Genetic analysis of durable resistance to yellow rust in bread wheat

Yellow rust, caused by Puccinia striiformis, is one of the most damaging diseases affecting bread wheat in temperate regions. Although resistance to yellow rust is frequently overcome by new virulent races, a durable form of resistance in the French bread wheat Camp Rémy (CR) has remained effective since its introduction in 1980. We used 217 F₇ recombinant inbred lines (RILs) derived from the cross between CR and the susceptible cultivar Récital to identify and map quantitative trait loci (QTLs) involved in durable yellow rust resistance. Six significant QTLs that were stable over a 4-year period were detected. Two QTLs, denoted QYr.inra-2DS and QYr.inra-5BL.2, were located on the short arm of chromosome 2D and the long arm of chromosome 5B, respectively. Each explained on average 25–35% of the observed phenotypic variation and were probably inherited from Cappelle Desprez, a parent of CR that confers durable adult plant resistance to yellow rust. QYr.inra-2DS probably corresponds to the Yr16 gene. The most consistent QTL, designated QYr.inra-2BL, was located on the centromeric region of chromosome 2B and explained 61% of the phenotypic variation in 2003. This QTL was responsible for seedling-stage resistance and may correspond to a cluster of genes, including Yr7. The remaining QTLs were mapped to the short arm of chromosome 2B (R²=22–70%) and to the long arm of chromosomes 2A (R²=0.20–0.40) and 5B (R²=0.18–0.26). This specific combination of seedling and adult plant resistance genes found in CR and CD may constitute the key to their durable resistance against yellow rust.     

Genetic analysis of Aegilops tauschii -derived seedling resistance to leaf rust in synthetic hexaploid wheat

Seedling resistance to leaf rust available in the synthetic hexaploid wheat line Syn137 was characterised by means of cytogenetic and linkage mapping. Monosomic analysis located a single dominant gene for leaf rust resistance on chromosome 5D. Molecular mapping not only confirmed this location but also positioned the gene to the distal part of the long arm of chromosome 5D. A test of allelism showed that the gene, tentatively named LrSyn137, is independent but closely linked to Lr1. It appears that Syn137 is occasionally heterogeneous for Lr1 since the analysis of the Lr1-specific marker RGA567-5 in the genetic mapping population indicated the presence of Lr1. Syn137 represents another source of genetic variation that can be useful for the diversification of leaf rust resistance in wheat cultivars.     

Inheritance of adult field resistance to yellow rust disease among broad-based hexaploid spring wheat germplasm

 Complete F₁ and F₂ diallel crosses were used to investigate the inheritance of yellow rust resistance among eight bread wheat lines, developed by CIMMYT for the East African Highlands, which showed a wide response to this disease. Both diallel sets were grown at a site with a high incidence of yellow rust, although for one season, during which the F₁ diallel was grown, disease incidence was unusually low. Analyses disclosed the presence of additive, dominance and epistatic effects among those genes controlling rust resistance, with the former being the most important. At normal disease levels, excluding two arrays having resistant common parents removed non-allelic interactions from the F₁ diallels. For all F₂ diallels, and the remaining F₁ diallel, omitting two arrays based on susceptible parents removed these interactions. Local selection of material from a broadly based germplasm appears to be a feasible method of developing adapted cultivars resistant to endemic diseases. Received: 1 March 1998 / Accepted: 19 March 1998     

Breeding for mature-plant resistance to yellow rust in wheat

In recent years several varieties of wheat, such as Rothwell Perdix and Maris Envoy, have shown good resistance to yellow rust when first produced, but because their resistance was determined by simply inherited major genes, they have later been severely attacked by newly arising physiologic races of the pathogen. Other varieties, such as Little Joss, Atle and Maris Widgeon, though slightly attacked by several races, have never suffered severe damage even when exposed to high levels of inoculum. The inheritance of this non-race-specific type of resistance was studied in a cross between Little Joss and a susceptible but shorter-strawed variety, Nord Desprez. Resistance appeared to be under complex control. It was found possible to select short-strawed resistant plants, using simple techniques in the field.     

