Urmil Bansal

The Gene Sr33, an Ortholog of Barley Mla Genes, Encodes Resistance to Wheat Stem Rust Race Ug99

Resistance May Not Be Futile Recently, Ug99, a particularly devastating strain of wheat stem rust fungus, has emerged, which could potentially threaten food security. Now, two genes have been cloned that offer resistance to Ug99. Saintenac et al. (p. 783, published online 27 June) cloned Sr35 from Triticum monococcum, a diploid wheat species not often cultivated. Periyannan et al. (p. 786, published online 27 June) cloned Sr33 from Aegilops tauschii, a diploid wild grass that contributed to the hexaploid genome of cultivated wheat. The genes both encode proteins that show features typical of other disease resistance proteins and offer opportunities to slow the pace of Ug99 progression. Two resistance genes are identified that could protect wheat from a virulent fungus that can severely reduce crop yields. Wheat stem rust, caused by the fungus Puccinia graminis f. sp. tritici, afflicts bread wheat (Triticum aestivum). New virulent races collectively referred to as “Ug99” have emerged, which threaten global wheat production. The wheat gene Sr33, introgressed from the wild relative Aegilops tauschii into bread wheat, confers resistance to diverse stem rust races, including the Ug99 race group. We cloned Sr33, which encodes a coiled-coil, nucleotide-binding, leucine-rich repeat protein. Sr33 is orthologous to the barley (Hordeum vulgare) Mla mildew resistance genes that confer resistance to Blumeria graminis f. sp. hordei. The wheat Sr33 gene functions independently of RAR1, SGT1, and HSP90 chaperones. Haplotype analysis from diverse collections of Ae. tauschii placed the origin of Sr33 resistance near the southern coast of the Caspian Sea.

Breeding triple rust resistant wheat cultivars for Australia using conventional and marker-assisted selection technologies

Stem rust susceptibility of European wheats under Australian conditions posed a significant threat to wheat production for the early British settlers in Australia. The famous Australian wheat breeder, William Farrer, tackled the problem of stem rust susceptibility through breeding fast-maturing wheat cultivars. South-eastern Australia suffered a severe stem rust epidemic in 1973, which gave rise to a national approach to breeding for rust resistance. The National Wheat Rust Control Program was set up in 1975, modelled on the University of Sydney’s own rust resistance breeding program, at the University of Sydney Plant Breeding Institute, Castle Hill (now Cobbitty). Back-crossing of a range of sources of resistance provided genetically diverse germplasm for evaluation in various breeding programs. Current efforts are directed to building gene combinations through marker-assisted selection. Major genes for resistance to stem rust and leaf rust are being used in the back-crossing program of the ACRCP to create genetic diversity among Australian germplasm. Stripe rust and to a lesser extent leaf rust resistance in the Australian germplasm is largely based on combinations of adult plant resistance genes and our knowledge of their genomic locations has increased. Additional genes, other than Yr18/Lr34 and Yr29/Lr46, appeared to control adult plant resistance to both leaf rust and stripe rust. Two adult-plant stem rust resistance genes have also been identified. The development of selection technologies to achieve genotype-based selection of resistance gene combinations in the absence of bioassays has evolved in the last 5 years. Robust molecular markers are now available for several commercially important rust resistance genes. Marker-assisted selection for rust resistance is performed routinely in many wheat-breeding programs. Modified pedigree and limited back-cross methods have been used for breeding rust-resistant wheat cultivars in the University of Sydney wheat-breeding program. The single back-cross methodology has proved more successful in producing cultivars with combinations of adult plant resistance genes.

A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes.

BackgroundBread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines.ResultsA sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies.ConclusionsEvidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets.

