Genome‐wide exploration of bacterial leaf blight resistance and fine mapping of major resistance gene ( <i>Bb13</i> ) in upland cotton ( <i>Gossypium hirsutum</i> L.)

Cotton bacterial blight (CBB), caused by Xanthomonas citri subsp. malvacearum (Xcm), continues to pose a significant threat to upland cotton (Gossypium spp.) production across the US Cotton Belt. To elucidate the genetic basis of resistance to race 18 of CBB and identify potential novel resistance sources, we conducted genome-wide association studies (GWASs) using a diversity panel of 661 upland cotton accessions that included elite US germplasm, tropical landraces, and University of Arkansas germplasm releases. GWAS identified a single 3.3 Mb region on chromosome D02 corresponding to the BB13 locus as the primary determinant of race 18 resistance, with no additional major loci detected, indicating Bb13 as the predominant race 18 resistance source in upland cotton. Population genetic analyses suggested uneven distribution of the Bb13 gene across US breeding programs and landraces, likely originating from the African cultivar S295. Linkage mapping in six recombinant inbred line (RIL) populations confirmed segregation of race 18 resistance at the BB13 locus. Fine mapping using PCR allele competitive extension (PACE) markers delimited BB13 locus to a 154.28 kb interval containing nine candidate genes, six of which have homologs implicated in plant disease resistance pathways. The PACE marker CBB16, co-segregating with resistance in both the diversity panel and RIL populations, was identified as a diagnostic marker for Bb13. Local haplotyping further revealed marker groups and haplotypes associated with CBB resistance. Results from this study provide key genomic tools for breeding CBB-resistant cultivars and establish the foundation for positional cloning of the Bb13 gene.