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Selection for resistance to plant diseases is a continuous effort on the part of plant breeders. Sources of genetic resistance are often limited, despite considerable discovery efforts. Stem rust and stripe rust are two diseases of particular importance in barley (Hordeum vulgare L.) production. The present work aims to develop and deploy genotypes with resistance to these diseases that can be used in future breeding efforts. The Woodies, Woody-1 (DH160733; Reg. no. GP-218, PI 704479) and Woody-2 (DH160754; Reg. no. GP-219, PI 704480), are two doubled-haploid genotypes produced via F1 anther culture named in honor of the late Lynn “Woody” Gallagher. These two-row spring habit barley germplasm accessions were released by the Oregon Agricultural Experiment Station in 2023. These genotypes have demonstrated resistance to both stem and stripe rust at the seedling and adult plant stage in trials conducted between 2018 and 2023. The genetic basis of this resistance appears to be a novel quantitative trait locus conferring resistance to both diseases on chromosome 5H that is different from the known rpg4/Rpg5 complex for stem rust resistance found on the same chromosome. Seed can be requested from the Oregon State University Barley Breeding Program or from the NLGRP Germplasm repository.

Aegilops umbellulata serve as an important reservoir for novel biotic and abiotic stress tolerance for wheat improvement. However, chromosomal rearrangements and evolutionary trajectory of this species remain to be elucidated. Here, we present a comprehensive investigation into Ae. umbellulata genome by generating a high-quality near telomere-to-telomere genome assembly of PI 554389 and resequencing 20 additional Ae. umbellulata genomes representing diverse geographical and phenotypic variations. Our analysis unveils complex chromosomal rearrangements, most prominently in 4U and 6U chromosomes, delineating a distinct evolutionary trajectory of Ae. umbellulata from wheat and its relatives. Furthermore, our data rectified the erroneous naming of chromosomes 4U and 6U in the past and highlighted multiple major evolutionary events that led to the present-day U-genome. Resequencing of diverse Ae. umbellulata accessions revealed high genetic diversity within the species, partitioning into three distinct evolutionary sub-populations and supported by extensive phenotypic variability in resistance against several races/pathotypes of five major wheat diseases. Disease evaluations indicated the presence of several novel resistance genes in the resequenced lines for future studies. Resequencing also resulted in the identification of six new haplotypes for Lr9, the first resistance gene cloned from Ae. umbellulata. The extensive genomic and phenotypic resources presented in this study will expedite the future genetic exploration of Ae. umbellulata, facilitating efforts aimed at enhancing resiliency and productivity in wheat., (© 2024 The Author(s). Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

Wheat stem rust caused by Puccinia graminis f. sp. tritici (Pgt) threatens wheat production worldwide. The objective of this study was to characterize wheat stem rust resistance in 'Linkert', a variety with adult plant resistance effective to emerging wheat stem rust pathogen strain Ug99. Two doubled haploid (DH) populations and one recombinant inbred line (RIL) population were developed with 'Linkert' as a stem rust resistant parent. Hard red spring wheat variety 'Forefront' and genetic stock 'LMPG' were used as stem rust susceptible parents of the DH populations. Breeding line 'MN07098-6' was used as a susceptible parent of the RIL population. Both DH and RIL populations with their parents were evaluated both at the seedling stage and in the field against Pgt races. Genotyping data of the DH populations were generated using the wheat iSelect 90k SNP assay. The RIL population was genotyped by genotyping-by-sequencing. We found QTL consistently associated with wheat stem rust resistance on chromosome 2BS for the Linkert/Forefront DH population and the Linkert/MN07098-6 RIL population both in Ethiopia and Kenya. Additional reliable QTL were detected on chromosomes 5BL (125.91 cM) and 4AL ( Sr7a ) for the Linkert/LMPG population in Ethiopia and Kenya. Different QTL identified in the populations reflect the importance of examining the genetics of resistance in populations derived from adapted germplasm (Forefront and MN07098-6) in addition to a genetic stock (LMPG). The associated markers in this study could be used to track and select for the identified QTL in wheat breeding programs., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Edae, Kosgey, Bajgain, Ndung'u, Gemechu, Bhavani, Anderson and Rouse.)

Barley leaf rust, caused by Puccinia hordei , is an important disease of barley worldwide. The pathogen can develop new races that overcome resistance genes, emphasizing the need for monitoring its virulence. This study characterized 519 P. hordei isolates collected in the United States from the 1989 to 2000 and 2010 to 2020 survey periods on 15 Rph (Reaction to Puccinia hordei ) genes. We analyzed linearized infection type data to detect virulence patterns across the United States and in five geographical regions: Pacific/West (PW), Southwest (SW), Midwest (MW), Northeast (NE), and Southeast (SE). Over 32 years, we observed high mean infection scores for Rph1.a , Rph4.d , and Rph8.h ; intermediate scores for Rph2.b , Rph9.i , Rph10.o , Rph11.p , and Rph13.x ; and low scores for Rph3.c , Rph5.e , Rph5.f , Rph7.g , Rph9.z , Rph14.ab , and Rph15.ad . Virulence for Rph2.b , Rph3.c , Rph5.e , Rph9.z , Rph10.o , Rph11.p , and Rph13.x significantly differed between the two survey periods. From 1989 to 2020, regional patterns of virulence were found for Rph5.e , Rph5.f , Rph7.g , and Rph14.ab , while regionalities of virulence for Rph3.c , Rph9.i , Rph9.z were only observed in the 2010 to 2020 survey period. Virulence associations were also detected in the P. hordei population. Notably, isolates that were virulent to Rph5.e and Rph6.f were more likely to be avirulent to Rph7.g and Rph13.x , and vice versa. In decreasing order of effectiveness, Rph15.ad , Rph5.e , Rph3.c , Rph9.z , Rph7.g , Rph5.f , and Rph14.ab were the most effective Rph genes in the United States from 1989 to 2020. Pyramiding Rph15.ad with other widely effective Rph and adult plant resistance genes may provide long-lasting resistance against P. hordei ., Competing Interests: The author(s) declare no conflict of interest.

Most rust resistance genes thus far isolated from wheat have a very limited number of functional alleles. Here, we report the isolation of most of the alleles at wheat stem rust resistance gene locus SR9. The seven previously reported resistance alleles (Sr9a, Sr9b, Sr9d, Sr9e, Sr9f, Sr9g, and Sr9h) are characterised using a synergistic strategy. Loss-of-function mutants and/or transgenic complementation are used to confirm Sr9b, two haplotypes of Sr9e (Sr9e_h1 and Sr9e_h2), Sr9g, and Sr9h. Each allele encodes a highly related nucleotide-binding site leucine-rich repeat (NB-LRR) type immune receptor, containing an unusual long LRR domain, that confers resistance to a unique spectrum of isolates of the wheat stem rust pathogen. The only SR9 protein effective against stem rust pathogen race TTKSK (Ug99), SR9H, differs from SR9B by a single amino acid. SR9B and SR9G resistance proteins are also distinguished by only a single amino acid. The SR9 allelic series found in the B subgenome are orthologs of wheat stem rust resistance gene Sr21 located in the A subgenome with around 85% identity in protein sequences. Together, our results show that functional diversification of allelic variants at the SR9 locus involves single and multiple amino acid changes that recognize isolates of wheat stem rust., (© 2023. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Control of stem rust, caused by Puccinia graminis f.sp. tritici, a highly destructive fungal disease of wheat, faces continuous challenges from emergence of new virulent races across wheat-growing continents. Using combinations of broad-spectrum resistance genes could impart durable stem rust resistance. This study attempted transfer of Sr59 resistance gene from line TA5094 (developed through CSph1bM-induced T2DS·2RL Robertsonian translocation conferring broad-spectrum resistance). Poor agronomic performance of line TA5094 necessitates Sr59 transfer to adapted genetic backgrounds and utility evaluations for wheat improvement. Based on combined stem rust seedling and molecular analyses, 2070 BC1F1 and 1230 BC2F1 plants were derived from backcrossing BAJ#1, KACHU#1, and REEDLING#1 with TA5094. Genotyping-by-sequencing (GBS) results revealed the physical positions of 15,116 SNPs on chromosome 2R. The adapted genotypes used for backcrossing were found not to possess broad-spectrum resistance to selected stem rust races, whereas Sr59-containing line TA5094 showed resistance to all races tested. Stem rust seedling assays combined with kompetitive allele-specific PCR (KASP) marker analysis successfully selected and generated the BC2F2 population, which contained the Sr59 gene, as confirmed by GBS. Early-generation data from backcrossing suggested deviations from the 3:1 segregation, suggesting that multiple genes may contribute to Sr59 resistance reactions. Using GBS marker data (40,584 SNPs in wheat chromosomes) to transfer the recurrent parent background to later-generation populations resulted in average genome recovery of 71.2% in BAJ#1*2/TA5094, 69.8% in KACHU#1*2/TA5094, and 70.5% in REEDLING#1*2/TA5094 populations. GBS data verified stable Sr59 introgression in BC2F2 populations, as evidenced by presence of the Ph1 locus and absence of the 50,936,209 bp deletion in CSph1bM. Combining phenotypic selections, stem rust seedling assays, KASP markers, and GBS data substantially accelerated transfer of broad-spectrum resistance into adapted genotypes. Thus, this study demonstrated that the Sr59 resistance gene can be introduced into elite genetic backgrounds to mitigate stem rust-related yield losses., Competing Interests: There are no competing interests among the author., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)

