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Key message: A novel light intensity-dependent lesion mimic mutant with enhanced disease resistance was physiologically, biochemically, and genetically characterized, and the causative gene was fine mapped to a 1.28 Mbp interval containing 17 high-confidence genes. Lesion mimic mutants are ideal for studying disease resistance and programmed cell death photosynthesis in plants to improve crop yield. In this study, a novel light intensity-dependent lesion mimic mutant (MC21) was obtained from the wheat variety Chuannong16 (CN16) by ethyl methane sulfonate treatment. The mutant initially developed tiny lesion spots on the basal part of the leaves, which then gradually proceeded down to leaf sheaths, stems, shells, and awns at the flowering stage. The major agronomic traits were significantly altered in the mutant compared to that in the wild-type CN16. Furthermore, the mutant exhibited a lesion phenotype with degenerated chloroplast structure, decreased chlorophyll content, increased level of reactive oxygen species, and increased resistance to stripe rust and powdery mildew. Genetic analysis indicated that the lesion phenotype was controlled by a novel single semi-dominant nuclear gene. The target gene was mapped on chromosome arm 2AL located between Kompetitive Allele Specific PCR (KASP) markers, KASP-4211 and KASP-5353, and tentatively termed as lesion mimic 5 (Lm5). The fine mapping suggested that Lm5 was located in a 1.28 Mbp interval between markers KASP-5825 and KASP-9366; 17 high-confidence candidate genes were included in this genomic region. This study provides an important foundational step for further cloning of Lm5 using a map-based approach. [ABSTRACT FROM AUTHOR]

Stripe rust (caused by Puccinia striiformis f. sp. tritici) is one of the most severe diseases affecting wheat production. The disease is best controlled by developing and growing resistant cultivars. Chinese wheat (Triticum aestivum) landraces have excellent resistance to stripe rust. The objectives of this study were to identify wheat landraces with stable resistance and map quantitative trait loci (QTL) for resistance to stripe rust from 271 Chinese wheat landraces using a genome-wide association study (GWAS) approach. The landraces were phenotyped for stripe rust responses at the seedling stage with two predominant Chinese races of P. striiformis f. sp. tritici in a greenhouse and the adult-plant stage in four field environments and genotyped using the 660K wheat single-nucleotide polymorphism (SNP) array. Thirteen landraces with stable resistance were identified, and 17 QTL, including eight associated to all-stage resistance and nine to adult-plant resistance, were mapped on chromosomes 1A, 1B, 2A, 2D, 3A, 3B, 5A, 5B, 6D, and 7A. These QTL explained 6.06–16.46% of the phenotypic variation. Five of the QTL, QYrCL.sicau-3AL , QYrCL.sicau-3B.4 , QYrCL.sicau-3B.5 , QYrCL.sicau-5AL.1 and QYrCL.sicau-7AL , were likely new. Five Kompetitive allele specific PCR (KASP) markers for four of the QTL were converted from the significant SNP markers. The identified wheat landraces with stable resistance to stripe rust, significant QTL, and KASP markers should be useful for breeding wheat cultivars with durable resistance to stripe rust. [ABSTRACT FROM AUTHOR]

