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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Cereal Crops Research » Research » Publications at this Location » Publication #330116
Title: Validation of genome-wide association studies as a tool to identify virulence factors in Parastagonospora nodorum

Author
item GAO, YUANYUAN - North Dakota State University
item LIU, ZHAOHUI - North Dakota State University
item Faris, Justin
item RICHARDS, JONATHAN - North Dakota State University
item BRUEGGEMAN, ROBERT - North Dakota State University
item LI, XUEHUI - North Dakota State University
item OLIVER, RICHARD - Curtin University
item MCDONALD, BRUCE - Swiss Federal Institute Of Technology Zurich
item Friesen, Timothy

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/8/2016
Publication Date: 8/15/2016
Publication URL: https://handle.nal.usda.gov/10113/63343
Citation: Gao, Y., Liu, Z., Faris, J.D., Richards, J., Brueggeman, R.S., Li, X., Oliver, R.P., McDonald, B.A., Friesen, T.L. 2016. Validation of genome-wide association studies as a tool to identify virulence factors in Parastagonospora nodorum. Phytopathology. 106(10):1177-1185.

Interpretive Summary: Septoria nodorum blotch is caused by the fungal pathogen Parastagonospora nodorum. P. nodorum causes disease by secreting virulence factors called necrotrophic effectors. We have identified nine necrotrophic effector-host dominant sensitivity gene interactions, and we have cloned three of the necrotrophic effector (NE) genes, including SnToxA, SnTox1 and SnTox3. genome wide association study (GWAS) is a way to use natural genetic variation to identify genomic regions responsible for virulence including necrotrophic effectors. Using this technique we identified strong marker trait associations (MTA) with P. nodorum virulence that mapped to SnTox3 and SnToxA, validating the GWAS model. A novel locus associated with P. nodorum virulence was also identified as a result of this analysis. Our results also showed that the rate of linkage disequilibrium (LD) decay in P. nodorum, and likely other fungi, is high compared to plants and animals. Based on our results with the SnToxA and SnTox3 regions, markers are needed every 9 or 8 kb, respectively, or in every gene, to guarantee that genes associated with a quantitative trait such as virulence are not missed.

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