Key Message: The diploid wheat recessive stem rust resistance gene SrTm4 was fine-mapped to a 754-kb region on chromosome arm 2A m L and potential candidate genes were identified. Race Ug99 of Puccinia graminis f. sp. tritici (Pgt), the causal agent of wheat stem (or black) rust is one of the most serious threats to global wheat production. The identification, mapping, and deployment of effective stem rust resistance (Sr) genes are critical to reduce this threat. In this study, we generated SrTm4 monogenic lines and found that this gene confers resistance to North American and Chinese Pgt races. Using a large mapping population (9522 gametes), we mapped SrTm4 within a 0.06 cM interval flanked by marker loci CS4211 and 130K1519, which corresponds to a 1.0-Mb region in the Chinese Spring reference genome v2.1. A physical map of the SrTm4 region was constructed with 11 overlapping BACs from the resistant Triticum monococcum PI 306540. Comparison of the 754-kb physical map with the genomic sequence of Chinese Spring and a discontinuous BAC sequence of DV92 revealed a 593-kb chromosomal inversion in PI 306540. Within the candidate region, we identified an L-type lectin-domain containing receptor kinase (LLK1), which was disrupted by the proximal inversion breakpoint, as a potential candidate gene. Two diagnostic dominant markers were developed to detect the inversion breakpoints. In a survey of T. monococcum accessions, we identified 10 domesticated T. monococcum subsp. monococcum genotypes, mainly from the Balkans, carrying the inversion and showing similar mesothetic resistant infection types against Pgt races. The high-density map and tightly linked molecular markers developed in this study are useful tools to accelerate the deployment of SrTm4-mediated resistance in wheat breeding programs., (© 2023. The Author(s).)

Key Message: The leaf rust resistance gene in Thatcher wheat derivative 78-1 was mapped to chromosome 1DS with SNP markers and designated as Lr83. 'Thatcher' wheat near isogenic line RL6149, a putative derivative of Triticum dicoccoides, was previously determined to carry leaf rust resistance gene Lr64 on chromosome arm 6AL and a second gene temporarily named LrX on chromosome arm 1DS. The objective of this study was to map and characterize LrX in a population of recombinant inbred lines (RILs) that segregated for a single gene. Thatcher line 78-1 with LrX was crossed with Thatcher and individual F 2 seedlings and F 6 RILs were evaluated for leaf rust response. The 208 F 2 plants segregated for a single recessive gene and 148 F 6 lines for a single gene. The RILs and parents were characterized by genotyping by sequencing (GBS). Six GBS markers and five Kompetitive Allele-Specific PCR (KASP) markers were used to map LrX on the distal region of chromosome arm 1DS. LrX was 1 centiMorgan (cM) proximal to marker K-IWB38437 and 0.4 cM distal to GBS marker 1D_9037138. Line 78-1 was crossed with Thatcher wheat lines with Lr21, Lr42, and Lr60 for allelism tests. LrX mapped 19.49 cM from Lr21 and 11.93 cM from Lr42. In the cross of line 78-1 with the Thatcher line with Lr60, one recombinant in 1,003 F 2 plants was found. LrX and Lr60 are at tightly linked loci on the distal region of chromosome arm 1DS. The gene in line 78-1 was designated as Lr83. Cytological examination of RL6149 provided no evidence of transfer of a chromosome segment of an A- or B-genome chromosome to chromosome 1D., (© 2023. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Detecting plant disease severity could help growers and researchers study how the disease impacts cereal crops to make timely decisions. Advanced technology is needed to protect cereals that feed the increasing population using fewer chemicals; this may lead to reduced labor usage and cost in the field. Accurate detection of wheat stem rust, an emerging threat to wheat production, could inform growers to make management decisions and assist plant breeders in making line selections. A hyperspectral camera mounted on an unmanned aerial vehicle (UAV) was utilized in this study to evaluate the severity of wheat stem rust disease in a disease trial containing 960 plots. Quadratic discriminant analysis (QDA) and random forest classifier (RFC), decision tree classification, and support vector machine (SVM) were applied to select the wavelengths and spectral vegetation indices (SVIs). The trial plots were divided into four levels based on ground truth disease severities: class 0 (healthy, severity 0), class 1 (mildly diseased, severity 1-15), class 2 (moderately diseased, severity 16-34), and class 3 (severely diseased, highest severity observed). The RFC method achieved the highest overall classification accuracy (85%). For the spectral vegetation indices (SVIs), the highest classification rate was recorded by RFC, and the accuracy was 76%. The Green NDVI (GNDVI), Photochemical Reflectance Index (PRI), Red-Edge Vegetation Stress Index (RVS1), and Chlorophyll Green (Chl green) were selected from 14 SVIs. In addition, binary classification of mildly diseased vs. non-diseased was also conducted using the classifiers and achieved 88% classification accuracy. This highlighted that hyperspectral imaging was sensitive enough to discriminate between low levels of stem rust disease vs. no disease. The results of this study demonstrated that drone hyperspectral imaging can discriminate stem rust disease levels so that breeders can select disease-resistant varieties more efficiently. The detection of low disease severity capability of drone hyperspectral imaging can help farmers identify early disease outbreaks and enable more timely management of their fields. Based on this study, it is also possible to build a new inexpensive multispectral sensor to diagnose wheat stem rust disease accurately.

Stem rust of wheat (Triticum spp.), caused by Puccinia graminis f. sp. tritici (Pgt), is one of the most impactful wheat diseases because of its threat to global wheat production. While disease mitigation has primarily been achieved through the deployment of resistant wheat varieties, emerging new virulent races continue to pose risks to the crop. For example, races such as Ug99 (TTKSK), TKTTF, and TTRTF have caused epidemics in different wheat growing regions of the world in recent years. A continual search for new and effective sources of resistance is therefore necessary to safeguard wheat production. This study assessed a breeding panel from the Ethiopian Institute of Agricultural Research (EIAR) wheat breeding program for seedling and field plant resistance to TTRTF and reports genomic regions conferring resistance to TTRTF. Trait correlations (r) were medium to strong (range = .38-.71) and heritabilities were moderate (.32-.56). Association analysis for resistance to TTRTF resulted in detection of 20 markers in 11 chromosomes; the marker S1B_175439851 was associated with resistance at both seedling and adult plant stages. Models with two to four QTL combinations reduced seedling and field disease severity by 12-48 and 9-17%, respectively. Genomic prediction for TTRTF resistance resulted in low to moderately-high predictions (mean correlations of .25-.47). Identification of resistant lines and QTL in the EIAR population is expected to assist in selection toward improved resistance to TTRTF. Specifically, the application of genomic selection (GS) in identifying resistant lines in future related breeding populations will further assist breeding efforts against this new stem rust pathogen race., (© 2022 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)

Puccinia graminis f.sp. tritici (Pgt) causes stem rust disease in wheat that can result in severe yield losses. The factors driving the evolution of its virulence and adaptation remain poorly characterized. We utilize long-read sequencing to develop a haplotype-resolved genome assembly of a U.S. isolate of Pgt. Using Pgt haplotypes as a reference, we characterize the structural variants (SVs) and single nucleotide polymorphisms in a diverse panel of isolates. SVs impact the repertoire of predicted effectors, secreted proteins involved in host-pathogen interaction, and show evidence of purifying selection. By analyzing global and local genomic ancestry we demonstrate that the origin of 8 out of 12 Pgt clades is linked with either somatic hybridization or sexual recombination between the diverged donor populations. Our study shows that SVs and admixture events appear to play an important role in broadening Pgt virulence and the origin of highly virulent races, creating a resource for studying the evolution of Pgt virulence and preventing future epidemic outbreaks., (© 2022. The Author(s).)

