Most of the current stem rust resistance genes (Sr) in Canadian wheat varieties are ineffective against the Pgt race Ug99 lineage, which pose a major threat to wheat production worldwide. Several stem rust resistance genes, including Sr33, Sr35, Sr36, SrCad/Sr42 and Sr43, are effective against race TTKSK. Although Sr36 is ineffective against Ug99 race TTTSK, it is still potentially useful for pyramiding genes to develop germplasm with durable stem rust resistance. For this purpose, we made crosses among RL5405 (Sr33), RL6099 (Sr35), Lang (Sr36), AC Cadillac (SrCad/Sr42), and RWG34 (Sr43) containing the respective Sr genes. A total of 54 doubled haploid (DH) lines were produced from the F1 from AC Cadillac/Lang//RWG34/RL5405, and 82 DH lines were obtained from RWG34/RL5405//RL6099. The DH progeny were tested at the seedling stage with race TTKSK and susceptible lines were discarded. We putatively developed 12 genotypes with multiple Sr gene combinations, including Sr33+Sr36+SrCad/Sr42+Sr43, Sr33+Sr36+SrCad/Sr42, Sr33+Sr36+Sr43, Sr33+SrCad/Sr42+Sr43, Sr36+SrCad/Sr42+Sr43, Sr35+Sr33+Sr43, Sr33+Sr36, Sr33+Sr43, Sr36+SrCad/Sr42, Sr36+Sr43, Sr35+Sr33, and Sr35+Sr43, based on positive association with linked PCR markers. Another population with 63 DH lines was derived from (Hoffman*2/RL6099)//(Hoffman*2/Lang) to combine the Fusarium head blight (FHB) resistance of Hoffman (Fhb1) with Sr35 and Sr36. We found 17 of 63 DH lines containing both Sr35 and Sr36 based also on linked PCR markers. This indicated that the combination Sr35+Sr36 was pyramided into the Canadian cultivar Hoffman; this derivative will be useful for development of cultivars resistant to Ug99 and FHB in Canada.
Primary Author: Jin, Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, Canada
Diploid A genome wheat species harbor immense genetic variability which has been targeted and proven useful in wheat crop improvement. Further, the development and deployment of sequence based markers in wheat using survey sequences from next generation sequencing has opened avenues for comparative analysis, gene transfer and marker assisted selection (MAS) using high throughput cost effective genotyping techniques. Chromosome 2A of wheat is known to harbor several economically important genes. The present study aimed at in silico identification of genes corresponding to full length cDNAs and mining of SSRs and ISBPs from 2A draft sequence assembly of Chinese Spring for marker development. In totality, 1029 primer pairs (478 gene based, 501 SSRs and 50 ISBPs) were used to screen for polymorphism in diploid A genome species i.e., T. monococcum and T. boeoticum that identified 221 polymorphic loci. Out of these, 119 markers were mapped in T. monococcum X T. boeoticum RIL population. The enriched 2A genetic map constituted 161 mapped markers with final map length of 549.6 cM. Further, the utility of this enriched genetic map was demonstrated towards the fine mapping of adult plant resistance (APR) QTL, QYrtm.pau-2A against stripe rust. Using composite interval mapping, a QTL was detected between G45 and G54 markers explaining 19% of phenotypic variance. The primer sequences of the two genic markers were used to find the scaffold of 343 kb from IWGSC WGA V0.4 data. Thirty five simple sequence repeat markers were designed from the scaffold sequence which are being used for the fine mapping of QYrtm.pau-2A.
