or genotyping17^,26^,37. Mislabeling, misclassification (misidentification), and mixing of samples are common problems in genebanks15 and have been reported in several species, including multiple Oryza species26^,73^,74, Dioscorea spp.75, Brassica spp 76. and Solanum spp.77. The percentage of mislabeled or misclassified samples reported in the literature is highly variable depending on sample size, the species, and the methods used for assessing the error rates, which varied from 3 to 21%26^,73^,74^,75^,76^,77. In one of our recent studies, we found that 3.1% of 3,134 of accessions from four rice species were either mislabeled or misclassified26, which can easily be checked using a subset of the diagnostic SNPs that we developed in the previous study. Misclassification and mislabeling not only restrict the effective use of the germplasm for various purposes but also provide an erroneous estimate of intra-accession and inter-accession genetic diversity; in such cases, the presence of larger intra-accession genetic diversity can be an indication of errors rather than genetics/biological.

Both Robinson-Foulds and SPR distances computed as measures of disagreements between a pair of phylogenies revealed that the phylogenetic tree constructed from the 15 individuals in Set-2 had the highest concordance with those in Set-12 (RF = 0.15, SPR = 7), followed by Set-11 (RF = 0.37, SPR = 21). All other values suggest a low to moderate concordance among pairs of phylogenies (Supplementary Table S10). It should be noted, however, that the concordance among pairs of phylogenies may be confounded by multiple factors, including topological features (the number of shared/non-shared subtrees) between a pair of trees, path length information (finding the nearest neighbor interchange to transform one tree into another), edge weights, and branch scores58^,78^,79^,80, all of which are of little relevance in characterizing genebank collections. In germplasm characterization, phylogenetic trees are primarily used to understand the broader pattern of evolutionary relationships; the level of genetic divergence; the definition of groups (populations or sub-populations); the selection of subsets of accessions that capture the genetic variation of a given group; and the identification of potential duplicates. In such cases, it is often difficult for genetic resource scientists to determine the true historical relationships between any groups of accessions other than using the bootstrapping method for assessing the accuracy or confidence in phylogenetic trees81. Although some studies advocate for bootstrapping, other studies believe that bootstrap values are a poor measure of repeatability82 depending on (1) the methods used for computing similarity/dissimilarity matrices; (2) the algorithm/methodology implemented in constructing the phylogenetic trees and for assessing disagreements between pairs of trees80, and (3) the lack of clear-cut threshold bootstrap values (which vary from 70 to 100%) that is used to judge whether a given node is good or not. Furthermore, displaying nodal support bootstrap values is difficult for large datasets83^,84, which are typical of large-scale germplasm curation and characterization studies.

Cost and technical feasibility

The availability of high throughput and relatively low-cost NGS technologies have provided genebank researchers a better opportunity to explore the genetic potential of their collections15. The current DNA extraction and genotyping cost of a single sample with DArTseq technology through a commercial vendor range from the US $22 to $30 per sample (the actual cost depends on sample size), which returns between 22,000 to 47,000 polymorphic SNPs in rice. A small sample size can underestimate genetic diversity parameters, and excessive sampling inflates costs2. Sampling 5–15 plants per accession instead of one provides more intra-accession information, but it does inflate sampling, DNA extraction, and genotyping cost 4–14-fold. In the present study, for example, genotyping of 5, 10, and 15 individuals incurred an additional cost per accession of US $88, $198, and $308, respectively. Currently, the AfricaRice genebank holds 21,300 accessions (https://www.genesys-pgr.org/), which would cost ~ US $2.4 and $7.1 million for genotyping 5 and 15 individuals per accession, respectively, compared to $468,600 for genotyping either a single individual or a bulk. Because we arrived at broadly similar conclusions regardless of sampling methods for most applications, we do not believe the additional information obtained by genotyping 5–15 individuals justify the multi-fold increase in cost. Furthermore, sampling of 5–15 individuals per accession across thousands of accessions raises another concern in that the technical feasibility of sampling, processing, and tracking so many individuals, followed by managing the high-density genotypic data, will be extremely challenging85^,86^,87. Recently, our team genotyped 4,115 rice accessions with ~ 32,000 SNPs using DArTseq, which generated 650-megabytes of data. If each accession had been represented by 5–15 individuals, the total number of samples would have been 21–62 thousands and approximately 3.2–9.8 gigabytes of data, and data analysis with existing statistical programs would have been extremely challenging. Genotyping of all 21,300 accessions with 5–15 individuals could lead to a daunting file size of 16.8 to 50.5-gigabytes.

