Skip to main content
ARS Home » Southeast Area » New Orleans, Louisiana » Southern Regional Research Center » Cotton Fiber Bioscience Research » Research » Publications at this Location » Publication #246356
Title: A SNP Haplotype Associated with a gene resistant to Xanthomonas axonopodis pv. malvacearum in Upland Cotton (Gossyium hirsutum L.)

Author
item XIAO, JINHUA - Monsanto Corporation
item Fang, David
item BHATTI, MUHAMMAD - Monsanto Corporation
item HENDRIX, BILL - Monsanto Corporation
item CANTRELL, ROY - Monsanto Corporation

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/14/2009
Publication Date: 1/1/2010
Citation: Xiao, J., Fang, D.D., Bhatti, M., Hendrix, B., Cantrell, R.G. 2009. A SNP Haplotype Associated with a gene resistant to Xanthomonas axonopodis pv. malvacearum in Upland Cotton (Gossyium hirsutum L.). Molecular Breeding.25(4):593-602

Interpretive Summary: Cotton bacterial blight is a serious cotton disease caused by bacterium. In the US, yield losses caused by this disease in some years were as high as 3.4%. Breeding bacterial blight resistant cotton varieties is not easy due to difficulties in evaluating disease resistance in large populations. Development of DNA markers associated with resistance trait will greatly assist the integration of bacterial blight resistance into elite cotton varieties. In this research, resistance to cotton bacterial blight Race 18 was evaluated in 285 F5 families derived from resistant variety ‘DeltaOpal’ crossed by susceptible variety ‘DP388’. The cotton bacterial blight resistance in ‘DeltaOpal’ is controlled by one single dominant gene designated B12. Three simple sequence repeat (SSR) markers (one kind of DNA marker) were identified as closely linked to B12 that resides on chromosome 14. The association between the SSR marker CIR246 and B12 was validated among 16 diverse varieties. Furthermore, single nucleotide polymorphism (SNP, another type of DNA marker) markers closely linked to the marker CIR246 were used to screen ‘DeltaOpal’ and ‘DP388’ for polymorphism. The polymorphic SNP markers were run on the F5 population and the four SNP markers spanning 3.4 cM (unit to measure genetic distance) were found to flank the resistance gene. The linkage between B12 and the 4-SNP marker haplotype (combination of more than 2 closely-linked markers) was validated using additional 18 elite cotton lines. This 4-SNP marker haplotype can be used to select bacterial blight resistant individuals in breeding or for screening germplasm collections for their bacterial blight resistance with great accuracy.

Technical Abstract: An F5 population of 285 families with each tracing back to a different F2 plant , derived from a cotton bacterial blight resistant line ‘DeltaOpal’ and a susceptible line ‘DP388’, was artificially inoculated with bacterial blight race 18 (Xanthomonas campestris pv. Malvacearum) to assay their resistance or susceptibility to the disease. The segregation in the F5 population indicates that the resistance was conditioned by a single dominant gene designated B12. Simple sequence repeat (SSR) markers identified as putatively linked to the resistance gene by bulked segregant analysis were confirmed on the entire F5 population. Three SSR markers, CIR246, BNL3545 and BNL3644 on chromosome 14, were found closely linked to B12. The association between marker CIR246 and B12 was validated among 354 plants of 16 diverse varieties. Based on Monsanto SSR/SNP (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 F5 population and the four SNP markers spanning 3.4 cM were found to flank the resistance gene. The linkage between B12 and the 4-SNP marker haplotype was validated using 18 elite cotton lines. This 4-SNP marker haplotype can be used to select bacterial blight resistant individuals in breeding or for screening germplasm collections for their bacterial blight resistance with great accuracy.