Background: Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is a serious foliar disease of wheat. Identification of novel stripe rust resistance genes and cultivation of resistant cultivars are considered to be the most effective approaches to control this disease. In this study, we evaluated the infection type (IT), disease severity (DS) and area under the disease progress curve (AUDPC) of 143 Chinese wheat landrace accessions for stripe rust resistance. Assessments were undertaken in five environments at the adult-plant stage with Pst mixture races under field conditions. In addition, IT was assessed at the seedling stage with two prevalent Pst races (CYR32 and CYR34) under a controlled greenhouse environment. Results: Seventeen accessions showed stable high-level resistance to stripe rust across all environments in the field tests. Four accessions showed resistance to the Pst races CYR32 and CYR34 at the seedling stage. Combining phenotypic data from the field and greenhouse trials with 6404 markers that covered the entire genome, we detected 17 quantitative trait loci (QTL) on 11 chromosomes for IT associated with seedling resistance and 15 QTL on seven chromosomes for IT, final disease severity (FDS) or AUDPC associated with adult-plant resistance. Four stable QTL detected on four chromosomes, which explained 9.99–23.30% of the phenotypic variation, were simultaneously associated with seedling and adult-plant resistance. Integrating a linkage map of stripe rust resistance in wheat, 27 QTL overlapped with previously reported genes or QTL, whereas four and one QTL conferring seedling and adult-plant resistance, respectively, were mapped distantly from previously reported stripe rust resistance genes or QTL and thus may be novel resistance loci. Conclusions: Our results provided an integrated overview of stripe rust resistance resources in a wheat landrace diversity panel from the southern autumn-sown spring wheat zone of China. The identified resistant accessions and resistance loci will be useful in the ongoing effort to develop new wheat cultivars with strong resistance to stripe rust. [ABSTRACT FROM AUTHOR]

The discovery of functional genes underlying agronomic traits is of great importance for wheat improvement. Here we designed a new wheat exome capture probe panel based on IWGSC RefSeq v1.0 genome sequence information and developed an effective algorithm, varBScore, that can sufficiently reduce the background noise in gene mapping and identification. An effective method, termed b ulked s egregant e xome capture seq uencing (BSE-Seq) for identifying causal mutations or candidate genes was established by combining the use of a newly designed wheat exome capture panel, sequencing of bulked segregant pools from segregating populations, and the robust algorithm varBScore. We evaluated the effectiveness of varBScore on SNP calling using the published dataset for mapping and cloning the yellow rust resistance gene Yr7 in wheat. Furthermore, using BSE-Seq, we rapidly identified a wheat yellow leaf mutant gene, ygl1 , in an ethyl methanesulfonate (EMS) mutant population and found that a single mutation of G to A at 921 position in the wild type YGL1 gene encoding magnesium-chelatase subunit chlI caused the leaf yellowing phenotype. We further showed that mutation of YGL1 through CRISPR/Cas9 gene editing led to a yellow phenotype on the leaves of transgenic wheat, indicating that ygl1 is the correct causal gene responsible for the mutant phenotype. In summary, our approach is highly efficient for discovering causal mutations and gene cloning in wheat. [ABSTRACT FROM AUTHOR]

Chinese endemic wheat, comprising Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum), Yunnan hulled wheat (T. aestivum ssp. yunnanense), and Xinjiang rice wheat (T. petropavlovskyi), are genetically and morphologically unique. To examine the adult plant resistance to stripe rust among Chinese endemic wheat germplasms, a panel of 213 accessions was inoculated with mixed virulent races of wheat stripe rust (Puccinia striiformis f. sp. tritici) in four different field environments. Four traits associated with stripe rust resistance, infection type, final disease severity, disease index, and area under the disease progress curve, were used to evaluate the accessions. The phenotypic datasets were used for 55K single-nucleotide polymorphism (SNP) array-based genome-wide association studies to identify effective resistance loci. Eighty-nine accessions with stable resistance were identified in at least three of the four environments by phenotypic evaluation. Eleven markers located on chromosomes 1A, 2B, 5A, 5D, 7B, and 7D by the genome-wide association studies analysis showed significant associations with at least two resistance-associated traits in two of the environments. These loci, corresponding to seven genomic regions based on linkage disequilibrium decay distance, explained 9.3 to 26.0% of the total phenotypic variation. Five quantitative trait loci (QTLs) on chromosomes 1A, 2B, 7B, and 7D overlapped or were in close proximity to previously reported QTLs based on the consensus and physical maps using the reference sequence of bread wheat (IWGSC RefSeq v1.0). The other two QTLs were potential novel QTLs given their physical positions. Haplotype variants of QTL QYr.sicau-2BS showed subspecies-specific inheritance of the stripe rust resistance locus. Resistant loci among Chinese endemic wheat germplasms could be introduced into common wheat cultivars, and the high-confidence SNP markers will aid in marker-assisted selection in breeding for stripe rust disease resistance. [ABSTRACT FROM AUTHOR]

