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ARS Home » Southeast Area » New Orleans, Louisiana » Southern Regional Research Center » Cotton Fiber Bioscience Research » Research » Publications at this Location » Publication #242311
Title: A New SNP Haplotype associated with blue disease resistance gene in cotton (Gossypium hirsutum L.)

Author
item Fang, David
item XIAO, JINHUA - Monsanto Corporation
item CANCI, PAULO - Monsanto Corporation
item CANTRELL, ROY - Monsanto Corporation

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/12/2009
Publication Date: 12/4/2009
Citation: Fang, D.D., Xiao, J., Canci, P.C., Cantrell, R.G. 2009. A New SNP Haplotype associated with blue disease resistance gene in cotton (Gossypium hirsutum L.). Journal of Theoretical and Applied Genetics. 120:943-953.

Interpretive Summary: Cotton blue disease (CBD) is a very serious cotton disease caused by virus. If not properly controlled, CBD can reduce cotton yield production as high as 80%. Breeding CBD 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 CBD resistance into elite cotton varieties. In this research, resistance to CBD was evaluated in 364 F2.3 families of 3 populations derived from resistant variety ‘Delta Opal’. The CBD resistance in ‘Delta Opal’ is controlled by one single dominant gene designated Cbd. Two simple sequence repeat (SSR) markers (one kind of DNA marker) were identified as linked to Cbd that resides on chromosome 10. SSR marker DC20027 was 0.75 cM away from Cbd. DC20027 marker fragments amplified from 3 relative species and 13 cotton varieties whose CBD resistance was known were cloned and sequenced. One single nucleotide polymorphism (SNP) (another kind of DNA marker) was identified. Screening SNP markers previously mapped on chromosome 10 identified an additional 3 SNP markers that were associated with Cbd. An association between a 4-SNP-marker combination and Cbd was developed. Application of these SNP markers will facilitate cotton breeders to bring this critical trait into elite cotton varieties.

Technical Abstract: Resistance to cotton blue disease (CBD) was evaluated in 364 F2.3 families of 3 populations derived from resistant variety ‘Delta Opal’. The CBD resistance in ‘Delta Opal’ was controlled by one single dominant gene designated Cbd. Two simple sequence repeat (SSR) markers were identified as linked to Cbd by bulked segregant analysis. Cbd resides at the telomere region of chromosome 10. SSR marker DC20027 was 0.75 cM away from Cbd. DC20027 marker fragments amplified from 3 diploid species and 13 cotton varieties whose CBD resistance was known were cloned and sequenced. One single nucleotide polymorphism (SNP) was identified at the 136th position by sequence alignment analysis. Screening SNP markers previously mapped on chromosome 10 identified an additional 3 SNP markers that were associated with Cbd. An association between a 4-SNP marker haplotype and Cbd was developed. Taqman® assays enables marker assisted selection for high levels of resistance in breeding programs for this critical trait. Key words: Cotton, blue disease, SSR, SNP, haplotype, marker assisted selection, bulked segregant analysis