Genetic analysis of durable leaf rust resistance in winter wheat

Quantitative resistance that delays the epidemic development of leaf rust in wheat is an important source for durable resistance breeding. The Swiss winter wheat variety ’Forno’ shows a high level of quantitative resistance against leaf rust. This resistance has been effective for more than 10 years and can therefore be considered to be durable. In order to map quantitative trait loci (QTL) for durable leaf rust resistance we analysed 204 F₅ recombinant inbred lines (RILs) of the cross between the winter wheat ’Forno’ and the winter spelt ’Oberkulmer’ for their level of leaf rust resistance (LR) and leaf tip necrosis (LTN) in four different environments. Both traits showed a continuous distribution and were significantly correlated (r=−0.5). Across environments we detected 8 QTL for leaf rust resistance (6 inherited from ’Forno’) and 10 QTL for the quantitative expression of LTN (6 inherited from ’Forno’). Of the 6 QTL responsible for the durable leaf rust resistance of ’Forno’, 1 major QTL coincided with a thaumatin locus on 7BL explaining 35% of the phenotypic variance. Four QTL for LR coincided with QTL for LTN. At these loci the alleles of ’Forno’ increased the level of resistance as well as the extent of LTN, indicating pleiotropy. Received: 1 July 1999 / Accepted: 30 July 1999     

Genetic analysis of durable resistance against leaf rust in durum wheat

The Italian durum wheat cultivar Creso possesses a high level of durable resistance to leaf rust based on both hypersensitive and non-hypersensitive components. In order to investigate the genetic basis of this resistance, a segregating population composed of 123 recombinant inbred lines (RILs) derived from the cross Creso × Pedroso, was evaluated for disease severity in adult plants under field conditions. Furthermore, the resistance of parents and RILs was evaluated by assessing macroscopically the latency period and microscopically the number and type of pathogen colonies formed following artificial inoculation with a specific isolate. This experiment was performed at controlled conditions at two developmental stages. Besides some minor QTLs, one major QTL explaining both reduction of disease severity in the field and increased latency period was found on the long arm of chromosome 7B, and closely associated PCR-based and DArT markers were identified. Daniela Marone and Ana I. Del Olmo contributed equally to the work.     

Mapping‐by‐sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat

Previously we extended the utility of mapping‐by‐sequencing by combining it with sequence capture and mapping sequence data to pseudo‐chromosomes that were organized using wheat–Brachypodium synteny. This, with a bespoke haplotyping algorithm, enabled us to map the flowering time locus in the diploid wheat Triticum monococcum L. identifying a set of deleted genes (Gardiner et al., 2014). Here, we develop this combination of gene enrichment and sliding window mapping‐by‐synteny analysis to map the Yr6 locus for yellow stripe rust resistance in hexaploid wheat. A 110 MB NimbleGen capture probe set was used to enrich and sequence a doubled haploid mapping population of hexaploid wheat derived from an Avalon and Cadenza cross. The Yr6 locus was identified by mapping to the POPSEQ chromosomal pseudomolecules using a bespoke pipeline and algorithm (Chapman et al., 2015). Furthermore the same locus was identified using newly developed pseudo‐chromosome sequences as a mapping reference that are based on the genic sequence used for sequence enrichment. The pseudo‐chromosomes allow us to demonstrate the application of mapping‐by‐sequencing to even poorly defined polyploidy genomes where chromosomes are incomplete and sub‐genome assemblies are collapsed. This analysis uniquely enabled us to: compare wheat genome annotations; identify the Yr6 locus – defining a smaller genic region than was previously possible; associate the interval with one wheat sub‐genome and increase the density of SNP markers associated. Finally, we built the pipeline in iPlant, making it a user‐friendly community resource for phenotype mapping.     

Molecular mapping of leaf rust resistance gene Lr15 in hexaploid wheat

Leaf rust is a widespread and commonly occurring rust disease of wheat. Genetic resistance is the most economical method of reducing losses due to leaf rust. Lr15 has been shown to be present on wheat chromosome 2D and is reported to be a seedling resistance gene. However, tightly linked markers associated with Lr15 have not been reported to date. To identify molecular markers linked to Lr15, an F₂ mapping population of Thatcher × Thatcher-Lr15 was generated. Available wheat simple sequence repeat markers were utilized in parental screening and polymorphic markers were used to analyze the entire population of 221 plants. Phenotypic evaluations of the F₂-derived F₃ progenies with Puccinia triticina Eriks. pathotype 162A (93R15) confirmed the monogenic inheritance of Lr15. The linkage group representing chromosome 2DS was constructed at LOD 4.0 which revealed the closest flanking markers Xgwm4562 and Xgwm102 at a distance of 3.1 and 9.3 cM, respectively. Furthermore, utilization of these flanking markers in combination has successfully identified wheat lines with or without Lr15. These markers could potentially be useful in gene pyramiding with other genes to enhance rust resistance in wheat.     

