Favorable Loci Identified for Stripe Rust Resistance in Chinese Winter Wheat Accessions via Genome-Wide Association Study.

Stripe rust (or yellow rust), caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat worldwide. Currently, the utilization of resistant cultivars is the most viable way to reduce yield losses. In this study, a panel of 188 wheat accessions from China was evaluated for stripe rust resistance, and genome-wide association studies were performed using high-quality Diversity Arrays Technology markers. According to the phenotype and genotype data, a total of 26 significant marker-trait associations were identified, representing 18 quantitative trait loci (QTLs) on chromosomes 1B, 2A, 2B, 3A, 3B, 5A, 5B, 6B, 7B, and 7D. Of the 18 QTLs, almost all were associated with adult plant resistance (APR) except QYr.nwsuaf-6B.2, which was associated with all-stage resistance (also known as seedling resistance). Three of the 18 QTLs were mapped far from previously identified Pst resistance genes and QTLs and were considered potentially new loci. The other 15 QTLs were mapped close to known resistance genes and QTLs. Subsequent haplotype analysis for QYr.nwsuaf-2A and QYr.nwsuaf-7B.3 revealed the degrees of resistance of the panel in the APR stage. In summary, the favorable alleles identified in this study may be useful in breeding for disease resistance to stripe rust.

Mapping of a Recessive Gene for All-Stage Resistance to Stripe Rust in a Wheat Line Derived from Cultivated Einkorn (Triticum monococcum).

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive fungal diseases of wheat. Cultivated einkorn (Triticum monococcum L. ssp. monococcum, 2n = 2x = 14, AmAm), one of the founder crops of agriculture, harbors unexploited genetic sources for wheat improvement. An advanced wheat line, Z15-1949, with 42 chromosomes, selected from the hybrids of Pst-susceptible common wheat cultivar Crocus and resistant T. monococcum accession 10-1, exhibits high resistance to a mixture of the prevalent Chinese Pst races. Genetic analysis on F1, F2, and F2:3 generations of the cross between Z15-1949 and Pst-susceptible common wheat SY95-71 indicated that the resistance of Z15-1949 was conferred by a recessive gene, tentatively designated as YrZ15-1949. This gene was mapped to the short arm of chromosome 7D using the Wheat 55K single nucleotide polymorphism array, flanked by markers KASP-1949-2 and KASP-1949-10 within a 3.3-cM genetic interval corresponding to a 1.12-Mb physical region in the Chinese Spring reference genome V2.0. The gene differs from previously reported Yr genes on 7D based on their physical positions and is probably a novel gene. YrZ15-1949 would be a valuable resource for developing Pst-resistant wheat cultivars, and the linked markers could be used for marker-assisted selection.

Identification and Molecular Mapping of the Gene YrFL in Wheat Cultivar Flanders with Durable Resistance to Stripe Rust.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most severe diseases of wheat (Triticum aestivum L.) worldwide. Identification and characterization of resistance genes is advantageous to cultivating wheat varieties with durable resistance, which is the most economic and effective strategy to control stripe rust. Flanders, a common wheat cultivar released in France in 1986, confers effective resistance to stripe rust both at the seedling and adult plant stages. To elucidate the genetic basis of resistance in Flanders, F1, F2, and F2:3 generations derived from the cross Mingxian169 × Flanders were evaluated with the most prevalent Chinese Pst race CYR33 at the seedling stage. Inheritance analysis showed that the stripe rust resistance of Flanders was controlled by a single dominant gene, temporarily designated as YrFL. Bulked segregant analysis (BSA) combined with a wheat 660K single-nucleotide polymorphism (SNP) array indicated that polymorphic SNP markers were mainly located in the 0 to 150 Mb on wheat chromosome 5A. One hundred and eleven kompetitive allele-specific PCR (KASP) and 39 simple sequence repeat (SSR) markers on chromosome 5A were used to locate the YrFL. Linkage analysis mapped YrFL with 19 KASP and three SSR markers on wheat chromosome 5AS, and the genetic distances of the closest flanking markers AX108925494 and Xbarc56 to YrFL were 0.6 and 2.0 cM, respectively. Chromosome location, resistance characterization, and molecular marker positions indicated that YrFL is likely a novel stripe rust resistance gene on wheat chromosome 5AS and could be pyramided with other resistance genes to improve resistance in wheat breeding programs.

Genome-wide association study for resistance in bread wheat (Triticum aestivum L.) to stripe rust (Puccinia striiformis f. sp. tritici) races in Argentina.