Barley leaf rust (BLR), caused by Puccinia hordei, is best controlled through genetic resistance. An efficient resistance breeding program prioritizes the need to identify, characterize, and map new sources of resistance as well as understanding the effectiveness, structure, and function of resistance genes. In this study, three mapping populations were developed by crossing Israelian barley lines "AGG-396," "AGG-397," and "AGG-403" (carrying unknown leaf rust resistance) with a susceptible variety "Gus" to characterize and map resistance. Genetic analysis of phenotypic data from rust testing F 3 s with a P. hordei pathotype 5457 P+ revealed monogenic inheritance in all three populations. Targeted genotyping-by-sequencing of the three populations detected marker trait associations in the same genomic region on the short arm of chromosome 2H between 39 and 57 Mb (AGG-396/Gus), 44 and 64 Mb (AGG-397/Gus), and 31 and 58 Mb (AGG-403/Gus), suggesting that the resistance in all three lines is likely conferred by the same locus (tentatively designated RphAGG396 ). Two Kompetitive allele-specific PCR (KASP) markers, HvGBSv2-902 and HvGBSv2-932, defined a genetic distance of 3.8 cM proximal and 7.1 cM distal to RphAGG396 , respectively. To increase the marker density at the RphAGG396 locus, 75 CAPS markers were designed between two flanking markers. Integration of marker data resulted in the identification of two critical recombinants and mapping RphAGG396 between markers- Mloc-28 (40.75 Mb) and Mloc-41 (41.92 Mb) narrowing the physical window to 1.17 Mb based on the Morex v2.0 reference genome assembly. To enhance map resolution, 600 F 2 s were genotyped with markers- Mloc-28 and Mloc-41 and nine recombinants were identified, placing the gene at a genetic distance of 0.5 and 0.2 cM between the two markers, respectively. Two annotated NLR (nucleotide-binding domain leucine-rich repeat) genes (r2.2HG0093020 and r2.2HG0093030) were identified as the best candidates for RphAGG396 . A closely linked marker was developed for RphAGG396 that can be used for marker-assisted selection., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Mehnaz, Dracatos, Dinh, Forrest, Rouse, Park and Singh.)

The winter wheat (Triticum aestivum L.) line CI13227 has been characterized as having adult plant resistance to leaf rust caused by Puccinia triticina Eriks (Pt). Line CI13227 was crossed with the susceptible spring wheat 'Thatcher' (Tc) and a Tc*2/CI13227 F 6 line with adult plant leaf rust resistance designated as 411A was derived. Line 411A was crossed with Tc to develop an F 6 recombinant inbred line (RIL) population. The parents and 120 F 6 lines were assessed for leaf rust severity at the flag leaf stage in five field plot tests from 2011 through 2015 and were genotyped for single-nucleotide polymorphism (SNP) markers with the Illumina iSelect 90K wheat bead array. A total of 2,384 SNP markers segregated among the RILs. Completely linked SNPs were removed, and 474 markers that covered 2,605 centimorgans (cM) were used for linkage map construction. Quantitative trait loci (QTL) on chromosome 2AL with logarithm of odds (LOD) values 2.34-7.88, on chromosome 4BS with LOD values 1.35- 4.66, and on chromosome 7AL with LOD values 2.92-7.81 were associated with significant reduction in leaf rust severity in the field plot tests. Recombinant inbred lines that had combinations of two or three of the QTL had significantly lower leaf rust severity than RILs that lacked any resistance QTL. Kompetitive allele specific polymerase chain reaction (KASP) markers were developed for the SNPs that were closely linked with the three QTL to facilitate marker-based selection of the leaf rust resistance in breeding programs., (Published 2022. This article is a U.S. Government work and is in the public domain in the USA. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)

Key Message: Stem rust resistance genes, SrRL5271 and Sr672.1 as well as SrCPI110651, from Aegilops tauschii, the diploid D genome progenitor of wheat, are sequence variants of Sr46 differing by 1-2 nucleotides leading to non-synonymous amino acid substitutions. The Aegilops tauschii (wheat D-genome progenitor) accessions RL 5271 and CPI110672 were identified as resistant to multiple races (including the Ug99) of the wheat stem rust pathogen Puccinia graminis f. sp. tritici (Pgt). This study was conducted to identify the stem rust resistance (Sr) gene(s) in both accessions. Genetic analysis of the resistance in RL 5271 identified a single dominant allele (SrRL5271) controlling resistance, whereas resistance segregated at two loci (SR672.1 and SR672.2) for a cross of CPI110672. Bulked segregant analysis placed SrRL5271 and Sr672.1 in a region on chromosome arm 2DS that encodes Sr46. Molecular marker screening, mapping and genomic sequence analysis demonstrated SrRL5271 and Sr672.1 are alleles of Sr46. The amino acid sequence of SrRL5271 and Sr672.1 is identical but differs from Sr46 (hereafter referred to as Sr46_h1 by following the gene nomenclature in wheat) by a single amino acid (N763K) and is thus designated Sr46_h2. Screening of a panel of Ae. tauschii accessions identified an additional allelic variant that differed from Sr46_h2 by a different amino acid (A648V) and was designated Sr46_h3. By contrast, the protein encoded by the susceptible allele of Ae. tauschii accession AL8/78 differed from these resistance proteins by 54 amino acid substitutions (94% nucleotide sequence gene identity). Cloning and complementation tests of the three resistance haplotypes confirmed their resistance to Pgt race 98-1,2,3,5,6 and partial resistance to Pgt race TTRTF in bread wheat. The three Sr46 haplotypes, with no virulent races detected yet, represent a valuable source for improving stem resistance in wheat., (© 2022. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Wheat line Tr129 is resistant to stem rust, caused by Puccinia graminis f. sp. tritici (Pgt). The resistance in Tr129 was reportedly derived from Aegilops triuncialis, but the origin and genetics of resistance have not been confirmed. Here, genomic in situ hybridization (GISH) showed that no Ae. triuncialis chromatin was present in Tr129. Genetic and phenotypic analysis was conducted on F 2 and DH populations from the cross RL6071/Tr129. Seedlings were tested with six Pgt races and were genotyped using an Illumina iSelect 90 K SNP array and kompetitive allele specific PCR (KASP) markers. Mapping and phenotyping showed that Tr129 carried four stem rust resistance (Sr) genes on chromosome arms 2BL (Sr9b), 4AL (Sr7b), 6AS (Sr8a), and 6DS (SrTr129). SrTr129 co-segregated with markers for SrCad, however Tr129 has a unique haplotype suggesting the resistance could be new. Analysis of a RL6071/Peace population revealed that like SrTr129, SrCad is ineffective against three North American races. This new understanding of SrCad will guide its use in breeding. Tr129 and the DNA markers reported here are useful resources for improving stem rust resistance in cultivars., (© 2022. The Author(s).)

Wheat stem (or black) rust, caused by Puccinia graminis f. sp. tritici (Pgt), has been historically among the most devastating global fungal diseases of wheat. The recent occurrence and spread of new virulent races such as Ug99 have prompted global efforts to identify and isolate more effective stem rust resistance (Sr) genes. Here, we report the map-based cloning of the Ug99-effective SrTm5 gene from diploid wheat Triticum monococcum accession PI 306540 that encodes a typical coiled-coil nucleotide-binding leucine-rich repeat protein. This gene, designated as Sr22b, is a new allele of Sr22 with a rare insertion of a large (13.8-kb) retrotransposon into its second intron. Biolistic transformation of an ~112-kb circular bacterial artificial chromosome plasmid carrying Sr22b into the susceptible wheat variety Fielder was sufficient to confer resistance to stem rust. In a survey of 168 wheat genotypes, Sr22b was present only in cultivated T. monococcum subsp. monococcum accessions but absent in all tested tetraploid and hexaploid wheat lines. We developed a diagnostic molecular marker for Sr22b and successfully introgressed a T. monococcum chromosome segment containing this gene into hexaploid wheat to accelerate its deployment and pyramiding with other Sr genes in wheat breeding programmes. Sr22b can be a valuable component of gene pyramids or transgenic cassettes combining different resistance genes to control this devastating disease., (© 2021 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Adult plant resistance (APR) to wheat stem rust has been one of the approaches for resistance breeding since the evolution of the Ug99 race group and other races. This study was conducted to dissect and understand the genetic basis of APR to stem rust in spring wheat line 'Copio'. A total of 176 recombinant inbred lines (RILs) from the cross of susceptible parent 'Apav' with Copio were phenotyped for stem rust resistance in six environments. Composite interval mapping using 762 genotyping-by-sequencing markers identified 16 genomic regions conferring stem rust resistance. Assays with gene-linked molecular markers revealed that Copio carried known APR genes Sr2 and Lr46 / Yr29 / Sr58 in addition to the 2NS/2AS translocation that harbors race-specific genes Sr38 , Lr37 , and Yr17 . Three quantitative trait loci (QTLs) were mapped on chromosomes 2B, two QTLs on chromosomes 3A, 3B, and 6A each, and one QTL on each of chromosomes 2A, 1B, 2D, 4B, 5D, 6D, and 7A. The QTL QSr.umn.5D is potentially a new resistance gene and contributed to quantitative resistance in Copio. The RILs with allelic combinations of Sr2 , Sr38 , and Sr58 had 27 to 39% less stem rust coefficient of infection in all field environments compared with RILs with none of these genes, and this gene combination was most effective in the U.S. environments. We conclude that Copio carries several genes that provide both race-specific and non-race-specific resistance to diverse races of stem rust fungus and can be used by breeding programs in pyramiding other effective genes to develop durable resistance in wheat.