Primary Author: Jindal, Punjab Agricultural University
A number of rusts affect grain crops in Sweden, but stem rust on oats and stripe (yellow) rust on wheat appear to create the greatest problems in production. The epidemiology of these diseases is intimately connected to the overall cropping patterns of these two crops. In Sweden, oats are only sown in the spring, thus forcing any overwintering pathogen to survive a Swedish winter. This is easiest for Puccinia graminis f. sp. avenae, which apparently completes its full, sexual life cycle on the abundant barberry plants. The presence of barberry and clear indications of sexual reproduction by P. graminis suggests that Pgt could be a problem on wheat, but there are only sporadic reports of stem rust on wheat. Wheat cultivars grown in Sweden possess few effective genes for resistance to stem rust, and the lack of rust is probably due to a lack of Pgt in the region. Given the resurgence of barberry in the landscape this implies that stem rust on wheat could be a major problem if (or when) the pathogen returns. P. striiformis, in contrast, can survive the Swedish winters on fall sown cereal crops, and thus it is the fittest clones that survive and dominate in the population. A large number of factors can affect this fitness, most markedly resistance genes in the cultivated wheat, but it is also possible that extended asexual reproduction can reduce the fitness of these persistent clones (Muller's ratchet) so that they can be displaced by fitter clones. Despite the widespread occurrence of barberry plants, we have not found any aecia of P. striiformis, although there does seem to be some genetic variation in the alternate host. Simple models that simulate the appearance and competition between different clonal lineages of the pathogen indicate that fitter individuals will eventually dominate the population, but their initial appearance will be difficult, since they are only detectable after enough generations have passed to increase the population size above a detectable level.
Primary Author: Jonathan Yuen, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences
Wheat rust is a group of deadly, constantly changing fungal pathogens that pose a serious threat worldwide and also equally most important in Pakistan. Three participatory wheat seed value chain workshops conducted in Pakistan in 2014 indicated the predominance of informal seed systems in Khyber Pakhtunkhwa and Pothwar region of Punjab. A relatively old and rust susceptible variety Sahar06 was covering nearly 50% area of irrigated wheat in Punjab while the coverage of TD-1 was nearly 75 % of wheat area in Sindh. Predominance of mega susceptible varieties with informal seed systems can be an important recipe for the outbreak of rust diseases threatening the stability of wheat production systems in Pakistan. It is challenging to continue to improve and sustain wheat productivity by reducing vulnerability of wheat varieties to rust diseases, both in time and space when more than 70% of wheat seed used comes from farmers' own farm saved seeds mostly of old and obsolete varieties. To address this, 17 recently released rust resistant wheat varieties with diversity in genetic background, adaptation and good yield potential have been deployed through a network of partners to nearly 10,000 smallholder farmers in parts of 62 districts of Pakistan. Varietal deployment was done by coordinating on farm participatory varietal selection with agronomic interventions and village level seed multiplication and marketing. Though, rusts pathogens can evolve into new strains that are more virulent and damaging to wheat crops, nevertheless, some of these varieties do carry known genes conferring resistance to yellow, leaf or stem rusts thereby help avert any sudden rust epidemics. This effort will be instrumental in improving the access to new seed varieties in the grassroots level and widening the genetic bases of wheat that will help in buffering the rust incidence and contribute to household food security of smallholder farmers in Pakistan.
Primary Author: Joshi, CIMMYT-Pakistan
Wheat stem (Sr), leaf (Lr) and stripe (Yr) rust pathogens are among the most destructive fungal diseases threatening global wheat production. We utilized 2300 wheat accession including worldwide landraces, cultivars, breeding materials and 341 synthetic accessions backcrossed with three widely grown Australian cultivars (Annuello, Yitpi and Correll) to investigate rust resistance under wide environmental conditions. The germplasm was genotyped with 90K SNP chip, and was phenotyped for two seasons in three different environments against Sr and Lr and in four different environments against Yr. Different environments for each trait showed significant correlation with mean r values of 0.53, 0.23 and 0.66 for Lr, Sr and Yr; respectively. Single-trait genome wide association (GWAS) revealed several environment-specific QTL and multi-environmental QTL distributed on all chromosomes except 6D. Multi-trait GWAS confirmed a cluster of Yr QTL on chromosome 3B (within 8.3 cM) as well as a QTL for Sr and Lr on chromosome 3D. Linkage disequilibrium and comparative mapping showed that at least three Yr QTL exists within the 3B cluster including the durable rust resistance gene Sr2/Yr30. The same region was effective against Sr resistance but did not pass the stringent significant threshold in two environments. The 3D QTL was found mainly in the synthetic germplasm with Annuello background which is known to carry the Ag. elongatum 3D translocation carrying Sr24/Lr24 resistance gene. Interestingly, estimating the SNP effect using BayesR method showed that the correlation among the highest 5% QTL effects across environments were lower than that for the small effect QTL with differences in r values of 0.25 and 0.2 for Lr and Yr respectively. These results indicate the importance of small effect QTL that cannot be captured using GWAS in achieving durable rust resistance. The detected QTL in this study are useful resources for improving bread wheat resistance to rust diseases.
