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New Research Links microRNA with Increased Rice Yield

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A Chinese research team led by investigators from Sun Yat-Sen University last week reported on the discovery of a single microRNA that, when overexpressed, can boost rice yield by as much as 25 percent.

Because the miRNA — miR-397 — is highly conserved across different grain species, the scientists speculated that its manipulation may also be useful for increasing yield in other crops.

Rice yield is known to be associated with grain size and the number of grains per panicle, and while several genes have been identified as regulating these traits, knowledge of the gene networks controlling yield is “limited,” according to the researchers.

“Exploring new genes that modulate these traits would help us better understand the relevant molecular mechanisms and would also facilitate the breeding of new varieties with higher yields,” they wrote in their paper, which appeared in Nature Biotechnology.

In recent years, there have been reports that another miRNA — miR-156 — negatively controls the number of panicle branches and yield in rice, suggesting that the small, non-coding RNAs play a role in how much grain can be obtained from the plants.

In light of these data, the researchers from Sun Yat-Sen University set out to identify miRNAs that may positively regulate grain size, number, and yield.

An initial screen of rice seeds identified several miRNAs that are preferentially highly expressed in rice seeds but downregulated during post-embryonic development, including the highly conserved miR-397, the scientists wrote in their study.

Hypothesizing that the miRNA’s expression could contribute to the regulation of seed development or another related trait, the team generated overexpression rice lines in which either miR-397a or miR-397b — the two isoforms of the miRNA — was driven by a constitutively active promoter.

RNA blot hybridization showed that the expression of the miRNA was elevated in the transgenic lines. During ripening, the plants were also found to have “strongly” drooping panicles, indicating an increased grain weight or panicle size, and grew taller than wild-type plants.

When measured, the rice grains from the transgenic plants were substantially longer and wider, were slightly thicker, and overall had a higher weight than their wild-type counterparts.

Looking beyond these obvious yield-related traits, the scientists examined at other agricultural parameters and found the transgenic lines to have a greater number of primary and secondary branches and effective grains per main panicle. In both transgenic lines, the primary panicles were also slightly longer than in unmodified plants.

In addition, the transgenic plants had “slightly reduced” tiller numbers and began to form heads about a week earlier than transgenic plants — two characteristics the researchers suggested would reduce the waste of photosynthetic production by the later tillers and shorten the planting cycle.

Aiming to test their observations under real-world conditions, the investigators conducted plot field experiments with the transgenic lines in Beijing, and discovered that the plants had a greater grain yield than wild-type plants, ranging from 17 percent to 24.9 percent depending on which miR-397 isoform was being overexpressed.

Notably, there were no observable differences between transgenic and wild-type rice in terms of rice quality, indicating that overexpression of miR-397 does not influence traits related to the grain’s cooking or consumption, the scientists wrote in Nature Biotechnology.

In an effort to understand just how miR-397 was influencing grain yield, the team examined the transgenic plants’ peduncle vascular bundles, noting that data in the literature indicate that the number of vascular bundles in these stems corresponds to the panicle branches and grain number.

Both the diameter of the peduncles, as well as the number of vascular bundles contained within, were found to be greater in the transgenic plants compared with wild-type ones, leading the researchers to conclude that miR-397 affects vascular bundle formation, potentially accounting for the observed increased panicle branching and higher grain number.

The investigators then looked for the downstream targets of miR-397, including laccase, which had been predicted other groups to be a target of the miRNA in rice, tobacco, and Arabidopsis thaliana.

A series of experiments indicated that the miRNA downregulates OsLAC, a gene whose product is a laccase-like protein found to be involved in plant sensitivity to the brassinosteroid class of plant hormones. In doing so, the miRNA enhanced brassinosteroid signaling, although not accumulation, which in turn boosts grain yield.

Given that miR-397 is conserved in a variety of other crop species, the researchers concluded that their findings may not only help increase grain yields in rice, but also other cereal crops.

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