Wheat stem (or black) rust is one of the most devastating fungal diseases, threatening global wheat production. Identification, mapping, and deployment of effective resistance genes are critical to addressing this challenge. In this study, we mapped and characterized one stem rust resistance ( Sr ) gene from the tetraploid durum wheat variety Kronos (temporary designation SrKN ). This gene was mapped on the long arm of chromosome 2B and confers resistance to multiple virulent Pgt races, such as TRTTF and BCCBC. Using a large mapping population (3,366 gametes), we mapped SrKN within a 0.29 cM region flanked by the sequenced-based markers pku4856F2R2 and pku4917F3R3 , which corresponds to 5.6- and 7.2-Mb regions in the Svevo and Chinese Spring reference genomes, respectively. Both regions include a cluster of nucleotide binding leucine-repeat (NLR) genes that likely includes the candidate gene. An allelism test failed to detect recombination between SrKN and the previously mapped Sr9e gene. This result, together with the similar seedling resistance responses and resistance profiles, suggested that SrKN and Sr9e may represent the same gene. We introgressed SrKN into common wheat and developed completely linked markers to accelerate its deployment in the wheat breeding programs. SrKN can be a valuable component of transgenic cassettes or gene pyramids that includes multiple resistance genes to control this devastating disease., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Li, Hua, Rouse, Li, Pang, Bai, Shen, Luo, Li, Zhang, Wang, Dubcovsky and Chen.)

Resistance breeding is an effective approach against wheat stem rust caused by Puccinia graminis f. sp. tritici (Pgt). The synthetic hexaploid wheat line Largo (pedigree: durum wheat "Langdon" × Aegilops tauschii PI 268210) was found to have resistance to a broad spectrum of Pgt races including the Ug99 race group. To identify the stem rust resistance (Sr) genes, we genotyped a population of 188 recombinant inbred lines developed from a cross between the susceptible wheat line ND495 and Largo using the wheat Infinium 90 K SNP iSelect array and evaluated the population for seedling resistance to the Pgt races TTKSK, TRTTF, and TTTTF in the greenhouse conditions. Based on genetic linkage analysis using the marker and rust data, we identified six quantitative trait loci (QTL) with effectiveness against different races. Three QTL on chromosome arms 6AL, 2BL, and 2BS corresponded to Sr genes Sr13c, Sr9e, and a likely new gene from Langdon, respectively. Two other QTL from PI 268210 on 2DS and 1DS were associated with a potentially new allele of Sr46 and a likely new Sr gene, respectively. In addition, Sr7a was identified as the underlying gene for the 4AL QTL from ND495. Knowledge of the Sr genes in Largo will help to design breeding experiments aimed to develop new stem rust-resistant wheat varieties. Largo and its derived lines are particularly useful for introducing two Ug99-effective genes Sr13c and Sr46 into modern bread wheat varieties. The 90 K SNP-based high-density map will be useful for identifying the other important genes in Largo., (© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.)

Leaf rust, caused by Puccinia triticina ( Pt ), stripe rust caused by Puccinia striiformis f. sp. tritici ( Pst ), and stem rust caused by Puccinia graminis f. sp. tritici ( Pgt ) are major diseases to wheat production globally. Host resistance is the most suitable approach to manage these fungal pathogens. We investigated the phenotypic and genotypic structure of resistance to leaf rust, stem rust, and stripe rust pathogen races at the seedling stage in a collection of advanced durum wheat breeding lines and cultivars adapted to Upper Mid-West region of the United States. Phenotypic evaluation showed that the majority of the durum wheat genotypes were susceptible to Pt isolates adapted to durum wheat, whereas all the genotypes were resistant to common wheat type- Pt isolate. The majority of genotypes were resistant to stripe rust and stem rust pathogen races. The durum panel genotyped using Illumina iSelect 90 K wheat SNP assay was used for genome-wide association mapping (GWAS). The GWAS revealed 64 marker-trait associations (MTAs) representing six leaf rust resistance loci located on chromosome arms 2AS, 2AL, 5BS, 6AL, and 6BL. Two of these loci were identified at the positions of Lr52 and Lr64 genes, whereas the remaining loci are most likely novel. A total of 46 MTAs corresponding to four loci located on chromosome arms 1BS, 5BL, and 7BL were associated with stripe rust response. None of these loci correspond to designated stripe rust resistance genes. For stem rust, a total of 260 MTAs, representing 22 loci were identified on chromosome arms 1BL, 2BL, 3AL, 3BL, 4AL, 5AL, 5BL, 6AS, 6AL, 6BL, and 7BL. Four of these loci were located at the positions of known genes/alleles ( Sr7b , Sr8155B1 , Sr13a , and Sr13b ). The discovery of known and novel rust resistance genes and their linked SNPs will help diversify rust resistance in durum wheat., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Aoun, Rouse, Kolmer, Kumar and Elias.)

AC Taber is a hard red spring wheat cultivar that has had long-lasting resistance to the leaf rust fungus Puccinia triticina . The objective of this study was to determine the chromosome location of the leaf rust resistance genes in AC Taber. The leaf rust-susceptible cultivar Thatcher was crossed with AC Taber to develop an F 6 recombinant inbred line (RIL) population. The RILs and parents were evaluated for segregation of leaf rust resistance in five field plot tests and in two seedling tests to race BBBDB of P. triticina . A genetic map of the RIL population was developed using 90,000 single nucleotide polymorphism markers with the Illumina Infinium iSelect 90K wheat bead array. Quantitative trait loci (QTLs) with significant effects for lower leaf rust severity in the field plot tests were found on chromosomes 2BS and 3BS. The same QTLs also had significant effects for lower infection type in seedlings to leaf rust race BBBDB. The gene on 2BS was the adult plant resistance gene Lr13 , and the gene on 3BS mapped to the same region as the adult plant resistance gene Lr74 and other QTLs for leaf rust resistance. Kompetitive allele-specific PCR assay markers linked to the 2BS and 3BS regions were developed and should be useful for marker-based selection of these genes.

