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Leaf rust (LR) and stem rust (SR) are threats to global wheat production and new races frequently overcome resistance genes deployed in wheat cultivars. Identification of new sources of resistance is a major goal for many pre-breeding programs. The objective of this study was to investigate the genetic basis of resistance to LR and SR in a diverse South American wheat panel. Molecular markers for known resistance genes and GBS were used to dissect genetic components. The wheat panel of 122 lines was characterized under field conditions at La Estanzuela Research Station, Uruguay, for disease severity (DS) to LR (2014 and 2015) and SR (2015), and LTN (leaf tip necrosis). Final DS for LR ranged between 0 and 95%, with mean values of 40% (2014) and 46% (2015). For SR, final DS ranged between 0 and 50%, with a mean value of 5%. The frequencies of positive diagnostic resistance markers among accessions were 20.5% for Lr34/Sr57, 6.6% for Lr68, 3.3% for Sr2/Lr27, 23% for Sr31/Lr26, 20.5% for Sr24/Lr24, 9.4% for Sr25/Lr19, and 0% for Sr39/Lr35. Of all the LR/SR resistance genes, only the effect of Lr68 was significant when predicting LR DS. Seventeen lines were identified with combinations of two genes, but no combination conferred a significantly improved level of resistance. Preliminary GWAS analysis for LR response on a subset of 86 lines revealed several QTLs, with a major QTL explained by Lr68. Lines with good levels of resistance to LR and SR, high expression of LTN, and absence of markers for the studied resistance genes were identified, indicating that there are other genes involved in resistance. Future research involving the testing of additional molecular markers for other known resistance genes, and a deeper GWAS analysis, will provide further information about the resistance genes present in this wheat panel.
Grain yield is the most important economic trait in wheat breeding. The detailed understanding of the genetic architecture of grain yield is crucial and the determining factor to optimize genomics-assisted selection strategies in wheat. First, we performed a marker and haplotype-based genome-wide association study (GWAS) for grain yield (GY) and yield stability coefficient (Pi) on 4,302 advanced breeding lines from five CIMMYT international bread wheat trails grown in multiple (optimally irrigated and stress) environments. All lines were genotyped using genotyping-by-sequencing. A haplotype map was built based on linkage disequilibrium between markers. Twenty-nine markers and 16 haplotypes were associated with GY and Pi across two and three germplasm trials with allelic effects ranging from 2 to 11% across environments. Secondly, we performed genomic prediction, testing eight different prediction models incorporating single markers (base model), haplotypes, epistatic interactions, and significant markers/haplotypes identified in GWAS. Initial results show that by including haplotypes and epistatic interactions among haplotypes (main effect and genome-wide), prediction accuracies range between 0.33-0.49 for GY, a 3 to 22.5% improvement over the base model. Despite the identification of significant marker/haplotype trait associations across traits and environments in GWAS, accounting for these markers in genomic prediction does not improve the prediction models. Our results suggest that the haplotype-based approach can increase prediction ability, but that the knowledge of the genetic architecture of grain yield might not have significant consequence on genomic-assisted selection.
The Green Revolution involved the deployment of reduced height (Rht) genes to generate shorter wheat varieties with increased grain yields. It also contributed to a reduction in genetic diversity in the modern gene pool. Therefore, the pre- Green Revolution tall wheat landraces may provide a reservoir of genetic variation for economic traits such as rust resistance. Considering the breakdown of a suite of rust resistance genes through the emergence of currently predominant pathotypes (e.g. Ug99 and high temperature adapted isolates of the stripe rust pathogen) after three decades of Green Revolution, the discovery, characterisation and deployment of diverse sources of resistance remains a high priority. We have screened the Watkins wheat landrace collection and discovered, characterised and formally named a suite of new rust resistance genes including Yr47, Yr51, Yr57, Yr63 and Sr49. In addition, genotypes carrying potentially new genes for resistance to three rust pathogens are currently being investigated by students from seven nations representing three continents (Australia, Asia and Africa). Yr47, Yr51, Yr57 and Lr52 have been backcrossed into modern cultivars including the widely adapted cultivar PBW343 (Atilla) using markers developed in our research program. Development of triple rust resistant derivatives in modern wheat backgrounds is in progress. Stocks carrying Yr47, Yr51, Yr57 and Lr52 have been mutated to facilitate cloning of these loci for their eventual use in development of multi-gene cassettes for transformation.
