Genetic and biochemical analyses identify a major locus, GH-PA1, underlying pollen carotenoid accumulation and pigmentation in upland cotton

The cotton genus Gossypium shows wide variation for pollen color. Pima cotton (G. barbadense), which is known for premium fiber quality, is characterized by yellow/orange pollen, while the widely cultivated upland cotton (G. hirsutum) usually has cream-colored pollen. We conducted a genome-wide association study using a diversity panel of 136 accessions of upland cotton genotyped with the cottonSNP63K array and identified three significant marker-trait associations for pollen color within a 226 kb region on chromosome A05. Phenotyping of two recombinant inbred line (RIL) populations derived from the parental accessions DES 56 (white pollen), and Sealand #2 and Southland M1 (yellow pollen) at the F1 and F5 generations showed that the yellow pollen color was controlled by a single dominant gene at a locus designated as GH-PA1. Molecular mapping using two RIL populations genotyped with SNP markers further localized GH-PA1 locus to a 5.36 cM region on chromosome A05. The flanking markers (i12529Gh and i12525Gh) of the GH-PA1 locus in the linkage map identified a 112.83 kb region in the sequence-based physical map. This genomic region consisted of four putative genes, with one predicted to encode phytoene synthase of the carotenoid biosynthetic pathway was identified as a probable candidate gene controlling the yellow pollen color. Analysis of phytochemicals confirmed higher carotenoid content in yellow- than in white-colored pollen grains, while no significant differences in flavonoids were found. Deciphering the molecular-genetic architecture of GH-PA1 could aid in the understanding of the role of phytochemicals in cotton pollen physiology and adaptation.