Stripe rust (also known as yellow rust), caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), is a common and serious fungal disease of wheat (Triticum aestivum L.) worldwide. To identify effective stripe rust resistance loci, a genome-wide association study was performed using 152 wheat landraces from the Yellow and Huai River Valleys in China based on Diversity Arrays Technology and simple sequence repeat markers. Phenotypic evaluation of the degree of resistance to stripe rust at the adult-plant stage under field conditions was carried out in five environments. In total, 19 accessions displayed stable, high degrees of resistance to stripe rust development when exposed to mixed races of Pst at the adult-plant stage in multi-environment field assessments. A marker–trait association analysis indicated that 51 loci were significantly associated with adult-plant resistance to stripe rust. These loci included 40 quantitative trait loci (QTL) regions for adult-plant resistance. Twenty identified resistance QTL were linked closely to previously reported yellow rust resistance genes or QTL regions, which were distributed across chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4A, 4B, 5B, 6B, 7A, 7B, and 7D. Six multi-trait QTL were detected on chromosomes 1B, 1D, 2B, 3A, 3B, and 7D. Twenty QTL were mapped to chromosomes 1D, 2A, 2D, 4B, 5B, 6A, 6B, 6D, 7A, 7B, and 7D, distant from previously identified yellow rust resistance genes. Consequently, these QTL are potentially novel loci for stripe rust resistance. Among the 20 potentially novel QTL, five (QDS.sicau-2A , QIT.sicau-4B , QDS.sicau-4B.2 , QDS.sicau-6A.3 , and QYr.sicau-7D) were associated with field responses at the adult-plant stage in at least two environments, and may have large effects on stripe rust resistance. The novel effective QTL for adult-plant resistance to stripe rust will improve understanding of the genetic mechanisms that control the spread of stripe rust, and will aid in the molecular marker-assisted selection-based breeding of wheat for stripe rust resistance. [ABSTRACT FROM AUTHOR]

Key message: A major, likely novel stripe rust resistance QTL for all-stage resistance on chromosome arm 1BL identified in a 1.76-cM interval using a saturated linkage map was validated in four populations with different genetic backgrounds. Stripe rust is a globally important disease of wheat. Identification and utilization of new resistance genes are essential for breeding resistant cultivars. Wheat line 20828 has exhibited high levels of stripe rust resistance for over a decade. However, the genetics of stripe rust resistance in this line has not been studied. A set of 199 recombinant inbred lines (RILs) were developed from a cross between 20828 and a susceptible cultivar Chuannong 16. The RIL population was genotyped with the Wheat55K SNP (single nucleotide polymorphism) array and SSR (simple sequence repeat) markers and evaluated in four environments with current predominant Puccinia striiformis f. sp. tritici t races including CYR32, CYR33 and CYR34. Four stable QTL were located on chromosomes 1B (2 QTL), 4A and 6A. Among them, the major QTL, QYr.sicau-1B.1 (LOD = 23–28, PVE = 16–39%), was localized to a 1.76-cM interval flanked by SSR markers Xwmc216 and Xwmc156 on chromosome 1BL. Eight resistance genes were previously identified in the physical interval of QYr.sicau-1B.1. Compared with previous studies, QYr.sicau-1B.1 is a new gene for resistant to stripe rust. It was further verified by analysis of the closely linked SSR markers Xwmc216 and Xwmc156 in four other populations with different genetic backgrounds. QYr.sicau-1B.1 reduced the stripe rust disease index by up to 82.8%. Three minor stable QTL (located on chromosomes 1B, 4A and 6A, respectively) also added to the resistance level of QYr.sicau-1B.1. Our results provide valuable information for further fine mapping and cloning as well as molecular-assisted breeding with QYr.sicau-1B.1. [ABSTRACT FROM AUTHOR]