BACKGROUND: Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of the wheat crop. It causes significant reductions in both grain yield and grain quality. In recent years, new and more virulent races have overcome many of the known resistance genes in Argentinian germplasm. In order to identify loci conferring resistance to the local races of Pst for effective utilization in future breeding programs, a genome-wide association study (GWAS) was performed using a collection of 245 bread wheat lines genotyped with 90 K SNPs. RESULTS: To search for adult plant resistance (APR) the panel was evaluated for disease severity (DS) and area under disease progress curve (AUDPC) in field trials during two years under natural infection conditions. To look for seedling or all-stage resistance (ASR) the panel was evaluated to determine infection type (IT) under greenhouse conditions against two prevalent races in Argentina. The phenotypic data showed that the panel possessed enough genetic variability for searching for sources of resistance to Pst. Significant correlations between years were observed for Pst response in the field and high heritability values were found for DS (H2 = 0.89) and AUDPC (H2 = 0.93). Based on GWAS, eight markers associated with Pst resistance (FDR < 0.01) were identified, of these, five were associated with ASR (on chromosomes 1B, 2A, 3A and 5B) and three with APR (on chromosomes 3B and 7A). These markers explained between 2% and 32.62% of the phenotypic variation. Five of the markers corresponded with previously reported Yr genes/QTL, while the other three (QYr.Bce.1B.sd.1, QYr.Bce.3A.sd and QYr.Bce.3B.APR.2) might be novel resistance loci. CONCLUSION: Our results revealed high genetic variation for resistance to Argentinian stripe rust races in the germplasm used here. It constitutes a very promising step towards the improvement of Pst resistance of bread wheat in Argentina. Also, the identification of new resistance loci would represent a substantial advance for diversifying the current set of resistance genes and to advance in the improvement of the durable resistance to the disease.

Studying Stem Rust and Leaf Rust Resistances of Self-Fertile Rye Breeding Populations.

Stem rust (SR) and leaf rust (LR) are currently the two most important rust diseases of cultivated rye in Central Europe and resistant cultivars promise to prevent yield losses caused by those pathogens. To secure long-lasting resistance, ideally pyramided monogenic resistances and race-nonspecific resistances are applied. To find respective genes, we screened six breeding populations and one testcross population for resistance to artificially inoculated SR and naturally occurring LR in multi-environmental field trials. Five populations were genotyped with a 10K SNP marker chip and one with DArTseqTM. In total, ten SR-QTLs were found that caused a reduction of 5-17 percentage points in stem coverage with urediniospores. Four QTLs thereof were mapped to positions of already known SR QTLs. An additional gene at the distal end of chromosome 2R, Pgs3.1, that caused a reduction of 40 percentage points SR infection, was validated. One SR-QTL on chromosome 3R, QTL-SR4, was found in three populations linked with the same marker. Further QTLs at similar positions, but from different populations, were also found on chromosomes 1R, 4R, and 6R. For SR, additionally seedling tests were used to separate between adult-plant and all-stage resistances and a statistical method accounting for the ordinal-scaled seedling test data was used to map seedling resistances. However, only Pgs3.1 could be detected based on seedling test data, even though genetic variance was observed in another population, too. For LR, in three of the populations, two new large-effect loci (Pr7 and Pr8) on chromosomes 1R and 2R were mapped that caused 34 and 21 percentage points reduction in leaf area covered with urediniospores and one new QTL on chromosome 1R causing 9 percentage points reduction.

Genetic dissection of stripe rust resistance in a Tunisian wheat landrace Aus26670.

The deployment of combinations of resistance genes in future wheat cultivars can save yield losses caused by the stripe rust pathogen (Puccinia striiformis f. sp. tritici; Pst). This relies on the availability and identification of genetically diverse sources of resistance. A Tunisian landrace Aus26670 displayed high level of stripe rust resistance against Australian Pst pathotypes. This landrace was crossed with a susceptible line Avocet 'S' (AvS) to generate 123 F7 recombinant inbred lines (RILs). The Aus26670/AvS RIL population was evaluated against three Pst pathotypes individually in greenhouse and against mixture of Pst pathotypes under field conditions for three consecutive years. Genetic analysis of the seedling stripe rust response variation data indicated the presence of an all-stage resistance (ASR) gene, and it was named YrAW12. This gene is effective against Australian Pst pathotypes 110 E143A + and 134 E16A + Yr17 + Yr27 + and is ineffective against the pathotype 239 E237A-Yr17 + Yr33 + . The RIL population was genotyped using the targeted genotyping-by-sequencing (tGBS) assay. YrAW12 was mapped in the 754.9-763.9 Mb region of the physical map of Chinese Spring and was concluded to be previously identified stripe rust resistance gene Yr72. QTL analysis suggested the involvement of four genomic regions which were named: QYr.sun-1BL/Yr29, QYr.sun-5AL, QYr.sun-5BL and QYr.sun-6DS, in controlling stripe rust resistance in Aus26670. Comparison of genomic regions detected in this study with previously reported QTL indicated the uniqueness of QYr.sun-5AL (654.5 Mb) and QYr.sun-6DS (1.4 Mb). Detailed mapping of these genomic regions will lead to permanent designation of these loci. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-021-01248-7.

