Un-Edited Verison
Grain traits traced to 'dark matter' of rice
genome
Date:
December 18, 2019
Source:
Washington University in St. Louis
Summary:
Research
finds that a sizeable amount of domestication-related changes in rice reflects
selection on traits that are determined by a portion of the genome that does
not transcribe proteins.
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FULL STORY
Rice plant (stock image).
Domesticated rice has fatter seed
grains with higher starch content than its wild rice relatives -- the result of
many generations of preferential seed sorting and sowing. But even though rice
was the first crop to be fully sequenced, scientists have only documented a few
of the genetic changes that made rice into a staple food for more than half the
world's population.
New research now finds that a
sizeable amount of domestication-related changes in rice reflects selection on
traits that are determined by a portion of the genome that does not transcribe
proteins.
Xiaoming Zheng, a biologist with
the Institute of Crop Sciences at the Chinese Academy of Agricultural Sciences,
is the first author of newly published paper in Science Advances, "Genome-wide analyses reveal the role of non-coding
variation in complex traits during rice domestication." Qingwen Yang and
Jun Liu, also from the Institute of Crop Sciences in the Chinese Academy of
Agricultural Sciences, and Kenneth M. Olsen from Washington University in St.
Louis are also communicating authors of this paper.
Noncoding RNAs are suspected to
play very important roles in regulating growth and development, but they're
only beginning to be characterized.
"Despite almost 20 years of
genomics and genome-enabled studies of crop domestication, we still know
remarkably little about the genetic basis of most domestication traits in most
crop species," said Olsen, professor of biology in Arts & Sciences at
Washington University.
"Early studies tended to go
for 'low-hanging fruit' -- simple traits that were controlled by just one or
two genes with easily identifiable mutations," Olsen said. "Far more
difficult is figuring out the more subtle developmental changes that were
critical for a lot of the changes during crop domestication.
"This study offers a step in
that direction, by examining one regulatory mechanism that has been critical
for modulating domestication-associated changes in rice grain
development."
Diversity of traits
A large proportion of the DNA in
the chromosomes of many plants and animals comprises genes that do not encode
instructions for making proteins -- up to 98% of the genome for any given
species. But this genetic information is poorly understood. Some scientists
have called this stuff the 'dark matter' of the genome, or even dismissed it as
'junk DNA' -- but it appears to have played an outsized role in rice
development.
In this study, researchers found
that key changes that occurred during rice domestication more than 9,000 years
ago could be tied back to molecules called long-noncoding RNAs (lncRNAs), a
class of RNA molecules with a length of more than 200 nucleotides.
About 36 percent of the genetic
information recorded in the rice genome can be tracked back to noncoding
regions, but more than 50 percent of the diversity of traits important to
agriculture is linked to these same areas, the researchers found.
"For the first time, the
lncRNAs in noncoding region of cultivated rice and wild rice was deeply
annotated and described," Zheng said.
"Our transgenic experiments
and population genetic analysis convincingly demonstrate that selection on
lncRNAs contributed to changes in domesticated rice grain quality by altering
the expression of genes that function in starch synthesis and grain
pigmentation," she said.
Working with several hundred rice
samples and more than 260 Gbs of sequence, the researchers employed sensitive
detection techniques to quantify and robustly track lncRNA transcription in
rice. The new study validates some previously identified lncRNAs and also
provides new information on previously undescribed molecules.
This new study adds fuel to
speculation by some researchers that most adaptive differences between groups
of plants or animals are due to changes in gene regulation, and not protein
evolution.
"Based on our findings, we
propose that selection on lncRNAs could prove to be a broader mechanism by
which genome-wide patterns of gene expression can evolve in many species,"
Zheng said.
This rice study also opens eyes
and possibly new doors for producing new crops and grains through precision
breeding.
Story Source:
Materials provided by Washington University in St. Louis. Original written by Talia Ogliore. Note: Content may be edited for style and length.
Journal Reference:
1.
X.