Deployment of cultivars with genetic resistance is an effective approach to control the diseases of powdery mildew (PM) and yellow rust (YR). Chinese wheat cultivar XK0106 exhibits high levels of resistance to both diseases, while cultivar E07901 has partial, adult plant resistance (APR). The aim of this study was to map resistance loci derived from the two cultivars and analyze their effects against PM and YR in a range of environments. A doubled haploid population (388 lines) was used to develop a framework map consisting of 117 SSR markers, while a much higher density map using the 90K Illumina iSelect SNP array was produced with a subset of 80 randomly selected lines. Seedling resistance was characterized against a range of PM and YR isolates, while field scores in multiple environments were used to characterize APR. Composite interval mapping (CIM) of seedling PM scores identified two QTLs (QPm.haas-6A and QPm.haas-2A), the former being located at the Pm21 locus. These QTLs were also significant in field scores, as were Qpm.haas-3A and QPm.haas-5A. QYr.haas-1B-1 and QYr.haas-2A were identified in field scores of YR and were located at the Yr24/26 and Yr17 chromosomal regions respectively. A second 1B QTL, QYr.haas-1B-2 was also identified. QPm.haas-2A and QYr.haas-1B-2 are likely to be new QTLs that have not been previously identified. Effects of the QTLs were further investigated in multiple environments through the testing of selected lines predicted to contain various QTL combinations. Significant additive interactions between the PM QTLs highlighted the ability to pyramid these loci to provide higher level of resistance. Interactions between the YR QTLs gave insights into the pathogen populations in the different locations as well as showing genetic interactions between these loci. [ABSTRACT FROM AUTHOR]

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating fungal disease of wheat. The wild emmer gene, Yr15 (Wtk1), which confers a strong broad-spectrum resistance to Pst isolates, is composed of kinase and pseudokinase domains. The analysis of 361 wild emmer accessions from a wide range of natural habitats confirms that functional Wtk1 is distributed mainly along a narrow axis from Mt. Carmel to Mt. Hermon regions, in the northern part of Israel, where environmental conditions are favorable to the onset of stripe rust. An analysis of full-length Wtk1 DNA sequences from 49 wild emmer accessions identified three haplotypes and extremely low nucleotide diversity (π = 0.00002). The sequence diversity of Wtk1 is 9.5 times lower than that of broad-spectrum partial resistance gene Yr36 (π = 0.00019), and both are in sharp contrast to the high level of nucleotide diversity previously reported for race-specific resistance genes (e.g., Lr10 and Pm3). However, the nonfunctional wtk1 sequences possess high level of nucleotide diversity (π = 0.07). These results may reflect the different resistance mechanisms and the different evolutionary processes that shaped these resistance genes. Yr15 was absent in 189 Chinese wheat landraces and was present in only 1.02% of the 583 tested modern Chinese wheat cultivars. These results corroborate our previous results showing that Yr15 was absent in 94% of a worldwide collection of 513 wheat cultivars, therefore indicating the importance of Yr15 in wheat stripe rust resistance breeding programs in China and elsewhere around the globe. [ABSTRACT FROM AUTHOR]

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a global threat to wheat production. Aegilops tauschii, one of the wheat progenitors, carries the YrAS2388 locus for resistance to Pst on chromosome 4DS. We reveal that YrAS2388 encodes a typical nucleotide oligomerization domain-like receptor (NLR). The Pst-resistant allele YrAS2388R has duplicated 3' untranslated regions and is characterized by alternative splicing in the nucleotide-binding domain. Mutation of the YrAS2388R allele disrupts its resistance to Pst in synthetic hexaploid wheat; transgenic plants with YrAS2388R show resistance to eleven Pst races in common wheat and one race of P. striiformis f. sp. hordei in barley. The YrAS2388R allele occurs only in Ae. tauschii and the Ae. tauschii-derived synthetic wheat; it is absent in 100% (n = 461) of common wheat lines tested. The cloning of YrAS2388R will facilitate breeding for stripe rust resistance in wheat and other Triticeae species. Stripe rust is a serious threat to wheat production. Here, the authors reveal that the resistance gene, only present in the wheat progenitor Aegilops tauschii and its derived synthetic wheat, encodes a nucleotide oligomerization domain-like receptor and confers resistance in common wheat and barley. [ABSTRACT FROM AUTHOR]

