Genetic basis of the agronomic traits of white and brown fiber upland cotton in China revealed by a genome-wide association study

Gossypium hirsutum L. represents the largest source of textile fibre, and China is one of the largest cotton producing and consuming countries in the world. To investigate the genetic architecture of the agronomic traits of white fiber upland cotton in China, a diverse and nation-wide population containing 503 G. hirsutum accessions was collected for GWAS on 16 agronomic traits. The accessions were planted in four places from 2012 to 2013 for phenotyping. The CottonSNP63K array and a published high-density map based on this array were used for genotyping. A total of 324 SNPs and 160 candidate quantitative trait loci (QTL) regions were identified as significantly associated with the 16 agronomic traits. A network was established for multi-effects in QTLs and inter-associations among traits. Thirty-eight associated regions had pleiotropic effects controlling more than one trait. To understand the genetic basis of brown fibre cotton, an F2 population was constructed to genetically map the dark brown fiber gene in an introgression line with mutant dark brown fiber derived from an interspecific hybridization between Gossypium hirsutum cv. Handan208 and G. barbadense Pima90-53. On the other hand, in order to comprehensively reveal the genetic basis of brown fiber, 100 accessions with light to dark brown fibers were collected, together with 109 re-sequenced white fiber accessions randomly selected from Upland cotton, to construct an association mapping panel. The 100 brown fiber accessions were genotyped by re-sequencing, and phenotyped with 21 of the 109 white fiber accessions in three environments to map quantitative trait loci (QTL) related to fiber color, yield and quality traits by genome-wide association study (GWAS). The brown fibre region, Lc1, was fine-mapped and dissected it into two loci, qBF-A07-1 and qBF-A07-2. The qBF-A07-1 locus mediates the initiation of brown fibre generation, whereas the shade of the brown fibre is affected by the interaction between qBF-A07-1 and qBF-A07-2. Haploid analysis of the signals significantly associated with these two loci showed that most tetraploid modern brown cotton accessions exhibit the introgression signature of G. barbadense. Ten quantitative trait loci (QTLs) for fibre yield and 19 QTLs were identified for fibre quality and found that qBF-A07-2 negatively affects fibre yield and quality through an epistatic interaction with qBF-A07-1. This study sheds light on the genetics of fibre colour and lint-related traits in brown fibre cotton, which will guide the elite cultivars breeding of brown fibre cotton.