RICEPLUS MAGAZINE

Friday, June 19, 2020

19th June,2020 Daily Global Regional Local Rice E-Newsletter

Study finds 'dark matter' DNA is vital for rice reproduction

Regions of DNA that give rise to non-coding RNA are required for proper development of plant reproductive organs.

OKINAWA INSTITUTE OF SCIENCE AND TECHNOLOGY (OIST) GRADUATE UNIVERSITY

VIDEO: THE STAMENS IN MUTANT STRAINS CONTAIN ANTHERS - THE PART OF THE STAMEN THAT HOUSES POLLEN - THAT ARE SHORTER AND MORE CURLED THAN IN WILDTYPE STRAINS. view more

CREDIT: OIST

Researchers from the Okinawa Institute of Science and Technology Graduate University (OIST) have shed light on the reproductive role of 'dark matter' DNA - non-coding DNA sequences that previously seemed to have no function.

Their findings, published today in Nature Communications, have revealed that a specific non-coding genomic region is essential for the proper development of the male and female reproductive organs in rice.

"Rice is one of the major global crops and is the staple food in many countries, including Japan," said Dr. Reina Komiya, senior author of the research paper and associate researcher from the OIST Science and Technology Group. "Further research into how these genomic regions affect plant reproduction could potentially lead to increased productivity and more stable yields of rice."

Many previous developmental studies have focused on genes - the sections of DNA that provide instructions for making proteins. But in complex creatures like plants and animals, a large fraction of the genome - typically between 90-98% - doesn't actually code for proteins.

The vast expanse of this 'junk DNA' has long puzzled biologists, with many dubbing it the 'dark matter' of the genome. But recent research suggests that many of these non-coding genomic regions may have a function after all, giving rise to non-coding RNA.

Scientists have now identified numerous types of non-coding RNA, ranging from small molecules only 20-30 nucleotide bases in length to long molecules of over 200 nucleotides. Although studies show that non-coding RNA plays a vital role in the regulation of gene expression - the process where a gene's instructions are used to make RNA or protein - the precise function of each specific non-coding RNA remains poorly understood.

Dr. Komiya is particularly interested in reproduction-specific RNAs. "These are non-coding RNAs that are produced as the reproductive system forms. I wanted to uncover what role they play in the development of stamens and pistils, the male and female reproductive organs in plants."

Making mutants

In the study, Dr. Komiya's group focused on a reproduction-specific microRNA - a major class of small non-coding RNAs - called microRNA2118.

The scientists created mutant rice strains by deleting a region of the genome that contains multiple copies of the specific DNA sequence that gives rise to microRNA2118. They found that the mutant strains were sterile and showed abnormalities in the structure of the stamens and pistils.

"This means that the role of microRNA2118 in the proper development of the stamens and pistils is essential for plant fertility," said Dr. Komiya.

Revealing RNA and probing proteins

In order to delve deeper into how microRNA2118 controlled development of the anther, the scientists then identified which other molecules were affected by microRNA2118.

They found that microRNA2118 triggered the cleavage of long non-coding RNA, producing many tiny RNA molecules, called secondary small RNAs.

"Interestingly, these small RNAs were rich in uracil, one of the four nucleotide bases found in RNA, which is very unusual compared to other small RNAs," said Dr. Komiya. "We hope to find out the exact function of these small RNAs - and whether this difference in nucleotide composition is important - in further research."

The scientists also discovered that two Argonaute proteins that were only produced in the stamen were dependent on the presence of microRNA2118. Previous research has shown that Argonaute proteins team up with small RNAs to carry out many regulatory functions, such as silencing genes and cleaving RNA.

Dr. Komiya's group therefore proposes that the Argonaute proteins may interact with microRNA2118 to trigger production of the secondary small RNAs. The proteins may also interact with the secondary small RNAs to silence specific regions of the genome. The team hopes to elucidate exactly how the Argonaute proteins and secondary small RNAs affect development of the plant reproductive system in further research.

