Genome-wide Mapping for Stripe Rust Resistance Loci in Common Wheat Cultivar Qinnong 142

Mapping QTLs for adult-plant resistance to powdery mildew and stripe rust using a recombinant inbred line population derived from cross Qingxinmai × 041133

A recombinant inbred line (RIL) population derived from wheat landrace Qingxinmai and breeding line 041133 exhibited segregation in resistance to powdery mildew and stripe rust in five and three field tests, respectively. A 16K genotyping by target sequencing (GBTS) single-nucleotide polymorphism (SNP) array-based genetic linkage map was used to dissect the quantitative trait loci (QTLs) for disease resistance. Four and seven QTLs were identified for adult-plant resistance (APR) against powdery mildew and stripe rust. QPm.caas-1B and QPm.caas-5A on chromosomes 1B and 5A were responsible for the APR against powdery mildew in line 041133. QYr.caas-1B, QYr.caas-3B, QYr.caas-4B, QYr.caas-6B.1, QYr.caas-6B.2, and QYr.caas-7B detected on the five B-genome chromosomes of line 041133 conferred its APR to stripe rust. QPm.caas-1B and QYr.caas.1B were co-localized with the pleiotropic locus Lr46/Yr29/Sr58/Pm39/Ltn2. A Kompetitive Allele Specific Polymorphic (KASP) marker KASP_1B_668028290 was developed to trace QPm/Yr.caas.1B. Four lines pyramiding six major disease resistance loci, PmQ, Yr041133, QPm/Yr.caas-1B, QPm.caas-2B.1, QYr.caas-3B, and QPm.caas-6B, were developed. They displayed effective resistance against both powdery mildew and stripe rust at the seedling and adult-plant stages.

Identification and fine-mapping of QYrAS286-2BL conferring adult-plant resistance to stripe rust in cultivated emmer wheat

KEY MESSAGE

A novel major adult-plant stripe rust resistance QTL derived from cultivated emmer wheat was mapped to a 123.6-kb region on wheat chromosome 2BL. Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat. Identification of new sources of resistance and their utilization in breeding programs is the effectively control strategy. The objective of this study was to identify and genetically characterize the stripe rust resistance derived from the cultivated emmer accession AS286. A recombinant inbred line population, developed from a cross between the susceptible durum wheat line langdon and AS286, was genotyped using the Wheat55K single nucleotide polymorphism array and evaluated in field conditions with a mixture of the prevalent Chinese Pst races (CYR32, CYR33, CYR34, Zhong4, and HY46) and in growth chamber with race CYR34. Three QTLs conferring resistance were mapped on chromosomes 1BS, 2BL, and 5BL, respectively. The QYrAS286-1BS and QYrAS286-2BL were stable with major effects, explaining 12.91% to 18.82% and 11.31% to 31.43% of phenotypic variation, respectively. QYrAS286-5BL was only detected based on growth chamber seedling data. RILs harboring both QYrAS286-1BS and QYrAS286-2BL showed high levels of stripe rust resistance equal to the parent AS286. The QYrAS286-2BL was only detected at the adult-plant stage, which is different from previously named Yr genes and inherited as a single gene. It was further mapped to a 123.6-kb region using KASP markers derived from SNPs identified by bulked segregant RNA sequencing (BSR-Seq). The identified loci enrich our stripe rust resistance gene pool, and the flanking markers developed here could be useful in marker-assisted selection for incorporating QYrAS286-2BL into wheat cultivars.

