Transcriptome Analysis of Short Fiber Mutant Ligon lintless-1 (Li1) Reveals Critical Genes and Key Pathways in Cotton Fiber Elongation and Leaf Development

For efficient spinning and superior fabric production, long fiber length is a desired trait for cotton production. To unveil the molecular basis of the cotton fiber length regulation, a short fiber mutant, Ligon lintless-1 (Li1), is selected to compare with its corresponding wild type (WT). Li1 is a monogenic dominant cotton mutant causing extremely short fibers (<6mm) on mature seeds with visible pleiotropic effects on vegetative growth and development. In this research, we compared the transcriptome of fiber bearing ovules at 1 DPA, 3 DPA, 8 DPA and leaf between Li1 mutant and WT. A total of 7,852 differentially expressed genes (DEGs) were detected in ovules and leaves, which mainly participated in sugar, secondary metabolite and lipid metabolism pathways based on KEGG analysis. The common DEGs at 1 DPA and 3 DPA were involved in the responses to endogenous stimulus, signal transduction and long-chain fatty acid biosynthesis. For 3 DPA, 8 DPA and leaf, the common DEGs were involved in the responses to auxin and receptor kinases related pathway. Further analysis showed that 37 genes involved in very-long-chain fatty acid biosynthesis were suppressed in Li1 mutant during fiber fast elongation development. Most of the DEGs involved in cell wall metabolism, such cellulose synthase, expansin family, and glycosyl hydrolase were differentially expressed at 3 DPA and 8 DPA. Our results provide new insights into the mechanisms of fiber elongation, and offer novel genes as potential objects for fiber length improvement.