In the last 20 years, stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt), has re-emerged as a major threat to wheat and barley production in Africa and Europe. In contrast to wheat with 60 designated stem rust (Sr) resistance genes, barley's genetic variation for stem rust resistance is very narrow with only ten resistance genes genetically identified. Of these, only one complex locus consisting of three genes is effective against TTKSK, a widely virulent Pgt race of the Ug99 tribe which emerged in Uganda in 1999 and has since spread to much of East Africa and parts of the Middle East. The objective of this study was to assess the functionality, in barley, of cloned wheat Sr genes effective against race TTKSK. Sr22, Sr33, Sr35 and Sr45 were transformed into barley cv. Golden Promise using Agrobacterium-mediated transformation. All four genes were found to confer effective stem rust resistance. The barley transgenics remained susceptible to the barley leaf rust pathogen Puccinia hordei, indicating that the resistance conferred by these wheat Sr genes was specific for Pgt. Furthermore, these transgenic plants did not display significant adverse agronomic effects in the absence of disease. Cloned Sr genes from wheat are therefore a potential source of resistance against wheat stem rust in barley., (© 2020 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Stem rust caused by Puccinia graminis f. sp. tritici ( Pgt ) remains a constraint to wheat production in East Africa. In this study, we characterized the genetics of stem rust resistance, identified QTLs, and described markers associated with stem rust resistance in the spring wheat line CI 14275. The 113 recombinant inbred lines, together with their parents, were evaluated at the seedling stage against Pgt races TTKSK, TRTTF, TPMKC, TTTTF, and RTQQC. Screening for resistance to Pgt races in the field was undertaken in Kenya, Ethiopia, and the United States in 2016, 2017, and 2018. One gene conferred seedling resistance to race TTTTF, likely Sr7a . Three QTL were identified that conferred field resistance. QTL QSr.cdl-2BS.2 , that conferred resistance in Kenya and Ethiopia, was validated, and the marker Excalibur_c7963_1722 was shown to have potential to select for this QTL in marker-assisted selection. The QTL QSr.cdl-3B.2 is likely Sr12 , and QSr.cdl-6A appears to be a new QTL. This is the first study to both detect and validate an adult plant stem rust resistance QTL on chromosome arm 2BS. The combination of field QTL QSr.cdl-2BS.2 , QSr.cdl-3B.2 , and QSr.cdl-6A has the potential to be used in wheat breeding to improve stem rust resistance of wheat varieties., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Kosgey, Edae, Dill-Macky, Jin, Bulbula, Gemechu, Macharia, Bhavani, Randhawa and Rouse.)

The identification and characterization of resistance genes should outpace the rapid emergence of new P. graminis f. sp. tritici races, such as TTRTF and TTKTT, to mitigate stem rust damage to wheat. The objective of the current study was to identify and characterize P. graminis f. sp. tritici race resistance association signals. A total of 250 North American spring wheat lines were evaluated at the seedling stage with a total of seven isolates including TKKTP, TKTTF, TKTTF, TRTTF, TTRTF, TTKSK, and TTKTT. The lines were genotyped by a GBS platform and 9,042 SNPs were used for identification of chromosome regions associated with resistance against the seven isolates. Strong association signals were detected on chromosomes 6BL (Sr11 gene region) and 4AL, likely Sr7a, for resistance against both TKKTP and TKTTF. Similarly, association signals were also detected on chromosomes 4AL (race TTRTF resistance) and 4BS (race TTKSK and TTKTT resistance). Association analysis based on mean phenotypic differences between closely related isolates identified QTL that were not elucidated by direct association mapping of the responses, individually. Overall, with the exception of race TRTTF, each race shared at least one association signal with another race. However, the number of race-specific association signals are larger than that of association signals common among races suggesting the need for identifying and characterizing QTL/genes for newly emerging stem rust pathogen races. There was also high concordance between PCA-based GWAS association signals and association signals from that of both single and multi-locus mixed models., (© 2020 The Authors. The Plant Genome published by Wiley Periodicals, Inc. on behalf of Crop Science Society of America.)

In the last 20 years, severe wheat stem rust outbreaks have been recorded in Africa, Europe, and Central Asia. This previously well controlled disease, caused by the fungus Puccinia graminis f. sp. tritici , has reemerged as a major threat to wheat cultivation. The stem rust ( Sr ) resistance gene Sr22 encodes a nucleotide-binding and leucine-rich repeat receptor which confers resistance to the highly virulent African stem rust isolate Ug99. Here, we show that the Sr22 gene is conserved among grasses in the Triticeae and Poeae lineages. Triticeae species contain syntenic loci with single-copy orthologs of Sr22 on chromosome 7, except Hordeum vulgare , which has experienced major expansions and rearrangements at the locus. We also describe 14 Sr22 sequence variants obtained from both Triticum boeoticum and the domesticated form of this species, T. monococcum , which have been postulated to encode both functional and nonfunctional Sr22 alleles. The nucleotide sequence analysis of these alleles identified historical sequence exchange resulting from recombination or gene conversion, including breakpoints within codons, which expanded the coding potential at these positions by introduction of nonsynonymous substitutions. Three Sr22 alleles were transformed into wheat cultivar Fielder and two postulated resistant alleles from Schomburgk (hexaploid wheat introgressed with T. boeoticum segment carrying Sr22 ) and T. monococcum accession PI190945, respectively, conferred resistance to P. graminis f. sp. tritici race TTKSK, thereby unequivocally confirming Sr22 effectiveness against Ug99. The third allele from accession PI573523, previously believed to confer susceptibility, was confirmed as nonfunctional against Australian P. graminis f. sp. tritici race 98-1,2,3,5,6.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Wheat ( Triticum aestivum L.) rusts are a worldwide production problem. Plant breeders have used genetic resistance to combat these fungi. However, single-gene resistance is rapidly overcome as a result of frequent occurrence of new virulent fungal strains. Thus, a supply of new resistance sources is continually needed, and new resistance sources are limited within hexaploid wheat genetic stocks. Wild relatives are able to be a resource for new resistance genes but are hindered because of chromosome incapability with domesticated wheats. Twenty-eight double-haploid hexaploid wheat /Amblyopyrum muticum (Boiss.) Eig introgression lines, with introgressions covering the majority of the T genome, were evaluated for resistance to Puccinia triticina Erikss., P. graminis Pers.:Pers. f.sp. tritici Erikss. & E. Henning, and P. striiformis Westend. f.sp. tritici Erikss.. At the seedling level, four lines were resistant to races of P. triticina , six lines were resistant to P. graminis , and 15 lines were resistant to P. striiformis . At the adult stage, 16 lines were resistant to P. triticina . Line 355 had resistance to all three rusts and line 161 had resistance to all tested races of P. triticina . Some of these lines will require further work to reduce the size of the introgressed segment; however, lines 92 and 355 have very small fragments and can be used directly as new resistance donors., Competing Interests: The authors declare that there are no conflicts of interest., (© 2020 The Authors. Crop Science published by Wiley Periodicals LLC on behalf of Crop Science Society of America. This article has been contributed to by US Government employees and their work is in the public domain in the USA.)

Stem rust is an important disease of wheat that can be controlled using resistance genes. The gene SuSr-D1 identified in cultivar 'Canthatch' suppresses stem rust resistance. SuSr-D1 mutants are resistant to several races of stem rust that are virulent on wild-type plants. Here we identify SuSr-D1 by sequencing flow-sorted chromosomes, mutagenesis, and map-based cloning. The gene encodes Med15, a subunit of the Mediator Complex, a conserved protein complex in eukaryotes that regulates expression of protein-coding genes. Nonsense mutations in Med15b.D result in expression of stem rust resistance. Time-course RNAseq analysis show a significant reduction or complete loss of differential gene expression at 24 h post inoculation in med15b.D mutants, suggesting that transcriptional reprogramming at this time point is not required for immunity to stem rust. Suppression is a common phenomenon and this study provides novel insight into suppression of rust resistance in wheat.

Wheat stem rust, caused by Puccinia graminis Pers. f. sp. tritici (Pgt), is a devastating fungal disease threatening global wheat production. The present paper reports the identification of stem rust resistance gene Sr60, a race-specific gene from diploid wheat Triticum monococcum L. that encodes a protein with two putative kinase domains. This gene, designated as WHEAT TANDEM KINASE 2 (WTK2), confers intermediate levels of resistance to Pgt. WTK2 was identified by map-based cloning and validated by transformation of a c.10-kb genomic sequence including WTK2 into susceptible common wheat variety Fielder (Triticum aestivum L.). Transformation of Fielder with WTK2 was sufficient to confer Pgt resistance. Sr60 transcripts were transiently upregulated 1 d post-inoculation with Pgt, but not in mock-inoculated plants. The upregulation of Sr60 was associated with stable upregulation of several pathogenesis-related genes. The Sr60-resistant haplotype found in T. monococcum was not found in polyploid wheat, suggesting an opportunity to introduce a novel resistance gene. Sr60 was successfully introgressed into hexaploid wheat, and we developed a diagnostic molecular marker to accelerate its deployment and pyramiding with other resistance genes. The cloned Sr60 also can be a useful component of transgenic cassettes including other resistance genes with complementary resistance profiles., (© 2019 The Authors. New Phytologist © 2019 New Phytologist Trust.)

