Peter Bulli

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.)

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 responsible for large yield losses worldwide. To identify new sources of resistance we performed a genome-wide association study (GWAS) using a worldwide collection of 1000 spring wheat accessions. Adult plants were evaluated under field conditions in six environments in the western United States, and seedlings were tested with four Pst races. A single-nucleotide polymorphism (SNP) Infinium 9K-assay provided 4585 SNPs suitable for GWAS. High correlations among environments and high heritabilities were observed for stripe rust infection type and severity. Greater levels of Pst resistance were observed in a subpopulation from Southern Asia than in other groups. GWAS identified 97 loci that were significant for at least three environments, including 10 with an experiment-wise adjusted Bonferroni probability < 0.10. These 10 quantitative trait loci (QTL) explained 15% of the phenotypic variation in infection type, a percentage that increased to 45% when all QTL were considered. Three of these 10 QTL were mapped far from previously identified Pst resistance genes and QTL, and likely represent new resistance loci. The other seven QTL mapped close to known resistance genes and allelism tests will be required to test their relationships. 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.

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

The 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. The 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. Our 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.

Genetic Architecture of Resistance to Stripe Rust in a Global Winter Wheat Germplasm Collection

Virulence shifts in populations of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, are a major challenge to resistance breeding. The majority of known resistance genes are already ineffective against current races of Pst, necessitating the identification and introgression of new sources of resistance. Germplasm core collections that reflect the range of genetic and phenotypic diversity of crop species are ideal platforms for examining the genetic architecture of complex traits such as resistance to stripe rust. We report the results of genetic characterization and genome-wide association analysis (GWAS) for resistance to stripe rust in a core subset of 1175 accessions in the National Small Grains Collection (NSGC) winter wheat germplasm collection, based on genotyping with the wheat 9K single nucleotide polymorphism (SNP) iSelect assay and phenotyping of seedling and adult plants under natural disease epidemics in four environments. High correlations among the field data translated into high heritability values within and across locations. Population structure was evident when accessions were grouped by stripe rust reaction. GWAS identified 127 resistance loci that were effective across at least two environments, including 20 with significant genome-wide adjusted P-values. Based on relative map positions of previously reported genes and QTL, five of the QTL with significant genome-wide adjusted P-values in this study represent potentially new loci. This study provides an overview of the diversity of Pst resistance in the NSGC winter wheat germplasm core collection, which can be exploited for diversification of stripe rust resistance in breeding programs.

Mapping a Large Number of QTL for Durable Resistance to Stripe Rust in Winter Wheat Druchamp Using SSR and SNP Markers

Winter wheat Druchamp has both high-temperature adult-plant (HTAP) resistance and all-stage resistance to stripe rust caused by Puccinia striiformis f. sp. tritici (Pst). The HTAP resistance in Druchamp is durable as the variety has been resistant in adult-plant stage since it was introduced from France to the United States in late 1940s. To map the quantitative trait loci (QTL) for stripe rust resistance, an F8 recombinant inbred line (RIL) population from cross Druchamp × Michigan Amber was phenotyped for stripe rust response in multiple years in fields under natural infection and with selected Pst races under controlled greenhouse conditions, and genotyped with simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. Composite interval mapping (CIM) identified eight HTAP resistance QTL and three all-stage resistance QTL. Among the eight HTAP resistance QTL, QYrdr.wgp-1BL.2 (explaining 2.36-31.04% variation), QYrdr.wgp-2BL (2.81–15.65%), QYrdr.wgp-5AL (2.27–17.22%) and QYrdr.wgp-5BL.2 (2.42–15.13%) were significant in all tests; and QYrdr.wgp-1BL.1 (1.94–10.19%), QYrdr.wgp-1DS (2.04–27.24%), QYrdr.wgp-3AL (1.78–13.85%) and QYrdr.wgp-6BL.2 (1.69–33.71%) were significant in some of the tests. The three all-stage resistance QTL, QYrdr.wgp-5BL.1 (5.47–36.04%), QYrdr.wgp-5DL (9.27–11.94%) and QYrdr.wgp-6BL.1 (13.07-20.36%), were detected based on reactions in the seedlings tested with certain Pst races. Among the eleven QTL detected in Druchamp, at least three (QYrdr.wgp-5DL for race-specific all-stage resistance and QYrdr.wgp-3AL and QYrdr.wgp-6BL.2 for race non-specific HTAP resistance) are new. All these QTL, especially those for durable HTAP resistance, and their closely linked molecular markers could be useful for developing wheat cultivars with durable resistance to stripe rust.