Conclusions

Using high-density DArTseq genotype data generated with the Illumina NGS technology, we assessed six leaf (DNA) sampling methods to determine if an obvious advantage in genotyping multiple individuals per accessions existed to justify the multi-fold increase in cost and technical complexity of handling/managing large number of samples per accession as compared to genotyping either a randomly selected individual or a bulk. Overall, we arrived at broadly similar conclusions in terms of overall SNPs polymorphism and heterozygosity/heterogeneity; molecular diversity indices within and between accessions and groups; the genetic dissimilarity between accessions and groups; population structure; and genetic differentiation. Genotyping 5–15 individuals per accession provided better information for understanding not only the level of intra-accession genetic diversity but also for detecting outliers over genotyping a randomly selected individual; however, the additional information obtained was not enough to justify the 4–14-fold increase in cost and technical challenges in managing the large-sample size associated with genebank genomics studies. Both Robinson-Foulds and SPR distances computed as measures of disagreements between a pair of phylogenies revealed that the phylogenetic tree constructed from the 15 individuals in Set-2 had the highest concordance with those in Set-12 (10 individuals), followed by Set-11 (5 individuals), suggesting that at least 5–10 plants should be genotyped per accession individually or in a bulk. Furthermore, the identification of suspected outliers in 26 of the 90 accessions, which accounted for 3.5–10.0% of the single DNA samples in Set-2, lead us to recommend genotyping of 5–10 plants individually or in a bulk instead of a single individual per accession. Results from this study provide highly useful information to other researchers involved in genetic resources characterization using genebank genomics.

Data availability

All relevant data are within the paper and its Supporting Information Files.

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Acknowledgments

The present study was supported by a grant given to the AfricaRice genebank from the Global Diversity Crop Trust (GDCT) through CGIAR Systems Organization and by the Federal Ministry for Economic Cooperation and Development, Germany.

Author information

Affiliations

1. Africa Rice Center (AfricaRice), M’bé Research Station, 01 B.P. 2551, Bouaké, Côte d’Ivoire

Arnaud Comlan Gouda, Marie Noelle Ndjiondjop, Alphonse Goungoulou, Sèdjro Bienvenu Kpeki & Kassa Semagn

2. Université Nationale Des Sciences, Technologies, Ingénierie Et Mathématiques (UNSTIM), Abomey, Benin

Gustave L. Djedatin

3. Corn Host Plant Resistance Research Unit, United States Department of Agriculture-Agricultural Research Service, Mississippi State, USA

Marilyn L. Warburton

4. Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada

Amidou N’Diaye

Contributions

A.C.G. was responsible for sample preparation, preliminary data analyses and drafting the manuscript; S.B.K. and A.G. compiled passport data and assisted in sample preparation; M.N.N. and K.S. conceived, designed, secure funding, supervised the study, analyzed the data, and edited the paper; A.N. imputed the S.N.P. genotype data and contributed in analysis; M.L.W. and G.L.D. contributed to and edited the paper. All authors read and approved the paper.

Corresponding authors

Correspondence to Marie Noelle Ndjiondjop or Kassa Semagn.

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Gouda, A.C., Ndjiondjop, M.N., Djedatin, G.L. et al. Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing. Sci Rep 10, 13995 (2020). https://doi.org/10.1038/s41598-020-70842-0

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· Received03 February 2020

· Accepted27 July 2020

· Published19 August 2020

· DOIhttps://doi.org/10.1038/s41598-020-70842-0

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· DNA sequencing

· Natural variation in plants

· Next-generation sequencing

· Population genetics

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https://www.nature.com/articles/s41598-020-70842-0