Primary Author: Joukhadar, La Trobe University
Climatic changes permit the spread of plant diseases to new areas. To ensure grain production meets the needs of the growing world population, wheat breeding must combine multiple disease resistances in single cultivars in order to maintain current yield potential. Over the last three decades, classical mapping and association studies have identified disease resistance loci for individual diseases, but few studies have investigated loci that confer resistance to multiple diseases. To address this limitation, we extensively surveyed the literature to identify wheat genomic regions harboring resistance to multiple diseases. We identified 174 trait-linked markers distributed across all wheat chromosomes, except chromosome 4A, and the numbers of disease resistance loci in each region ranged from two to ten. Our survey suggests that some regions of the genome contain multiple disease resistance genes, or genes with pleiotropic effects. We are using the Chinese Spring flow sorted chromosome survey contigs to investigate the genic contents of genomic regions containing multiple disease trait loci to address this question.
Primary Author: Joukhadar, Department of Animal, Plant and Soil Sciences, La Trobe University, Australia
The quest for durable rust resistance in wheat is burgeoning with the emergence of new virulent races. Breeders challenged with this unceasing plant-pathogen arms race have to devise strategies for effective evaluation and exploitation of the rust resistance genes. Considering the likely presence of useful variation for rust resistance in CIMMYT’s international bread wheat screening nurseries (IBWSN), we implemented genomic prediction in the 45th and 46th IBWSN entries to determine their genomic estimated breeding values (GEBV’s) for leaf, stem and stripe rust resistance. The 350 lines (45th IBWSN) and 329 lines (46th IBWSN) were phenotyped in replicated trials over two to three years in El Batan, Mexico (leaf rust); Njoro, Kenya (stem rust) and Toluca, Mexico (stripe rust). The filtered genotyping data for these two nurseries comprised of 6,786 and 11,218 genotyping by sequencing (GBS) markers. Our objective was to compare the GEBV’s estimated by four different models: multiple linear regression (MLR) with QTL-linked markers as fixed effects; Genomic-best linear unbiased prediction (G-BLUP); G-BLUP mixed model which includes QTL linked markers as fixed effects and Bayesian least absolute shrinkage and selection operator (LASSO). We observed that the prediction accuracies (calculated using 10-fold cross validation) were the highest for stripe rust (0.52 to 0.61), followed by stem rust (0.42 to 0.65) and leaf rust (0.15 to 0.45). Among the models, the MLR gave the lowest prediction accuracies (0.15,0.42 and 0.52), while G-BLUP (0.45,0.59 and 0.59), mixed G-BLUP (0.38,0.65 and 0.62) and the Bayesian LASSO (0.45,0.58 and 0.61) yielded relatively higher and almost similar accuracies. Overall, our results are promising and indicate that using genome-wide markers is advantageous than including only significant QTL-linked markers. We hope that implementing genomic prediction in breeding programs, would help to achieve rapid gains from selection and revolutionize our efforts in combating the rust pathogen.