Identification of a new source of stripe rust resistance Yr82 in wheat.

KEY MESSAGE: Stripe rust resistance gene, Yr82, was mapped in chromosome 3BL using SNP markers. Yr82 interacted with Yr29 to produce lower stripe rust responses at the adult plant stage. Landrace Aus27969 produced low infection types against Australian Puccinia striiformis f. sp. tritici (Pst) pathotypes. A recombinant inbred line (RIL) F7 population from the Aus27969/Avocet S cross was developed. Monogenic segregation for seedling stripe rust response was observed among the RIL population, and the resistance locus was named Yr82. Bulk segregant analysis performed using the iSelect wheat 90 K Infinium SNP array located Yr82 in the long arm of chromosome 3B. The RIL population was screened against stripe rust under field conditions and was genotyped with targeted genotyping-by-sequencing assay. QTL analysis detected the involvement of chromosomes 1B and 3B in controlling stripe rust resistance carried by Aus27969. Incorporation of Yr82 and marker SNPLr46G22 into the linkage map showed that the QTL in 1B and 3B represented Yr29 and Yr82, respectively. Kompetitive allele-specific PCR (KASP) markers sun KASP_300 and KASP_8775 flanked Yr82 distally and proximally, respectively, each at 2 cM distance. These Yr82-linked markers were polymorphic among 84% of Australian cultivars and can be used for marker-assisted selection of Yr82.

QTL mapping for seedling and adult plant resistance to stripe and leaf rust in two winter wheat populations.

The two recombinant inbred line (RIL) populations developed by crossing Almaly × Avocet S (206 RILs) and Almaly × Anza (162 RILs) were used to detect the novel genomic regions associated with adult plant resistance (APR) and seedling or all-stage resistance (ASR) to yellow rust (YR) and leaf rust (LR). The quantitative trait loci (QTLs) were detected through multi-year phenotypic evaluations (2018-2020) and using high-throughput DArTseq genotyping technology. RILs exhibited significant genetic variation with p < 0.001, and the coefficient of variation ranged from 9.79% to 47.99% for both LR and YR in all Environments and stages of evaluations. The heritability is quite high and ranged between 0.47 and 0.98. We identified nine stable QTLs for YR APR on chromosomes 1B, 2A, 2B, 3D, and 4D and four stable QTLs for LR APR on chromosomes 2B, 3B, 4A, and 5A. Furthermore, in silico analysis revealed that the key putative candidate genes such as cytochrome P450, protein kinase-like domain superfamily, zinc-binding ribosomal protein, SANT/Myb domain, WRKY transcription factor, nucleotide sugar transporter, and NAC domain superfamily were in the QTL regions and probably involved in the regulation of host response toward pathogen infection. The stable QTLs identified in this study are useful for developing rust-resistant varieties through marker-assisted selection (MAS).

Population structure and genetic basis of the stripe rust resistance of 140 Chinese wheat landraces revealed by a genome-wide association study.

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.

Mapping Stem Rust (Puccinia graminis f. sp. secalis) Resistance in Self-Fertile Winter Rye Populations.

Rye stem rust caused by Puccinia graminis f. sp. secalis can be found in all European rye growing regions. When the summers are warm and dry, the disease can cause severe yield losses over large areas. To date only little research was done in Europe to trigger resistance breeding. To our knowledge, all varieties currently registered in Germany are susceptible. In this study, three biparental populations of inbred lines and one testcross population developed for mapping resistance were investigated. Over 2 years, 68-70 genotypes per population were tested, each in three locations. Combining the phenotypic data with genotyping results of a custom 10k Infinium iSelect single nucleotide polymorphism (SNP) array, we identified both quantitatively inherited adult plant resistance and monogenic all-stage resistance. A single resistance gene, tentatively named Pgs1, located at the distal end of chromosome 7R, could be identified in two independently developed populations. With high probability, it is closely linked to a nucleotide-binding leucine-rich repeat (NB-LRR) resistance gene homolog. A marker for a competitive allele-specific polymerase chain reaction (KASP) genotyping assay was designed that could explain 73 and 97% of the genetic variance in each of both populations, respectively. Additional investigation of naturally occurring rye leaf rust (caused by Puccinia recondita ROEBERGE) revealed a gene complex on chromosome 7R. The gene Pgs1 and further identified quantitative trait loci (QTL) have high potential to be used for breeding stem rust resistant rye.