Association mapping of North American spring wheat breeding germplasm reveals loci conferring resistance to Ug99 and other African stem rust races

Abstract

BackgroundThe recently identified Puccinia graminis f. sp. tritici (Pgt) race TTKSK (Ug99) poses a severe threat to global wheat production because of its broad virulence on several widely deployed resistance genes. Additional virulences have been detected in the Ug99 group of races, and the spread of this race group has been documented across wheat growing regions in Africa, the Middle East (Yemen), and West Asia (Iran). Other broadly virulent Pgt races, such as TRTTF and TKTTF, present further difficulties in maintaining abundant genetic resistance for their effective use in wheat breeding against this destructive fungal disease of wheat. In an effort to identify loci conferring resistance to these races, a genome-wide association study was carried out on a panel of 250 spring wheat breeding lines from the International Maize and Wheat Improvement Center (CIMMYT), six wheat breeding programs in the United States and three wheat breeding programs in Canada.ResultsThe lines included in this study were grouped into two major clusters, based on the results of principal component analysis using 23,976 SNP markers. Upon screening for adult plant resistance (APR) to Ug99 during 2013 and 2014 in artificial stem rust screening nurseries at Njoro, Kenya and at Debre Zeit, Ethiopia, several wheat lines were found to exhibit APR. The lines were also screened for resistance at the seedling stage against races TTKSK, TRTTF, and TKTTF at USDA-ARS Cereal Disease Laboratory in St. Paul, Minnesota; and only 9 of the 250 lines displayed seedling resistance to all the races. Using a mixed linear model, 27 SNP markers associated with APR against Ug99 were detected, including markers linked with the known APR gene Sr2. Using the same model, 23, 86, and 111 SNP markers associated with seedling resistance against races TTKSK, TRTTF, and TKTTF were identified, respectively. These included markers linked to the genes Sr8a and Sr11 providing seedling resistance to races TRTTF and TKTTF, respectively. We also identified putatively novel Sr resistance genes on chromosomes 3B, 4D, 5A, 5B, 6A, 7A, and 7B.ConclusionOur results demonstrate that the North American wheat breeding lines have several resistance loci that provide APR and seedling resistance to highly virulent Pgt races. Using the resistant lines and the SNP markers identified in this study, marker-assisted resistance breeding can assist in development of varieties with elevated levels of resistance to virulent stem rust races including TTKSK.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0628-9) contains supplementary material, which is available to authorized users.

Spectral Reflectance for Indirect Selection and Genome‐Wide Association Analyses of Grain Yield and Drought Tolerance in North American Spring Wheat

“…3). This finding was consistent with the prior study using this germplasm collection (Bajgain et al, 2015). The modelbased structure analysis, however, identified five subgroups that were regrouped and aligned to these two primary clusters.…”

“…The SNP marker location and position were obtained from the wheat 90K consensus map (Wang et al, 2014). The results were compared with previous reports in the same association mapping population (Bajgain et al, 2015) and different wheat panels (Chao et al, 2010;Edae et al, 2014). Average map distance of markers in genetic linkage and LD-decay threshold were visualized in scatter plots of r 2 against map distance (cM).…”

“…A previous analysis indicated that a kinship-mixed linear model, which accounts for pairwise relatedness in mixed linear model, was optimum to identify MTAs for stem rust resistance in this panel (Bajgain et al, 2015). We tested this model along with three other models: general linear model with population structure (Price et al, 2006); mixed linear model with population structure and full relationship matrix (Yu et al, 2006), and a mixed linear model with population structure and compressed relationship matrix (Zhang et al, 2010).…”

“…Average map distance of markers in genetic linkage and LD-decay threshold were visualized in scatter plots of r 2 against map distance (cM). The results were compared with previous reports in the same association mapping population (Bajgain et al, 2015) and different wheat panels (Chao et al, 2010;Edae et al, 2014). The LD block creation procedure in JMP genomics 6.0 (SAS Institute, 2013) was used to create LD blocks at a more stringent D prime threshold.…”

Characterizing and Validating Stripe Rust Resistance Loci in US Pacific Northwest Winter Wheat Accessions (Triticum aestivumL.) by Genome‐wide Association and Linkage Mapping

“…These MTAs were characterized from the advanced generations of PNW breeding materials that have improved agronomic traits. Incorporating these resistance alleles into diverse PNW wheat germplasm reduces linkage drag and facilitates adaptation to the local environment and, thus, will be more efficient than using MTAs detected from landraces (Bajgain et al, 2015).…”