M. Zheng, J. Chen, H. B. Pang, S. Liu, Q. Gao, J. R. Wang, W. H. Qiao, H. Wang,
J. Liu, K. M. Olsen, and Q. W. Yang. Genome-wide analyses reveal the role of
noncoding variation in complex traits during rice domestication. Science
Advances, 2019 DOI: 10.1126/sciadv.aax3619
Cite This Page:
Washington University in St. Louis. "Grain traits traced to
'dark matter' of rice genome." ScienceDaily. ScienceDaily, 18 December
2019. <www.sciencedaily.com/releases/2019/12/191218153533.htm>.
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FROM AROUND THE WEB
India can increase food output by growing sorghum, millets in rice
areas: Study
India can enhance its food production by planting crops such as
sorghum and millets
India can enhance its food
production, and improve its environmental footprint by reducing its reliance on
rice, and planting crops such as sorghum and millets, according to a study.
The researchers, including those
from the Indian School of Business in Hyderabad and the Indian Institute of
Public Health in Delhi, said the country has tripled its cereal production over
the past 50 years, with rice contributing almost half of this produce.
In their study, published in the
journal PNAS, they said that rice does not offer the nutritional benefits of
some other cereals, such as sorghum and millets, and added that the staple crop
is grown in areas that are not necessarily suited to rice production.
While the reliance on rice since
the Green Revolution succeeded in feeding a large population, the scientists
said, it also pushed out a lot of traditional cereals that are still consumed
in India but to a lesser extent.
They added that these traditional
cereals like sorghum and millets are more nutritious and less environmentally
damaging than rice.
"We've found that those
traditional cereals have a higher nutritional quality and also tend to use less
water, require less energy to be grown, and emit fewer greenhouse gases on a
per kilogram basis," said study co-author Kyle Davis from the University
of Delaware in the US.
Davis explained that rice is
flood irrigated and requires a lot of water to grow -- a burden in India which
is already experiencing widespread depletion of groundwater resources.
Additionally, the researchers
said, the standing water in rice fields contributed to bacteria undergoing
respiration without air, a process which causes them to emit methane -- a potent
greenhouse gas -- into the atmosphere.
This side effect is not present
in the other cereals which are not flood irrigated, so the scientists said
their cultivation does not produce any methane emissions.
"These traditional cereals
also tend to be less sensitive to variability in temperature and precipitation
so they're more resilient to climate variability," Davis said.
He added that there are also many
places where the yields of these cereals are comparable to, or higher than
rice.
"For all of those reasons,
we wanted to look at whether there were opportunities to replace some rice
production with some of these traditional cereals without reducing food supply
in the country," Davis said.
The current study also pinpoints
which districts in which Indian states could see the largest improvements from
the cultivation of millets.
"If the government had to
prioritise a few states, they could point to our results and say for example
'Ok, these are the places where our largest water savings are going to happen
so we should focus here," Davis explained.
According to the study, the next
step for the government would be to quantify the willingness of local
populations to increase the amount of these different cereals in their diets.
It noted that the government may
also need to make economic considerations to protect the livelihoods of
farmers, since asking a farmer to switch to a different crop might mean that
they have different fertilizer requirements or would have to buy more seed.
READ MORE
According to Davis, the
government subsidy programs in India for farmers would also have to be modified
to make sure that they accommodate the changes.
While the study only looked at
decreasing the rice area, and increasing some of the space allocated for other
cereals, he said, India could also look at regions producing cotton or
sugarcane -- water-intensive crops that don't contribute to nutrition -- and
replace them with sorghum and millets.
The study said all these
transitions could have positive environmental and nutritional benefits.
"You often see agriculture
presented as causing environmental problems, when in fact agriculture is the
solutions to many challenges. Our study shows there are opportunities to
realise a number of different benefits through more thoughtful agricultural
practices, and it shows that a single intervention can change multiple outcomes
for the better," Davis said.