Slow stripe rusting in Chinese wheat Jimai 44 conferred by Yr29 in combination with a major QTL on chromosome arm 6AL

YrJ44, a more effective slow rusting gene than Yr29, was localized to a 3.5-cM interval between AQP markers AX-109373479 and AX-109563479 on chromosome 6AL. "Slow rusting" (SR) is a type of adult plant resistance (APR) that can provide non-specific durable resistance to stripe rust in wheat. Chinese elite wheat cultivar Jimai 44 (JM44) has maintained SR to stripe rust in China since its release despite exposure to a changing and variable pathogen population. An F2:6 population comprising 295 recombinant inbred lines (RILs) derived from a cross between JM44 and susceptible cultivar Jimai 229 (JM229) was used in genetic analysis of the SR. The RILs and parental lines were evaluated for stripe rust response in five field environments and genotyped using the Affymetrix Wheat55K SNP array and 13 allele-specific quantitative PCR-based (AQP) markers. Two stable QTL on chromosome arms 1BL and 6AL were identified by inclusive composite interval mapping. The 1BL QTL was probably the pleiotropic gene Lr46/Yr29/Sr58. QYr.nwafu-6AL (hereafter named YrJ44), mapped in a 3.5-cM interval between AQP markers AX-109373479 and AX-109563479, was more effective than Yr29 in reducing disease severity and relative area under the disease progress curve (rAUDPC). RILs harboring both YrJ44 and Yr29 displayed levels of SR equal to the resistant parent JM44. The AQP markers linked with YrJ44 were polymorphic and significantly correlated with stripe rust resistance in a panel of 1,019 wheat cultivars and breeding lines. These results suggested that adequate SR resistance can be obtained by combining YrJ44 and Yr29 and the AQP markers can be used in breeding for durable stripe rust resistance.

Molecular characterization and validation of adult-plant stripe rust resistance gene Yr86 in Chinese wheat cultivar Zhongmai 895

KEY MESSAGE

Adult-plant stripe rust resistance gene Yr86 in Chinese wheat cultivar Zhongmai 895 was mapped to the physical interval 710.2-713.2 Mb on the long arm of chromosome 2A. Adult-plant resistance to stripe rust is generally more durable than all-stage resistance. Chinese wheat cultivar Zhongmai 895 showed stable stripe rust resistance at the adult-plant stage. To map the genetic loci underlying its resistance, 171 doubled haploid (DH) lines from a Yangmai 16/Zhongmai 895 cross were genotyped with the wheat 660 K SNP chip. Disease severities of the DH population and parents were assessed in four environments. A major QTL designated QYryz.caas-2AL was mapped to interval 703.7-715.3 Mb on the long arm of chromosome 2A using both chip-based and KASP (kompetitive allele-specific PCR) marker-based methods, explaining 31.5 to 54.1% of the phenotypic variances. The QTL was further validated in an F₂ population of cross Emai 580/Zhongmai 895 with 459 plants and a panel of 240 wheat cultivars using KASP markers. Three reliable KASP markers predicted a low frequency (7.2-10.5%) of QYryz.caas-2AL in the test panel and remapped the gene to the physical interval 710.2-713.2 Mb. Based on different physical positions or genetic effects from known genes or QTL on chromosome arm 2AL, the gene was predicted to be a new one for adult-plant stripe rust resistance and was named Yr86. Twenty KASP markers linked to Yr86 were developed in this study based on wheat 660 K SNP array and genome re-sequencing. Three of them are significantly associated with stripe rust resistance in natural population. These markers should be useful for marker-assisted selection and also provide a starting point for fine mapping and map-based cloning of the new resistance gene.

Rapid and Sensitive Detection of Fungicide-Resistant Crop Fungal Pathogens Using an Isothermal Amplification Refractory Mutation System

Fungicide abuse leads to the emergence of fungicide-resistant fungal pathogens, thus posing a threat to agriculture and food safety. Here, we developed an isothermal amplification refractory mutation system (termed iARMS) allowing us to resolve genetic mutations, enabling rapid, sensitive, and potentially field-applicable detection of fungicide-resistant crop fungal pathogens. iARMS yielded a limit of detection of 25 aM via a cascade signal amplification strategy of recombinase polymerase amplification (RPA) and Cas12a-mediated collateral cleavage at 37 °C within 40 min. Specificity for fungicide-resistant Puccinia striiformis (P. striiformis) detection was guaranteed by RPA primers and the flexible sequence of gRNA. The iARMS assay allowed us to detect as low as 0.1% cyp51-mutated P. striiformis that showed resistance to the demethylase inhibitor (DMI), which was 50 times more sensitive than the sequencing techniques. Thus, it is promising for the discovery of rare fungicide-resistant isolates. We applied iARMS to investigate the emergence of fungicide-resistant P. striiformis in western China and found that its proportion was over 50% in Qinghai, Sichuan, and Xinjiang Province. iARMS can serve as a molecular diagnostic tool for crop diseases and facilitate precision plant disease management.