Wheat stem rust, caused by Puccinia graminis f. sp. tritici , is a re-emerging disease exemplified by recent epidemics caused by new virulent races. Understanding the sources and origins of genetic variations in the pathogen populations globally can facilitate the development of better strategies in disease management. We analyzed 68 wheat stem rust samples collected between 2013 and 2015 from Georgia where stem rust incidences are frequent and the alternate host, common barberry, is present. A total of 116 single-pustule isolates were derived and evaluated on stem rust differential lines to determine the virulence phenotypes and 23 races were identified, many of which were detected for the first time. Unique virulence combinations including, Sr22+Sr24 and Sr13b+Sr35+Sr37 were detected. These virulence combinations pose new challenges to breeding programs because many of these genes are used in breeding for resistance to the Ug99 race group. Sixty-one isolates were genotyped using a custom single-nucleotide polymorphism chip and 17 genotypes were identified. The 2013 isolates contained 11 multilocus genotypes compared with isolates of 2014 and 2015, with five and three genotypes, respectively. The higher levels of virulence and genotypic diversity observed in the 2013 samples strongly indicated that sexual recombination occurs in the Georgian P. graminis f. sp. tritici population, and that the Caucasus region of Eurasia may be an important source of new races.[Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Key Message: Two stem rust resistance genes identified on chromosome arms 2BL and 6AL of the cultivated emmer wheat accession PI 193883 can be used for protecting modern varieties against Ug99 strains. The wheat research community consistently strives to identify new genes that confer resistance to stem rust caused by the fungal pathogen Puccinia graminis f. sp. tritici Eriks & E. Henn (Pgt). In the current study, our objective was to identify and genetically characterize the stem rust resistance derived from the cultivated emmer accession PI 193883. A recombinant inbred line population developed from a cross between the susceptible durum wheat line Rusty and PI 193883 was genotyped and evaluated for reaction to Pgt races TTKSK, TRTTF, and TMLKC. Two QTLs conferring resistance were identified on chromosome arms 2BL (QSr.fcu-2B) and 6AL (QSr.fcu-6A). The stem rust resistance gene (Sr883-2B) underlying QSr.fcu-2B was recessive, and based on its physical location it is located proximal to the Sr9 region. QSr.fcu-6A was located in the Sr13 region, but PI 193883 is known to carry the susceptible haplotype S4 for Sr13, indicating that the gene underlying QSr.fcu-6A (Sr883-6A) is likely a new allele of Sr13 or a gene residing close to Sr13. Three IWGSC scaffold-based simple sequence repeat (SSR) and two SNP-based semi-thermal asymmetric reverse PCR (STARP) markers were developed for the Sr883-2B region, and one STARP marker was developed for Sr883-6A. Sr883-2B was epistatic to Sr883-6A for reaction to TTKSK and TRTTF, and the two genes had additive effects for TMLKC. These two genes and the markers developed in this research provide additional resources and tools for the improvement in stem rust resistance in durum and common wheat breeding programs.

Bread wheat improvement using genomic tools is essential for accelerating trait genetic gains. Here we report the genomic predictabilities of 35 key traits and demonstrate the potential of genomic selection for wheat end-use quality. We also performed a large genome-wide association study that identified several significant marker-trait associations for 50 traits evaluated in South Asia, Africa and the Americas. Furthermore, we built a reference wheat genotype-phenotype map, explored allele frequency dynamics over time and fingerprinted 44,624 wheat lines for trait-associated markers, generating over 7.6 million data points, which together will provide a valuable resource to the wheat community for enhancing productivity and stress resilience.

Many disease resistance genes that have been transferred from wild relatives to cultivated wheat have played a significant role in wheat production worldwide. Ae. umbellulata is one of the species within the genus Aegilops that have been successfully used as sources of resistance genes to leaf rust, stem rust and powdery mildew. The objectives of the current work was to validate the map position of a major QTL that confers resistance to the stem rust pathogen races Ug99 (TTKSK) and TTTTF with an independent bi-parental mapping population and to refine the QTL region with a bulk segregant analysis approach. Two F2 bi-parental mapping populations were developed from stem rust resistant Ae. umbellulata accessions (PI 298905 and PI 5422375) and stem rust susceptible accessions (PI 542369 and PI 554395). Firstly, one of the two populations was used to map the chromosome location of the resistance gene. Later on, the 2nd population was used to validate the chromosome location in combination with a bulk segregant analysis approach. For the bulk segregant analysis, RNA was extracted from a bulk of leaf tissues of 12 homozygous resistant F3 families, and a separate bulk of 11 susceptible homozygous F3 families derived from the PI 5422375 and PI 554395 cross. The RNA samples of the two bulks and the two parents were sequenced for SNPs identification. Stem rust resistance QTL was validated on chromosome 2U of Ae. umbellulata in the same region in both populations. With bulk segregant analysis, the QTL position was delimited within 3.2 Mbp. Although there were a large number of genes in the orthologous region of the detected QTL on chromosome 2D of Ae. tauschii, we detected only two Ae. umbellulata NLR genes which can be considered as a potential candidate genes., Competing Interests: The authors have declared that no competing interests exist.

In Ethiopia, breeding rust resistant wheat cultivars is a priority for wheat production. A stem rust epidemic during 2013 to 2014 on previously resistant cultivar Digalu highlighted the need to determine the effectiveness of wheat lines to multiple races of Puccinia graminis f. sp. tritici in Ethiopia. During 2014 and 2015, we evaluated a total of 97 bread wheat and 14 durum wheat genotypes against four P. graminis f. sp. tritici races at the seedling stage and in single-race field nurseries. Resistance genes were postulated using molecular marker assays. Bread wheat lines were resistant to race JRCQC, the race most virulent to durum wheat. Lines with stem rust resistance gene Sr24 possessed the most effective resistance to the four races. Only three lines with adult plant resistance possessed resistance effective to the four races comparable with cultivars with Sr24 . Although responses of the wheat lines across races were positively correlated, wheat lines were identified that possessed adult plant resistance to race TTKSK but were relatively susceptible to race TKTTF. This study demonstrated the importance of testing wheat lines for response to multiple races of the stem rust pathogen to determine if lines possessed non-race-specific resistance. Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Leaf rust caused by Puccinia triticina Erikss. ( Pt ) and stem rust caused by Puccinia graminis f. sp. tritic i Erikss. & E. Henn ( Pgt ) are serious constraints to production of durum wheat ( Triticum turgidum L). The objective of this study was to identify leaf rust resistance ( Lr ) and stem rust resistance ( Sr ) genes/QTL in Portuguese durum landrace PI 192051. Four Pt -isolates, representing three virulence phenotypes (BBBQJ, BBBSJ & EEEEE) and six Pgt -races TTKSK, JRCQC, TKTTF, QFCFC, TPMKC and TMLKC were used to evaluate 180 recombinant inbred lines (RILs) derived from the cross Rusty (rust susceptible) × PI 192051-1 (rust resistant) at the seedling stage. The RILs were also phenotyped at the adult-plant stage in a stem rust nursery in Ethiopia in 2017. The RILs were genotyped using the Illumina iSelect 9K wheat SNP array. PI 192051-1 carries a previously unidentified major Sr gene designated as QSr.ace-7A on chromosome arm 7AS and Lr gene Lr.ace-4A in the pericentromeric region of chromosome 4A. In addition, three minor Sr QTL QSr.ace-1A , QSr.ace-2B and QSr.ace-4A were mapped in PI 192051-1 on chromosomes 1AL, 2BL, and 4A, respectively Lr.ace-4A could be co-located or tightly linked to QSr.ace-4A Markers linked to the identified QTL/genes can be used for marker assisted selection. These findings enrich the genetic basis of rust resistance in both durum and common wheat., (Copyright © 2019 Aoun et al.)

Dasypyrum villosum is a wild relative of common wheat ( Triticum aestivum L.) with resistance to Puccinia graminis f. tritici , the causal agent of stem rust, including the highly virulent race TTKSK (Ug99). In order to transfer resistance, T. durum - D. villosum amphiploids were initially developed and used as a bridge to create wheat- D. villosum introgression lines. Conserved ortholog set (COS) markers were used to identify D. villosum chromosome introgression lines, which were then subjected to seedling P. graminis f. tritici resistance screening with race TTKSK. A COS marker-verified line carrying chromosome 2V with TTKSK resistance was further characterized by combined genomic in situ and fluorescent in situ analyses to confirm a monosomic substitution line MS2V(2D) (20″ + 1' 2V[2D]). This is the first report of stem rust resistance on 2V, which was temporarily designated as SrTA10276-2V . To facilitate the use of this gene in wheat improvement, a complete set of previously developed wheat- D. villosum disomic addition lines was subjected to genotyping-by-sequencing analysis to develop D. villosum chromosome-specific markers. On average, 350 markers per chromosome were identified. These markers can be used to develop diagnostic markers for D. villosum -derived genes of interest in wheat improvement.

