A SNP haplotype associated with a gene resistant to Xanthomonas axonopodis pv. malvacearum in upland cotton (Gossypium hirsutum L.)

An F(4:5) population of 285 families with each tracing back to a different F(2) plant, derived from a cotton bacterial blight resistant line 'DeltaOpal' and a susceptible line 'DP388', was artificially inoculated with bacterial blight race 18 (Xanthomonas axonopodis pv. malvacearum) to assay their resistance or susceptibility to the disease. The segregation in the F(4:5) population indicates that the resistance was conditioned by a single dominant gene designated B (12.) Simple sequence repeat (SSR) markers identified as putatively linked to the resistance gene by bulked segregant analysis were confirmed on the entire F(4:5) population. Three SSR markers, CIR246, BNL3545 and BNL3644 on chromosome 14, were found closely linked to B (12) . The association between CIR246 and B (12) was validated among 354 plants of 16 diverse varieties. Based on Monsanto SSR/single nucleotide polymorphism (SNP) consensus map, SNP markers closely linked to CIR246 were used to screen 'DeltaOpal' and 'DP388' for polymorphism. The polymorphic SNP markers were run on the F(4:5) population and the four SNP markers spanning 3.4 cM were found to flank the resistance gene on chromosome 14. The linkage between B (12) and the 4-SNP marker haplotype was validated using 18 elite cotton lines. This 4-SNP marker haplotype can be used for marker assisted selection for bacterial blight resistance breeding programs or for screening germplasm collections for this locus rapidly.