High density mapping of wheat stripe rust resistance gene QYrXN3517-1BL using QTL mapping, BSE-Seq and candidate gene analysis

Fine mapping of a major stripe rust resistance locus QYrXN3517-1BL to a 336 kb region that includes 12 candidate genes. Utilization of genetic resistance is an effective strategy to control stripe rust disease in wheat. Cultivar XINONG-3517 (XN3517) has remained highly resistant to stripe rust since its release in 2008. To understand the genetic architecture of stripe rust resistance, Avocet S (AvS) × XN3517 F₆ RIL population was assessed for stripe rust severity in five field environments. The parents and RILs were genotyped by using the GenoBaits Wheat 16 K Panel. Four stable QTL from XINONG-3517 were detected on chromosome arms 1BL, 2AL, 2BL, and 6BS, named as QYrXN3517-1BL, QYrXN3517-2AL, QYrXN3517-2BL, and QYrXN3517-6BS, respectively. Based on the Wheat 660 K array and bulked segregant exome sequencing (BSE-Seq), the most effective QTL on chromosome 1BL is most likely different from the known adult plant resistance gene Yr29 and was mapped to a 1.7 cM region [336 kb, including twelve candidate genes in International Wheat Genome Sequencing Consortium (IWGSC) RefSeq version 1.0]. The 6BS QTL was identified as Yr78, and the 2AL QTL was probably same as QYr.caas-2AL or QYrqin.nwafu-2AL. The novel QTL on 2BL was effective in seedling stage against the races used in phenotyping. In addition, allele-specifc quantitative PCR (AQP) marker nwafu.a5 was developed for QYrXN3517-1BL to assist marker-assisted breeding.

Fine Mapping of Stripe-Rust-Resistance Gene YrJ22 in Common Wheat by BSR-Seq and MutMap-Based Sequencing

Identification and accurate mapping of new resistance genes are essential for gene pyramiding in wheat breeding. The YrJ22 gene is a dominant stripe-rust-resistance gene located at the distal end of chromosome 2AL, which was identified in a leading Chinese-wheat variety, Jimai 22, showing high resistance to CYR32, a prevalent race of Puccinia striiformis tritici (Pst) in China. In the current study, 15 F₁ and 2273 F₂ plants derived from the cross of Jimai 22/Avocet S were used for the fine-mapping of YrJ22. The RNA-Seq of resistant and susceptible bulks of F₂ plants (designated BSR-Seq) identified 10 single-nucleotide polymorphisms (SNP) in a 12.09 Mb physical interval on chromosome 2AL. A total of 1022 EMS-induced M₃ lines of Jimai 22 were screened, to identify susceptible mutants for MutMap analysis. Four CAPS markers were developed from SNPs identified using BSR-Seq and MutMap. A linkage map for YrJ22 was constructed with 11 CAPS/STS and three SSR markers. YrJ22 was located at a 0.9 cM genetic interval flanked by markers H736 and H400, corresponding to a 340.46 kb physical region (768.7-769.0 Mb), including 13 high-confidence genes based on the Chinese Spring reference genome. TraesCS2A01G573200 is a potential candidate-gene, according to linkage and quantitative real-time PCR (qPCR) analyses. The CAPS marker H732 designed from an SNP in TraesCS2A01G573200 co-segregated with YrJ22. These results provide a useful stripe-rust-resistance gene and molecular markers for marker-assisted selection in wheat breeding and for further cloning of the gene.

