Integrative genomic structural variation analysis unveils genetic architecture underlying important traits in Gossypium barbadense.

Key message: Through GWAS incorporating SVs, we identified 143 loci in Gossypium barbadense, including pleiotropic loci governing fiber quality (FQ1 and FQ2), maturity (GS1), and trichome development (LH1 and SH1). Gossypium barbadense is renowned for its exceptional fiber quality, yet its limited environmental adaptability has resulted in genetic research lagging far behind that of G. hirsutum. Here, we generated a comprehensive genomic variation map of 326 G. barbadense accessions, encompassing SNPs, InDels, and structural variations (SVs). Integrative genome-wide association studies (GWAS) of 25 traits identified 143 significant loci. The SV-based GWAS uncovered 61 loci linked to targeted traits, 53 of which were novel loci and undetectable using SNPs alone. Five pleiotropic hotspots were associated with fiber quality (FQ1, FQ2), maturity and plant architecture (GS1), and trichome development (LH1, SH1). We demonstrated additive effects of two fiber quality loci (FQ1 and FQ2) on D10 and D11, where pyramiding favorable haplotypes simultaneously improve fiber length (FL) and micronaire (FM). Transcriptome analysis further implicated Gbar_D10G011020 and Gbar_D11G011510 as candidate genes for FQ1 and FQ2, respectively. The genetic basis of trichome development was deciphered through the pleiotropic locus LH1 (A06), regulating leaf and stem trichomes in G. barbadense. Concurrently, the stem hair-specific locus SH1 on D08 harbored GbSTR, which synergizes with LH1 to increase stem trichome. Our study establishes a genomic framework for comprehensively identification of causal variations underlying key traits in G. barbadense, providing actionable loci and genes for more efficient genetic enhancement of both G. hirsutum and G. barbadense.