Resistance offers the best means of control of the cereal rusts, but must be strategically deployed so as to avoid exposure of single major genes, which have faltered so many times in the past. The pyramiding of multiple effective resistance genes is a strategy that has proven effective in a number of wheat production areas around the world. However, the process of incorporating multiple resistance genes into a single cultivar using standard breeding techniques is time consuming, laborious, and hampered by the problem of linkage drag. If a suite of effective resistance genes could be efficiently cloned and transferred into wheat as a cassette, it would accelerate the development of durably resistant varieties without the problem of linkage drag. Toward this end, we have developed a resistance gene cloning technology based on resistance gene enrichment sequencing (RenSeq) of EMS-derived mutant R gene alleles. As a proof of concept test, we successfully ‘re’-cloned the already characterized gene Sr33 and are now targeting the cloning of eight other effective resistance genes. For the identification of susceptible mutants for the cloning of Sr32 from Aegilops speltoides, we screened 1,109 M2 families with race TPMKC — as a surrogate for race TTKSK. Five susceptible M2 mutants were confirmed by progeny testing. These mutants were also susceptible to race TTKSK. For the population involving Sr1644 from Ae. sharonensis, 1,649 M2 families were screened, yielding 33 M2 families that appeared to segregate for susceptibility. Thirteen of 33 families were confirmed as bona fide susceptible mutants by progeny tests in the M3 generation. Identification of susceptible EMS mutants of Sr32 and Sr1644 suggests that the underlying resistance in these lines is conferred by single genes. We will report on progress to clone and characterize these genes using R gene exome capture and sequencing technology (RenSeq).
Wild species are sources and donors of many valuable traits for wheat improvement. We studied winter wheat introgression lines for productivity traits, disease resistance, and protein, globulin, gliadin and glutenin contents as well as grain mineral concentrations. Laboratory and field studies allowed selection in populations segregating for resistance to yellow rust and leaf rust. Lines 1718, 1721-9, 1721-4, 1675 and 1727 had the highest yields (6.2 t/ha) and stable leaf rust and stem rust resistances, but were still variable in response to stripe rust (30-80 S). Lines 1718 (Bezostaya 1 x Ae. cylindrica, genomes CCDD) and 1721 (Bezostaya 1 x T. militinae2 - 6, ABG) were resistant to stripe rust in trials at yield levels of 3.7-7.6 t/ha and from 5.7 to 8.2 t/ha, respectively. Line 1675 (Zhetisu x T. kiharae, ABGD) was resistant to all three rusts. Line 1676 (Steklovidnaya 24 x T. timopheevi, ABG) was resistant to LR and SR at a yield level of 8.3 t/ha, and 1671 (Zhetisu x T. militinae, ABG) was resistant to YR and SR at a yield level of 7.5 t/ha. Protein contents of the lines ranged from 13.6 to 18.4%, and grain mineral contents were above average.
The shortage of stem rust resistance genes effective against the Ug99 group prompted recent efforts to increase the number of resistance genes available to breeders. We are fortunate that many new and/or cytogenetically improved rust resistance genes are now being shared with the global wheat breeding community by their developers. If we are poor stewards of these resources, the new resistance genes will eventually be defeated, and we will waste the efforts and investments that have been made. However, if we are good stewards, we should have enough resistance to achieve sustainable, durable resistance. Stewardship can be defined as the careful and responsible management of something entrusted to one’s care. What should we do to safeguard the new resistance genes? Diversification of resistance is often suggested as a way to reduce the risk of large scale epidemics. Although diversification is generally a good idea, it cannot be at the expense of leaving new genes exposed and vulnerable. A durable combination (pyramid) must be designed so that the component genes protect each other. They should reduce the probability of simultaneous pathogen mutations to virulence and they should avoid stepwise erosion of the pyramid by preventing significant reproduction of any new race that is virulent on component genes. We need pyramids to be immune or nearly immune not only to current races, but to anticipated mutants. This objective should be achievable with three or more major genes or a combination of major and minor genes. Successful gene stewardship will depend on several things. On the technical side, we will need very good markers for each gene. Each breeding program will require strong genotyping support to assemble and then validate pyramids. Most importantly, successful stewardship will require that we organize our user community to cooperate more closely. We will need to decide which genes require special stewardship and which do not. Every user of the stewardship pool resource will need to participate in earnest. It only takes one cultivar with an unprotected gene to give the pathogen a stepping stone to greater virulence. As they say, a chain is only as strong as the weakest link
