The genetic basis for Gossypium hirsutum race latifolium, the putative ancestor of cultivated upland cotton, emerging from the semi-wild races to be domesticated into cultivated upland cotton is unknown. Here, we reported a high-quality genome assembly of G. latifolium. Comparative genome analyses revealed substantial variations in both gene group composition and genomic sequences across 13 cotton genomes, including the expansion of photosynthesis-related gene groups in G. latifolium compared with other races and the pivotal contribution of structural variations (SVs) to G. hirsutum domestication. Based on the resequencing reads and constructed pan-genome of upland cotton, co-selection regions and SVs with significant frequency differences among different populations were identified. Genes located in these regions or affected by these variations may characterize the differences between G. latifolium and other races, and could be involved in maintenance of upland cotton domestication phenotypes. These findings may assist in mining genes for upland cotton improvement and improving the understanding of the genetic basis of upland cotton domestication.

Structural variation is a major type of genetic variation that can potentially induce powerful genetic effects. In this study, we examined the Inv(A07)p1.09p2.23 genetic inversion in brown fibre cotton at the individual and population genetics levels. A dark-brown fibre mutant that resulted from a distant hybridization between Gossypium barbadense and G. hirsutum, and a natural population including 30 dark-brown, 70 light-brown and 21 white fibre cotton accessions were collected to perform a functional study of this micro-inversion. The results showed that Inv(A07)p1.09p2.23 can be detected by high-throughput resequencing method, and induce micro-deletion, gene disruption (Ghir_A07G000980) and abnormal gene expression in the breakpoint regions. Inv(A07)p1.09p2.23 existed in only dark-brown fibre cotton, had undergone negative selection in elite brown fibre cultivars, and was significantly associated with fibre colour and nine fibre traits. In the Inv(A07)p1.09p2.23 region, nucleotide diversity was lower, recombination was absent, and linkage disequilibrium was higher. Overall, this inversion event in dark-brown fibre cotton produced significant genetic effects, and this study will guide us to better understand the genetic effects of inversion events in dark-brown fibre cotton.

With increasing demand for high-quality cotton, it is desirable to identify genes involved in fiber development for molecular improvement of cotton. In this study, 780 differentially expressed genes (DEGs) were identified in developing fibers at 10 days post-anthesis (DPA) in Gossypium hirsutum acc. DH962 and G. hirsutum cv. Jimian 5 using RNA-seq. Of 15 stable QTL for fiber quality identified in the same two parents in previous studies, 4, 3, 6, 1, and 1 QTL were associated with fiber length (FL), fiber strength (FS), micronaire (MIC), fiber elongation (FE) and fiber length uniformity ratio (FU), respectively. Integration of DEGs and QTL allowed the identification of 31 genes in 9 QTL regions, of which 25 were highly expressed in fibers based on the transcriptome datasets and 9 were preferentially expressed in different stages of fiber development. Gh_A01G0453 (GhDTX19), Gh_D07G1581 and Gh_D04G0942 were expressed specifically in 5 and 10 DPA fibers, with Gh_D04G0942 showing low expression in other tissues except pistil. Gh_D07G1799 (GhGAUT9), Gh_D11G0326 (GhVPS29), Gh_D11G0333 (GhTCP14), and Gh_D11G0334 (GhNRP2) were preferentially expressed in 5 or 10 DPA fibers; Gh_A01G0397 (GhABCG10) and Gh_D07G1744 were expressed specifically in 20 and 25 DPA fibers. These results suggest candidate genes for molecular improvement of cotton fiber quality.

Plant architecture traits influence crop yield. An understanding of the genetic basis of cotton plant architecture traits is beneficial for identifying favorable alleles and functional genes and breeding elite cultivars. We collected 121 cotton accessions including 100 brown-fiber and 21 white-fiber accessions, genotyped them by whole-genome resequencing, and phenotyped them in multiple environments. This genome-wide association study (GWAS) identified 11 quantitative trait loci (QTL) for two plant architecture traits: plant height and fruit spur branch number. Negative-effect alleles were enriched in the elite cultivars. Based on these QTL, gene annotation information, and published QTL, candidate genes and natural genetic variations in four QTL were identified. Ghir_D02G017510 and Ghir_D02G017600 were identified as candidate genes for qD02-FSBN-1, and a premature start codon gain variation was found in Ghir_D02G017510. Ghir_A12G026570, the candidate gene of qA12-FSBN-2, belongs to the pectin lyase-like superfamily, and a significantly associated SNP, A12_105366045 (T/C), in this gene represents an amino acid change. The QTL, candidate genes, and associated natural variations in this study are expected to lay a foundation for studying functional genes and developing breeding programs for desirable architecture in brown-fiber cotton.