• Chinese wheat landraces were assessed for stripe rust resistance at the seedling stage and the adult-plant stage. • Performed a genome-wide association study to ASR and APR stripe rust using DArT markers. • Identified ten potential novel ASR and APR loci for wheat stripe rust. Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is one of the most devastating foliar diseases in wheat. Host resistance is the most effective strategy for the management of the disease. To screen for accessions with stable resistance and identify effective stripe rust resistance loci, a genome-wide association study (GWAS) was conducted using a panel of 140 Chinese wheat landraces. The panel was evaluated for stripe rust response at the adult-plant stage at six field-year environments with mixed races and at the seedling stage with two separate predominant races of the pathogen, and genotyped with the genome-wide Diversity Arrays Technology markers. The panel displayed abundant phenotypic variation in stripe rust responses, with 9 landraces showing stable resistance to the mixture of Pst races at the adult-plant stage in the field and 10 landraces showing resistance to individual races at the seedling stage in the greenhouse. GWAS identified 12 quantitative trait loci (QTL) significantly (P ≤ 0.001) associated to stripe rust resistance using the field data of at least two environments and 18 QTL using the seedling data with two races. Among these QTL, 10 were presumably novel, including 4 for adult-plant resistance mapped to chromosomes 1B (QYrcl.sicau-1B.3), 4A (QYrcl.sicau-4A.3), 6A (QYrcl.sicau-6A.2) and 7B (QYrcl.sicau-7B.2) and 6 for all-stage resistance mapped to chromosomes 2D (QYrcl.sicau-2D.1), 3B (QYrcl.sicau-3B.3), 3D (QYrcl.sicau-3D), 4B (QYrcl.sicau-4B), 6A (QYrcl.sicau-6A.1) and 6D (QYrcl.sicau-6D). The landraces with stable resistance can be used for developing wheat cultivars with effective resistance to stripe rust. [ABSTRACT FROM AUTHOR]

• Chinese wheat landraces were assessed for stripe rust resistance at the adult-plant stage. • Performed a genome-wide association study to APR stripe rust using DArT array and SSR markers. • Identified eight potential novel APR loci for wheat stripe rust. • Haplotype analysis revealed that accessions carrying APR loci showed enhanced degrees of resistance. Stripe rust (Yr), caused by the fungal pathogen Puccinia striiformis f. sp. tritici , is a devastating foliar disease of wheat in China. Chinese wheat landraces originating from the middle and lower reaches of the Yangtze River are potential stripe-rust resistance resources. To identify APR genes for stripe-rust resistance, a panel of 188 accessions derived from the middle and lower reaches of the Yangtze River were inoculated with a mixture of Chinese P. striiformis f. sp. tritici races and resistance evaluated under field conditions in five environments at adult-plant stages. Seventy-three accessions showed degrees of stable resistance. Combining phenotypic datasets from multiple field experiments with high-quality Diversity Arrays Technology and simple sequence repeat markers, we detected 21 marker-trait associations spanning 18 quantitative trait loci (QTLs) on chromosomes 1B, 2A, 2B, 3B, 4A, 5A, 5B, 6B, and 6D, respectively. Single QTLs explained 9.67% to 16.14% of the observed phenotypic variation. Nine QTLs co-localized with previously reported Yr genes or genomic regions. The remaining QTLs were potential novel loci associated with adult-stage stripe-rust resistance. Two novel QTLs, QYr.sicau-3B.2 and QYr.sicau-5B.3 , located on chromosomes 3B and 5B significantly explained 16.14% and 11.16% of the phenotypic variation, respectively. Haplotype analysis revealed that accessions carrying APR variants or their combinations showed enhanced degrees of resistance. The potentially novel loci or genomic regions associated with adult-stage resistance may be useful to improve stripe-rust resistance in current wheat cultivars and for future isolation of stripe-rust resistance genes. [ABSTRACT FROM AUTHOR]