The genetics of non-host disease resistance in wheat to barley yellow rust

Non-host resistance is investigated as a potential source of durable resistance. However, the genetics of non-host resistance between closely related plant species and their corresponding pathogens would indicate that in these interactions, non-host resistance primarily involves major genes that operate on a gene-for-gene principal similar to that seen in host resistance. Wheat is a non-host of the barley-attacking form of the fungus responsible for yellow rust, i.e. Puccinia striiformis f. sp. hordei. While P. striiformis f. sp. hordei is generally unable to infect wheat, a partial susceptibility was exhibited by the wheat variety Chinese 166. Consequently, in the cross Lemhi × Chinese 166 two major QTLs for resistance to P. striiformis f. sp. hordei were identified: one on chromosome 1D and a second on 2B. These two QTLs accounted for 43.5% and 33.2% of the phenotypic variance for resistance to barley yellow rust, respectively. In addition, two QTLs of smaller effect were also identified: one on chromosome 5A, contributing 5.1% of the variance and a second on chromosome 6A, contributing 10.9% to the phenotype. The QTL on 6A was derived from the susceptible variety, Chinese 166. In all cases the resistance towards P. striiformis f. sp. hordei was associated with a visual chlorosis/necrosis response typical of race-specific host resistance.     

Inheritance of resistance to wheat yellow rust at adult plant stage

In order to investigate on inheritance and gene action for resistance to yellow rust, the resistant line C.B227 was crossed with the susceptible variety Avocet. Parents (P1 and P2) and the resulting F1, F2 and F3 generations were planted in a randomised complete block design with two replications in the field. The plants were inoculated with 70E0A⁺ pathotype of yellow rust in the research station of Gharakhil, Iran, and evaluated for resistance at adult plant stage. Disease severity and infection type of flag leaf were recorded for each single plant and final coefficient of infection was calculated. The results of weighted ANOVA indicated that the difference among the generations was significant (p?<?0.01) for the trait final infection type. Generation mean analysis showed that dominant effect was more important than additive one. The degree of dominance indicated the presence of complete dominance. Additive, dominance and epistasic additive?×?additive [i] effects were important in genetic control of resistance. The results of generation variance analysis were consistent with generation mean analysis.     

西科麦2028抗条锈性的遗传分析

西科麦2028是地理远缘小麦材料的杂交后代,具有突出的抗条锈病性能。为了解西科麦2028对小麦条锈病的抗性遗传规律,以西科麦2028和铭贤169的杂交群体为研究对象,采用我国目前小麦条锈菌流行小种CYR31、CYR32、CYR33、Su11-4对供试群体进行成株期接种,分析杂交后代的抗病性及分布情况。结果表明:西科麦2028对CYR31的抗病性由3对显性基因控制;对CYR32由2对显性和1对隐性基因控制;对CYR33由1对显性基因控制;对Su11-4由1对显性和1对隐性基因控制。     

An EST-SSR marker linked with yellow rust resistance in wheat

Expressed sequenced tags containing simple sequence repeats (EST-SSRs) were used to identify molecular markers associated with yellow rust resistance in wheat (Triticum aestivum L.). A cross between yellow rust resistant (PI178383) and susceptible (Harmankaya99) wheat genotypes was performed and respective DNA pools from the resistant and susceptible F₂ seedlings were constructed. 78 EST-SSR primers were used for bulked segregant analysis and one EST-SSR marker (Pk54), identified as 200 bp fragment, was present in the resistant parent and resistant F₂ hybrids but not in the susceptible ones. 108 wheat genotypes differing in yellow rust resistance were screened with Pk54 and 68 % of the wheat genotypes, known to be yellow rust resistant, had the Pk54 marker, further suggesting that the presence of this marker correlates with yellow rust resistance.     

Genetic analysis and molecular mapping of crown rust resistance in common wheat

Key Message

This is the first report on genetic analysis and genome mapping of major dominant genes for near non-host resistance to barley crown rust ( Puccinia coronata var. hordei ) in common wheat.

