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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVEMENT OF HARD RED SPRING AND DURUM WHEAT FOR DISEASE RESISTANCE AND QUALITY USING GENETICS AND GENOMICS

Location: Cereal Crops Research

Title: Association Mapping of Spot Blotch Resistance in Wild Barley

Authors
item Roy, Joy -
item Smith, Kevin -
item Muehlbauer, Gary -
item Chao, Shiaoman
item Close, Timothy -
item Steffenson, Brian -

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 25, 2010
Publication Date: August 1, 2010
Repository URL: http://hdl.handle.net/10113/43879
Citation: Roy, J.K., Smith, K.P., Muehlbauer, G.J., Chao, S., Close, T.J., Steffenson, B.J. 2010. Association Mapping of Spot Blotch Resistance in Wild Barley . Molecular Breeding. 26:243-256.

Interpretive Summary: Spot blotch, caused by Cochliobolus sativus, is an important foliar disease of barley. The disease has been controlled for over 40 years through the deployment of cultivars with durable resistance derived from line 'NDB112'. The pathogen strains of C. sativus that can overcome NDB112 resistance have been detected in the Northern Plains region; thus, many commercial cultivars are vulnerable to spot blotch epidemics. To increase the diversity of spot blotch resistance in cultivated barley, we evaluated 318 diverse wild barley accessions comprising the Wild Barley Diversity Collection (WBDC) for reaction to C. sativus at the seedling stage. Most of the accessions were from the Fertile Crescent, with fewer numbers from Central Asia, North Africa, and the Caucasus region. A high frequency of resistance was found in the WBDC as 95 percent (302/318) of the accessions exhibited low infection responses, indicating that these accessions may carry novel resistance genes. To identify and map resistance genes on barley chromosome, we utilized a genetic mapping strategy called association mapping (AM) to find DNA markers closely associated with the trait using a mechanism known as linkage disequilibrium (LD). LD is the association of a gene or DNA marker with its neighboring DNA markers, which form a block that can be passed on from parents to progeny without breaking up. It facilitates mapping of a complex trait with finer resolution. In contrast to conventional linkage mapping where mapping populations need to be developed by crossing two parents with genetic difference followed by an analysis of co-segregation of the markers with the trait among progeny, individuals used in AM need not be closely related, creation of mapping populations therefore is not required. The WBDC was genotyped with over 3,400 DNA markers, including 2,878 single nucleotide polymorphic (SNP) markers, which is a marker system that can differentiate individuals based on variations detected at the level of a single nucleotide base in the genome. Results from AM analysis identified twenty-three locations distributed on each of the seven barley chromosomes containing genes responsible for spot blotch resistance. About half of the genes mapped to chromosome locations where spot blotch resistance genes were previously reported based on linkage analysis, offering validation for the AM approach. The other genes mapped to unique genomic regions and may represent new spot blotch resistance. This study demonstrates that AM is an effective technique for identifying and mapping genes for disease resistance in a wild crop progenitor.

Technical Abstract: Spot blotch, caused by Cochliobolus sativus, is an important foliar disease of barley. The disease has been controlled for over 40 years through the deployment of cultivars with durable resistance derived from line 'NDB112.' Pathotypes of C. sativus with virulence for the NDB112 resistance have been detected in the region;thus, many commercial cultivars are vulnerable to spot blotch epidemics. To increase the diversity of spot blotch resistance in cultivated barley, we evaluated 318 diverse wild barley accessions comprising the Wild Barley Diversity Collection (WBDC) for reaction to C. sativus at the seedling stage and utilized an association mapping (AM) approach to identify and map resistance loci. A high frequency of resistance was found in the WBDC as 95% (302/318) of the accessions exhibited low infection responses. The WBDC was genotyped with 558 Diversity Array Technology (DArT(r)) and 2,878 single nucleotide polymorphic (SNP)markers and subjected to structure analysis before running the AM procedure. Twenty-three QTL for spot blotch resistance were identified with DArT and SNP markers. These QTL were found on each of the seven barley chromosomes and explained from 2.0 to 3.9% of the phenotypic variance. About half of the QTL mapped to chromosome bins where spot blotch resistance loci were previously reported, offering validation for the AM approach. The other QTL mapped to unique genomic regions and may represent new spot blotch resistance loci. This study demonstrates that AM is an effective technique for identifying and mapping QTL for disease resistance in a wild crop progenitor.

Last Modified: 9/22/2014
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