Primary Author: Juliana, Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, USA
Durum wheat production is globally important, but grain yield has been stagnating in recent decades. In order to ensure that its production maintains the pace with increasing demand, breeding for high grain yield must be supported by molecular-based methods. Genomic estimated breeding values for selection and genome scan were assessed as molecular tools holding maximum potential for durum wheat breeding. Four recombinant inbred line populations bred by inter-mating elite were sown in yield trials at five sites. All progenies were characterized using "genotyping by sequencing" method. A consensus map was developed, and missing genotypes were imputed using a Hidden Markov model to reach a total of 1987 polymorphic markers. Models accounting for genotype environment interactions were used to estimate the genetic component of each measured trait. Hence, Bayesian ridge regression was used to determine the predicted values and their relative accuracy in several combinations, testing full-sibs and half-sibs as training population for grain yield and 1,000 kernel weight. The high level of accuracy achieved suggests that GEBV for selection holds great potential for durum wheat breeding, as long as full-sibs are used as training populations, in combination with statistical models that account for G?E. In order to test the exploitability of genome scan to guide breeding crosses, a separate genome-wide association study was conducted. 288 elite were sown in the south of Morocco and at two sites along the Senegal River for two years. These sites show a temperature differential of 10?C. Implementing a GE model facilitated identifying the most heat tolerant among the tested entries. 8,173 polymorphic SNPs were inquired, and several associations could be identified between markers and the ability to withstand the heat gradient. Hence, GWAS holds great potential to increase genetic gain in breeding via increased accuracy in determining the crosses to be made.
Primary Author: kabbaj, Mohamed 5 university/ICARDA
Landraces and wild relatives of wheat are rich repositories of new rust resistance genes. Landraces are preferred over wild relatives for the absence of deleterious effects associated with large alien segments. A common wheat landrace, AUS 27969 (ex Portugal), from the Watkins Collection was resistant under field conditions and produced seedling infection type (IT) 2C against the widely virulent Australian Puccinia striiformis f. sp. tritici (Pst) pathotype 134 E16 A+ Yr17+ Yr27+. AUS 27969 was crossed with the susceptible genotype Avocet S (AvS) and the distribution of F3 lines conformed to monogenic segregation [40 non-segregating resistant (NSR), 93 segregating (Seg), and 37 non-segregating susceptible (NSS); ?2 = 1.61, P2d.f. >0.05] when tested with the same pathotype at the seedling stage. The population is currently being selfed to F6. DNA from NSR and NSS lines will be sent for high throughput analysis to identify the genomic region carrying the resistance gene. Resistance-linked SNPs will be mapped on the F6 RIL population. The resistance gene will be backcrossed into modern Australian wheat backgrounds.
Primary Author: Kandiah, The University of Sydney, Plant Breeding Institute, Australia
Pst is highly variable, and new races that overcome newly released resistant cultivars are regular events. The widely virulent race V26 (virulent to Yr26) has a significant potential to cause epidemics in China. In this study teliospores from a single urediniospore isolate of V26 (No. Pinglan 17-7) produced on the Nanjing wheat line 92R137 (Yr26) were induced to germinate and infect Berberis shensiana as a sexual host. One hundred and eighteen single aeciospore (SA) selfed progeny and the V26 parent were typed for pathogenicity on a set of differentials comprising 22 Yrnear-isogenic wheat lines (NILs). Virulence phenotyping was conducted twice for all isolates, and similar results were obtained each time. The V26 isolate (No. Pinglan 17-7) was avirulent on differentials with Yr5, Yr6, Yr8, Yr15, Yr43, YrSp, YrTr1 and virulent on those with Yr1, Yr2, Yr4, Yr7, Yr9, Yr10, Yr17, Yr25, Yr26, Yr27, Yr28, Yr32, Yr44, YrV23, and YrExp2. The progeny were all virulent to Yr1, Yr2 (Kalyansona), Yr7, Yr9, Yr10, Yr17, Yr25, Yr26, YrV23 (Vilmorin 23) and YrExp2, and all avirulent to Yr5, Yr8, Yr15, and YrTr1, suggesting that V26 is homozygous at the corresponding pathogenicity loci. Various segregation ratios were apparent for other Yrgenes (P values ranging from 0.6to 0.09).These included3 avirulent: 1 virulent with respect to Yr6 and Yr43, 1 avirulent : 3 virulent forYr27 and Yr28, 1 avirulent : 15 virulent forYr4, Yr32, and Yr44,and 13 avirulent : 3 virulent for YrSp. Among the 118 progeny，27 of new pathotypes were identified as compared with the avirulence/virulence loci of the parent isolate. A study of the population based on markers and development of a molecular map is in progress.
Primary Author: Kang, State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, P.R. China