Identification and genomic characterization of major effect bacterial blight resistance locus (BB-13) in Upland cotton (Gossypium hirsutum L.)

Abstract Cotton bacterial leaf blight (CBB), caused by Xanthomonas citri subsp. malvacearum (Xcm) has been periodically a damaging disease in the U.S.A. Identification and deployment of genetic resistance in the cotton cultivars is the most economical and efficient means of reducing the crop losses due to CBB. In the current study, a combined genome-wide association study (GWAS) and linkage-mapping approach was used to map the CBB resistance gene in Upland cotton. An elite diversity panel of 380 accessions, genotyped with the Cotton 63K single nucleotide polymorphism (SNP) array and phenotyped with race-18 of CBB was used in the GWAS. The GWAS localized the CBB resistance to a 2.01 Mb region in the long arm of chromosome D02. Mapping of this CBB resistance was further resolved using linkage mapping in an F6 recombinant inbred line (RIL) population derived from Acala Maxxa × Arkot 8102. The CBB resistance in Arkot 8102 showed monogenic inheritance. The CBB resistance locus (BB-13) was mapped within the 0.95 cM interval near the telomeric region in the long arm of chromosome D02. Flanking SNP markers, i25755Gh (p = 19.29) and i46775Gh (p = 19.29) of the BB-13 locus from the linkage analysis showed the highest significant marker-trait associations (MTAs) in the GWAS study. Using these SNPs, we targeted the BB-13 locus to a 371 Kb genomic region on chromosome D02. Candidate gene analysis identified thirty putative gene sequences in the targeted region. Nine of the thirty putative genes were involved in disease resistance in plants.