Background: Sea island cotton (Gossypium barbadense) has markedly superior high quality fibers, which plays an important role in the textile industry and acts as a donor for upland cotton (G. hirsutum) fiber quality improvement. The genetic characteristics analysis and the identification of key genes will be helpful to understand the mechanism of fiber development and breeding utilization in sea island cotton. Results: In this study, 279 sea island cotton accessions were collected from different origins for genotyping and phenotyping fiber quality traits. A set of 6303 high quality single nucleotide polymorphisms (SNPs) were obtained by high-density CottonSNP80K array. The population characteristics showed that the sea island cotton accessions had wide genetic diversity and were clustered into three groups, with Group1 closely related to Menoufi, an original sea island cotton landrace, and Group2 and Group3 related to widely introduced accessions from Egypt, USA and Former Soviet Union. Further, we used 249 accessions and evaluated five fiber quality traits under normal and salt environments over 2 years. Except for fiber uniformity (FU), fiber length (FL) and fiber elongation (FE) were significantly decreased in salt conditions, while fiber strength (FS) and fiber micronaire (MIC) were increased. Based on 6303 SNPs and genome-wide association study (GWAS) analysis, a total of 34 stable quantitative trait loci (QTLs) were identified for the five fiber quality traits with 25 detected simultaneously under normal and salt environments. Gene Ontology (GO) analysis indicated that candidate genes in the 25 overlapped QTLs were enriched mostly in “cellular and biological process”. In addition, “xylem development” and “response to hormone” pathways were also found. Haplotype analyses found that GB_A03G0335 encoding an E3 ubiquitin-protein ligase in QTL TM6004 had SNP variation (A/C) in gene region, was significantly correlated with FL, FS, FU, and FE, implying a crucial role in fiber quality. Conclusions: The present study provides a foundation for genetic diversity of sea island cotton accessions and will contribute to fiber quality improvement in breeding practice.

Upland cotton (Gossypium hirsutum L.) is the most important source of natural fiber in the world. Early-maturity upland cotton varieties are commonly planted in China. Nevertheless, lint yield of early-maturity upland cotton varieties is strikingly lower than that of middle- and late-maturity ones. How to effectively improve lint yield of early maturing cotton, becomes a focus of cotton research. Here, based on 72,792 high-quality single nucleotide polymorphisms of 160 early-maturing upland cotton accessions, we performed genome-wide association studies (GWASs) for lint percentage (LP), one of the most lint-yield component traits, applying one single-locus method and six multi-locus methods. A total of 4 and 45 significant quantitative trait nucleotides (QTNs) were respectively identified to be associated with LP. Interestingly, in two of four planting environments, two of these QTNs (A02_74713290 and A02_75551547) were simultaneously detected via both one single-locus and three or more multi-locus GWAS methods. Among the 42 genes within a genomic region (A02: 74.31–75.95 Mbp) containing the above two peak QTNs, Gh_A02G1269, Gh_A02G1280, and Gh_A02G1295 had the highest expression levels in ovules during seed development from 20 to 25 days post anthesis, whereas Gh_A02G1278 was preferentially expressed in the fibers rather than other organs. These results imply that the four potential candidate genes might be closely related to cotton LP by regulating the proportion of seed weight and fiber yield. The QTNs and potential candidate genes for LP, identified in this study, provide valuable resource for cultivating novel cotton varieties with earliness and high lint yield in the future.

The boll opening rate (BOR) is an early maturity trait that plays a crucial role in cotton production in China, as BOR has a significant effect on defoliant spraying and picking time of unginned cotton, ultimately determining yield and fiber quality. Therefore, elucidating the genetic basis of BOR and identifying stably associated loci, elite alleles, and potential candidate genes can effectively accelerate the molecular breeding process. In this study, we utilized the mixed linear model (MLM) algorithm to perform a genome-wide association study (GWAS) based on 4,452,629 single-nucleotide polymorphisms (SNPs) obtained through whole-genome resequencing of a natural population of 418 upland cotton accessions and phenotypic BOR data acquired from five environments. A total of 18 SNP loci were identified on chromosome D11 that are stable and significantly associated with BOR in multiple environments. Moreover, a significant SNP peak (23.703–23.826 Mb) was identified, and a GH-D11G2034 gene and favorable allelic variation (GG) related to BOR were found in this genomic region, significantly increasing cotton BOR. Evolutionary studies have shown that GH-D11G2034 may have been subjected to artificial selection throughout the variety selection process. This study provides valuable insights and suggests that the GH-D11G2034 gene and its favorable allelic variation (GG) could be potential targets for molecular breeding to improve BOR in upland cotton. However, further research is needed to validate the function of this gene and explore its potential applications in cotton breeding programs. Overall, this study contributes to the advancement of genetic improvement in early maturity and has important implications for the sustainable development of the cotton industry.

Upland cotton (Gossypium hirsutum L.) dominates Xinjiang’s cotton production, but the narrow genetic base of modern cultivars limits further yield gains. Here, 356 Xinjiang upland cotton accessions (184 northern, 172 southern) were genotyped at 280 elite trait locus–trait combinations (270 unique markers) using a liquid-phase chip. Pairwise kinship was inferred with the KING-robust estimator and cross-validated by IBS similarity, population structure was examined by PCA, and a marker-weighted comprehensive elite genotype index (S) was constructed. The overall missing rate was 0.43%, and five identical and 101 near-identical accession pairs were detected. PC1 and PC2 explained only 9.81% and 7.29% of the variation, with substantial regional overlap. Index S ranged from 0.39 to 0.57, led by Tkuo, Y80, Ba 44435, Ziyu R040068 and Youzhi 5; salt tolerance (0.07), lint yield (0.14), seed index (0.19) and fiber strength (0.22) showed the lowest carriage of the marker-defined elite alleles scored here. After excluding close relatives, 62,252 crosses (98.52%) satisfied the constraint, and 30 crosses (19 inter-regional) were recommended, the best being Ziyu TY112 × Tkuo (joint coverage U = 0.65). These parents and crosses provide candidates for parental selection, pending field validation.

Upland cotton (Gossypium hirsutum L.) dominates Xinjiang's cotton production, but the narrow genetic base of modern cultivars limits further yield gains. Here, 356 Xinjiang upland cotton accessions (184 northern, 172 southern) were genotyped at 280 elite trait locus–trait combinations (270 unique markers) using a liquid-phase chip. Pairwise kinship was inferred with the KING-robust estimator and cross-validated by IBS similarity, population structure was examined by PCA, and a marker-weighted comprehensive elite genotype index (S) was constructed. The overall missing rate was 0.43%, and five identical and 101 near-identical accession pairs were detected. PC1 and PC2 explained only 9.81% and 7.29% of the variation, with substantial regional overlap. Index S ranged from 0.39 to 0.57, led by Tkuo, Y80, Ba 44435, Ziyu R040068 and Youzhi 5; salt tolerance (0.07), lint yield (0.14), seed index (0.19) and fiber strength (0.22) were the main deficiencies. After excluding close relatives, 62,252 crosses (98.52%) satisfied the constraint, and 30 crosses (19 inter-regional) were recommended, the best being Ziyu TY112 × Tkuo (joint coverage U = 0.65). These parents and crosses provide candidates for parental selection, pending field validation.