Lagos trains, empowers 800 rice farmers

ON AUGUST 18, 202011:10 PMIN AGRIC Kindly Share This Story:FacebookTwitterEmailWhatsAppPinterestShare Governor Babajide Sanwo-Olu of Lagos State. By Olasunkanmi Akoni Lagos State Government has empowered no fewer than 800 rice farmers in the state with preferred high-yielding Farrow 44 seeds, brand new high-quality knapsack sprayers, rain boots and farm coats. The state Acting Commissioner for Agriculture, Ms. Abisola Olusanya, who gave out the empowerment tools on Tuesday, at the beginning of a three-day capacity building and training of the rice farmers on current production practices in the rice value chain, explained that the strategic intervention by the state government was informed by the need to boost the farming activities of rice farmers in the state. She stressed that the empowerment of the rice farmers was also geared towards ensuring the sustainable supply of paddy by the rice farmers, particularly bearing in mind the imminent completion of the state-owned Imota Rice Mill project. ALSO READ: Edo farmers to cultivate rice, maize, soya beans, others on 10,000 hectares “It is expected that if these farming techniques are adopted by the farmers in the next planting season, it will result in an increase in paddy production in the state to an expected average yield of four tonnes per hour,” Olusanya stated. She explained that the capacity building and training was expected to give all participating farmers the opportunity to gain hands-on experience in modern and improved rice farming techniques. Olusanya added: “Due to the fact that the state has limited agricultural cultivable land area and with the increasing rate of small and large scale Rice Mills across the nation, there is a strain on the state getting a constant supply of paddy to feed the mill when it becomes fully operational. “It is to this end that the ministry has embarked on the sensitisation of rice farmers to train and disseminate the current production practices and empowerment geared towards sustainable supply of paddy by Lagos rice farmers towards the Imota Rice Mill project.” She noted that the 32 metric tonne per hour rice mill at Imota was nearing completion, stressing that at full capacity, it would produce 115,200mt of milled rice which would require about 280,000mt of paddy per year, hence the need to stock enough paddy to ensure a smooth take-off of the mill. According to her, the training was necessary in order to bridge the rice demand deficit of the residents of the state and the Federal Government’s current ban on importation of rice. She stated that the training would take place in 20 locations cut across Ikorodu, Epe, Badagry, Gboyinbo, Idena, Obada, Ito Ikin, and Ise adding that they would be trained on global best practices and the most effective ways to grow their rice. Responding, the National Deputy President, Rice Farmers’ Association of Nigeria, Mr. Segun Atho, appreciated the state government for the training initiative. He noted that the training and capacity building would go a long way in providing the needed paddy for rice production for the nearly-completed Imota Rice Mill, while simultaneously improving the economic status of rice farmers in the state.

https://www.vanguardngr.com/2020/08/lagos-trains-empowers-800-rice-farmers/

Iranian customs bans rice imports as of August 22

August 19, 2020 - 14:19

According to Orounaqi, nearly 800,000 tons of rice was imported into the country and was cleared from various customs in the previous Iranian calendar year (ended on March 19).

According to the Secretary of Iran Rice Association Jamil Alizadeh Shayeq, Iranian farmers managed to produce 2.6 million tons of rice during the past Iranian calendar year 1398.

Iran’s annual rice consumption stands at about three million tons. That means nearly 400,000 tons of the product is required to be imported into the country, according to Shayeq.

However, customs data show that nearly 700,000 tons of rice was imported into the country in the first quarter of the previous year (March 21-June 21, 2019).

Based on official statistics, over 620,000 hectares of the country’s agricultural lands are under rice cultivation, of which 520,000 hectares are in Mazandaran, Gilan and Golestan provinces.

https://www.tehrantimes.com/news/451440/Iranian-customs-bans-rice-imports-as-of-August-22

Agri exports grow by 23% to ₹25,553 cr in Q1 of current fiscal

T V Jayan New Delhi | Updated on August 19, 2020 Published on August 19, 2020

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Exports of non-basmati rice, sugar and onion see substantial increase

A substantial increase in exports of non-basmati rice, sugar and onion has helped India push up exports of agricultural commodities during the first three months of the current fiscal by 23 per cent to ₹25,553 crore as against the export earning of ₹20,735 crore in the corresponding period in the last financial year, according to data released by the Agriculture Ministry.

While the export of non-basmati rice went up by 70 per cent to ₹5,800 crore in the first quarter of 2020-21, that of onions was up by 48 per cent to ₹1,197 crore. However, growth in basmati export remained flat at ₹8,591 crore while that of tea dipped by nearly 28 per cent to ₹1013 crore.