Single nucleotide polymorphism (SNP) is one of the most broadly distributed types of molecular variation in a genome which, along with the availability of costand labor-effective genotyping platforms, make it the marker of choice for many crops. Our work is aimed at the development of a dense set of genetically mapped SNP markers for low-cost high-throughput genotyping of wheat germplasm. Next generation sequencing of normalized cDNA libraries was used for developing gene-associated SNPs in polyploid wheat. A total of 7.5 million 454 reads were generated from cDNA libraries of 10 wheat cultivars from US and Australia and processed for discovering SNPs using a bioinformatical pipeline specifically designed for variant discovery in polyploid transcriptomes. A total of 25,000 high-quality SNPs distributed among 14,500 EST contigs were identified. All these SNPs were validated by comparison with RNAseq data generated from an additional set of 17 U.S. and Australian cultivars. A total of 9,000 genome-wide common SNPs were selected for designing an Illumina iSelect assay. Preliminary testing showed that more than 95% of SNPs produce high-quality genotype calls with up to 70% being polymorphic in a diverse sample of U.S. and Australian cultivars with a minor allele frequency >0.05. The assay is currently being used for studying patterns of genetic diversity in a worldwide collection of wheat cultivars and for developing a high-density SNP map. A long term goal of this initiative is to advance wheat research and breeding by developing genetic and genomic tools for efficient analysis of agronomic traits using high-resolution linkage and association mapping and deploying SNP markers in breeding programs
Full nonhost resistance can be defined as immunity, displayed by an entire plant species against all genotypes of a plant pathogen. The genetic basis of (non)host-status of plants is hard to study, since identification of the responsible genes would require interspecific crosses that suffer from sterility and abnormal segregation. There are some plant/potential pathogen combinations where only 10% or less of the accessions are at most moderately susceptible. These may be regarded as marginal host or near-nonhost, and can provide insights into the genes that determine whether a plant species is a host or a nonhost to a would-be pathogen. Barley (Hordeum vulgare L.) is a near-nonhost to several rust pathogens (Puccinia) of cereals and grasses. By crossing and selection we developed an experimental line, SusPtrit, with high susceptibility to at least nine different heterologous rust taxa such as the wheat and Agropyron leaf rusts (caused by P. triticina and P. persistens, respectively). On the basis of SusPtrit and several regular, fully resistant barley accessions, we developed mapping populations. We established that the near-nonhost resistance to heterologous rusts inherits polygenically (QTLs). The QTLs have different and overlapping specificities. In addition, an occasional R-gene is involved. In each population, different sets of loci were implicated in resistance. Very few resistance genes were common between the populations, suggesting a high redundancy in barley for resistance factors. Selected QTLs have been introduced into near-isogenic lines to be fine-mapped. Our results show that the barley- Puccinia system is ideal to investigate the genetics of host-status to specialized plant pathogens.
With the TTKS family of races virulent on most genes currently providing protection against stem rust worldwide, identifying, mapping, and deploying resistance genes effective against these races has become critical. We present here a genetic map of Sr35. Both parents of our diploid mapping population (DV92/G3116, 142 SSD lines) are resistant to TTKSK, but the population segregates for resistance to TRTTF (Yemen) and RKQQC (US). Race analysis suggests that G3116 carries Sr21 and DV92 both Sr21 and Sr35. Resistance to TRTTF and RKQQC was mapped to a 6 cM interval on chromosome 3AmL between markers BF483299 and CJ656351. This interval corresponds to a 178-kb region in Brachypodium which contains only 16 annotated genes and exhibits a small inversion (including 2 genes) and a putative insertion (2 genes) relative to rice and sorghum. This map contains closely-linked markers to Sr35 and provides the initial step for this gene's positional cloning.
Rust diseases remain a significant threat to the production of most cereals including wheat. New sources of resistance are continually sought by breeders to combat the emergence of new pathogen races. Rice is atypical in that it is an intensively grown cereal with no known rust pathogen. The resistance of rice to cereal rust diseases is referred to as nonhost resistance (NHR), a resistance mechanism that has only recently become genetically tractable. In this report, the mechanisms of rice NHR to wheat stem rust and other cereal rust diseases are explored and the potential for transferring this durable disease resistance to wheat is considered. Approaches being undertaken for the molecular-genetic dissection of rice NHR to rust are described.