A plastid lipid-associated protein-encoding gene (GhPAP) that positively regulates fiber strength was identified via genetic mapping and transcriptomic analysis of a stable QTL on chromosome D06 of upland cotton.

Abstract

Key message: GhPAP was identified as a candidate gene associated with cotton fiber development via genetic mapping and transcriptomic analysis. GhPAP increases fiber strength by modulating cell wall thickness and fiber helix formation. Cotton fiber strength (FS), length (FL), and fineness are economically important quality-related traits. Although many genes related to fiber quality were identified recently, the molecular mechanism controlling fiber quality remains largely unknown. In this study, an FS/FL-related stable QTL was mapped to a 2.92 Mb region containing 81 putative coding genes on chromosome D06 by combining SLAF-BSA-seq and InDel analyses of a bi-parental recombinant inbred line (RIL) population. Five genes in the QTL region were differentially expressed between two near-isogenic RILs, A_dh (with long and strong fibers) and A_dl (with short and weak fibers), during fiber development. GhPAP (Ghi_D06G06106) was subsequently identified as the most likely candidate gene according to its sequence variations and annotation information. The functional validation of GhPAP revealed an association between reduced FS and decreased GhPAP expression in plants due to virus-induced gene silencing (VIGS), leading to a significant decrease in GhPAP-VIGS fiber helix formation and thickness. GhPAP expression positively affected FS in four cotton lines with distinct breeding histories. Additionally, GhPAP overexpression in Arabidopsis thaliana resulted in slower elongation and thicker cell walls in roots and stems (compared with the control). Moreover, SNPs in the GhPAP promoter region were significantly correlated with FS and FL. Notably, a KASP marker was developed for selecting cotton genotypes according to FS and FL. This study identified a new and important gene and developed a KASP marker applicable for future molecular breeding of high-quality cotton.