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> News > State > Telangana Millets can
boost child growth by 50%: Study Hans News Service | 19 Dec 2019
1:14 AM IST HIGHLIGHTS In a latest study it was found that millet-based mid-day
meals can boost growth by 50% in just three months. Children rated the meals,
which were... Patancheru: In a latest study it was found that millet-based
mid-day meals can boost growth by 50% in just three months. Children rated the
meals, which were designed by scientists and chefs and included little millet
as a rice substitute, over 4.5 on 5 for taste. This Smart Food study,
'Acceptance and impact of millet based mid-day meal on nutritional status of
adolescent school going children in a peri-urban region of Karnataka state in
India,' published in the journal Nutrients, was undertaken by The Akshaya Patra
Foundation and the International Crops Research Institute for the Semi-Arid
Tropics (ICRISAT). ADVERTISEMENT "It is not good enough just to say we are
going to add millets to the meal," said Dr S Anitha, a nutritionist at
ICRISAT and the study's corresponding author. "The type of millet, its
variety, how it is cooked and the foods it is combined with are some of the key
elements that can make a difference in nutrition. For instance, the amount of
iron available in a meal can be doubled by selecting the right variety of
millet. This is the first known scientific study of millet based meals in a school
feeding program." ADVERTISEMENT The researchers gave the study group
children meals including idli, khichdi, upma and bisibella bath in which rice
was replaced by pearl millet (bajra), ragi (finger millet) or little millet
(kutki). The anthropometric measurements at the end of the feeding program were
compared with that of control group children who consumed fortified rice with
sambar. More On Millets Child growth ICRISAT Telangana
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NEWS
Border Closure: Oyo/Osun Customs seizes
2,540 bags of rice, clothes, others worth N142m
Published
20 hours ago
on
December 18, 2019
By
In spite of the Federal
Government’s partial closure of borders against smuggling, the Osun/Oyo Area
Command of the Nigerian Customs Service has been able to arrest and impound 25
vehicles used to convey 2,540 (50kg) bags of parboiled rice, 15 bags of sugar;
40 bales of second hand clothes and shoes, as well as, 500 pieces of tyres with
a Duty Paid Value of N142,896,113.00.
This disclosure was made at the Ibadan Command Headquarters on Wednesday by the Controller, Abdullahi Argungu while addressing journalists and conveying them round the seized items at its Ijokodo Barracks, Ibadan.
The Controller, who said that the border closure was indeed making positive impacts in the area of “security control, illegal immigration regulation, encouragement of our local farmers, as well as, encouragement of patronage of made in Nigeria goods and agricultural products”, excitedly disclosed that the Command projected annual revenue target of N30bn while it exceeded it by 59 per cent, ploughing in N34,686,875,967.80 as against the N21,954,286,381.10 recorded in 2018.
Though the Controller said that no government can stop smuggling completely, he boasted that his Command would continue to ensure ot is reduced to the barest minimum level.
He lamented that the recalcitrant smugglers were employing series of hazardous tactics in moving through bushes where seven vehicles were seized. “They are deadly because they create roads by themselves in the bushes and they usually move in the night. We get them tracked through intelligence reports,” he said.
This disclosure was made at the Ibadan Command Headquarters on Wednesday by the Controller, Abdullahi Argungu while addressing journalists and conveying them round the seized items at its Ijokodo Barracks, Ibadan.
The Controller, who said that the border closure was indeed making positive impacts in the area of “security control, illegal immigration regulation, encouragement of our local farmers, as well as, encouragement of patronage of made in Nigeria goods and agricultural products”, excitedly disclosed that the Command projected annual revenue target of N30bn while it exceeded it by 59 per cent, ploughing in N34,686,875,967.80 as against the N21,954,286,381.10 recorded in 2018.
Though the Controller said that no government can stop smuggling completely, he boasted that his Command would continue to ensure ot is reduced to the barest minimum level.
He lamented that the recalcitrant smugglers were employing series of hazardous tactics in moving through bushes where seven vehicles were seized. “They are deadly because they create roads by themselves in the bushes and they usually move in the night. We get them tracked through intelligence reports,” he said.
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NEWS
Protests rage in India against citizenship
law amid restrictions
Published
7 hours ago
on
December 19, 2019
By
Big rallies are expected across
India on Thursday as the tumultuous and angry reaction builds against a
citizenship law seen as discriminatory against the country’s 200 million
Muslims.
Indian Prime Minister Narendra
Modi’s move to drive the Citizenship Amendment Act (CAA) through parliament
last week has ignited nationwide protests that have often turned violent, with
six people killed and students attacked.
