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Durum wheat is the tenth most important crop in the world, but its cultivation is mostly limited to harsh, arid, and heat prone marginal lands. Breeding for tolerance to these conditions is often considered the most strategic approach to ensure adaptation, especially when paired with best agronomical practices. The word 'adaptation' summarizes all the research efforts conducted to identify the many traits controlling the mechanisms for withstanding or escaping the traceries of the environment. It can be summarized as "GGE vs E". The durum wheat breeding program of ICARDA deploys targeted phenotyping methods in combination with genomic scans to dissect these 'adaptive' traits into simple loci. These loci can then be pyramided via a combination of international field testing, markers assisted selection, genetically-driven crossing schemes, and genomic selection to derive climate-ready cultivars. Here, several examples of this approach are presented and their implications for 'adaptation' are discussed.
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.
Two broad categories of resistance genes in wheat have been described. One group represents the so called seedling resistance or the ‘gene for gene’ class that often provides strong resistance to some but not all strains of a rust species. The other category referred to as adult plant resistance provide partial resistance that is expressed in adult plants during the critical grain filling stage of wheat development. A few seedling rust resistance genes have been cloned in wheat and other cereals and are predominantly from the nucleotide binding site/leucine rich repeat class which is associated with localized cell death at the pathogen entry site. Until recently, the molecular basis of race non-specific, partial and slow rusting adult plant resistance genes were unknown. Gene products that differ from known plant resistance genes were revealed from the recent cloning of the Yr18, Yr36 and Lr34 adult plant genes in wheat. The available range of diverse resistance gene sequences provide entry points for developing genebased markers and will facilitate selection of germplasm containing unique resistance gene combinations.