The past, present and future of breeding rust resistant wheat.

The fungus Puccinia triticina Eriks (Pt) is the cause of leaf rust, one of the most damaging diseases, which significantly reduces common wheat yields. In Pt-resistant adult plants, an APR-type resistance is observed, which protects the plant against multiple pathogen races and is distinguished by its persistence under production conditions. With a more complete understanding of the molecular mechanisms underlying the function of APR genes, it will be possible to develop new strategies for resistance breeding in wheat. Currently, mainly APR genes, such as Lr34, Lr46, and Lr67, are principally involved in resistance breeding as they confer durable resistance to multiple fungal races occurring under different climatic and environmental conditions. However, the mechanisms underlying the defence against pathogens mediated by APR genes remain largely unknown. Our research aimed to shed light on the molecular mechanisms related to resistance genes and miRNAs expression, underlying APR resistance to leaf rust caused by Pt. Furthermore, the present study aimed to identify and functionally characterize the investigated miRNAs and their target genes in wheat in response to leaf rust inoculation. The plant material included hybrid forms of wheat from the F2 and BC1F1 generations, obtained by crossing the resistance cultivar Glenlea (CItr 17272) with agriculturally important Polish wheat cultivars. Biotic stress was induced in adult plants via inoculation with Pt fungal spores under controlled conditions. The RT-qPCR method was used to analyze the expression profiles of selected APR genes at five time points (0, 6, 12, 24, and 48 hpi). The results presented here demonstrate the differential expression of APR genes and miRNAs at stages of leaf rust development at selected timepoints after inoculation. We analyzed the expression of three leaf rust resistance genes, using different genetic backgrounds in F2 and BC1F1 segregation materials, in leaf tissues after Pt infection. Our goal was to investigate potential differences resulting from the genetic background found in different generations of hybrid forms of the same parental forms. Gene ontology analysis predicted 190 target genes for tae-miR5384-3p and 167 target genes for tae-miR9653b. Our findings revealed distinct expression profiles for genes, with the highest expression levels observed mainly at 6, 24, and 48 hpi. The candidate gene Lr46-Glu2 displayed an upregulation, suggesting its potential involvement in the immune response against Pt infection.