Abstract

Barley crown rust, caused by Puccinia coronata var. hordei, primarily occurs on barley (Hordeum vulgare L.) in the Great Plain regions of the United States. However, a few genotypes of common wheat (Triticum aestivum L.) were susceptible to this pathogen among 750 wheat accessions evaluated. To investigate the genetics of crown rust resistance in wheat, a susceptible winter wheat accession PI 350005 was used in crosses with two resistant wheat varieties, Chinese Spring and Chris. Analysis of F₁ plants and F₂ populations from these two crosses indicated that crown rust resistance is controlled by one and two dominant genes in Chris and Chinese Spring, respectively. To determine the chromosome location of the resistance gene Cr1 in Chris, a set of 21 monosomic lines derived from Chris was used as female parents to cross with a susceptible spring type selection (SSTS35) derived from the PI 350005/Chris cross. Monosomic analysis indicated that Cr1 is located on chromosome 5D in Chris and one of the crown rust resistance genes is located on chromosome 2D in Chinese Spring. The other gene in Chinese Spring is not on 5D and thus is different from Cr1. Molecular linkage analysis and QTL mapping using a population of 136 doubled haploid lines derived from Chris/PI 350005 further positioned Cr1 between SSR markers Xwmc41-2 and Xgdm63 located on the long arm of chromosome 5D. Our study suggests that near non-host resistance to crown rust in these different common wheat genotypes is simply inherited.     

Genomic regions conferring resistance to multiple fungal pathogens in synthetic hexaploid wheat

Fungal diseases are among the most devastating biotic stresses and often cause significant losses in wheat production worldwide. A set of 173 synthetic hexaploid wheat (SHW) characterized for resistance against fungal pathogens that cause leaf, stem and yellow rusts, yellow leaf spot, Septoria nodorum and crown rot were used in genome-wide association study (GWAS). Diversity Arrays Technology (DArT) and DArTSeq markers were employed for marker–trait association in which 74 markers associated with 35 quantitative trait loci (QTL) were found to be significantly linked with disease resistances using a unified mixed model (P = 10^?3 to 10^?5); Of these 15 QTL originated from D genome. Six markers on 1BL, 3BS, 4BL, 6B, and 6D conferred resistance to two diseases representing 10 of the 35 QTL. A further set of 147 SHW genotyped with DArT only markers validated 11 QTL detected in the previous 173 SHW. We also confirmed the presence of the gene Lr46/Yr29/Sr58/Pm39/Ltn2 on 1BL in the SHW germplasm. In addition, gene–gene interactions between significantly associated loci and all loci across the genome revealed five significant interactions at FDR <0.05. Two significant leaf rust and one stem rust interactions were thought to be synergistic, while another two QTL for yellow leaf spot involved antagonistic relations. To the best of our knowledge, this is the first GWAS for six fungal diseases using SHW. Identification of markers associated with disease resistance to one or more diseases represents an important resource for pyramiding favorable alleles and introducing multiple disease resistance from SHW accessions into current elite wheat cultivars.     

Detection and validation of genomic regions associated with resistance to rust diseases in a worldwide hexaploid wheat landrace collection using BayesR and mixed linear model approaches

Key message

BayesR and MLM association mapping approaches in common wheat landraces were used to identify genomic regions conferring resistance to Yr, Lr, and Sr diseases.

Abstract

Deployment of rust resistant cultivars is the most economically effective and environmentally friendly strategy to control rust diseases in wheat. However, the highly evolving nature of wheat rust pathogens demands continued identification, characterization, and transfer of new resistance alleles into new varieties to achieve durable rust control. In this study, we undertook genome-wide association studies (GWAS) using a mixed linear model (MLM) and the Bayesian multilocus method (BayesR) to identify QTL contributing to leaf rust (Lr), stem rust (Sr), and stripe rust (Yr) resistance. Our study included 676 pre-Green Revolution common wheat landrace accessions collected in the 1920–1930s by A.E. Watkins. We show that both methods produce similar results, although BayesR had reduced background signals, enabling clearer definition of QTL positions. For the three rust diseases, we found 5 (Lr), 14 (Yr), and 11 (Sr) SNPs significant in both methods above stringent false-discovery rate thresholds. Validation of marker–trait associations with known rust QTL from the literature and additional genotypic and phenotypic characterisation of biparental populations showed that the landraces harbour both previously mapped and potentially new genes for resistance to rust diseases. Our results demonstrate that pre-Green Revolution landraces provide a rich source of genes to increase genetic diversity for rust resistance to facilitate the development of wheat varieties with more durable rust resistance.

