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Matthew N Rouse - One of the best experts on this subject based on the ideXlab platform.
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identification and characterization of sr22b a new allele of the wheat stem rust resistance gene sr22 effective against the Ug99 race group
Plant Biotechnology Journal, 2021Co-Authors: Jing Luo, Matthew N Rouse, Jorge Dubcovsky, Wenjun Zhang, Lei Hua, Caixia Gao, Yanpeng Wang, Shisheng ChenAbstract: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 a ~112-kb circular BAC 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 programs. Sr22b can be a valuable component of gene pyramids or transgenic cassettes combining different resistance genes to control this devastating disease.
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extensive genetic variation at the sr22 wheat stem rust resistance gene locus in the grasses revealed through evolutionary genomics and functional analyses
Molecular Plant-microbe Interactions, 2020Co-Authors: Matthew N Rouse, Burkhard Steuernagel, Asyraf Md M Hatta, Sreya Ghosh, Naveenkumar Athiyannan, Terese Richardson, Michael AyliffeAbstract: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.
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identification and characterization of wheat stem rust resistance gene sr21 effective against the Ug99 race group at high temperature
PLOS Genetics, 2018Co-Authors: Shisheng Chen, Matthew N Rouse, Jorge Dubcovsky, Wenjun Zhang, Stephen BolusAbstract: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.
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mapping and characterization of wheat stem rust resistance genes srtm5 and sr60 from triticum monococcum
Theoretical and Applied Genetics, 2018Co-Authors: Shisheng Chen, Shiaoman Chao, Matthew N Rouse, Wenjun Zhang, Yan Guo, Jordan Briggs, Felix Dubach, Jorge DubcovskyAbstract:The new stem rust resistance gene Sr60 was fine-mapped to the distal region of chromosome arm 5AmS, 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 7AmL, 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 5AmS 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.
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Dissection of the multigenic wheat stem rust resistance present in the Montenegrin spring wheat accession PI 362698
BMC, 2018Co-Authors: Jason D. Zurn, Shiaoman Chao, Matthew N Rouse, Colin W. Hiebert, Zacharias A Pretorius, Godwin Macharia, Meriem Aoun, Michael J. Bonman, Maricelis AcevedoAbstract:Abstract 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
Yue Jin - One of the best experts on this subject based on the ideXlab platform.
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characterization of puccinia graminis f sp tritici isolates derived from an unusual wheat stem rust outbreak in germany in 2013
Plant Pathology, 2017Co-Authors: P Olivera D Firpo, Les J Szabo, Maria Newcomb, Douglas G Luster, Kerstin Flath, N Sommerfeldtimpe, Melissa L Carter, Yue JinAbstract:An unusual stem rust infestation occurred in German wheat fields in summer 2013. This study analysed 48 isolates derived from 17 Puccinia graminis f. sp. tritici (Pgt) samples and six races were identified: TKTTF, TKKTF, TKPTF, TKKTP, PKPTF and MMMTF. Infection type and genotypic data confirmed that none of these races belonged to the TTKS (Ug99) race group. German isolates of race TKTTF are phenotypically different to the ones responsible for the stem rust epidemic in Ethiopia in 2013–2014. Forty isolates were genotyped using a custom SNP array. Phylogenetic analysis showed that these 40 isolates represented two distinct lineages (clade IV and clade V). Thirty-eight isolates clustered into clade IV, which previously was defined by Ethiopian isolates of race TKTTF. Race TKKTP is of special concern due to its combined virulence to stem rust resistance genes Sr24, SrTmp and Sr1RSAmigo. The vulnerability to race TKKTP in US and international winter wheat was confirmed as 55% of North American and international cultivars and breeding lines resistant to race TTKSK (Ug99) became susceptible to TKKTP. Races identified in Germany in 2013 confirmed the presence of virulence to important resistance genes that are effective against race TTKSK. This information should be useful for breeders to select diverse and effective resistance genes in order to provide more durable stem rust resistance and reduce the use of fungicides.
