Fine mapping and targeted genomic analyses of photoperiod‐sensitive gene (GB_PPD1) in Pima cotton (Gossypium barbadense L.)

Cotton grown in the United States are day‐length insensitive annuals and are grown under long‐day summers. Photoperiod sensitivity, present in tropical wild and landraces endemic to the center of origin and diversity, is a major barrier for the introgression of tropical gene pool into the US cotton. Previously, we mapped the major photoperiod response locus Gb_Ppd1 on chromosome D06 of Pima cotton (Gossypium barbadense L.). In the current study, an F2 population of 2112 gametes was used to fine map the Gb_Ppd1 locus. Two sequence‐tagged‐site and nine kompetitive allele‐specific polymerase chain reaction (KASP) markers were developed and the Gb_Ppd1 locus was fine mapped to 1.1 cM region flanked by novel markers 17‐KASP‐8, 17‐KASP‐10, and 15‐PR‐10A. The closely linked markers identified 2.10 Mb region in the G. barbadense genome that contained 18 putative gene sequences. A candidate gene Gbar_D06G014560 showed high homology to VASCULAR PLANT ONE ZINC FINGER PROTEIN 1 involved in photoperiodism in Arabidopsis. We evaluated the diagnostic polymorphisms for the flanking markers on a diversity panel of 91 Pima accessions. These markers would be useful in marker‐assisted selection of photoperiod response in cotton breeding. Further, quantitative gene expression analysis indicated that the CONSTANS (CO)/FLOWERING LOCUS T (FT) system is conserved in the photoperiod response pathway in Pima cotton, while CO and FT are likely not the causal genes underlying flowering time at the Gb_Ppd1 locus. The Gb_Ppd1 gene may be an upstream regulatory sequence in the FT gene pathway that controls photoperiodism in photoperiod‐sensitive cotton by affecting the CO/FT interaction under long‐day‐length conditions. Core Ideas The major effect photoperiod response locus (Gb_Ppd1) of Pima cotton was fine mapped to a 1.1 cM region flanked by new markers 15‐PR‐10A and 17‐KASP‐10. Targeted genomic mapping of Gb_Ppd1 locus identified 18 putative genes in 2.10 Mb region of Gossypium barbadense genome. Candidate gene analyses identified a homolog of VASCULAR PLANT ONE ZINC FINGER PROTEIN 1 as a candidate gene for Gb_Ppd1 locus. Quantitative expression analysis indicated that the CO/FT system in the photoperiod response pathway is likely conserved in Pima cotton, while CO is likely not the causal gene at the Gb_Ppd1 locus.