The law gives migrants fleeing
persecution from neighbouring Afghanistan, Pakistan and Bangladesh an easier
path to citizenship, except that Muslims – 14 percent of India’s population – are
excluded.
Critics say it is further proof
that Modi, emboldened by a resounding election victory this year, is moving
quickly to reshape India as a Hindu nation and weaken its secular foundations,
reports al-Jazeera.
India’s Supreme Court turned down a
pleaon Wednesday to halt implementation of the law but said it would hold
hearings next month on the sweeping measure.
More rallies amid prohibitory
orders
During the past week of unrest,
hundreds of people have been arrested, authorities have cut the internet in
some flashpoint areas and banned large gatherings in others.
Police have fired tear gas into
crowds and been accused of beating protesters, including women and students,
fuelling the anger.
Protest organisers have flagged
plans for major rallies on Thursday in major cities across India, including the
capital of New Delhi.
Police refused a march permit for
one of two major demonstrations planned in New Delhi, officials said.
Organisers said they planned to march anyway.
With more demonstrations likely,
authorities in the southern state of Karnataka have moved to ban large public
gatherings in at least three major cities, a police official said.
The restrictions will come into
force on Thursday morning, including in the state capital Bengaluru where offices
of dozens of multinational companies including Walmart Inc’s Flipkart, Uber,
Infosys and Wipro, are based.
Similar restrictions were also
imposed in Lucknow, capital of northern Uttar Pradesh state.
Ban on gatherings in capital
In New Delhi, authorities on
Wednesday also imposed a ban on gatherings of more than four people in some of
its Muslim-dominated districts.
Police fired shots in the air in a
Muslim-dominated part of the capital to repel thousands of demonstrators
throwing stones and glass bottles, demanding the law be withdrawn.
At a protest in front of New
Delhi’s Jamia Millia Islamia university, which was stormed by policeon Sunday
night, leaving 200 students injured, 70-year old Fasiur Rehman accused Modi’s
administration of targeting Muslims.
“This government wants to turn us
into second-class citizens,” he said, as several hundred protesters around him
raised slogans, held up banners, and waved the Indian flag.
The crowd of mostly young people
defied the ban on large gatherings.
“We are really very angry with the
BJP government… they have taken racism to the extreme point,” Taiba Hadis, 18,
told AFP news agency at the rally.
“They are questioning our
existence, and it is high time for us to speak up.”
Protests across India
In the financial capital of Mumbai,
hundreds of people rallied on Wednesday carrying placards with the words:
“India is Ours” and chanting “We Are All One”.
“We just cannot go along with this
bill. I can’t believe we now have to prove our citizenship after living in
India for so many years,” Tabeer Rizvi told AFP as the Mumbai crowd burst into
a Hindi version of the US civil rights movement anthem: “We shall overcome”.
“I am not surprised to see people
of all religions come out to protest this bill.”
Rallies were also held in other
states including Assam, West Bengal, Tamil Nadu and Telangana on Wednesday.
In the northeastern state of Assam,
which has seen some of the most violent protests against the CAA, thousands of
people came out on the streets of several cities on Wednesday.
“We shall continue with our
agitation till we get a favourable response from the Supreme Court,” said
Samujjal Bhattacharya of the All Assam Students’ Union.
In West Bengal state, where some
protests have also turned violent, four people were injured in scuffles in the
Uttar Dinajpur district after a procession against the CAA, local official
Arvind Meena said.
‘Excessive force’
The UN secretary-general’s
spokesman Stephane Dujarric said on Tuesday the global body was “concerned
about the violence and alleged use of excessive force by security forces that
we’ve seen that have been taking place”.
The United States’ State Department
urged New Delhi to “protect the rights of its religious minorities in keeping
with India’s constitution and democratic values”.
At a news conference with his
Indian counterpart on Wednesday, US Secretary of State Mike Pompeo said
Washington cares deeply about protecting religious rights everywhere, but gave
a muted answer on the issue.
“We honour Indian democracy as they
have a robust debate inside India on the issue,” he said.
India’s Foreign Minister
Subrahmanyam Jaishankar repeated the government’s line that it was a measure
designed to address the needs of persecuted religious minorities.
