Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important disease of wheat worldwide. Exploring new resistance genes is essential for breeding resistant wheat cultivars. PI 182103, a spring wheat landrace originally from Pakistan, has shown a high level of resistance to stripe rust in fields for many years, but genes for resistance to stripe rust in the variety have not been studied. To map the resistance gene(s) in PI 182103, 185 recombinant inbred lines (RILs) were developed from a cross with Avocet Susceptible (AvS). The RIL population was genotyped with simple sequence repeat (SSR) and single nucleotide polymorphism markers and tested with races PST-100 and PST-114 at the seedling stage under controlled greenhouse conditions and at the adult-plant stage in fields at Pullman and Mt. Vernon, Washington under natural infection by the stripe rust pathogen in 2011, 2012, and 2013. A total of five quantitative trait loci (QTL) were detected. QyrPI182103.wgp-2AS and QyrPI182103.wgp-3AL were detected at the seedling stage, QyrPI182103.wgp-4DL was detected only in Mt. Vernon field tests, and QyrPI182103.wgp-5BS was detected in both seedling and field tests. QyrPI182103.wgp-7BL was identified as a high-temperature adult-plant resistance gene and detected in all field tests. Interactions among the QTL were mostly additive, but some negative interactions were detected. The 7BL QTL was mapped in chromosomal bin 7BL 0.40 to 0.45 and identified as a new gene, permanently designated as Yr79. SSR markers Xbarc72 and Xwmc335 flanking the Yr79 locus were highly polymorphic in various wheat genotypes, indicating that the molecular markers are useful for incorporating the new gene for potentially durable stripe rust resistance into new wheat cultivars.

Tyee, one of the wheat cultivars used to differentiate races of Puccinia striiformis f. sp. tritici in the United States, was identified to have a single gene for all-stage resistance, tentatively named YrTye. To map the gene, Tyee was crossed with ‘Avocet Susceptible’ (AvS). Genetic analysis of the F₁, F₂, F_2:3, and BC₁ progenies confirmed a single dominant gene for resistance to race PSTv-37 that is avirulent to YrTye. A mapping population of 135 F₂ plants was phenotyped with PSTv-37 and the derived F_2:3 lines were tested with races PSTv-37, PSTv-40, and PSTv-79. The F₂ mapping population was genotyped with simple sequence repeat (SSR) markers. A genetic map comprising 13 SSR markers located YrTye in chromosome 3AS flanked distally by SSR marker wmc11 and proximally by wmc532 at 2.6 and 3.4 cM, respectively. Amplification of Chinese Spring 3A deletion lines placed the gene in the distal bin 3AS4-0.45 to 1.00. Because YrTye is different from all formally named Yr genes in chromosomal location, we permanently name the gene Yr76. A near-isogenic line of spring common wheat was developed and selected by testing F₃ lines derived from a AvS*4/Tyee cross with Tyee-avirulent and virulent races and the flanking markers. The specific SSR alleles flanking Yr76 were validated using cultivars and breeding lines with and without the gene, and showed high polymorphisms. The specificity of Yr76 is useful in differentiating P. striiformis f. sp. tritici races, and its tightly linked markers will be useful in developing resistant cultivars when combining the gene with other genes for resistance to stripe rust.

Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh most important crop in the world and is mainly cultivated for its underground storage root (SR). The genetic studies of this species have been hindered by a lack of high-quality reference sequence due to its complex genome structure. Diploid Ipomoea trifida is the closest relative and putative progenitor of sweetpotato, which is considered a model species for sweetpotato, including genetic, cytological, and physiological analyses. Here, we generated the chromosome-scale genome sequence of SR-forming diploid I. trifida var. Y22 with high heterozygosity (2.20%). Although the chromosome-based synteny analysis revealed that the I. trifida shared conserved karyotype with Ipomoea nil after the separation, I. trifida had a much smaller genome than I. nil due to more efficient eliminations of LTR-retrotransposons and lack of species-specific amplification bursts of LTR-RTs. A comparison with four non-SR-forming species showed that the evolution of the beta-amylase gene family may be related to SR formation. We further investigated the relationship of the key gene BMY11 (with identity 47.12% to beta-amylase 1) with this important agronomic trait by both gene expression profiling and quantitative trait locus (QTL) mapping. And combining SR morphology and structure, gene expression profiling and qPCR results, we deduced that the products of the activity of BMY11 in splitting starch granules and be recycled to synthesize larger granules, contributing to starch accumulation and SR swelling. Moreover, we found the expression pattern of BMY11, sporamin proteins and the key genes involved in carbohydrate metabolism and stele lignification were similar to that of sweetpotato during the SR development. We constructed the high-quality genome reference of the highly heterozygous I. trifida through a combined approach and this genome enables a better resolution of the genomics feature and genome evolutions of this species. Sweetpotato SR development genes can be identified in I. trifida and these genes perform similar functions and patterns, showed that the diploid I. trifida var. Y22 with typical SR could be considered an ideal model for the studies of sweetpotato SR development.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most serious plant diseases worldwide. Resistant cultivars are the most effective way to control the disease. YrTr1 is an important stripe rust resistance gene that has been used in wheat breeding programs and is represented in the host differential set to identify P. striiformis f. sp. tritici races in the United States. To map YrTr1, AvSYrTr1NIL was backcrossed to its recurrent parent Avocet S (AvS). Seedlings of BC₇F₂, BC₇F₃, and BC₈F₁ populations were tested with YrTr1-avirulent races under controlled conditions, and BC₇F₂ plants were genotyped using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. YrTr1 was mapped to the short arm of chromosome 1B using four SSR and seven SNP markers. The genetic distances of YrTr1 from the nearest flanking markers IWA2583 and IWA7480 were 1.8 and 1.3 centimorgans (cM), respectively. DNA amplification of a set of 21 Chinese Spring (CS) nulli-tetrasomic lines and seven CS 1B deletion lines with three SSR markers confirmed the chromosome arm location and further placed the gene in chromosomal bin region 1BS18 (0.5). The gene was determined to be about 7.4 cM proximal to Yr10. Based on multirace response array and chromosomal location, YrTr1 was determined to be different from other permanently named stripe rust resistance genes in chromosome arm 1BS and was named Yr85.

Sweetpotato (Ipomoea batatas L.), an important food and industrial crop in the world, has a highly heterozygous hexaploid genome, making the development of single nucleotide polymorphism (SNP) markers challenging. Identifying SNP loci and developing practical SNP markers are crucial for genomic and genetic research on sweetpotato. A restriction site-associated DNA sequencing analysis of 60 sweetpotato accessions in this study yielded about 7.97 million SNPs. Notably, 954 candidate SNPs were obtained from 21,681 high-quality SNPs. Based on their stability and polymorphism, 274 kompetitive allele specific PCR (KASP) markers were then developed and uniformly distributed on chromosomes. The 274 KASP markers were used to genotype 93 sweetpotato accessions to evaluate their utility for assessing germplasm and analyzing genetic diversity and population structures. These markers had respective mean values of 0.24, 0.34, 0.31, and 0.25 for minor allele frequency, heterozygosity, gene diversity, and polymorphic information content (PIC). Their genetic pedigree led to the division of all accessions into three primary clusters, which were found to be both interrelated and independent. Finally, 74 KASP markers with PIC values greater than 0.35 were selected as core markers. These markers were used to construct the DNA fingerprints of 93 sweetpotato accessions and were able to differentiate between all accessions. To the best of our knowledge, this is the first attempt at the development and application of KASP markers in sweetpotato. However, due to sweetpotato’s polyploidy, heterozygosity and the complex genome, the KASP marker conversion rate in this study was relatively low. To improve the KASP marker conversion rate, and accuracies in SNP discovery and marker validation, further studies including more accessions from underrepresented regions are needed in sweetpotato.