The emergence of new races of Puccinia graminis f. sp. tritici, the causal pathogen of wheat stem rust, has spurred interest in developing durable resistance to this disease in wheat. Nonhost resistance holds promise to help control this and other diseases because it is durable against nonadapted pathogens. However, the genetic and molecular basis of nonhost resistance to wheat stem rust is poorly understood. In this study, the model grass Brachypodium distachyon, a nonhost of P. graminis f. sp. tritici, was used to genetically dissect nonhost resistance to wheat stem rust. A recombinant inbred line (RIL) population segregating for response to wheat stem rust was evaluated for resistance. Evaluation of genome-wide cumulative single nucleotide polymorphism allele frequency differences between contrasting pools of resistant and susceptible RILs followed by molecular marker analysis identified six quantitative trait loci (QTL) that cumulatively explained 72.5% of the variation in stem rust resistance. Two of the QTLs explained 31.7% of the variation, and their interaction explained another 4.6%. Thus, nonhost resistance to wheat stem rust in B. distachyon is genetically complex, with both major and minor QTLs acting additively and, in some cases, interacting. These findings will guide future research to identify genes essential to nonhost resistance to wheat stem rust.

Races belonging to Ug99 lineage of stem rust fungus Puccinia graminis f. sp. tritici ( Pgt ) continue to pose a threat to wheat ( Triticum aestivum L.) production in various African countries. Growing resistant varieties is the most economical and environmentally friendly control measure. Recombinant inbred line (RIL) populations from the crosses of susceptible parent 'Cacuke' with the resistant parents 'Huhwa' and 'Yaye' were phenotyped for resistance at the seedling stage to Pgt race TTKSK (Ug99) and in adult plants in field trials at Njoro, Kenya for two seasons in 2016. Using the Affymetrix Axiom breeders SNP array, two stem rust resistance genes, temporarily designated as SrH and SrY , were identified and mapped on chromosome arm 2BL through selective genotyping and bulked segregant analysis (BSA), respectively. Kompetitive allele specific polymorphism (KASP) markers and simple sequence repeat (SSR) markers were used to saturate chromosome arm 2BL in both RIL populations. SrH mapped between markers cim109 and cim114 at a distance of 0.9 cM proximal, and cim117 at 2.9 cM distal. SrY was flanked by markers cim109 and cim116 at 0.8 cM proximal, and IWB45932 at 1.9 cM distal. Two Ug99-effective stem rust resistance genes derived from bread wheat, Sr9h and Sr28 , have been reported on chromosome arm 2BL. Infection types and map position in Huhwa and Yaye indicated that Sr28 was absent in both the parents. However, susceptible reactions produced by resistant lines from both populations against Sr9h -virulent race TTKSF+ confirmed the presence of a common resistance locus Sr9h in both lines. Test of allelism is required to establish genetic relationships between genes identified in present study and Sr9h . Marker cim117 linked to SrH was genotyped on set of wheat lines with Huhwa in the pedigree and is advised to be used for marker assisted selection for this gene, however, a combination of phenotypic and genotypic assays is desirable for both genes especially for selection of Sr9h in breeding programs.

Recent stem rust epidemics in eastern Africa and elsewhere demonstrated that wheat stem rust is a re-emerging disease posing a threat to wheat production worldwide. The cultivated wheat gene pool has a narrow genetic base for resistance to virulent races, such as races in the Ug99 race group. Wild relatives of wheat are a tractable source of stem rust resistance genes. Aegilops species in the tertiary genepool have not been exploited to any great extent as a source of stem rust resistance. We evaluated 1,422 accessions of Aegilops spp. for resistance to three highly virulent races (TTKSK, TRTTF, and TTTTF) of Puccinia graminis f. sp. tritici . Species studied include Ae. biuncialis, Ae . caudata, Ae. comosa, Ae. cylindrica, Ae. geniculata, Ae. neglecta, Ae. peregrina, Ae. triuncialis , and Ae. umbellulata that do not share common genomes with cultivated wheat. High frequencies of resistance were observed as 977 (68.8%), 927 (65.2%), and 850 (59.8%) accessions exhibited low infection types to races TTKSK, TTTTF, and TRTTF, respectively. Contingency table analyses showed strong association for resistance to different races in several Aegilop s spp., indicating that for a given species, the resistance genes effective against multiple races. Inheritance studies in selected accessions showed that resistance to race TTKSK is simply inherited.

In the original publication, the IWGSC assembly is incorrectly referenced.

Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a devastating foliar disease. The Ug99 race group has combined virulence to most stem rust (Sr) resistance genes deployed in wheat and is a threat to global wheat production. Here we identified a coiled-coil, nucleotide-binding leucine-rich repeat protein (NLR) completely linked to the Ug99 resistance gene Sr21 from Triticum monococcum. Loss-of-function mutations and transgenic complementation confirmed that this gene is Sr21. Sr21 transcripts were significantly higher at high temperatures, and this was associated with significant upregulation of pathogenesis related (PR) genes and increased levels of resistance at those temperatures. Introgression of Sr21 into hexaploid wheat resulted in lower levels of resistance than in diploid wheat, but transgenic hexaploid wheat lines with high levels of Sr21 expression showed high levels of resistance. Sr21 can be a valuable component of transgenic cassettes or gene pyramids combining multiple resistance genes against Ug99.

Key Message: The new stem rust resistance gene Sr60 was fine-mapped to the distal region of chromosome arm 5A m S, and the TTKSK-effective gene SrTm5 could be a new allele of Sr22. The emergence and spread of new virulent races of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici; Pgt), including the Ug99 race group, is a serious threat to global wheat production. In this study, we mapped and characterized two stem rust resistance genes from diploid wheat Triticum monococcum accession PI 306540. We mapped SrTm5, a previously postulated gene effective to Ug99, on chromosome arm 7A m L, completely linked to Sr22. SrTm5 displayed a different race specificity compared to Sr22 indicating that they are distinct. Sequencing of the Sr22 homolog in PI 306540 revealed a novel haplotype. Characterization of the segregating populations with Pgt race QFCSC revealed an additional resistance gene on chromosome arm 5A m S that was assigned the official name Sr60. This gene was also effective against races QTHJC and SCCSC but not against TTKSK (a Ug99 group race). Using two large mapping populations (4046 gametes), we mapped Sr60 within a 0.44 cM interval flanked by sequenced-based markers GH724575 and CJ942731. These two markers delimit a 54.6-kb region in Brachypodium distachyon chromosome 4 and a 430-kb region in the Chinese Spring reference genome. Both regions include a leucine-rich repeat protein kinase (LRRK123.1) that represents a potential candidate gene. Three CC-NBS-LRR genes were found in the colinear Brachypodium region but not in the wheat genome. We are currently developing a Bacterial Artificial Chromosome library of PI 306540 to determine which of these candidate genes are present in the T. monococcum genome and to complete the cloning of Sr60.

Stem rust of wheat caused by the fungal pathogen Puccinia graminis f. sp. tritici historically caused major yield losses of wheat worldwide. To understand the genetic basis of stem rust resistance in contemporary North American spring wheat, genome-wide association analysis (GWAS) was conducted on an association mapping panel comprised of 250 elite lines. The lines were evaluated in separate nurseries each inoculated with a different P. graminis f. sp. tritici race for 3 years (2013, 2015, and 2016) at Rosemount, Minnesota allowing the evaluation of race-specificity separate from the effect of environment. The lines were also challenged with the same four races at the seedling stage in a greenhouse facility at the USDA-ARS Cereal Disease Laboratory. A total of 22,310 high-quality SNPs obtained from the Infinium 90,000 SNPs chip were used to perform association analysis. We observed often negative and sometimes weak correlations between responses to different races that highlighted the abundance of race-specific resistance and the inability to predict the response of the lines across races. Markers strongly associated with resistance to the four races at seedling and field environments were identified. At the seedling stage, the most significant marker-trait associations were detected in the regions of known major genes ( Sr6, Sr7a , and Sr9b ) except for race QFCSC where a strong association was detected on chromosome arm 1AL. We postulated the presence of Sr2, Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, Sr24, Sr25, Sr31 , and Sr57 ( Lr34 ) in this germplasm based on phenotypic and marker data. We found over half of the panel possessed three or more Sr genes, and most commonly included various combinations of Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12 , and Sr57 . Most of these genes confer resistance to specific P. graminis f. sp. tritici races accounting for the prevalent stem rust resistance in North American spring wheat.

