Combined genome and transcriptome analysis of elite fiber quality in Gossypium barbadense.

Abstract

Gossypium barbadense, which is one of several species of cotton, is well-known for its superior fiber quality. However, the genetic basis of its high-quality fiber remains largely unexplored. Here, we re-sequenced 269 G. barbadense accessions. Phylogenetic structure analysis showed that the set of accessions were clustered into three groups, G1 and G2 mainly included modern cultivars from Xinjiang, China, and G3 was related to widely introduced accessions in different regions worldwide. A genome-wide association study of five fiber quality traits across multiple field environments identified a total of 512 qtls (main effect QTLs) and 94 qtlEs (QTL-by-environment interactions) related to fiber quality, of which 292 qtls and 57 qtlEs co-located with previous studies. We extracted the genes located in these loci and performed expression comparison, local association analysis, and introgression segment identification. The results showed that high expression of hormone-related genes during fiber development, introgressions from G. hirsutum, and the recombination of domesticated elite allelic variation, were three major contributors to improve fiber quality of G. barbadense. In total, 839 candidate genes with encoding region variation associated with elite fiber quality were mined. We confirmed that haplotype GB_D03G0092H traced from G. hirsutum introgression, with a 1-bp deletion leading to a frameshift mutation compared with GB_D03G0092B, significantly improved fiber quality. GB_D03G0092H localized in the plasma membrane, while GB_D03G0092B in both the nucleus and plasma membrane. Overexpression of GB_D03G0092H in Arabidopsis (Arabidopsis thaliana) significantly improved the elongation of longitudinal cells. Our study systematically reveals the genetic basis of the superior fiber quality of G. barbadense and provides elite segments and gene resources for breeding high-quality cotton cultivars.