Bread wheat (Triticum aestivum) is one of the top three cultivated crops, and a major caloric source for humanity. Global wheat production is under threat due to the rapid evolution of highly virulent fungal pathogens such as Puccinia spp. that cause rust diseases. Losses due to rusts are routinely minimised through the deployment of host-mediated genetic resistance. However, the rust pathogens have the ability to evolve virulence and overcome the host resistance. Therefore, a continuous supply of new sources of resistance is essential for sustainable rust management. Wheat wild relatives are a valuable resource as they provide resistance against diverse rust forms.In this study, CPI110672, an accession of the D-genome progenitor Aegilops tauschii, was chosen for in-depth analysis as it resists three wheat rust diseases, namely leaf, stem and stripe rust. To determine whether the triple rust resistance is pleiotropic or involves multiple genes conferring specific resistance, we conducted genetic analysis using a mapping population derived from a cross between CPI110672 and CPI110717 (susceptible) accessions. Through rust infection screening, we determined the triple rust resistance was conferred by multiple genes. Two independent genes (Sr672a and Sr672b) segregated for stem rust resistance, while we identified monogenic segregation for stripe (Yr672) and leaf rust (Lr672) resistance. Genotyping by 90K Infinium single nucleotide polymorphism (90K SNP) chip analysis confirmed independent segregation where each of the resistances were linked with different SNP markers. Based on closely-associated SNPs and their physical position, the leaf rust resistance gene Lr672 and one of the stem rust resistance genes (Sr672a) were mapped to the short arm of chromosome 2D, whereas the stripe rust resistance gene mapped to chromosome arm 4DS. Converting the SNPs into Kompetitive Allele Specific (KASP) genotyping markers and mapping on the segregating population resulted in the identification of flanking markers for all three resistance genes.Anchoring the Sr672a flanking markers on to the Chinese Spring (CS) IWGSC RefSeq v1.0 and Ae. tauschii AL8/78 v4.0 reference genome sequences identified one candidate gene belonging to CC-NBS-LRR (CNL), the major class of resistance genes known in plants for rust resistance. The candidate gene was identified as a homologue of the recently cloned Sr46 gene. Screening using a gene specific marker for Sr46 confirmed that Sr672a was an allele of Sr46 with a single amino acid difference and hence designated as Sr46b. Validation of Sr46b by a transgenic complementation test confirmed that rust resistance is conferred by this allele, and indicated that the difference in one amino acid did not alter the rust resistance function. Further, we deployed Sr46b into a commercial cultivar through marker assisted selection. Also, we attempted to stack Sr46b with other stem rust resistance genes (Sr33 and Sr45) isolated from Ae. tauschii using speed breeding technology. Through speed breeding and marker assisted selection, we were able to select recombinant lines with multiple resistance genes combinations within 180 days.We used traditional map-based cloning in conjunction with a comparative genomics approach to fine mapping the leaf rust (Lr672) and stripe rust (Yr672) resistance genes. The whole genome sequence assemblies of parental accessions CPI110672, CPI110717 from the open wild wheat consortium (OWWC), John Innes Centre, UK and the recent version of reference sequences of CS-RefSeq v1.0 and AL8/78 v4.0 were used to fine map and identify candidate genes for Lr672 and Yr672.Based on previous studies, we identified the accession CPI110672 as synonymous with TA1675, the donor for the leaf rust resistance gene Lr39, thus confirming that Lr672 is Lr39. Anchoring the closely linked flanking markers in the CS-RefSeq v1.0 and AL8/78 v4.0 reference sequences delimited a 1.2 Mb genomic region in both reference genomes. Additionally, we also used the CPI110672 genome sequences to predict CNL genes mapped within the 1.2 Mb physical region of Lr39. Markers specific to the candidate genes co-segregated with the leaf rust phenotype in the CPI110672xCPI110717 F2:3 mapping population and hence was useful for marker assisted deployment of Lr39 resistance.Similarly, anchoring the Yr672 flanking markers narrowed down an approximately 500 kb region in both reference sequences. Evaluation of the CPI110672 CNL genes mapped collinear to the 500 kb reference sequences identified one candidate gene. Markers specific to the candidate CNL gene co-segregated with the stripe rust resistance phenotype in the F2:3 mapping population. Cloning and transgenic complementation tests confirmed the stripe rust resistance. Further, we deployed the Yr672 in the commercial cultivar using marker assisted backcross strategy.The major outcomes of this study include:• Understanding the genetic architecture of triple rust resistance in accession CPI110672• Cloning and validation of Sr46b and Yr672 rust resistance candidate genes• Fine mapping a leaf rust resistance (Lr39) gene• Development of breeder-friendly molecular markers for Sr46, Yr672 and Lr39• Marker assisted introgression of Sr46b and Yr672 into a commercial cultivar• Marker assisted pyramiding of Sr33/Sr45/Sr46b resistance genes using speed breeding technology