QTL mapping of multiple foliar disease and root-lesion nematode resistances in wheat

A genetic linkage map, based on a cross between the synthetic hexaploid CPI133872 and the bread wheat cultivar Janz, was established using 111 F1-derived doubled haploid lines. The population was phenotyped in multiple years and/or locations for seven disease resistance traits, namely, Septoria tritici blotch (Mycosphaeralla graminicola), yellow leaf spot also known as tan spot (Pyrenophora tritici-repentis), stripe rust (Puccinia striiformis f. sp. tritici), leaf rust (Puccinia triticina), stem rust (Puccinia graminis f. sp. tritici) and two species of root-lesion nematode (Pratylenchyus thornei and P. neglectus). The DH population was also scored for coleoptile colour and the presence of the seedling leaf rust resistance gene Lr24. Implementation of a multiple-QTL model identified a tightly linked cluster of foliar disease resistance QTL in chromosome 3DL. Major QTL each for resistance to Septoria tritici blotch and yellow leaf spot were contributed by the synthetic hexaploid parent CPI133872 and linked in repulsion with the coincident Lr24/Sr24 locus carried by parent Janz. This is the first report of linked QTL for Septoria tritici blotch and yellow leaf spot contributed by the same parent. Additional QTL for yellow leaf spot were detected in 5AS and 5BL. Consistent QTL for stripe rust resistance were identified in chromosomes 1BL, 4BL and 7DS, with the QTL in 7DS corresponding to the Yr18/Lr34 region. Three major QTL for P. thornei resistance (2BS, 6DS, 6DL) and two for P. neglectus resistance (2BS, 6DS) were detected. The recombinants combining resistance to Septoria tritici blotch, yellow leaf spot, rust diseases and root-lesion nematodes from parents CPI133872 and Janz constitute valuable germplasm for the transfer of multiple disease resistance into new wheat cultivars.

Development of wheat lines carrying stem rust resistance gene Sr39 with reduced Aegilops speltoides chromatin and simple PCR markers for marker-assisted selection

The use of major resistance genes is a cost-effective strategy for preventing stem rust epidemics in wheat crops. The stem rust resistance gene Sr39 provides resistance to all currently known pathotypes of Puccinia graminis f. sp. tritici (Pgt) including Ug99 (TTKSK) and was introgressed together with leaf rust resistance gene Lr35 conferring adult plant resistance to P. triticina (Pt), into wheat from Aegilops speltoides. It has not been used extensively in wheat breeding because of the presumed but as yet undocumented negative agronomic effects associated with Ae. speltoides chromatin. This investigation reports the production of a set of recombinants with shortened Ae. speltoides segments through induction of homoeologous recombination between the wheat and the Ae. speltoides chromosome. Simple PCR-based DNA markers were developed for resistant and susceptible genotypes (Sr39#22r and Sr39#50s) and validated across a set of recombinant lines and wheat cultivars. These markers will facilitate the pyramiding of ameliorated sources of Sr39 with other stem rust resistance genes that are effective against the Pgt pathotype TTKSK and its variants.

The wheat Sr50 gene reveals rich diversity at a cereal disease resistance locus.

We identify the wheat stem rust resistance gene Sr50 (using physical mapping, mutation and complementation) as homologous to barley Mla, encoding a coiled-coil nucleotide-binding leucine-rich repeat (CC-NB-LRR) protein. We show that Sr50 confers a unique resistance specificity different from Sr31 and other genes on rye chromosome 1RS, and is effective against the broadly virulent Ug99 race lineage. Extensive haplotype diversity at the rye Sr50 locus holds promise for mining effective resistance genes.

A robust molecular marker for the detection of shortened introgressed segment carrying the stem rust resistance gene Sr22 in common wheat

Stem rust resistance gene Sr22 transferred to common wheat from Triticum boeoticum and T. monococcum remains effective against commercially prevalent pathotypes of Pucciniagraminis f. sp. tritici, including Ug99 and its derivatives. Sr22 was previously located on the long arm of chromosome 7A. Several backcross derivatives (hexaploid) possessing variable sized Sr22-carrying segments were used in this study to identify a closely linked DNA marker. Expressed sequenced tags belonging to the deletion bin 7AL-0.74–0.86, corresponding to the genomic location of Sr22 were screened for polymorphism. In addition, RFLP markers that mapped to this region were targeted. Initial screening was performed on the resistant and susceptible DNA bulks obtained from backcross derivatives carrying Sr22 in three genetic backgrounds with short T. boeoticum segments. A cloned wheat genomic fragment, csIH81, that detected RFLPs between the resistant and susceptible bulks, was converted into a sequence tagged site (STS) marker, named cssu22. Validation was performed on Sr22 carrying backcross-derivatives in fourteen genetic backgrounds and other genotypes used for marker development. Marker cssu22 distinguished all backcross-derivatives from their respective recurrent parents and co-segregated with Sr22 in a Schomburgk (+Sr22)/Yarralinka (−Sr22)-derived recombinant inbred line (RIL) population. Sr22 was also validated in a second population, Sr22TB/Lakin-derived F4 selected families, containing shortened introgressed segments that showed recombination with previously reported flanking microsatellite markers.

