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New Data Published on RNAi-based Cotton Plant Improvement


Researchers from the Academy of Sciences of Uzbekistan (ASU) and Texas A&M University this month reported data showing that RNAi-based silencing of a photoreceptor gene in cotton can significantly enhance a number of traits related to the plant's commercial applications.

The effects, which were also shown to be transferrable to another cotton variety via conventional sexual hybridization, suggest that many of the desirable characteristics of high-quality but low-yielding Egyptian cotton can be obtained in Upland cotton, which produces lesser quality fibers but accounts for about 95 percent of the world's cotton given its high yield, according to one of the study's authors.

The genetic improvement of Upland cotton fiber quality has long been a key objective for cotton breeders, but has proven difficult due to issues of segregation distortion, Ibrokhim Abdurakhmonov, an ASU researcher and lead author of the new study, told Gene Silencing News this week. Specifically, there exists a negative correlation between fiber quality traits and yield components, and between fiber quality and boll maturity.

So rather than attempting, for instance, to introduce desirable Egyptian cotton traits into Upland cotton plants, "we [hypothesized] that Upland cotton fiber could be improved itself without integrating [other] cotton genes," Abdurakhmonov explained.

Light is known the be a key environmental factor controlling plant development and morphology, and plants respond to light through various photoreceptor systems including the phytochrome red/far-red (R/FR) photoreceptor gene family. And in cotton, this gene family has been shown to have a significant effect on the length and diameter of developing fibers.

As a PhD student at Texas A&M, Abdurakhmonov had studied the role of phytochrome genes in cotton, identifying one in particular — PHYA1 — that appeared to have a direct role in fiber length, he said. Aiming to build off this work, Abdurakhmonov began collaborating with former colleagues at Texas A&M, as well as partners at the US Department of Agriculture, to see if RNAi could be used to selectively inhibit this gene and boost cotton fiber length.

As described in a paper appearing this month in Nature Communications, the scientists created an RNAi construct based on a Hellsgate vector against a PHYA1-specific fragment with significant similarity to other phytochrome genes. Still, because "effective RNAi suppression typically requires 80-100 percent nucleotide identity, we anticipated that our construct would only target the PHYA1 genes," they wrote.

Transgenic plants were created using the vectors, and these showed "rapid and vigorous lateral and main root development," as well as elongated petioles, versus control plants. Fibers obtained from the transformed plants also proved to be at least 17 percent longer than those from control plants and displayed earlier flowering and earlier boll maturity.

Further analysis showed that the RNAi plant fibers were thicker and more uniform compared with fibers from control plants.

The phenotypes beyond fiber elongation weren't entirely expected as PHYA1 had not been linked to them before, but it was the early flowering phenotype that really caught the researchers' attention. PHYA1 expression, Abdurakhmonov noted, is directly associated with flowering, therefore its suppression should delay effect, not speed it up.

"When we checked gene expression, the results were very unusual," with around a 70 percent suppression of PHYA1 but as much as a 20-fold increase in other phytochrome genes, he said. The exact mechanism behind this outcome is not clear, but the investigators concluded that there is a compensatory effect between the genes.

Based on data on various phytochrome genes in different plant species, they believe that it is the upregulation of the non-target genes that is behind the non-fiber elongation phenotypes observed in the RNAi cotton. Increased PHYE expression, for example, has been shown to boost yield in tobacco and potatoes.

Notably, Abdurakhmonov and his colleagues were able to transfer the RNAi-associated traits obtained in the Upland cotton plants to a line of plants adapted to grow in Uzbekistan using conventional sexual crosses. The result was a plant that maintained the improved phenotypes but was "well-adapted for local growing conditions and cultivation practices," the researchers wrote in Nature Communications.

Overall, the findings show that "modulation of phytochrome photoreceptor activity using RNAi not only provides a solution to a longstanding problem for conventional cotton breeders … but may also lead to significantly increased income for cotton producers worldwide, thus opening a new paradigm in Upland cotton improvement," the team concluded.

With an eye toward commercializing their approach, Abdurakhmonov said that he and his colleagues have filed for patent protection on their discoveries and are preparing to test their plants in large field studies under various environmental conditions.