Triticum aestivum L., commonly known as bread wheat, characterized by a chromosomal composition of 2n = 6x = 42 (AABBDD), is a significant source of dietary protein and daily calorie intake for much of the global population. Stripe rust (Puccinia striiformis Westend. f. sp. tritici Eriks) and stem rust (Puccinia graminis f. sp. tritici Erikss & E. Henning) now pose substantial threats to overall wheat production worldwide, since most rust resistance genes in wheat have been overcome by virulent rust fungus races. It is essential to enhance genetic resistance against these devastating diseases. Wheat acquires crucial reservoirs of new resistance genes through introgressions from derivatives of Secale cereale, Leymus mollis, Leymus racemosus, and Thinopyrum junceiforme. This study systematically examined seedling resistance to various stripe rust races to identify new sources of resistance. Six wheat-rye introgression lines (SLU124, SLU125, SLU126, SLU127, SLU128 and SLU129) containing rye chromosomes 4R, 5R, and 6R were identified as carriers of previously undiscovered resistance genes against stripe rust races. Seedling assays confirmed that the stripe rust resistance in line SLU126 was retained over multiple generations. Using genotyping-by-sequencing (GBS) platforms and aligning putative GBS-SNPs with fully annotated rye NLR genes, three Kompetitive Allele-Specific PCR (KASP) markers were designed specifically for a chromosomal region at chromosome 6R, associated with two distinct stripe rust resistance genes. The development and validation of the wheat-rye cryptic translocation 6DS.6DL.6RL.6DL, featuring newfound stripe rust resistance genes, were conducted through seedling resistance assays and molecular analysis. The stripe rust resistance gene in family 29-N3-5 on the rye chromosome 6RL arm was provisionally designated YrSLU. Extensive molecular marker analysis and multiple-generation seedling assays revealed that stripe rust resistance in SLU124 is located on the 4RL chromosome arm of rye. Two KASP markers located on the 4RL chromosome were identified as being closely associated with two stripe rust resistance genes in resistant plants of a SLU124 population. Using marker-assisted gene pyramiding, stem rust resistance gene Sr59 and stripe rust resistance gene YrSLU were combined in a single wheat genotype. Overall, this thesis demonstrated the advantages of marker-assisted gene pyramiding in transferring multiple disease resistance genes within a single genotype. Incorporation of these resistance genes into wheat has expanded the gene pool for combating destructive diseases.

ABSTRACTThe leaf rust (Puccinia triticina f. sp. tritici), stripe rust (Puccinia striiformis f. sp. tritici), and stem rust (Puccinia graminis f. sp. tritici) are major fungal constraints affecting wheat production worldwide. Identifying and deploying wheat varieties with diverse resistance are the best ways to manage all the rusts. Therefore, a continuous search goes on to identify diverse germplasm with effective rust resistance that expresses at different stages of plant growth (seedling and adult plant). A set of 22 rust resistant wheat genotypes and 4 checks (controls), viz., Avocet‐Yr10, Avocet ‐Yr15, Agra Local, and respective positive checks were studied for characterising rust resistance genes using host–pathogen interactions complemented by molecular markers. Among 22 elite genotypes, 05 genotypes amplified 191 bp fragment with marker PSY1E1, confirmed the presence of gene Lr19/Sr25. These genotypes also expressed resistance to most virulent leaf rust pathotypes, 77‐5 and 77‐9 in host–pathogen interaction test (HPI). Seven genotypes showed the presence of Lr34/Yr18/Sr57/Pm38/Ltn1 in homozygous state, whereas G4 showed its presence in heterozygous condition. Among 22 genotypes, 16 genotypes possessed Yr10. Five genotypes (22.7%) exhibited two gene combinations, Lr19/Sr25, and Yr10 as revealed through the detection of 191 bp fragment with marker PSY1E1 and 260 bp fragment with co‐dominantly inherited microsatellite marker Xpsp3000, respectively. All five genotypes (G2, G3, G8, G9, and G18) also expressed brown glumes controlled by the gene Rg1 tightly linked to Yr10 on the 1BS chromosome. Broad spectrum rust resistance present in these lines in good agronomic backgrounds could be used as potent genetic donors for diverse and durable rust resistance breeding programmes in wheat.

