A genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a worldwide collection of hexaploid spring wheat (Triticum aestivum L.)

Authors: MACAFERRI, MARCO - University Of Bologna; ZHANG, JUNLI - University Of California; BULLI, PETER - Washington State University; ABATE, ZEWDIE - University Of California; Chao, Shiaoman; CANTU, DARIO - University Of California; BOSSOLINI, ELIGIO - University Of California; Chen, Xianming; PUMPHREY, MICHAEL - Washington State University; DUBCOVSKY, JORGE - Howard Hughes Medical Institute

Submitted to: Genes, Genomes, and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/17/2015
Publication Date: 1/20/2015
Publication URL: http://handle.nal.usda.gov/10113/60474
Citation: Macaferri, M., Zhang, J., Bulli, P., Abate, Z., Chao, S., Cantu, D., Bossolini, E., Chen, X., Pumphrey, M., Dubcovsky, J. 2015. A genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a worldwide collection of hexaploid spring wheat (Triticum aestivum L.). Genes, Genomes, and Genomics. 5(3):449-465.

Interpretive Summary: Stripe rust disease of wheat caused by a fungal pathogen poses a major threat to global wheat production and negatively impacts grain quality. Although multiple fungicide applications can control this pathogen, developing resistant varieties is the most efficient and environmentally sustainable means for reducing losses due to the disease. Because new races of the pathogen can evolve and defeat previously deployed resistance genes, it is critical to identify new sources of resistance genes to continue the efforts on combating the disease. In this study a worldwide collection of 875 spring wheat for resistance against the stripe rust pathogens was investigated. Resistance was evaluated both at the seedling stage in controlled environments and at the adult plant stage in multiple years and field locations in western U.S. Genetic analysis results have revealed at least ten chromosome regions strongly associated with the resistance. A comparison with previously known resistance genes indicated that seven out of the ten regions likely harbor novel sources of resistance. This study provides an integrated view of stripe rust resistance resources in spring wheat and identifies new resistance gene regions that will be useful to diversify the current set of resistance genes deployed to control this devastating disease.

Technical Abstract: New races of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, show high virulence to previously deployed resistance genes and are causing large yield losses worldwide. To identify new sources of resistance we performed a genome-wide association study (GWAS) using a worldwide collection of 875 spring wheat. Adult plants were evaluated under field conditions in six environments in western USA, and seedlings were tested with four Pst races. A single nucleotide polymorphism (SNP) Infinium 9K-assay provided 4,374 mapped SNPs suitable for GWAS. Population structure had a moderate effect on Pst response (R2 = 0.14-0.17). High correlations among environments and high heritabilities were observed for all Pst evaluations. GWAS identified 7 QTL (single or multiple linked SNPs) that were consistent across at least three environments and that showed an experiment-wise adjusted Bonferroni probability lower than 0.10. A second analysis excluding accessions with complete resistance identified 3 additional QTL for partial resistance. These 10 QTL explained 15% of the phenotypic variation in infection type, a percentage that increased to 19% when six significant pair-wise interactions were included in the model. A comparison with previously mapped Yr genes and Pst resistance QTL indicated that seven out of the 10 significant GWAS associations likely represent novel sources of resistance. In summary, this study provides an integrated view of stripe rust resistance resources in spring wheat and identifies new resistance loci that will be useful to diversify the current set of resistance genes deployed to control this devastating disease.