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New Study Uncovers Novel, Plant-specific microRNAs in Wheat

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NEW YORK (GenomeWeb) – A research team from the China Agricultural University (CAU) last month reported the results of a genome-wide survey of wheat microRNAs, finding more than 300 novel miRNAs belonging to 276 families, with nearly 200 specific to the plant.

Notably, 64 miRNAs were found to be preferentially expressed in developing or germinating grains, suggesting they play key roles in their development and offering an avenue for further research into whether the small, non-coding RNAs can be manipulated to improve yield.

Bread wheat, or Triticum aestivum, is one of the most widely cultivated crops in the world, providing an estimated 20 percent of calories consumed by humans, according to estimates by the United Nations' Food and Agricultural Organization.

To date, a number of research groups have looked at wheat miRNAs associated with development and stress response by sequencing small RNA populations or via bioinformatics, identifying miRNA families in various plant tissues, in seedlings, and in developing grains. But to date, the have been no attempts to identify and compare miRNAs in multiple tissues types or developmental stages on a whole-genome scale, the CAU team wrote in a paper appearing in BMC Plant Biology.

To fill in this gap, the researchers created 11 sequencing libraries using small RNAs extracted from dry grains, germinating seed embryos, seedling shoots, seedling leaves, seedling roots, stems in the jointing stage, young spikes of varying lengths, flag leaves, and developing grain eight days and 15 days after pollination.

The team systematically annotated a total of 689 miRNAs belonging to 536 families in the different tissues based on the draft wheat genome sequences, identifying 69 highly conserved miRNAs and 191 wheat-specific miRNAs at a genome-wide scale.

"This extremely large set of miRNAs is likely associated with the polyploid nature of wheat, which is reasonably consistent with the higher gene numbers, ranging from 94,000 to 96,000, reported in bread wheat than its diploid progenitor and other species such as rice, maize, and Arabidopsis," the scientists wrote in their paper.

The discovery of the highly conserved miRNAs, which were in 16 families, suggests that they are evolutionarily conserved in the plant kingdom. However, they also identified multiple wheat-specific variants of conserved miRNAs exhibiting nucleotide substitutions as compared to other species. This divergence within highly conserved miRNA families, the researchers noted, might suggest that they evolved at different rates.

In the study, a total of 524 potential targets were identified for 124 putative miRNA families through degradome sequencing. For highly conserved miRNAs, 122 target genes were identified, including 92 targets that are conserved among other species and 30 non-homologous target genes.

"These non-conserved targets of miRNAs might evolve specific properties and display unique functions in wheat growth and development," according to the BMC Plant Biology study.

The CAU groups also found 51 miRNAs from 36 families that are specifically expressed in developing grains, 28 of which are wheat-specific. A number of grain-abundant miRNAs specifically expressed in the embryo or endosperm during grain development were also uncovered. Notably, miR-156a specifically accumulated in the embryo and gradually increased in the days following pollination. In Arabidopsis embryos, miR-156 delays the production of maturation transcripts, suggesting that the miRNA might also be involved in late embryo maturation during wheat grain development.

The study also showed that 22-nucleotide miRNAs had markedly higher expression levels in seed tissues compared with other tissues. In light of a recent report indicating that these longer miRNAs trigger secondary siRNA biogenesis in plants, the CAU scientists wrote that the 22-nucleotide miRNAs that they found in their experiments might be involved in directing the generation of phased siRNAs during wheat seed germination and maturation.

In their study, northern blotting analysis showed that two 22-nucleotide miRNAs — tae-miR021b and tae-miR2003a — preferentially accumulated in the embryo rather than the endosperm, suggesting important roles for miRNA-mediated gene regulation in wheat grain.

Overall, the findings have added to the overall body of knowledge about wheat miRNAs, serving as a foundation for future studies into the functional role of the small RNAs in an important crop plant.

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