Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat in the world. Genetic resistance is the best strategy for control of the disease. Spring wheat landrace PI 181410 has shown high level resistance to stripe rust. The present study characterized the landrace to have both race-specific all-stage resistance and nonrace-specific high-temperature adult-plant (HTAP) resistance. To map quantitative trait loci (QTL) for the resistance in PI 181410, it was crossed with Avocet S (AvS), from which a recombinant inbred line population was developed. The F₅–F₈ populations were consecutively phenotyped for stripe rust response in multiple field environments under natural Pst infection, and the F₇ population was phenotyped in seedlings at low temperature and in adult-plant stage with selected Pst races in the greenhouse. The F₇ population was genotyped using the 90K wheat SNP chip. Three QTL, QYrPI181410.wgp-4AS, QYrPI181410.wgp-4BL, and QYrPI181410.wgp-5BL.1, from PI 181410 for all-stage resistance, were mapped on chromosome arms 4AS, 4BL, and 5BL, respectively. Four QTL, QYrPI181410.wgp-1BL, QYrPI181410.wgp-4BL, QYrPI181410.wgp-5AS, and QYrPI181410.wgp-5BL.2, were identified from PI 181410 for HTAP resistance and mapped to 1BL, 4BL, 5AS, and 5BL, respectively. Two QTL with minor effects on stripe rust response were identified from AvS and mapped to 2BS and 2BL. Four of the QTL from PI 181410 and one from AvS were potentially new. As the 4BL QTL was most effective and likely a new gene for stripe rust resistance, three kompetitive allele specific PCR (KASP) markers were developed for incorporating this gene into new wheat cultivars.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat worldwide. The disease is most preferably managed by developing and growing cultivars with high-level, durable resistance. To achieve high-level and long-lasting resistance, we developed a wheat line, RIL-Yr64/Yr15, by pyramiding Yr64 and Yr15, both on the chromosome 1BS and providing high resistance to all tested Pst races. To validate RIL-Yr64/Yr15 possessing both genes, we crossed it to Avocet S (AvS). The F₄ RILs from this cross were phenotyped with Pst races under controlled greenhouse conditions and also under natural Pst infection in the field. The population was genotyped with SSR markers previously reported to be linked to the resistance gene loci and with additional SSR and SNP-KASP markers along chromosome 1B. Both phenotype and genotype data confirmed the copresence of Yr64 and Yr15 in RIL-Yr64/Yr15, and the high-resolution linkage map dissected the chromosomal regions and traced their origins. New lines possessing these genes were selected from the F₅ population of cross AvS × RIL-Yr64/Yr15 by marker-assisted selection. These lines with the two highly effective genes should be more useful than individual gene lines for developing high-level, durable resistant wheat cultivars.

Rust fungi cause significant damage to wheat production worldwide. In order to mitigate disease impact and improve food security via durable resistance, it is important to understand the molecular basis of host–pathogen interactions. Despite a long history of research and high agricultural importance, still little is known about the interactions between the stripe rust fungus and wheat host on the gene expression level. Here, we present analysis of the molecular interactions between a major wheat pathogen—Puccinia striiformis f. sp. tritici (Pst)—in resistant and susceptible host backgrounds. Using plants with durable nonrace-specific resistance along with fully susceptible ones allowed us to show how gene expression patterns shift in compatible versus incompatible interactions. The pathogen showed significantly greater number and fold changes of overexpressed genes on the resistant host than the susceptible host. Stress-related pathways including MAPK, oxidation–reduction, osmotic stress, and stress granule formation were, almost exclusively, upregulated in the resistant host background, suggesting the requirement of the resistance-countermeasure mechanism facilitated by Pst. In contrast, the susceptible host background allowed for broad overrepresentation of the nutrient uptake pathways. This is the first study focused on the stripe rust pathogen–wheat interactions, on the whole transcriptome level, from the pathogen side. It lays a foundation for the better understanding of the resistant/susceptible hosts versus pathogenic fungus interaction in a broader sense.

