Population structure, genetic diversity analyses and genome-wide association study of photoperiod sensitivity in Pima cotton (Gossypium barbadense L.).

backgroundPima cotton (Gossypium barbadense) producing superior quality fibers used for premium fabrics and a source of valuable genetic diversity to improve Upland cotton (G. hirsutum). However, current Pima cultivars lack premium quality traits and have a narrow genetic base. Germplasm and genomic resources for population-scale genetic studies and targeted breeding in Pima cotton are limited in the US. Additionally, photoperiod sensitivity is a barrier to introgress beneficial alleles from the tropical G. barbadense germplasm into US cotton.

resultsA 473-member diversity panel, comprising photoperiod-insensitive and sensitive accessions from over 50 countries, was assembled to assess genetic and phenotypic diversity and genomic analyses of photoperiod response in Pima cotton. Population genetic analyses of the panel using array-based SNP markers showed genetic diversity was low, as indicated by Nei's genetic distance of 0.156 and identity by state of 0.759. A core set of 41 accessions captured 99% of total allelic diversity, with smaller core sets developed for each photoperiod group. Population structure analysis revealed six subpopulations, including Peruvian germplasm, diversified Peruvian lines, Sea-Island types, American Pima cultivars, Egyptian accessions, and accessions from Russia/former Soviet Union. Phenotypically, photoperiod-insensitive accessions showed broad variability in fiber length (22.85-41.40 mm), strength (28.12-56.01 g tex⁻¹), and elongation (5.70-10.29%). Sea-Island types had longer fibers, while American Pima lines had stronger fibers. Genome-wide association studies of photoperiod response under long-day conditions identified a major genomic region on chromosome D06, along with novel marker-trait associations on A10 and D10. Targeted genomic analysis revealed candidate genes for photoperiod sensitivity, including VOZ1 at the Gb_Ppd locus on D06.

conclusionsThe diversity panel of Pima cotton assembled in the current study showed excellent phenotypic variation in fiber quality and morphological traits and could be used for population scale genetic studies. The identified structured sub-populations offer valuable parental lines for targeted cotton genetic improvement and core sets enable rapid trait discovery and breeding in cotton. GWAS uncovered three key genomic regions controlling photoperiod response, highlighting distinct genetic mechanisms for flowering time in Upland vs. Pima cotton. The VOZ1 at the Gb_Ppd locus on chromosome D06 was confirmed as a candidate gene for photoperiod sensitivity in tropical G. barbadense landraces laying the foundation for dissecting the molecular genetic architecture of flowering time in cotton.