Leaf rust, stripe rust and stem rust are the three important rusts of wheat. While stripe rust is confined to the cooler regions of North West India, stem rust requires a comparatively higher temperature to develop thus confined to Central and peninsular India. Leaf rust on the other hand occurs almost everywhere, wherever wheat is grown in India. Breeding for rust resistance is important for preventing the losses caused by the rust pathogen Puccinia spp. Over the years, judicious deployment of rust resistance genes has kept the rusts under control in India. However, continuous evolution of new virulent races of leaf, stem and stripe rusts have led to breakdown of many effective rust resistance genes. In view of the continuous evolution of new rust races, search and utilization of new rust resistance genes is essential. Resistance breeding using MAS technology have eliminated the creation of artificial rust epiphytotic for selection of rust resistance genes. Marker based selection has aided in incorporation of not only single but multiple genes for rust resistance. Three popular wheat varieties, HD2967, HD2733 and HD2932 were improved for rust resistance by incorporating rust resistance genes, Lr19, Lr24, LrTrK, Sr26, Yr5, Yr10 and Yr15. Apart from seedling resistance genes some APR genes such as Lr34, Lr46, Lr67 and Lr68 were also introgressed in these varieties to impart durable rust resistance. In some varieties such as HD2733 and HD3059 APR and seedling resistance genes were also combined. Several wheat varieties developed through MAS breeding have already replaced the old susceptible wheat varieties. Marker assisted backcross breeding can produce improved versions of the popular varieties or Near isogenic lines in shorter period of time. NILs may also be used effectively to deploy diverse genes in a given geographical area. Multiple NILs of a mega variety carrying different rust resistance genes can help in managing the rust disease by preventing the build up and spread of inoculums.

ABSTRACTGene pyramiding (assembling multiple desirable genes into a single genotype) via conventional methods to combat Asian rust resistance in soybean (Glycine max (L.) Merrill) and developing soybean varieties with durable resistance to this disease continues to be a challenge. Therefore, our objectives were to pyramid four Asian rust (caused by Phakopsora pachyrhizi) resistance (Rpp) genes, viz., Rpp1, Rpp2, Rpp3, and Rpp4 from their respective donors, PI200492 (Komata), PI230971, PI462312 (Ankur), and PI459025 (Bing Nan). Two single crosses (PI200492 × PI230971; PI462312 × PI459025) and a double-cross [(PI200492 × PI230971) × (PI462312 × PI459025)] were made for present study. The scoring of parents and crosses was done according to a 0–9 grading scale, where 0 = 0% disease intensity (absolutely resistant), 1 = 1% disease intensity (highly resistant), 3 = 1.1–10% disease intensity (moderately resistant), 5 = 10.1–25% disease intensity (moderately susceptible), 7 = 25.1–50% disease intensity (susceptible), and 9 = more than 50% disease intensity (highly susceptible). Out of four parents used, Rpp1 gene-donor plant introduction (PI)200492 (Komata) was immune to rust, with a disease grade of 0.92. Rpp2 and Rpp4 gene donors, PI230971 and [PI459025 (Bing Nan)], had reddish-brown (RB) lesions. Rpp3 gene-donor PI462312 (Ankur) showed a few, highly localized patches of tan lesions; however, it was not as susceptible as the susceptible check JS335. In cross-A (PI200492 × PI230971), all the F1s were rust resistant, whereas in the F2, 93.9% (845 plants) were either immune (11.0%, 99 plants) showing no infection or had RB lesions (82.9%, 746 plants) with resistant reaction and the remainder 6.1% (55 plants) had susceptible reaction. In cross-B (PI462312 × PI459025), 80.8% (63 plants) of the F1 had RB lesions and resistant reaction, whereas 19.2% (15 plants) had susceptible reaction. In its F2 population, 24.2% (217 plants) were susceptible. In cross-C [(PI200492 × PI230971) × (PI462312 × PI459025)], i.e., double-cross hybrid (DCH), 85.5% (77 plants) were either immune or had RB lesions, whereas the rest of the plants 14.5% (13 plants) showed susceptible reaction. Based on parental survey, four simple sequence repeat primers were short-listed for amplification of individual rust-resistance gene-specific markers in ten plants of each cross, viz., Satt191-210bp (Rpp1 gene), Sat_361-245bp (Rpp2 gene), Satt263-195bp (Rpp3 gene), and Rpp4TM-128bp (Rpp4 gene). In the single-cross hybrid (SCH)-A (PI200492 × PI230971), six plants had both Rpp1 and Rpp2 genes, whereas in another SCH-B (PI462312 × PI459025), seven plants had both Rpp3 and Rpp4 genes. In DCH [(PI200492 × PI230971) × (PI462312 × PI459025)], a single plant had all four Rpp genes, five plants had two Rpp genes, whereas a single susceptible plant had only Rpp3 gene. The homozygous rust-resistant segregants from these crosses can be used for improving rust resistance of otherwise adapted, high-yielding soybean genotypes.