Epistatic interaction effect between chromosome 1BL (Yr29) and a novel locus on 2AL facilitating resistance to stripe rust in Chinese wheat Changwu 357-9

Four stable QTL for adult plant resistance were identified in wheat line Changwu 357-9, including a new QTL on 2AL showing significant interaction with Yr29 to reduce stripe rust severity. Stripe rust (yellow rust) is a serious disease of bread wheat (Triticum aestivum L.) worldwide. Genetic resistance is considered the most economical, effective and environmentally friendly method to control the disease and to minimize the use of fungicides. The current study focused on characterizing the components of stripe rust resistance and understanding the interactions in Changwu 357-9 (CW357-9)/Avocet S RIL population. A genetic linkage map constructed using a new GenoBaits Wheat 16K Panel and the 660K SNP array had 5104 polymorphic SNP markers spanning 3533.11 cM. Four stable QTL, consistently identified across five environments, were detected on chromosome arms 1BL, 2AL, 3DS, and 6BS in Changwu357-9. The most effective QTL QYrCW357-1BL was Yr29. The 6BS QTL was identified as Yr78, which has been combined with the 1BL QTL in many wheat cultivars and breeding lines. The novel QTL on 2AL with moderate effect showed a stable and significant epistatic interaction with Yr29. The QTL on 3DL should be same as QYrsn.nwafu-3DL and enriches the overall stripe rust resistance gene pool for breeding. Polymorphisms of flanking AQP markers AX-110020417 (for QYrCW357-1BL), AX-110974948 (for QYrCW357-2AL), AX-109466386 (for QYrCW357-3DL), and AX-109995005 (for QYrCW357-6BS) were evaluated in a diversity panel including 225 wheat cultivars and breeding lines. These results suggested that these high-throughput markers could be used to introduce QYrCW357-1BL, QYrCW357-2AL, QYrCW357-3DL, and QYrCW357-6BS into commercial wheat cultivars. Combinations of these genes with other APR QTL should lead to higher levels of stripe rust resistance along with the beneficial effects of multi-disease resistance gene Yr29 on improving resistance to other diseases.

Genome-Wide Wheat 55K SNP-Based Mapping of Stripe Rust Resistance Loci in Wheat Cultivar Shaannong 33 and Their Alleles Frequencies in Current Chinese Wheat Cultivars and Breeding Lines

Wheat cultivar Shaannong 33 (SN33) has remained highly resistant to stripe rust in the field since its release in 2009. To unravel the genetic architecture of stripe rust resistance, seedlings of 161 recombinant inbred lines (RILs) from the cross Avocet S × SN33 were evaluated with two isolates (PST-Lab.1 and PST-Lab.2) of the stripe rust pathogen (Puccinia striiformis f. sp. tritici) in the greenhouse, and the RILs were evaluated in naturally or artificially inoculated field sites during two cropping seasons. The RILs and parents were genotyped with the wheat 55K single-nucleotide polymorphism array. Three genomic regions conferring seedling resistance were mapped on chromosomes 1DS, 2AS, and 3DS, and four consistent quantitative trait loci (QTL) for adult-plant resistance (APR) were detected on 1BL, 2AS, 3DL, and 6BS. The 2AS locus conferring all-stage resistance was identified as the resistant gene Yr17 located on 2NS translocation. The QTL identified on 1BL and 6BS likely correspond to Yr29 and Yr78, respectively. An APR QTL on 3DL explaining 5.8 to 12.2% of the phenotypic variation is likely to be new. Molecular marker detection assays with the 2NS segment (Yr17), Yr29, Yr78, and QYrsn.nwafu-3DL on a panel of 420 current Chinese wheat cultivars and breeding lines indicated that these genes were present in 11.4, 7.6, 14.8, and 7.4% of entries, respectively. The interactions among these genes and QTL were additive, suggesting their potential value in enhancing stripe rust resistance breeding materials as observed in the resistant parent. In addition, we also identified two leaf necrosis genes, Ne1 and Ne2; however, the F₁ plants from cross Avocet S × SN33 survived, indicating that SN33 probably has another allele of Ne1 which allows seed to be harvested.

