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Abstract
Cotton is one of the most important textile crops but little is known how microRNAs regulate cotton fiber development. Using a well-studied cotton fiberless mutant Xu-142-fl, we compared 54 miRNAs for their expression between fiberless mutant and its wildtype. In wildtype Xu-142, 26 miRNAs are involved in cotton fiber initiation and 48 miRNAs are related to primary wall synthesis and secondary wall thickening. Thirty three miRNAs showed different expression in fiber initiation between Xu-142 and Xu-142-fl. These miRNAs potentially target 723 protein-coding genes, including transcription factors, such as MYB, ARF, and LRR. ARF18 was newly predicted targets of miR160a, and miR160a was expressed at higher level in −2DPA of Xu-142-fl compared with Xu-142. Furthermore, the result of Gene Ontology-based term classification (GO), EuKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis shows that miRNA targets were classified to 222 biological processes, 64 cellular component and 42 molecular functions, enriched in 22 KOG groups, and classified into 28 pathways. Together, our study provides evidence for better understanding of miRNA regulatory roles in the process of fiber development, which is helpful to increase fiber yield and improve fiber quality.
Highlights
MicroRNAs (MiRNAs) are a category of endogenous non-coding single-stranded RNAs, which regulate gene expression at the post-transcription levels by degrading corresponding mRNAs or inhibiting mRNA translation[9,10]
34 conserved miRNA families were identified in cotton fiberless mutant Xu-142-fl and its wildtype Xu-142 using deep sequencing technology, and many of these miRNAs are significantly expressed between the two different cotton genotypes[24]
Our result shows that the majority of miRNAs were down-regulated in cotton fiber development, suggesting that those tested miRNAs may play positive role in different fiber development stages. 33 miRNAs showed different expression patterns in fiber initiation between Xu-142 and Xu-142-fl
Summary
MicroRNAs (MiRNAs) are a category of endogenous non-coding single-stranded RNAs, which regulate gene expression at the post-transcription levels by degrading corresponding mRNAs or inhibiting mRNA translation[9,10]. Xie et al (2015) identified 65 conserved miRNA families in cotton ovules with initiated fiber and leaves using the first-generation deep sequencing technology; among these miRNAs, the expression of 32 miRNA families were difference between ovule and leaf tissues[41] Those studies have been reported on miRNA expression related to fiber development, no single report has attempted to compare the miRNA expression profiles among multiple fiber development stages and the regulatory mechanism is still unclear. We studied the expression profiles of 54 miRNAs in cotton ovules, fibers, cotyledons, leaves and flower buds in a well-studied cotton fuzzless-lintless mutant (Xu-142-fl) and its wildtype Xu-142 We selected these 54 miRNAs based on previous reports; these miRNAs either play important role in plant development or are differentially expressed in a certain cotton fiber development stage. Our study show that those miRNAs target many transcription factors, suggesting that these miRNA get involved in cotton fiber development potentially through targeting different transcription factors
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