Here, we describe a strategy to improve broad-spectrum leaf rust resistance by marker-assisted combination of two partial resistance genes. One of them represents a novel partial adult plant resistance gene, named Lr75. Leaf rust caused by the fungal pathogen Puccinia triticina is a damaging disease of wheat (Triticum aestivum L.). The combination of several, additively-acting partial disease resistance genes has been proposed as a suitable strategy to breed wheat cultivars with high levels of durable field resistance. The Swiss winter wheat cultivar 'Forno' continues to show near-immunity to leaf rust since its release in the 1980s. This resistance is conferred by the presence of at least six quantitative trait loci (QTL), one of which is associated with the morphological trait leaf tip necrosis. Here, we used a marker-informed strategy to introgress two 'Forno' QTLs into the leaf rust-susceptible Swiss winter wheat cultivar 'Arina'. The resulting backcross line 'ArinaLrFor' showed markedly increased leaf rust resistance in multiple locations over several years. One of the introgressed QTLs, QLr.sfr-1BS, is located on chromosome 1BS. We developed chromosome 1B-specific microsatellite markers by exploiting the Illumina survey sequences of wheat cv. 'Chinese Spring' and mapped QLr.sfr-1BS to a 4.3cM interval flanked by the SSR markers gwm604 and swm271. QLr.sfr-1BS does not share a genetic location with any of the described leaf rust resistance genes present on chromosome 1B. Therefore, QLr.sfr-1BS is novel and was designated as Lr75. We conclude that marker-assisted combination of partial resistance genes is a feasible strategy to increase broad-spectrum leaf rust resistance. The identification of Lr75 adds a novel and highly useful gene to the small set of known partial, adult plant leaf rust resistance genes.

Stem rust [causal organism: Puccinia graminis f. sp. tritici (Pgt)], stripe rust [Puccinia striiformis f. sp. tritici (Pst)], and leaf rust [Puccinia triticina (Pt)] are important fungal diseases of wheat in Central Asia and worldwide. Therefore, identification of seedling and adult plant resistance (APR) genes is of major importance for the national wheat breeding program in many countries. The objectives of this study were to identify genes that confer seedling and APR resistances in widely grown wheat cultivars, landraces and advanced lines from Tajikistan. A total of 41 wheat accessions were inoculated with eleven races of Pgt, twelve races of Pst and nine races of Pt for postulation of Sr (stem rust), Yr (yellow or stripe rust), and Lr Lr (leaf rust) resistance genes at the seedling stage. In addition, all of the accessions were tested in field trials for the response to stem rust and stripe rust. Genes for seedling stem rust resistance (i.e. Sr5, Sr6, Sr11, Sr31, and Sr38), stripe rust resistance (Yr9, Yr17, and Y27), and leaf rust resistance (Lr16 and Lr26) were postulated in the Tajik wheat. The presence of the pleiotropic APR genes Sr2/Yr30/Lr27 (associated with pseudo-black chaff phenotype) and Lr34/Yr18/Sr57 (associated with leaf tip necrosis phenotype), and also Lr37 were assessed in the field and confirmed with linked molecular markers. In most of the wheat accessions, resistance genes could not be postulated because their infection types did not match the avirulence or virulence profile of the Pgt, Pst and Pt races tested. Six, seven, and nine accessions were identified that likely possess new genes for resistance to stem rust, stripe rust, and leaf rust, respectively, which have not been described previously. The research demonstrates the presence of effective seedling resistance and APR genes in widely grown wheat accessions that could facilitate further rust resistance breeding in the national wheat breeding program in Tajikistan.

