Whole-genome resequencing of 240 Gossypium barbadense accessions reveals genetic variation and genes associated with fiber strength and lint percentage

Key message Genetic variation in a G. barbadense population was revealed using resquencing. GWAS on G.barbadense population identified several candidate genes associated with fiber strength and lint percentage. Abstract Gossypium barbadense is the second-largest cultivated cotton species planted in the world, which is characterized by high fiber quality. Here, we described the global pattern of genetic polymorphisms for 240 G. barbadense accessions based on the whole-genome resequencing. A total of 3,632,231 qualified single-nucleotide polymorphisms (SNPs) and 221,354 insertion–deletions (indels) were obtained. We conducted a genome-wide association study (GWAS) on 12 traits under four environments. Two traits with more stable associated variants, fiber strength and lint percentage, were chosen for further analysis. Three putative candidate genes, HD16 orthology ( GB_D11G3437 ), WDL2 orthology ( GB_D11G3460 ) and TUBA1 orthology ( GB_D11G3471 ), on chromosome D11 were found to be associated with fiber strength, and one gene orthologous to Arabidopsis Receptor-like protein kinase HERK 1 ( GB_A07G1034 ) was predicated to be the candidate gene for the lint percentage improvement. The identified genes may serve as promising targets for genetic engineering to accelerate the breeding process for G. barbadense and the high-density genome variation map constructed in this work may facilitate our understanding of the genetic architecture of cotton traits.