Background: Research to identify and characterize stem rust resistance genes in common wheat, Triticum aestivum, has been stimulated by the emergence of Ug99-lineage races of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici (Pgt), in Eastern Africa. The Montenegrin spring wheat landrace PI 362698 was identified as a source of Pgt resistance. This accession exhibits resistance to multiple Ug99-lineage and North American Pgt races at seedling and adult-plant stages. A recombinant inbred population was developed by crossing the susceptible line LMPG-6 with a single plant selection of PI 362698. A genetic map was constructed using the Illumina iSelect 90 K wheat assay and the markers csLv34, NB-LRR3, and wMAS000003 and quantitative trait locus (QTL) analysis was performed., Results: QTL analysis identified five significant QTLs (α = 0.05) on chromosomes 2B, 3B, 6A, 6D, and 7A associated with wheat stem rust resistance. The QTL on chromosome 3B was identified using both field data from Kenya (Pgt Ug99-lineage races) and seedling data from Pgt race MCCF. This QTL potentially corresponds to Sr12 or a new allele of Sr12. The multi-pathogen resistance gene Sr57 located on chromosome 7D is present in PI 362698 according to the diagnostic markers csLv34 and wMAS000003, however a significant QTL was not detected at this locus. The QTLs on chromosomes 2B, 6A, and 6D were identified during seedling trials and are thought to correspond to Sr16, Sr8a, and Sr5, respectively. The QTL identified on chromosome 7A was detected using MCCF seedling data and may be Sr15 or a potentially novel allele of recently detected Ug99 resistance QTLs., Conclusions: The combination of resistance QTLs found in PI 362698 is like the resistance gene combination present in the broadly resistant cultivar Thatcher. As such, PI 362698 may not be a landrace as previously thought. PI 362698 has been crossed with North Dakota wheat germplasm for future breeding efforts. Additional work is needed to fully understand why the combination of genes present in PI 362698 and 'Thatcher' provide such durable resistance.

Leaf rust, caused by Puccinia triticina, and stem rust, caused by P. graminis f. sp. tritici, are important diseases of durum wheat. This study determined the inheritance and genomic locations of leaf rust resistance (Lr) genes to P. triticina race BBBQJ and stem rust resistance (Sr) genes to P. graminis f. sp. tritici race TTKSK in durum accessions. Eight leaf-rust-resistant genotypes were used to develop biparental populations. Accessions PI 192051 and PI 534304 were also resistant to P. graminis f. sp. tritici race TTKSK. The resulting progenies were phenotyped for leaf rust and stem rust response at seedling stage. The Lr and Sr genes were mapped in five populations using single-nucleotide polymorphisms and bulked segregant analysis. Five leaf-rust-resistant genotypes carried single dominant Lr genes whereas, in the remaining accessions, there was deviation from the expected segregation ratio of a single dominant Lr gene. Seven genotypes carried Lr genes different from those previously characterized in durum. The single dominant Lr genes in PI 209274, PI 244061, PI387263, and PI 313096 were mapped to chromosome arms 6BS, 2BS, 6BL, and 6BS, respectively. The Sr gene in PI 534304 mapped to 6AL and is most likely Sr13, while the Sr gene in PI 192051 could be uncharacterized in durum.

The Puccinia graminis f. sp. tritici ( Pgt ) Ug99 race group is virulent to most stem rust resistance genes currently deployed in wheat and poses a threat to global wheat production. The durum wheat ( Triticum turgidum ssp. durum ) gene Sr13 confers resistance to Ug99 and other virulent races, and is more effective at high temperatures. Using map-based cloning, we delimited a candidate region including two linked genes encoding coiled-coil nucleotide-binding leucine-rich repeat proteins designated CNL3 and CNL13. Three independent truncation mutations identified in each of these genes demonstrated that only CNL13 was required for Ug99 resistance. Transformation of an 8-kb genomic sequence including CNL13 into the susceptible wheat variety Fielder was sufficient to confer resistance to Ug99, confirming that CNL13 is Sr13 CNL13 transcripts were slightly down-regulated 2-6 days after Pgt inoculation and were not affected by temperature. By contrast, six pathogenesis-related ( PR ) genes were up-regulated at high temperatures only when both Sr13 and Pgt were present, suggesting that they may contribute to the high temperature resistance mechanism. We identified three Sr13 -resistant haplotypes, which were present in one-third of cultivated emmer and durum wheats but absent in most tested common wheats ( Triticum aestivum ). These results suggest that Sr13 can be used to improve Ug99 resistance in a large proportion of modern wheat cultivars. To accelerate its deployment, we developed a diagnostic marker for Sr13 The identification of Sr13 expands the number of Pgt -resistance genes that can be incorporated into multigene transgenic cassettes to control this devastating disease., Competing Interests: The authors declare no conflict of interest., (Copyright © 2017 the Author(s). Published by PNAS.)

Wheat stem rust, caused by Puccinia graminis f. sp. tritici Eriks. & E. Henn, can incur yield losses in susceptible cultivars of durum wheat, Triticum turgidum ssp. durum (Desf.) Husnot. Although several durum cultivars possess the stem rust resistance gene Sr13 , additional genes in durum wheat effective against emerging virulent races have not been described. Durum line 8155-B1 confers resistance against the P. graminis f. sp. tritici race TTKST, the variant race of the Ug99 race group with additional virulence to wheat stem rust resistance gene Sr24 However, 8155-B1 does not confer resistance to the first-described race in the Ug99 race group: TTKSK. We mapped a single gene conferring resistance in 8155-B1 against race TTKST, Sr8155B1 , to chromosome arm 6AS by utilizing Rusty/8155-B1 and Rusty*2/8155-B1 populations and the 90K Infinium iSelect Custom bead chip supplemented by KASP assays. One marker, KASP_6AS_IWB10558 , cosegregated with Sr8155B1 in both populations and correctly predicted Sr8155B1 presence or absence in 11 durum cultivars tested. We confirmed the presence of Sr8155B1 in cultivar Mountrail by mapping in the population Choteau/Mountrail. The marker developed in this study could be used to predict the presence of resistance to race TTKST in uncharacterized durum breeding lines, and also to combine Sr8155B1 with resistance genes effective to Ug99 such as Sr13 The map location of Sr8155B1 cannot rule out the possibility that this gene is an allele at the Sr8 locus. However, race specificity indicates that Sr8155B1 is different from the known alleles Sr8a and Sr8b ., (Copyright © 2017 Nirmala et al.)

Background: The narrow genetic basis of resistance in modern wheat cultivars and the strong selection response of pathogen populations have been responsible for periodic and devastating epidemics of the wheat rust diseases. Characterizing new sources of resistance and incorporating multiple genes into elite cultivars is the most widely accepted current mechanism to achieve durable varietal performance against changes in pathogen virulence. Here, we report a high-density molecular characterization and genome-wide association study (GWAS) of stripe rust and stem rust resistance in 190 Ethiopian bread wheat lines based on phenotypic data from multi-environment field trials and seedling resistance screening experiments. A total of 24,281 single nucleotide polymorphism (SNP) markers filtered from the wheat 90 K iSelect genotyping assay was used to survey Ethiopian germplasm for population structure, genetic diversity and marker-trait associations., Results: Upon screening for field resistance to stripe rust in the Pacific Northwest of the United States and Ethiopia over multiple growing seasons, and against multiple races of stripe rust and stem rust at seedling stage, eight accessions displayed resistance to all tested races of stem rust and field resistance to stripe rust in all environments. Our GWAS results show 15 loci were significantly associated with seedling and adult plant resistance to stripe rust at false discovery rate (FDR)-adjusted probability (P) <0.10. GWAS also detected 9 additional genomic regions significantly associated (FDR-adjusted P < 0.10) with seedling resistance to stem rust in the Ethiopian wheat accessions. Many of the identified resistance loci were mapped close to previously identified rust resistance genes; however, three loci on the short arms of chromosomes 5A and 7B for stripe rust resistance and two on chromosomes 3B and 7B for stem rust resistance may be novel., Conclusion: Our results demonstrate that considerable genetic variation resides within the landrace accessions that can be utilized to broaden the genetic base of rust resistance in wheat breeding germplasm. The molecular markers identified in this study should be useful in efficiently targeting the associated resistance loci in marker-assisted breeding for rust resistance in Ethiopia and other countries.