Exports of refined sugar, on the other hand, shot up by 80 per cent in FY21Q1 to ₹3,863 crore as compared to ₹2,144 crore in the corresponding quarter last year. Similarly, there is a decent 38 per cent increase in the export of raw sugar, raking in a sum of ₹1,616 crore, up from ₹1,168 crore in the same quarter in the last fiscal.

Soyameal exports fell to ₹751 crore from ₹880 crore in the same period last year, mustard and rapeseed meal registered a marginal 1 per cent growth to ₹432 crore.

Among other agri commodities that registered handsome increase are kabuli chana (94 per cent to ₹205 crore), Bengal gram (408 per cent to ₹140 crore) and tur (by 440 per cent to ₹81 crore). There was a slight 5 per cent decline in potato exports, which fetched ₹140 crore this first quarter of the current fiscal. Soyabean exports too dipped by 8 per cent to ₹84 crore, the data showed.

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https://www.thehindubusinessline.com/economy/agri-business/agri-exports-grow-by-23-per-cent-to-25553-cr-in-q1-of-current-fiscal/article32391731.ece#:~:text=A%20substantial%20increase%20in%20exports,in%20the%20last%20financial%20year%2C

Rice exporters urged to promote brand through safe production

Wednesday, 08/19/2020, 23:45

The golden time for Vietnam to promote its rice brand will come once the country is able to promptly expand production of ST25 rice in line with a safe process, according to rice exporters.

A large-scale rice field in the Mekong Delta (Source: www.sggp.org.vn)

Opportunities will be opened up for Vietnamese rice to further access the European market as the EU-Vietnam Free Trade Agreement (EVFTA) became effective at the beginning of August.

The rice variety ST25 won the first prize in the 2019 World’s Best Rice Contest and is favoured by domestic consumers.

Major rice exporters from the Mekong Delta are striving to meet demands of stringent markets.

The export price of Vietnamese five-percent broken rice currently hits its peak in the past 10 years, standing at US$473-477 per tonne, announced the Vietnam Food Association on August 18.

This is also the first time that the price of Vietnamese five-percent broken rice has been higher than that of Thailand.

Vietnam exported 3.9 million tonnes of rice in the first seven months of this year, earning US$1.9 billion, according to the Department of Agro Processing and Market Development under the Ministry of Agriculture and Rural Development.

The export volume fell 1.4% but the value increased by 10.9% over the same period last year.

https://english.vov.vn/economy/rice-exporters-urged-to-promote-brand-through-safe-production-417541.vov

China's early rice output rises 3.9 pct

Source: Xinhua| 2020-08-19 15:44:09|Editor: huaxia

BEIJING, Aug. 19 (Xinhua) -- China's early rice output reported a 3.9-percent increase in 2020 after seven consecutive years of decline, the National Bureau of Statistics (NBS) said Wednesday.

The output reached 27.29 million tonnes, up 1.03 million tonnes from 2019.

http://www.xinhuanet.com/english/2020-08/19/c_139302089.htm

China's 2020 early rice output rises on year despite flooding impact

08/19/2020 | 12:49am

China's early rice output in 2020 rose from last year due to a significant increase in planting acreage, the statistics bureau said on Wednesday, even as flooding and rains in the southern part of the country affected yields.

China produced 27.29 million tonnes of early rice in 2020, up 3.9% from the previous year, as various steps pushed farmers to grow more of the grain and favourable weather during spring planting season facilitated output, Li Suoqiang, head of agriculture division at the National Bureau of Statistics said.

Beijing had said in May it would draft a food security plan amid the COVID-19 pandemic, and the government has encouraged regions with good growing conditions to increase planting acreage of rice.

President Xi Jinping also urged the country to maintain a sense of crisis about food security and called food wastage "shameful," prompting local governments to launch campaigns and restaurants to raise penalties on buffet wastage.

China's early rice acreage in 2020 rose 6.8% to 4.75 million hectares, as local governments in major production regions issued grain subsidies to farmers and encouraged them to grow crops on farmland that used to lie fallow, as per a statistics bureau statement, citing Li.

However, early rice yield in 2020 fell as continuous heavy rains hit some regions in the south, including Anhui, Jiangxi, Hubei and Hunan provinces, where flooding destroyed all crops on some farmland, Li said.

Some regions in southern China were hit by heaviest rains in decades, which have also caused fresh outbreaks of animal disease, and taken away lives.

