Differential miRNA expression and regulatory mechanisms in pigmentation and fiber development of white and brown cotton (Gossypium hirsutum)

Cotton (Gossypium hirsutum) is a major global natural fiber crop used in the textile industry. Although white colored cotton remains the most popular form of cultivated cotton, colored varieties could replace chemically dyed fibers and provide more environmental friendly alternatives. In order to investigate the role of miRNAs in fiber color, we selected white and brown cotton varieties for comparative investigations. Through small RNA sequencing, a number of known miRNA families were discovered (74 in white cotton and 61 in brown cotton, with 44 shared) in which 11 miRNA families were significantly elevated in brown cotton variety. Functional enrichment and network analysis of target genes of these miRNAs revealed their regulatory role in secondary metabolite biosynthesis pathway, particularly the flavonoids pathway, which are known to be associated with fiber coloration. Pigmentation and developmental-related miRNA members such as miR396e-5p, miR167l, and miR1446 were also significantly enriched. Real-time PCR results suggest the regulatory role of miRNAs in these two cotton varieties. Furthermore, 30 and 25 novel miRNAs were also identified in white and brown cotton, respectively. Our findings also show miRNAs associated with fiber coloration and development through the intricate networks of miRNA and targets. Understanding these systems may provide novel insights on improving the fiber color and quality.