Cotton bacterial leaf blight (CBB), caused by Xanthomonas citri subsp. malvacearum (Xcm) has been periodically a damaging disease in the U.S.A. Identi cation and deployment of genetic resistance in the cotton cultivars is the most economical and e cient 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 F 6 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 signi cant 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 identi ed thirty putative gene sequences in the targeted region. Nine of the thirty putative genes were involved in disease resistance in plants. Key MessageIdenti cation and genomic characterization of major resistance locus against cotton bacterial blight (CBB) using GWAS and linkage mapping to enable genomics-based development of durable CBB resistance and gene discovery in cotton.

In cotton, most agronomic traits are controlled by polygenes. In this study, 110 F 6 recombinant inbred lines (RILs), derived from Upland cotton cross NC05AZ06 x NC11-2100, were used to develop a linkage map and to identify quantitative trait loci (QTL) for six fiber quality traits, three yield traits, and plant height. These RILs were genotyped using the CottonSNP63K array and phenotyped for fiber quality, yield traits, and plant height in 2-year field trials. Analysis of variance revealed significant (p < 0.05) differences among RILs for all traits studied, and the heritability estimates were moderate (30%-60%) to high (> 60%). Both positive and negative correlations were observed for fiber quality and yield traits. A total of 3,774 polymorphic SNP markers were used to develop a genetic map with an average marker density of 1.54 SNP/cM. Thirty QTL for fiber quality traits, yield traits, and plant height were detected on 15 different chromosomes, explaining 6.80%-20.02% of the phenotypic variance (PVE). Of these, 14 were major QTL (PVE > 10%), and three major QTL were detected in both years. Candidate gene analysis in the major QTL detected in both years and plant height QTL with PVE of 20.02% revealed five putative genes for fiber quality traits and one putative gene for plant height. The linkage map and identified QTL along with the candidate genes in the study could serve as additional breeding resources for Upland cotton genetic improvement.

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.