Rice resistance (R) genes have been effectively deployed to prevent blast disease caused by the fungal pathogen Magnaporthe oryzae, one of the most serious threats for stable rice production worldwide. Weedy rice competing with cultivated rice may carry novel or lost R genes. The quantitative trait locus qBR12.3b was previously mapped between two single nucleotide polymorphism markers at the 10,633,942-bp and 10,820,033-bp genomic positions in a black-hull-awned (BHA) weed strain using a weed-crop-mapping population under greenhouse conditions. In this study, we found a portion of the known resistance gene Ptr encoding a protein with four armadillo repeats and confers a broad spectrum of blast resistance. We then analyzed the sequences of the Ptr gene from weedy rice, Ptr^BHA, and identified a unique amino acid glutamine at protein position 874. Minor changes of protein conformation of the Ptr^BHA gene were predicted through structural analysis of Ptr^BHA, suggesting that the product of Ptr^BHA is involved in disease resistance. A gene-specific codominant marker HJ17-13 from Ptr^BHA was then developed to distinguish alleles in weeds and crops. The Ptr^BHA gene existed in 207 individuals of the same mapping population, where qBR12.3b was mapped using this gene-specific marker. Disease reactions of 207 individuals and their parents to IB-33 were evaluated. The resistant individuals had Ptr^BHA whereas the susceptible individuals did not, suggesting that HJ17-13 is reliable to predict qBR12.3b. Taken together, this newly developed marker, and weedy rice genotypes carrying qBR12.3b, are useful for blast improvement using marker assisted selection.

Puccinia striiformis Westend. f. sp. tritici, commonly known as stripe rust, is an economically important pathogen of wheat (Triticum aestivum L.). The hexaploid club spring wheat cultivar JD contains both all-stage and adult plant resistance genes and exhibited consistent high resistance to stripe rust in the field. In this study, we aimed to identify the quantitative trait loci (QTL) for stripe rust resistance using a BC1F7 backcross inbred lines (BILs) population derived from the cross of JD and the recurrent parental line Avocet. The population was phenotyped in field plots in Washington state at Spillman Agronomy Farm in Pullman and Mount Vernon Northwest Washington Research and Extension Center (NWREC) in between 2014 and 2016. A major QTL, tentatively designated as QYrJD.wsu-1B, conferring all-stage resistance in JD background, was identified, and mapped at the telomere region on the short arm of chromosome 1B using the genotyping by sequencing (GBS) method. This QTL was further characterized with SSR markers and found to have the greatest LOD score and phenotypic effect using SSR marker wmc798 on chromosome 1BS. Seven additional QTLs associated with adult plant resistance were identified in the JD background on chromosomes 2D, 3A, 3B, 4A, 6B, and 7A with partial phenotypic effects.

Wheat (Triticum aestivum L.) is one of the major crops and a staple food for approximately 35% of the world population. Wheat production is constantly threatened by stripe rust, one of the most devastating wheat diseases, which is caused by Puccinia striiformis f. sp. tritici (Pst). Improving the disease resistance of wheat cultivars is the most efficient and sustainable way to control stripe rust. In this study, we aimed to explore the novel resistance resources in a collection of 180 cultivated emmer wheat accessions (T. turgidum ssp. dicoccum) collected from 32 countries on five continents. The cultivated emmer wheat accessions were genotyped by wheat Illumina iSelect 9 K single-nucleotide polymorphism (SNP) array, and phenotypes were evaluated in a greenhouse using four races and in five field environments. Conducting a genome-wide association study, we identified 14 quantitative trait loci (QTLs) associated with stripe rust resistance. Two QTLs, QYr.emmer-4A.2 and QYr.emmer-6A, confer all-stage resistance, and 12 QTLs, located on chromosomes 1A, 2A, 2B, 3A, 3B, 4A, 5A, 5B, 7A, and 7B, confer adult plant resistance (APR) to stripe rust. Compared with the known stripe rust resistance QTLs, most of the QTLs identified in this study are very likely novel QTLs. The APR QTL, QYr.emmer-7A, was consistently detected among multiple data sets from different environments and was validated using a biparental mapping population. The SNPs, simple sequence repeat markers and the genomic loci identified in this study will provide very useful information for QTL mapping and resistance breeding programs.