QTL Analysis of Adult Plant Resistance to Stripe Rust in a Winter Wheat Recombinant Inbred Population

Stripe rust, caused by the fungus Puccinia striiformis f. sp. tritici, is a worldwide disease of wheat that causes devastating crop losses. Resistant cultivars have been developed over the last 40 years that have significantly reduced the economic impact of the disease on growers, but in heavy infection years it is mostly controlled through the intensive application of fungicides. The Pacific Northwest of the United States has an ideal climate for stripe rust and has one of the most diverse race compositions in the country. This has resulted in many waves of epidemics that have overcome most of the resistance genes traditionally used in elite germplasm. The best way to prevent high yield losses, reduce production costs to growers, and reduce the heavy application of fungicides is to pyramid multiple stripe rust resistance genes into new cultivars. Using genotyping-by-sequencing, we identified 4662 high quality variant positions in a recombinant inbred line population of 196 individuals derived from a cross between Skiles, a highly resistant winter wheat cultivar, and Goetze, a moderately to highly susceptible winter wheat cultivar, both developed at Oregon State University. A subsequent genome wide association study identified two quantitative trait loci (QTL) on chromosomes 3B and 3D within the predicted locations of stripe rust resistance genes. Resistance QTL, when combined together, conferred high levels of stripe rust resistance above the level of Skiles in some locations, indicating that these QTL would be important additions to future breeding efforts of Pacific Northwest winter wheat cultivars.

Molecular breeding for rust resistance in wheat genotypes

Rusts are a group of major diseases that have an adverse effect on crop production. Those targeting wheat are found in three principal forms: leaf, stripe, and stem rust. Leaf rust causes foliar disease in wheat; in Egypt, this causes a significant annual yield loss. The deployment of resistant genotypes has proved to be a relatively economical and environmentally sustainable method of controlling the disease. Gene pyramiding can be performed using traditional breeding techniques. Additionally, pathotypes can be introduced to examine specific leaf rust genes, or the breeder may conduct more complex breeding methods. Indirect selection via DNA markers linked to resistance genes may facilitate the transfer of targeted genes, either individually or in combination, even in a disease-free environment. The use of selective crosses to counter virulent races of leaf, stripe, and stem rust has resulted in the transfer of several resistance genes into new wheat germplasm from cultivated or wild species. Quantitative trait locus (QTL) technology has been adopted in a wide variety of novel approaches and is becoming increasingly recognized in wheat breeding. Moreover, several researchers have reported the transference of leaf and stripe rust resistance genes into susceptible wheat cultivars.

Genome-Wide Association Studies in Diverse Spring Wheat Panel for Stripe, Stem, and Leaf Rust Resistance

Among several important wheat foliar diseases, Stripe rust (YR), Leaf rust (LR), and Stem rust (SR) have always been an issue of concern to the farmers and wheat breeders. Evolution of virulent pathotypes of these rusts has posed frequent threats to an epidemic. Pyramiding rust-resistant genes are the most economical and environment-friendly approach in postponing this inevitable threat. To achieve durable long term resistance against the three rusts, an attempt in this study was made searching for novel sources of resistant alleles in a panel of 483 spring wheat genotypes. This is a unique and comprehensive study where evaluation of a diverse panel comprising wheat germplasm from various categories and adapted to different wheat agro-climatic zones was challenged with 18 pathotypes of the three rusts with simultaneous screening in field conditions. The panel was genotyped using 35K SNP array and evaluated for each rust at two locations for two consecutive crop seasons. High heritability estimates of disease response were observed between environments for each rust type. A significant effect of population structure in the panel was visible in the disease response. Using a compressed mixed linear model approach, 25 genomic regions were found associated with resistance for at least two rusts. Out of these, seven were associated with all the three rusts on chromosome groups 1 and 6 along with 2B. For resistance against YR, LR, and SR, there were 16, 18, and 27 QTL (quantitative trait loci) identified respectively, associated at least in two out of four environments. Several of these regions got annotated with resistance associated genes viz. NB-LRR, E3-ubiquitin protein ligase, ABC transporter protein, etc. Alien introgressed (on 1B and 3D) and pleiotropic (on 7D) resistance genes were captured in seedling and adult plant disease responses, respectively. The present study demonstrates the use of genome-wide association for identification of a large number of favorable alleles for leaf, stripe, and stem rust resistance for broadening the genetic base. Quick conversion of these QTL into user-friendly markers will accelerate the deployment of these resistance loci in wheat breeding programs.