Construction and characterization of new cloning vehicles I. Ampicillin-resistant derivatives of the plasmid pMB9

Wheat as a crop has benefited immensely from genetic improvement programmes but wheat production is still being challenged constantly by several diseases; among them, rusts are the most prominent. Leaf rust is the most widely distributed desease of wheat despite the fact that major emphasis has been made to develop rust resistant varieties. Deployment of major genes has often turned out to be non-durable and in India most of the genes identified from cultivated germplasm are not effective against the prevalent pathotypes of leaf rust. A spring type Triticum monococcum (acc. 14087) has maintained a high level of resistance to Indian isolates of leaf and stripe rust. Genetic studies using a set of 125 recombinant inbred lines (RILs), developed from a cross T. monococcum (acc. 14087)/T. boeoticum (acc. 5088) revealed that both T. monococcum and T. boeoticum have one APR gene that confers resistance to stripe rust and one seedling and one adult plant resistance gene for leaf rust. A genome linkage map with more than 150 markers, including RFLPs, SSRs and bin mapped ESTs, has been generated using the RIL population. QTL analysis revealed the presence of leaf and stripe rust resistance genes on chromosome 2A. Attempts were made to transfer both leaf and stripe rust resistance genes from T. monococcum to hexaploid wheat using T. durum cv N59 as a bridging species. Screening of F1 and backcross generations revealed that B genome of T. durum suppresses resistance of T. monococcum. With subsequent backcrosses one seedling and one APR gene for leaf rust and one APR gene for stripe rust resistance have been transferred from T. monococcum to bread wheat cv. WL711 and one APR gene for leaf rust has been transferred in PBW343 background. Chromosome number of the resistant plants varied from 39–kern0.5pt41. The leaf and stripe rust resistant plants are being analyzed with SSR markers that were found to be associated with leaf and stripe rust resistance genes based on QTL mapping in the RIL population

BackgroundThe resistance to leaf rust (Lr) caused by Puccinia triticina in wheat (Triticum aestivum L.) has been well studied over the past decades with over 70 Lr genes being mapped on different chromosomes and numerous QTLs (quantitative trait loci) being detected or mapped using DNA markers. Such resistance is often divided into race-specific and race-nonspecific resistance. The race-nonspecific resistance can be further divided into resistance to most or all races of the same pathogen and resistance to multiple pathogens. At the molecular level, these three types of resistance may cover across the whole spectrum of pathogen specificities that are controlled by genes encoding different protein families in wheat. The objective of this study is to predict and analyze genes in three such families: NBS-LRR (nucleotide-binding sites and leucine-rich repeats or NLR), START (Steroidogenic Acute Regulatory protein [STaR] related lipid-transfer) and ABC (ATP-Binding Cassette) transporter. The focus of the analysis is on the patterns of relationships between these protein-coding genes within the gene families and QTLs detected for leaf rust resistance.ResultsWe predicted 526 ABC, 1117 NLR and 144 START genes in the hexaploid wheat genome through a domain analysis of wheat proteome. Of the 1809 SNPs from leaf rust resistance QTLs in seedling and adult stages of wheat, 126 SNPs were found within coding regions of these genes or their neighborhood (5 Kb upstream from transcription start site [TSS] or downstream from transcription termination site [TTS] of the genes). Forty-three of these SNPs for adult resistance and 18 SNPs for seedling resistance reside within coding or neighboring regions of the ABC genes whereas 14 SNPs for adult resistance and 29 SNPs for seedling resistance reside within coding or neighboring regions of the NLR gene. Moreover, we found 17 nonsynonymous SNPs for adult resistance and five SNPs for seedling resistance in the ABC genes, and five nonsynonymous SNPs for adult resistance and six SNPs for seedling resistance in the NLR genes. Most of these coding SNPs were predicted to alter encoded amino acids and such information may serve as a starting point towards more thorough molecular and functional characterization of the designated Lr genes. Using the primer sequences of 99 known non-SNP markers from leaf rust resistance QTLs, we found candidate genes closely linked to these markers, including Lr34 with distances to its two gene-specific markers being 1212 bases (to cssfr1) and 2189 bases (to cssfr2).ConclusionThis study represents a comprehensive analysis of ABC, NLR and START genes in the hexaploid wheat genome and their physical relationships with QTLs for leaf rust resistance at seedling and adult stages. Our analysis suggests that the ABC (and START) genes are more likely to be co-located with QTLs for race-nonspecific, adult resistance whereas the NLR genes are more likely to be co-located with QTLs for race-specific resistance that would be often expressed at the seedling stage. Though our analysis was hampered by inaccurate or unknown physical positions of numerous QTLs due to the incomplete assembly of the complex hexaploid wheat genome that is currently available, the observed associations between (i) QTLs for race-specific resistance and NLR genes and (ii) QTLs for nonspecific resistance and ABC genes will help discover SNP variants for leaf rust resistance at seedling and adult stages. The genes containing nonsynonymous SNPs are promising candidates that can be investigated in future studies as potential new sources of leaf rust resistance in wheat breeding.