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genotype by sequencing facilitates genetic mapping of a stem rust resistance locus in aegilops umbellulata a wild relative of cultivated wheat
BMC Genomics, 2016Co-Authors: Erena A Edae, Matthew N Rouse, Yue Jin, Pablo D Olivera, Jesse PolandAbstract:Wild relatives of wheat play a significant role in wheat improvement as a source of genetic diversity. Stem rust disease of wheat causes significant yield losses at the global level and stem rust pathogen race TTKSK (Ug99) is virulent to most previously deployed resistance genes. Therefore, the objective of this study was to identify loci conferring resistance to stem rust pathogen races including Ug99 in an Aegilops umbelluata bi-parental mapping population using genotype-by-sequencing (GBS) SNP markers. A bi-parental F2:3 population derived from a cross made between stem rust resistant accession PI 298905 and stem rust susceptible accession PI 542369 was used for this study. F2 individuals were evaluated with stem rust race TTTTF followed by testing F2:3 families with races TTTTF and TTKSK. The segregation pattern of resistance to both stem rust races suggested the presence of one resistance gene. A genetic linkage map, comprised 1,933 SNP markers, was created for all seven chromosomes of Ae. umbellulata using GBS. A major stem rust resistance QTL that explained 80% and 52% of the phenotypic variations for TTTTF and TTKSK, respectively, was detected on chromosome 2U of Ae. umbellulata. The novel resistance gene for stem rust identified in this study can be transferred to commercial wheat varieties assisted by the tightly linked markers identified here. These markers identified through our mapping approach can be a useful strategy to identify and track the resistance gene in marker-assisted breeding in wheat.
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emergence and spread of new races of wheat stem rust fungus continued threat to food security and prospects of genetic control
Phytopathology, 2015Co-Authors: Ravi P Singh, Matthew N Rouse, Evans Lagudah, Yue Jin, Sridhar Bhavani, Zacharias A Pretorius, David Hodson, Les J Szabo, Michael Ayliffe, Julio HuertaespinoAbstract:Race Ug99 (TTKSK) of Puccinia graminis f. sp. tritici, detected in Uganda in 1998, has been recognized as a serious threat to food security because it possesses combined virulence to a large number of resistance genes found in current widely grown wheat (Triticum aestivum) varieties and germplasm, leading to its potential for rapid spread and evolution. Since its initial detection, variants of the Ug99 lineage of stem rust have been discovered in Eastern and Southern African countries, Yemen, Iran, and Egypt. To date, eight races belonging to the Ug99 lineage are known. Increased pathogen monitoring activities have led to the identification of other races in Africa and Asia with additional virulence to commercially important resistance genes. This has led to localized but severe stem rust epidemics becoming common once again in East Africa due to the breakdown of race-specific resistance gene SrTmp, which was deployed recently in the 'Digalu' and 'Robin' varieties in Ethiopia and Kenya, respectively. Enhanced research in the last decade under the umbrella of the Borlaug Global Rust Initiative has identified various race-specific resistance genes that can be utilized, preferably in combinations, to develop resistant varieties. Research and development of improved wheat germplasm with complex adult plant resistance (APR) based on multiple slow-rusting genes has also progressed. Once only the Sr2 gene was known to confer slow rusting APR; now, four more genes-Sr55, Sr56, Sr57, and Sr58-have been characterized and additional quantitative trait loci identified. Cloning of some rust resistance genes opens new perspectives on rust control in the future through the development of multiple resistance gene cassettes. However, at present, disease-surveillance-based chemical control, large-scale deployment of new varieties with multiple race-specific genes or adequate levels of APR, and reducing the cultivation of susceptible varieties in rust hot-spot areas remains the best stem rust management strategy.
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emergence and spread of new races of wheat stem rust fungus continued threat to food security and prospects of genetic control
Phytopathology, 2015Co-Authors: Ravi P Singh, Matthew N Rouse, Evans Lagudah, Yue Jin, Sridhar Bhavani, Zacharias A Pretorius, David Hodson, Les J Szabo, Michael Ayliffe, Julio HuertaespinoAbstract:Race Ug99 (TTKSK) of Puccinia graminis f. sp. tritici, detected in Uganda in 1998, has been recognized as a serious threat to food security because it possesses combined virulence to a large number of resistance genes found in current widely grown wheat (Triticum aestivum) varieties and germplasm, leading to its potential for rapid spread and evolution. Since its initial detection, variants of the Ug99 lineage of stem rust have been discovered in Eastern and Southern African countries, Yemen, Iran, and Egypt. To date, eight races belonging to the Ug99 lineage are known. Increased pathogen monitoring activities have led to the identification of other races in Africa and Asia with additional virulence to commercially important resistance genes. This has led to localized but severe stem rust epidemics becoming common once again in East Africa due to the breakdown of race-specific resistance gene SrTmp, which was deployed recently in the ‘Digalu’ and ‘Robin’ varieties in Ethiopia and Kenya, respectively. Enha...