(Reporting by Hallie Gu and Tom Daly; Editing by Shri Navaratnam and Uttaresh.V)

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Flood waters reach the toes of China's famous giant Buddha statue

By Rob Picheta, CNN

Updated 0328 GMT (1128 HKT) August 20, 2020

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(CNN)Floods in southern China have caused water from the Yangtze River to rise and reach the toes of a famous towering statue of the Buddha -- reportedly for the first time in decades.

Leshan's Giant Buddha, a 233 foot (71 meters) sitting buddha carved out of a hillside around 1,200 years ago, is part of a UNESCO World Heritage Site in China's Sichuan province.

It usually sits comfortably above the waters of the Yangtze -- the world's third longest river -- and tourists gather at its base.

Waters also threatened the Buddha's toes in this photo from August 12.

But the area was closed on Monday as river water rose high enough to touch the buddha's toes, which has not happened in at least seven decades, according to state-run media outlet Xinhua.

Police and staff put sandbags at the platform under the historic statue's feet, trying to build a dam to protect it from the rushing water -- but by the next morning, the rising water had already covered the toes.

The area remains closed as thousands of citizens evacuate to safety, and as emergency personnel begin search and rescue operations. Officials on Chinese social media posted that the area may re-open later this week after safety assessments are carried out.

This file photo shows tourists at the feet of the giant Buddha, which is usually untroubled by river water.

Summer flooding is not uncommon in the region -- but this year has seen the worst floods in decades, destroying the homes and livelihoods of millions of people as the country struggles to revive an economy battered by the coronavirus pandemic.

The floods, which began in earnest in June, have impacted at least 55 million people -- more than the entire population of Canada.

Some 2.24 million residents have been displaced, with 141 people dead or missing, the Ministry of Emergency Management said in July.

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At least 443 rivers nationwide have been flooded, with 33 of them swelling to the highest levels ever recorded, the Ministry of Water Resources said in July.

On Wednesday, the Ministry of Water Resources raised the national emergency response alert for flood control to level 2 -- the second highest in a four-tier system.

In Sichuan, where Leshan's Buddha is located, authorities activated the highest level of flood control response on Tuesday for the first time ever. Sections of the river and basin in the area were hit by floods "rarely seen in a hundred years," according to Xinhua.

The majority of these flooding rivers are in the vast basin of the Yangtze River, which flows from west to east through the densely populated provinces of central China. The river is the longest and most important waterway in the country, irrigating large swathes of farmland and linking a string of inland industrial metropolises with the commercial hub of Shanghai on the eastern coast.

'Everything is gone.' Flooding in China ruins farmers and risks rising food prices

The flooding has not only washed away people's homes and communities -- but their farms and food supply as well. Last month, floods destroyed thousands of acres of farmland in Jiangxi province alone. The broader Yangtze River basin accounts for 70% of the country's rice production.

China's Ministry of Emergency Management pegs the direct economic cost of the disaster at $21 billion in destroyed farmland, roads and other property.

Beijing has so far been able to secure food supplies by importing vast amounts of produce from other countries, and by releasing tens of millions of tons from strategic reserves -- but analysts warn that such measures can only be useful for so long.

CNN's Nectar Gan and Shanshan Wang contributed to this report.

https://edition.cnn.com/2020/08/19/asia/leshan-giant-buddha-flooding-scli-intl/index.html

Chefs reveal the one piece of equipment they couldn’t live without

BY BRINKWIRE ON AUGUST 19, 2020

The Michelin-starred Social Eating House maestro has one very simple, traditional item on his must-have list.

He says: ‘A good knife is your best friend in the kitchen – I prefer my Florentine’s cook knife.

‘But for extra thin slicing, you need a Japanese mandolin.

‘Get wafer thin potatoes for dauphinoise or boulangère. It’s great for salads and makes light work of slicing.’

A Japanese mandolin, also known as a vegetable slicer, works by quickly cutting through veggies such as carrots and potatoes in the same way a grater does but only using just a single blade.

British-Iranian Chef and food writer Sabrina Ghayour has dozens of awards to her name and hosts a very popular supper club in London, specialising in Persian and Middle Eastern flavours.

For her, the most important item in her kitchen is her food processor.

She told FEMAIL: ‘I can’t live without my Cuisinart food processor. It makes chopping and mixing a doddle in the kitchen. I can live without everything else! This small one is perfect for more snug kitchens too.

