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

The 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.