Leaf rust is an important disease, threatening wheat production annually. Identification of resistance genes or QTLs for effective field resistance could greatly enhance our ability to breed durably resistant varieties. We applied a genome wide association study (GWAS) approach to identify resistance genes or QTLs in 338 spring wheat breeding lines from public and private sectors that were predominately developed in the Americas. A total of 46 QTLs were identified for field and seedling traits and approximately 20–30 confer field resistance in varying degrees. The 10 QTLs accounting for the most variation in field resistance explained 26–30% of the total variation (depending on traits: percent severity, coefficient of infection or response type). Similarly, the 10 QTLs accounting for most of the variation in seedling resistance to different races explained 24–34% of the variation, after correcting for population structure. Two potentially novel QTLs (QLr.umn-1AL, QLr.umn-4AS) were identified. Identification of novel genes or QTLs and validation of previously identified genes or QTLs for seedling and especially adult plant resistance will enhance understanding of leaf rust resistance and assist breeding for resistant wheat varieties. We also developed computer programs to automate field and seedling rust phenotype data conversions. This is the first GWAS study of leaf rust resistance in elite wheat breeding lines genotyped with high density 90K SNP arrays.

Leaf rust (caused by Puccinia triticina Erikss. [Pt]) is increasingly impacting durum wheat (Triticum turgidum L. var. durum) production with the recent appearance of races with virulence to widely grown cultivars in many durum producing areas worldwide. A highly virulent P. triticina race on durum wheat was recently detected in Kansas. This race may spread to the northern Great Plains, where most of the US durum wheat is produced. The objective of this study was to identify sources of resistance to several races from the United States and Mexico at seedling stage in the greenhouse and at adult stage in field experiments. Genome-wide association study (GWAS) was used to identify single-nucleotide polymorphism (SNP) markers associated with leaf rust response in a worldwide durum wheat collection of 496 accessions. Thirteen accessions were resistant across all experiments. Association mapping revealed 88 significant SNPs associated with leaf rust response. Of these, 33 SNPs were located on chromosomes 2A and 2B, and 55 SNPs were distributed across all other chromosomes except for 1B and 7B. Twenty markers were associated with leaf rust response at seedling stage, while 68 markers were associated with leaf rust response at adult plant stage. The current study identified a total of 14 previously uncharacterized loci associated with leaf rust response in durum wheat. The discovery of these loci through association mapping (AM) is a significant step in identifying useful sources of resistance that can be used to broaden the relatively narrow leaf rust resistance spectrum in durum wheat germplasm. Abbreviations: AM, association mapping; ARS, Agricultural Research Service; CDL, Cereal Disease Laboratory; GWAS, genome-wide association study; IT, infection type; LD, linkage disequilibrium; MAF, minor allele frequency; MR, moderately resistant; MS, moderately susceptible; MSD, mean squared difference; NSGC, National Small Grain Collection; PC, principal component; PCA, principal component analysis; pFDR, positive false discovery rate; Pt, Puccinia triticina Erikss.; QTL, quantitative trait loci; R, resistant; S, susceptible; SNP, single-nucleotide polymorphism; SSR, simple-sequence repeat. Core Ideas• Thirteen durum wheat accessions showed resistance to all Puccinia triticina races tested• GWAS revealed 88 SNPs (37 loci) associated with leaf rust response in durum wheat• Associations were identified on all chromosomes except 1B and 7B• GWAS revealed 14 previously uncharacterized loci for leaf rust resistance

Silphium perfoliatum L. (cup plant, silphie) and S. integrifolium Michx. (rosinweed, silflower) are in the same subfamily and tribe as sunflower (Helianthus annuus L.). Silphium perfoliatum has been grown in many countries as a forage or bioenergy crop with forage quality approaching that of alfalfa (Medicago sativa L.) and biomass yield close to maize (Zea mays L.) in some environments. Silphium integrifolium has large seeds with taste and oil quality similar to traditional oilseed sunflower. Silphium species are all long‐lived, diploid perennials. Crops from this genus could improve the yield stability, soil, and biodiversity of agricultural landscapes because, in their wild state, they are deep rooted and support a wide diversity of pollinators. In contrast with premodern domestication, de novo domestication should be intentional and scientific. We have the luxury and obligation at this moment in history to expand the domestication ideotype from food and energy production to include (i) crop‐driven ecosystem services important for sustainability, (ii) genetic diversity to enable breeding progress for centuries, (iii) natural adaptations and microbiome associations conferring resource use efficiency and stress tolerance, and (iv) improving domestication theory itself by monitoring genetic and ecophysiological changes from predomestication baselines. Achieving these goals rapidly will require the use of next‐generation sequencing for marker development and an international, interdisciplinary team committed to collaboration and strategic planning.

We 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. Leaf 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.