Association mapping of leaf rust resistance loci in a spring wheat core collection

Key messageWe identified 15 potentially novel loci in addition to previously characterized leaf rust resistance genes from 1032 spring wheat accessions. Targeted AM subset panels were instrumental in revealing interesting loci.AbstractLeaf rust is a common disease of wheat, consistently reducing yields in many wheat-growing regions of the world. Although fungicides are commonly applied to wheat in the United States (US), genetic resistance can provide less expensive, yet effective control of the disease. Our objectives were to map leaf rust resistance genes in a large core collection of spring wheat accessions selected from the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection (NSGC), determine whether previously characterized race-nonspecific resistance genes could be identified with our panel, and evaluate the use of targeted panels to identify seedling and adult plant resistance (APR) genes. Association mapping (AM) detected five potentially novel leaf rust resistance loci on chromosomes 2BL, 4AS, and 5DL at the seedling stage, and 2DL and 7AS that conditioned both seedling and adult plant resistance. In addition, ten potentially novel race-nonspecific resistance loci conditioned field resistance and lacked seedling resistance. Analyses of targeted subsets of the accessions identified additional loci not associated with resistance in the complete core panel. Using molecular markers, we also confirmed the presence and effectiveness of the race-nonspecific genes Lr34, Lr46, and Lr67 in our panel. Although most of the accessions in this study were susceptible to leaf rust in field and seedling tests, many resistance loci were identified with AM. Through the use of targeted subset panels, more loci were identified than in the larger core panels alone.

Multi-locus mixed model analysis of stem rust resistance in winter wheat

Multi‐locus association mapping outperforms single‐locus genome scans in polyploid species. Single nucleotide polymorphism marker IWA435 reliably detects the 1BL.1RS rye translocation in diverse germplasm. Markers linked to three novel stem rust resistance loci were identified.

Unlocking Diversity in Germplasm Collections via Genomic Selection: A Case Study Based on Quantitative Adult Plant Resistance to Stripe Rust in Spring Wheat

Larger germplasm collections may be efficiently sampled via lower‐density genotyping methods. The selection population needs to be well represented in the training set. Good prospects for applying genomic selection to efficiently unlock the potential of plant genetic resources exist.

Loci associated with resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a core collection of spring wheat (Triticum aestivum)

Stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst) remains one of the most significant diseases of wheat worldwide. We investigated stripe rust resistance by genome-wide association analysis (GWAS) in 959 spring wheat accessions from the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection, representing major global production environments. The panel was characterized for field resistance in multi-environment field trials and seedling resistance under greenhouse conditions. A genome-wide set of 5,619 informative SNP markers were used to examine the population structure, linkage disequilibrium and marker-trait associations in the germplasm panel. Based on model-based analysis of population structure and hierarchical Ward clustering algorithm, the accessions were clustered into two major subgroups. These subgroups were largely separated according to geographic origin and improvement status of the accessions. A significant correlation was observed between the population sub-clusters and response to stripe rust infection. We identified 11 and 7 genomic regions with significant associations with stripe rust resistance at adult plant and seedling stages, respectively, based on a false discovery rate multiple correction method. The regions harboring all, except three, of the QTL identified from the field and greenhouse studies overlap with positions of previously reported QTL. Further work should aim at validating the identified QTL using proper germplasm and populations to enhance their utility in marker assisted breeding.