Phytoene synthase gene GbDYA modulates carotenoids accumulation and confers yellow anther and pollen antioxidant activity in cotton

Carotenoids are natural pigments that are widely distributed in the flowers, fruits, and seeds of many plant species. These compounds not only endow diverse colors but also exhibit antioxidant, immune-modulatory, anti-aging, and photoprotective properties. Although carotenoid metabolism has been studied extensively in microbial and plant science, the genetic mechanisms underlying carotenoid metabolism in cotton remain underexplored. Here, we isolated gene GbDYA that regulates a dark-yellow anther color by map-based cloning using a BC₁F₁ population derived from a cross of Gossypium barbadense acc. Hai7124 with dark-yellow anthers and G. hirsutum acc. TM-1 with light-yellow anthers backcrossed with TM-1. GbDYA encodes phytoene synthase, a key rate-limiting enzyme in the carotenoid biosynthesis pathway. A long terminal repeat retrotransposon in the first exon of GhDYA (an ortholog of GbDYA in G. hirsutum acc. TM-1) caused loss of function and led to the light-yellow anther color. GbDYA is predominantly expressed in the early stages of anther development. Transcriptome, RT-qPCR and KEGG enrichment analyses revealed that GbDYA influences the synthesis and accumulation of carotenoids in anthers by modulating expression of key genes in the carotenoid biosynthesis pathway. Integrated transcriptomic and metabolomic analyses indicated that the accumulation of lutein, violaxanthin, antherxanthin, cryptoxanthin, zeaxanthin, and β-carotene contributed to yellow coloration of anthers. Dual-luciferase and yeast one-hybrid assays confirmed that transcription factor GbMYB105 (GB_A11G3511) binds to the promoter of GbDYA and activates its expression. High-temperature stress treatment indicated that carotenoids accumulation in anthers enhances pollen antioxidant activity. This study unravels the role of GbDYA in conferring the anther coloration, and provides the potential utilization by modulating accumulation of carotenoids in anthers to enhance pollen viability in high-temperature tolerance breeding in cotton.