     

Resistance to wheat leaf rust and stem rust in Triticum tauschii and inheritance in hexaploid wheat of resistance transferred from T. tauschii.

Twelve accessions of Triticum tauschii (Coss.) Schmal. were genetically analyzed for resistance to leaf rust (Puccinia recondita Rob. ex Desm.) and stem rust (Puccinia graminis Pers. f.sp. tritici Eriks. and E. Henn.) of common wheat (Triticum aestivum L.). Four genes conferring seedling resistance to leaf rust, one gene conferring seedling resistance to stem rust, and one gene conferring adult-plant resistance to stem rust were identified. These genes were genetically distinct from genes previously transferred to common wheat from T. tauschii and conferred resistance to a broad spectrum of pathogen races. Two of the four seedling leaf rust resistance genes were not expressed in synthetic hexaploids, produced by combining tetraploid wheat with the resistant T. tauschii accessions, probably owing to the action of one or more intergenomic suppressor loci on the A or B genome. The other two seedling leaf rust resistance genes were expressed at the hexaploid level as effectively as in the source diploids. One gene was mapped to the short arm of chromosome 2D more than 50 cM from the centromere and the other was mapped to chromosome 5D. Suppression of seedling resistance to leaf rust in synthetic hexaploids derived from three accessions of T. tauschii allowed the detection of three different genes conferring adult-plant resistance to a broad spectrum of leaf rust races. The gene for seedling resistance to stem rust was mapped to chromosome ID. The degree of expression of this gene at the hexaploid level was dependent on the genetic background in which it occurred and on environmental conditions. The expression of the adult-plant gene for resistance to stem rust was slightly diminished in hexaploids. The production of synthetic hexaploids was determined to be the most efficient and flexible method for transferring genes from T. tauschii to T. aestivum, but crossing success was determined by the genotypes of both parents. Although more laborious, the direct introgression method of crossing hexaploid wheat with T. tauschii has the advantages of enabling selection for maximum expression of resistance in the background hexaploid genotype and gene transfer into an agronomically superior cultivar.     

Mutations in wheat showing altered field resistance to yellow and brown rust.

Intensive screening of a small population of mutagenised wheat lines revealed a large number of lines with altered resistance to both yellow and brown rust. The parental cultivar Guardian has an intermediate level of adult plant resistance to this disease; mutants were therefore isolated that showed either enhanced resistance or enhanced susceptibility to yellow rust. Seven lines were identified that gave an altered yellow rust disease phenotype as adult plants under both field and greenhouse conditions. Simultaneous field testing for brown rust infection identified two of these lines as having increased resistance to brown rust.     

Genetic analysis and location of gene for resistance to stripe rust in wheat international differential host Strubes Dickkopf

Strubes Dickkopf is the sixth differential in the world set for wheat stripe (yellow) rust. It is very important to clarify its genetic character of resistance to stripe rust and to develop the molecular markers linked to resistance genes. The NIL Taichung 29*6/Strubes Dickkopf, which was obtained by Strubes Dickkopf as the gene donor and Taichung 29 as the genetic background through backcross breeding, was crossed with the recurrent parent Taichung 29, inbred, and backcrossed to obtain the F₁, F₂ and BC₁ population. The genetic analysis of the cross Taichung 29/(Taichung 29*6/Strubes Dickkopf) was assessed by inoculating the rust race CYR26 at seedling stage. Bulked segregant analysis (BSA) and F₂ segregation analysis were used for detecting polymorphic primers to locate the gene. The resistance of the NIL Taichung 29*6/Strubes Dickkopf to CYR26 was controlled by a single dominant gene, named YrSD. The primer pair Xbarc59 on 5B was linked to YrSD and the genetic distance between Xbarc59 and YrSD was 2.4 cM. The molecular marker Xbarc59 closely linked to the gene YrSD could be used in marker-assisted selection for resistance to stripe rust in wheat breeding programmes.