Leaf rust, stem rust, and stripe rust are among the most important diseases of wheat and barley worldwide and are best controlled using genetic resistance. To increase the diversity of rust resistance in wheat and barley, a project was initiated to identify and characterise rust resistance genes from the wild species of Aegilops sharonensis (Sharon goatgrass) and Hordeum vulgare ssp. spontaneum (wild barley), respectively. One hundred and two accessions of Sharon goatgrass from Israel and 318 Wild Barley Diversity Collection (WBDC) accessions from the Fertile Crescent, Central Asia, North Africa, and the Caucasus region were evaluated for resistance to leaf rust, stem rust, and/or stripe rust. Sharon goatgrass exhibited a wide range of infection types (ITs) in response to leaf rust, stem rust, and stripe rust. The percentage of resistant accessions in Sharon goatgrass was 58.8–78.4% for leaf rust, 11.8–69.6% for stem rust, and 46.1% for stripe rust, depending on the race used and the plant growth stage. Genetic studies with Sharon goatgrass revealed oligogenic resistance to leaf rust and stem rust. Wild barley also exhibited a wide range of ITs to leaf rust and stem rust; however, the overall frequency of resistance was lower than for Sharon goatgrass. The percentage of resistant accessions in wild barley was 25.8% for leaf rust and 5.7–20.1% for stem rust, depending on the race used. Resistance to the new virulent stem rust race TTKS (i.e. Ug99), present in eastern Africa, was found in both Sharon goatgrass (70% of accessions) and wild barley (25% of 20 accessions tested). Association mapping for stem rust resistance was applied in the WBDC using Diversity Arrays Technology (DArT) markers. Using the highly conservative P value threshold of 0.001, 14 and 15 significant marker associations were detected when the number of subpopulations (K value) was set for 10 and 8, respectively. These significant associations were in 9 and 8 unique chromosome bins, respectively. Two significant marker associations were detected for resistance to the wheat stem rust race MCCF in the same bin as the rpg4/Rpg5 complex on chromosome 7(5H). The presence of a major stem rust resistance gene in this bin on chromosome 7(5H) was validated in a bi-parental mapping population (WBDC accession Damon × cv. Harrington) constructed with DArT markers. The results from this study indicate that Sharon goatgrass and wild barley are rich sources of rust resistance genes for cultivated wheat and barley improvement, respectively, and that association mapping may be useful for positioning disease resistance genes in wild barley.

