A genome-wide association study of field and seedling response to stem rust pathogen races reveals combinations of race-specific resistance genes in North American spring wheat

Authors: EDAE, ERENA; PUMPHREY, MICHAEL - WASHINGTON STATE UNIVERSITY; ROUSE, MATTHEW

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/10/2018
Publication Date: 1/30/2018
Citation: Edae, E.A., Pumphrey, M.O., Rouse, M.N. 2018. A genome-wide association study of field and seedling response to stem rust pathogen races reveals combinations of race-specific resistance genes in North American spring wheat. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2018.00052.
DOI: https://doi.org/10.3389/fpls.2018.00052

Interpretive Summary: Stem rust of wheat caused by the fungal pathogen Puccinia graminis f. sp. tritici historically caused major yield losses of wheat worldwide. To understand the genetic basis of stem rust resistance in conventional North American spring wheat, genome-wide association analysis (GWAS) was conducted on a panel of 250 conventional North American spring wheat lines. The lines were evaluated in four separate nurseries each inoculated with a different P. graminis f. sp. tritici race for three years (2013, 2015 and 2016) at Rosemount, Minnesota. The lines were also challenged with the same four races at the seedling stage in a greenhouse facility at the USDA-ARS Cereal Disease Laboratory. A total of 22,310 high-quality SNPs obtained from the Infinium 90,000 SNP chip were used to perform association analysis. Markers strongly associated with resistance to the four races at seedling and field environments were identified. At the seedling stage, the most significant marker-trait associations were detected in the regions of known major genes (Sr6, Sr7a and Sr9b) except for race QFCSC where a strong association was detected on chromosome arm 1AL. The markers that showed strong association signals may be useful to pyramid and track race-specific major stem rust resistance genes in wheat breeding programs. We postulated the presence of Sr2, Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, Sr24, and Sr57 (Lr34) in this germplasm based on phenotypic and marker data. We found that combinations of genes conferring resistance to specific P. graminis f. sp. tritici races accounts for the prevalent stem rust resistance in North American spring wheat.

Technical Abstract: Stem rust of wheat caused by the fungal pathogen Puccinia graminis f. sp. tritici historically caused major yield losses of wheat worldwide. To understand the genetic basis of stem rust resistance in conventional North American spring wheat, genome-wide association analysis (GWAS) was conducted on a panel of 250 conventional North American spring wheat lines. The lines were evaluated in four separate nurseries each inoculated with a different P. graminis f. sp. tritici race for three years (2013, 2015 and 2016) at Rosemount, Minnesota. The lines were also challenged with the same four races at the seedling stage in a greenhouse facility at the USDA-ARS Cereal Disease Laboratory. A total of 22,310 high-quality SNPs obtained from the Infinium 90,000 SNP chip were used to perform association analysis. Markers strongly associated with resistance to the four races at seedling and field environments were identified. At the seedling stage, the most significant marker-trait associations were detected in the regions of known major genes (Sr6, Sr7a and Sr9b) except for race QFCSC where a strong association was detected on chromosome arm 1AL. Markers presumably linked to Sr6 and Sr7a were associated with both seedling and field resistance to specific races. A field resistance QTL on chromosome arm 2DS was detected for response to race RCRSC and TPMKC. A QTL specific to field resistance was detected for QFCSC and TPMKC on 2BL. The markers that showed strong association signals may be useful to pyramid and track race-specific major stem rust resistance genes in wheat breeding programs. We postulated the presence of Sr2, Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, Sr24, and Sr57 (Lr34) in this germplasm based on phenotypic and marker data. We found that combinations of genes conferring resistance to specific P. graminis f. sp. tritici races accounts for the prevalent stem rust resistance in North American spring wheat.