"Reproduction is an important phenomenon of passing genetic information to the next generation and is essential for maintaining a stable yield supply. However, development of the reproductive system is complicated, and many aspects remain unknown," concluded Dr. Komiya. "This study shows that non-coding RNAs, derived from regions of the genome that were thought to be non-functional, are vital for plant reproduction. Exploring non-coding RNAs further is an exciting and important area of research."

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* This research was supported by the Japan Science and Technology Agency (JST) Strategic Creative Research Promotion Project PRESTO (creation of next-generation basic technology for control of plant life phenomena in the field) and Grant-in-Aid for Scientific Research on Innovative Areas (RNA taxonomy).

https://www.eurekalert.org/pub_releases/2020-06/oios-sf061720.php

The problem with shotguns

By: Cielito F. Habito - @inquirerdotnet

Philippine Daily Inquirer / 05:07 AM June 19, 2020

After three months of immobilizing the economy to flatten the COVID-19 curve, we have nothing to show for it but a battered economy and a pandemic curve that’s anything but flat.

Perhaps thinking that lockdown was enough, crucial testing and tracing received less attention than our more successful neighbors gave.

A reader described it as a shotgun solution that harmed too many people, when we could have used more focused rifle approaches like other countries used with far better results, and without choking their economies the way we did.

The problem with shotgun solutions is that they make governments complacent and lazy, as it’s far easier than figuring out and pursuing creative and effective rifle-focused cures. My favorite illustration had been our decades-old approach to “helping” our 2 million rice farmers, in an effort to achieve full rice self-sufficiency.

While that’s a worthy goal, it’s how we tried to achieve it that was all wrong—through a policy that hurt 100 million consumers in the process. Many thought the way to do it was to block imports and shield domestic producers from competition. What it did was to allow domestic rice prices to rise steadily over time until it reached 2-3 times what our neighbors pay for the same staple.

We could have given focused and effective help for our rice farmers to match the productivity of their counterparts in our neighbors, what with all the superior agricultural scientists we have, who actually taught many of their scientists. But government chose to allow them to slide into inefficiency, low productivity, and high costs, the effect of tightly controlling imports that only helped farmers by raising their prices.

Thus, we got by without providing them enough credit financing, and other needed support like irrigation, farm-to-market roads, mechanization, and postharvest facilities. Thankfully, we finally came to our senses and put the deadly shotgun aside, forcing our agriculture authorities to buckle down on rifle fixes, unburdening all of us consumers in the process.

Another example has been our tax breaks and other fiscal incentives aimed to attract investments. Over the years, we gave them out rather liberally, ultimately at great cost to taxpayers’ pockets. We came up with an Investment Priorities Plan in the name of selectivity, but for many years, that list was faulted for being a virtual catch-all. UP economist Dr. Renato Reside has tracked through the years how these fiscal incentives were for many firms redundant and little more than wasted gifts that never really made a difference.

Meanwhile, government got complacent in fixing the real things that made investors elusive—poor infrastructure, bad governance, and bad taxation. The pending CREATE tax reform package will change that, with more regionally competitive tax rates, and the capability to grant more flexible, rifle-focused incentives. It has passed the House, and our senators will hopefully pass it soon as well.

Still another shotgun has to do with the decades-old cry that it’s cheaper to ship corn from Bangkok to Manila than from Mindanao to Manila, for lack of competition.

The law on cabotage that prohibits foreign ships from moving cargo within the country hurts domestic producers, especially farmers, as a feed miller in Luzon, for example, would rather bring in corn from Thailand rather than source it from Mindanao where there’s lots of it.

Filipino consumers are also hurt by higher commodity prices that embody the higher costs incurred in moving them across our islands.

Cabotage is yet another shotgun policy that effectively sacrifices the interests of the wider majority of Filipinos as it tries to protect a few local shippers—even as there could be more rifle-focused ways to support the latter.

The amendment to the 1936-vintage Public Service Act would change that, by delisting domestic shipping as a public utility where the Constitution bars foreign competition. That’s another shotgun due to go soon.

Testing and tracing, focused support to our farmers and shippers, flexible, targeted incentives, and more—it’s time government dusted off its other rifles. They get far better results.

cielito.habito@gmail.com

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: https://opinion.inquirer.net/130933/the-problem-with-shotguns#ixzz6PoIHFCgX
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