Natural Variations in GhFLA9_D12 Confer Divergent Fiber Development and Lint Percentage via Cell Wall Plasticity Remodeling in Cotton.

Lint percentage (LP) is a core determinant of cotton yield. Here, we systematically characterized the evolutionary impacts and molecular mechanisms of GhFLA9_D12 on fiber development. Population genomics revealed a significant selective sweep at the locus, where the superior haplotype HapA (T/INS) correlates with higher LP and underwent continuous selection during modern breeding. This favorable variation was likely introgressed from G. barbadense into G. hirsutum. Mechanistically, GhFLA9_D12 regulates fiber development via divergent expression and protein functions. Transcriptionally, a 162-bp InDel in promoter mediates differential activation by GhAGL11, determining allele-specific expression. Biochemically, GhFLA9_D12 is secreted to the cell wall, binding polysaccharides (β-glucan, xylans, and pectins) to modulate plasticity. Crucially, a non-synonymous coding mutation alters its polysaccharide-binding preference. Consequently, overexpressing distinct alleles yields contrasting phenotypes in fiber strength and cell wall thickness, highlighting the role of allelic variation in fine-tuning cell wall architecture. Furthermore, GhFLA9_D12 undergoes essential glycosylation through interactions with prolyl 4-hydroxylase (GhP4H) and galactosyltransferase 1 (GhGalT1). In summary, this study elucidates how natural variations of GhFLA9_D12 orchestrate cell wall plasticity to determine LP, which advance our understanding of plant cell wall biosynthesis and provide elite genetic resources for synergistically improving cotton yield and quality.