Last year, the world-famous Dorchester hotel announced the appointment of their youngest ever head chef in the restaurant’s 88-year history, 26-year-old Tom Booton.

Tom, who’s worked in New York, Copenhagen and Iceland says his essential equipment is a simple – but high quality – pot, which will last a lifetime.

‘For me, it has to be a Le Creuset pot,’ he told FEMAIL.

‘From being great for slow cooking, roasting and even better for all the new budding sourdough bakers out there, it’s multi-purpose and stylish too.’

Known as a culinary classic and the Rolls Royce of pots and pans, the Le Creuset casserole dish has been loved by cooks across the world for nearly a century.

James Cochran, who made his name at the two Michelin-starred Ledbury, says the famous £1149 Thermomix is his go-to item.

James, who starred in BBC’s Great British Menu in 2018, told FEMAIL: ‘My favourite tool or piece of equipment would have to be the Thermomix. It’s an integral piece of machinery which can do so many things from making soups, to sauces, purées, ice cream bases – but then can be used a water bath and steamer too. It’s like your own personal sous chef!’

Owned by German company Vorwerk, the Thermomix is a 20-in-1 device that sous-vides, ferments, acts as rice cooker, and carameliser – and even cleans itself.

Alex Claridge, the chef owner of modern British fine dining establishment The Wilderness, warns that home cooks shouldn’t be fooled into buying too many on-trend items for the kitchen.

He says: ‘Don’t be fooled into buying lots of gadgets, Lakeland is not your friend.

‘Good cookery needs very little in terms of equipment; when I first started I had a few hobs and my knives.

‘Invest in a great stick blender (Bamix is my choice), and if you’re a baking enthusiast, a KitchenAid – which, if you look after it, will look after you for years to come.

‘Most importantly though, make sure you have great chefs’ knives – they are more important than any dehydrator, bread machine or waffle maker.’

Chef Tom Brown, who runs the Cornerstone in east London told Femail: ‘A good gadget to have in the kitchen which instantly upgrades dishes is a microplane – essentially a hand-held grater, which retails at around £10.

‘It’s perfect for finely zesting citrus for baking and dressings and mincing garlic, so you don’t have great big chunks. And even adding a ‘cheffy’ dusting of parmesan or truffle!’

Tom Aikens, one of the UK’s most acclaimed chefs, became the youngest British chef ever to be awarded two Michelin stars aged just 26.

He told FEMAIL: ‘I think, given so many of us – myself included – have been baking like crazy at the moment, it’ll have to be my KitchenAid! I’ve got a few, but my go-to is the Kitchen Aid 9 speed hand mixer.

‘The higher speeds mix heavy doughs and thick batters, and it also whips the perfect still egg whites too.

‘If you fancy making a bit of an investment though, I would recommend the stand mixer.

‘This machine can handle anything! It can be used for baking, breads, meringues, and also has an attachment for a juice extractor, vegetable sheet peeler and more. It’s so useful and multipurpose!’

British-Turkish chef Hus Vedat started his career working at his family’s butcher shop before training as a chef working in various top hotels.

He now runs Yosma, a Turkish tavern in Soho. He told FEMAIL: ‘Well, aside from your tongue – the most important tool in the kitchen, I would say, is my speed peeler.

‘It makes peeling carrots and potatoes take just minutes without accidentally removing too much and it’s a non-expensive gadget to help improve every kitchen.

‘I would recommend buying quite a number though – I always end up throwing mine away with the peelings or losing them!

‘I also love my falafel scoop – essential for me, though I imagine not for everyone…’

https://en.brinkwire.com/news/chefs-reveal-the-one-piece-of-equipment-they-couldnt-live-without/

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20th August,2020 Daily Global Regional Local Rice Digital Edition

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Exporters have also received big orders for the coming months.

Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing

Abstract

Introduction

Methods

Plant materials and genotyping

Statistical analyses

Results

Intra-accession diversity

Inter-accession diversity in multiple datasets

Genetic distance and population structure

Genetic differentiation

Discussion

Genetic diversity within and between accessions

Genetic relationship and population structure

Cost and technical feasibility

Conclusions

Data availability

References

Acknowledgments

Author information

Affiliations

Contributions

Corresponding authors

Ethics declarations

Competing interests

Additional information

Publisher's note

Supplementary information

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