Validation of Genome-Wide Association Studies as a Tool to Identify Virulence Factors inParastagonospora nodorum

• DOI: 10.1094/phyto-02-16-0113-fi
• Publication Date: 2016-07-20T14:23:18Z
• Authors: Yuanyuan Gao; Zhaohui Liu; Justin D. Faris; Jonathan Richards; Robert S. Brueggeman; Xuehui Li; Richard P. Oliver; Bruce A. McDonald; Timothy L. Friesen
• Keywords: Genome-wide Association Study; SNP

Parastagonospora nodorum is a necrotrophic fungal pathogen causing Septoria blotch on wheat. We have identified nine effector–host dominant sensitivity gene interactions, and we cloned three of the effector genes, including SnToxA, SnTox1, SnTox3. Because sexual populations P. are difficult to develop under lab conditions, genome-wide association study (GWAS) best population genomic approach identify regions associated with traits using natural populations. In this article, used global collection 191 isolates from which 2,983 single-nucleotide polymorphism (SNP) markers for SnToxA SnTox3 evaluate power GWAS two popular wheat breeding lines that were sensitive Strong marker trait associations (MTA) virulence mapped first set described above. A novel locus in genome was also as result analysis. To whether sufficient level saturation available, designed primers every 1 kb containing Polymerase chain reaction amplification performed across presence/absence scored genotype. The proximity necessary MTA flanking ranged 4 5 7 kb, respectively. Similar analysis locus. Using 45% missing data threshold, more SNP spanning 4.6-kb region at These results showed rate linkage disequilibrium (LD) decay and, likely, other fungi high compared plants animals. fast LD an advantage only if density attained. Based our regions, needed 9 or 8 respectively, gene, guarantee genes quantitative such not missed.