Stem rust has become a renewed threat to global wheat production after the emergence and spread of race TTKSK (also known as Ug99) and related races from Africa. To elucidate U.S. winter wheat resistance genes to stem rust, association mapping was conducted using a panel of 137 lines from cooperative U.S. winter wheat nurseries from 2008 and simple sequence repeat (SSR) and sequence tagged site (STS) markers across the wheat genome. Seedling infection types were evaluated in a greenhouse experiment using six U.S. stem rust races (QFCSC, QTHJC, RCRSC, RKQQC, TPMKC and TTTTF) and TTKSK, and adult plant responses to bulked U.S. races were evaluated in a field experiment. A linearization algorithm was used to convert the qualitative Stakman scale seedling infection types for quantitative analysis. Association mapping successfully detected six known stem rust seedling resistance genes in U.S. winter wheat lines with frequencies: Sr6 (12%), Sr24 (9%), Sr31 (15%), Sr36 (9%), Sr38 (19%), and Sr1RSAmigo (8%). Adult plant resistance gene Sr2 was present in 4% of lines. SrTmp was postulated to be present in several hard winter wheat lines, but the frequency could not be accurately determined. Sr38 was the most prevalent Sr gene in both hard and soft winter wheat and was the most effective Sr gene in the adult plant field test. Resistance to TTKSK was associated with nine markers on chromosome 2B that were in linkage disequilibrium and all of the resistance was attributed to the Triticum timopheevii chromosome segment carrying Sr36. Potential novel rust resistance alleles were associated with markers Xwmc326-203 on 3BL, Xgwm160-195 and Xwmc313-225 on 4AL near Sr7, Xgwm495-182 on 4BL, Xwmc622-147 and Xgwm624-146 on 4DL, and Xgwm334-123 on 6AS near Sr8. Xwmc326-203 was associated with adult plant resistance to bulked U.S. races and Xgwm495-182 was associated with seedling resistance to TTKSK.

Rice blast caused by Magnaporthe oryzae is the most destructive fungal disease in crops, greatly threatening rice production and food security worldwide. The identification and utilization of broad-spectrum resistance genes are considered to be the most economic and effective method to control the disease. In the past decade, many blast resistance ( R) genes have been identified, which mainly encode nucleotide-binding leucine-rich repeat (NLR) receptor family and confer limited race-specific resistance to the fungal pathogen. Resistance genes conferring broad-spectrum blast resistance are still largely lacking. In this study, we carried out a map-based cloning of the new blast R locus Pizh in variety ZH11. A bacterial artificial chromosome (BAC) clone of 165 kb spanning the Pizh locus was sequenced and identified 9 NLR genes, among which only Pizh-1 and Pizh-2 were expressed. Genetic complementation experiments indicated that Pizh-1 but not Pizh-2 alone could confer blast resistance. Intriguingly, both mutations on Pizh-1 and Pizh-2 by CRISPR-Cas9 abolished the Pizh-mediated resistance. We also observed that Pizh-1-mediated resistance was partially dependent on Pizh-2. Pizh-1 and Pizh-2 form a complex of NLRs through direct interaction. This suggests that Pizh-1 may function as the executor NLR and Pizh-2 as a 'helper' NLR that shares functional redundancy with other NLRs. Our current study provides not only a good tool for rice disease resistance breeding but also deep insight into NLR association and function in plant immunity. This article is part of the theme issue 'Biotic signalling sheds light on smart pest management'.

Leaf rust caused by Puccinia triticina Eriks is one of the most problematic diseases of wheat throughout the world. The gene Lr42 confers effective resistance against leaf rust at both seedling and adult plant stages. Previous studies had reported Lr42 to be both recessive and dominant in hexaploid wheat; however, in diploid Aegilops tauschii (TA2450), we found Lr42 to be dominant by studying segregation in two independent F2 and their F2:3 populations. We further fine-mapped Lr42 in hexaploid wheat using a KS93U50/Morocco F5 recombinant inbred line (RIL) population to a 3.7 cM genetic interval flanked by markers TC387992 and WMC432. The 3.7 cM Lr42 region physically corresponds to a 3.16 Mb genomic region on chromosome 1DS based on the Chinese Spring reference genome (RefSeq v.1.1) and a 3.5 Mb genomic interval on chromosome 1 in the Ae. tauschii reference genome. This region includes nine nucleotide-binding domain leucine-rich repeat (NLR) genes in wheat and seven in Ae. tauschii, respectively, and these are the likely candidates for Lr42. Furthermore, we developed two kompetitive allele-specific polymorphism (KASP) markers (SNP113325 and TC387992) flanking Lr42 to facilitate marker-assisted selection for rust resistance in wheat breeding programs.