Genome-Wide Linkage Mapping Reveals Stripe Rust Resistance in Common Wheat (Triticum aestivum) Xinong1376

Stripe rust, also known as yellow rust, is a significant threat to wheat yield worldwide. Adult plant resistance (APR) is the preferred way to obtain durable protection. Chinese winter wheat cultivar Xinong1376 has maintained acceptable APR to stripe rust in field environments. To characterize APR in this cultivar, 190 F₁₀ recombinant inbred lines (RILs) developed from Xiaoyan81 × Xinong1376 were evaluated for infection type and disease severity in fields either artificially or naturally inoculated. The population along with parents were genotyped using the Illumina 90K single-nucleotide polymorphism arrays. Six quantitative trait loci (QTL) were detected using the inclusive composite interval mapping method. QYr.nwafu-4AL and QYr.nwafu-6BL.3 conferred stable resistance in all environments, and likely corresponded to a gene-rich region on the long arm of chromosomes 4A and 6B. QYr.nwafu-5AL, QYr.nwafu-5BL, QYr.nwafu-3BL.1, and QYr.nwafu-3BL.2 were detected only in some environments but enhanced the level of resistance conferred by QYr.nwafu-4AL and QYr.nwafu-6BL.3. Kompetitive allele-specific PCR (KASP) markers developed for QYr.nwafu-4AL and QYr.nwafu-6BL.3 were confirmed in a subset of RILs and 133 wheat genotypes. The QTL on 4AL and 6BL with their linked KASP markers would be useful for marker-assisted selection to improve stripe rust resistance in breeding programs.

A major QTL co-localized on chromosome 6BL and its epistatic interaction for enhanced wheat stripe rust resistance

Co-localization of a major QTL for wheat stripe rust resistance to a 3.9-cM interval on chromosome 6BL across both populations and another QTL on chromosome 2B with epistatic interaction. Cultivars with diverse resistance are the optimal strategy to minimize yield losses caused by wheat stripe rust (Puccinia striiformis f. sp. tritici). Two wheat populations involving resistant wheat lines P10078 and Snb"S" from CIMMYT were evaluated for stripe rust response in multiple environments. Pool analysis by Wheat660K SNP array showed that the overlapping interval on chromosome 6B likely harbored a major QTL between two populations. Then, linkage maps were constructed using KASP markers, and a co-localized locus with large effect on chromosome 6BL was detected using QTL analysis in both populations. The coincident QTL, named QYr.nwafu-6BL.2, explained 59.7% of the phenotypic maximum variation in the Mingxian 169 × P10078 and 52.5% in the Zhengmai 9023 × Snb"S" populations, respectively. This co-localization interval spanning 3.9 cM corresponds to ~ 30.5-Mb genomic region of the newest common wheat reference genome (IWGSC RefSeq v.1.0). In addition, another QTL was also detected on chromosome 2B in Zhengmai 9023 × Snb"S" population and it can accelerate expression of QYr.nwafu-6BL.2 to enhance resistance with epistatic interaction. Allowing for Pst response, marker genotypes, pedigree analysis and relative genetic distance, QYr.nwafu-6BL.2 is likely to be a distinct adult plant resistance QTL. Haplotype analysis of QYr.nwafu-6BL.2 revealed specific SNPs or alleles in the target region from a diversity panel of 176 unrelated wheat accessions. This QTL region provides opportunity for further map-based cloning, and haplotypes analysis enables pyramiding favorable alleles into commercial cultivars by marker-assisted selection.