Development of wheat-Aegilops speltoides recombinants and simple PCR-based markers for Sr32 and a new stem rust resistance gene on the 2S#1 chromosome.

Key messageWheat–Aegilops speltoidesrecombinants carrying stem rust resistance genesSr32andSrAes1teffective against Ug99 and PCR markers for marker-assisted selection.AbstractWild relatives of wheat are important resources for new rust resistance genes but underutilized because the valuable resistances are often linked to negative traits that prevent deployment of these genes in commercial wheats. Here, we report ph1b-induced recombinants with reduced alien chromatin derived from E.R. Sears’ wheat–Aegilops speltoides 2D-2S#1 translocation line C82.2, which carries the widely effective stem rust resistance gene Sr32. Infection type assessments of the recombinants showed that the original translocation in fact carries two stem rust resistance genes, Sr32 on the short arm and a previously undescribed gene SrAes1t on the long arm of chromosome 2S#1. Recombinants with substantially shortened alien chromatin were produced for both genes, which confer resistance to stem rust races in the TTKSK (Ug99) lineage and representative races of all Australian stem rust lineages. Selected recombinants were back crossed into adapted Australian cultivars and PCR markers were developed to facilitate the incorporation of these genes into future wheat varieties. Our recombinants and those from several other labs now show that Sr32, Sr39, and SrAes7t on the short arm and Sr47 and SrAes1t on the long arm of 2S#1 form two linkage groups and at present no rust races are described that can distinguish these resistance specificities.

Exploring wheat landraces for rust resistance using a single marker scan

Marker-trait associations identified in diverse germplasm can be exploited in crop improvement programs. An attempt to establish such associations was made by evaluating 205 wheat landraces for stripe rust, leaf rust and stem rust responses in the field over three crop seasons. Diversity arrays technology was used to genotype the landraces and associations were identified using a single-marker scan. Sixty-eight markers were significantly associated with rust resistance. Several significantly associated loci coincided with the presence of known major genes or QTL for rust resistance. In contrast, many marker-rust response associations identified in this analysis for each of the three rust diseases uncovered new loci. Dual associations; stripe rust-leaf rust (1AL, 2BS, 2BL, 3DL, 5BS, 6BS and 7DL), leaf rust-stem rust (5BL) and stripe rust-stem rust (4BL and 6AS) resistance were also observed. These associations could enable a cost-effective targeted mapping of dual rust resistance. Some marker-trait associations identified in this study have been validated through genetic analyses and formal naming of resistance loci.

Inheritance and molecular mapping of a gene conferring seedling resistance against Puccinia hordei in the barley cultivar Ricardo

Genetic studies were undertaken to determine the inheritance and genomic location of uncharacterised seedling resistance to leaf rust, caused by Puccinia hordei, in the barley cultivar Ricardo. The resistance was shown to be conferred by a single dominant gene, which was tentatively designated RphRic. Bulk segregant analysis (BSA) and genetic mapping of an F3 mapping population using multiplex-ready SSR genotyping and Illumina GoldenGate SNP assay located RphRic in chromosome 4H. Given that this is the first gene for leaf rust resistance mapped on chromosome 4H, it was designated Rph21. The presence of an additional gene, Rph2, in Ricardo, was confirmed by the test of allelism. The seedling gene Rph21 has shown effectiveness against all Australian pathotypes of P. hordei tested since at least 1992 and hence represents a new and useful source of resistance to this pathogen.