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fine mapping and characterization of sr21 a temperature sensitive diploid wheat resistance gene effective against the puccinia graminis f sp tritici Ug99 race group
Theoretical and Applied Genetics, 2015Co-Authors: Matthew N Rouse, Yue Jin, Jorge Dubcovsky, Wenjun Zhang, Shisheng Chen, Eduard Akhunov, Yuming WeiAbstract:Key message The diploid wheat stem rust resistance gene Sr21 confers temperature‑sensitive resistance to isolates of the Ug99 group and maps to the middle of the long arm of chromosome 2A m .
Ravi P Singh - One of the best experts on this subject based on the ideXlab platform.
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identification and validation of single nucleotide polymorphic markers linked to Ug99 stem rust resistance in spring wheat
PLOS ONE, 2017Co-Authors: Shiaoman Chao, Ravi P Singh, Mark E SorrellsAbstract:Wheat stem rust (Puccinia graminis f. sp. tritici Eriks. and E. Henn.) is one of the most destructive diseases world-wide. Races belonging to Ug99 (or TTKSK) continue to cause crop losses in East Africa and threaten global wheat production. Developing and deploying wheat varieties with multiple race-specific genes or complex adult plant resistance is necessary to achieve durability. In the present study, we applied genome-wide association studies (GWAS) for identifying loci associated with the Ug99 stem rust resistance (SR) in a panel of wheat lines developed at the International Maize and Wheat Improvement Center (CIMMYT). Genotyping was carried out using the wheat 9K iSelect single nucleotide polymorphism (SNP) chip. Phenotyping was done in the field in Kenya by infection of Puccinia graminis f. sp. tritici race TTKST, the Sr24-virulent variant of Ug99. Marker-trait association identified 12 SNP markers significantly associated with resistance. Among them, 7 were mapped on five chromosomes. Markers located on chromosomes 4A and 4B overlapped with the location of the Ug99 resistance genes SrND643 and Sr37, respectively. Markers identified on 7DL were collocated with Sr25. Additional significant markers were located in the regions where no Sr gene has been reported. The chromosome location for five of the SNP markers was unknown. A BLASTN search of the NCBI database using the flanking sequences of the SNPs associated with Ug99 resistance revealed that several markers were linked to plant disease resistance analogues, while others were linked to regulatory factors or metabolic enzymes. A KASP (Kompetitive Allele Specific PCR) assay was used for validating six marker loci linked to genes with resistance to Ug99. Of those, four co-segregated with the Sr25-pathotypes while the rest identified unknown resistance genes. With further investigation, these markers can be used for marker-assisted selection in breeding for Ug99 stem rust resistance in wheat.
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genetic gain from phenotypic and genomic selection for quantitative resistance to stem rust of wheat
The Plant Genome, 2015Co-Authors: Jessica Rutkoski, Sridhar Bhavani, Ravi P Singh, Julio Huertaespino, Jesse Poland, Jeanluc Jannink, Mark E SorrellsAbstract:Stem rust of wheat (Triticum aestivum L.) caused by Puccinia graminis f. sp. tritici Eriks. and E. Henn. is a globally important disease that can cause severe yield loss. Breeding for quantitative stem rust resistance (QSRR) is important for developing cultivars with durable resistance. Genomic selection (GS) could increase rates of genetic gain for quantitative traits, but few experiments comparing GS and phenotypic selection (PS) have been conducted. Our objectives were to (i) compare realized gain from GS based on markers only with that of PS for QSRR in spring wheat using equal selection intensities; (ii) determine if gains agree with theoretical expectations; and (iii) compare the impact of GS and PS on inbreeding, genetic variance, and correlated response for pseudo-black chaff (PBC), a correlated trait. Over 2 yr, two cycles of GS were performed in parallel with one cycle of PS, with each method replicated twice. For GS, markers were generated using genotyping-by-sequencing, the prediction model was initially trained using historical data, and the model was updated before the second GS cycle. Overall, GS and PS led to a 31 11 and 42 12% increase in QSRR and a 138 22 and 180 70% increase in PBC, respectively. Genetic gains were not significant but were in agreement with expectations. Per year, gains from GS and PS were equal, but GS led to significantly lower genetic variance. This shows that while GS and PS can lead to equal rates of short-term gains, GS can reduce genetic variance more rapidly. Further work to develop efficient GS implementation strategies in spring wheat is warranted. Stem rust of wheat caused by the fungal pathogen P. graminis is a globally widespread and highly damaging disease capable of causing severe yield losses in susceptible cultivars (Park, 2007). In 1998, a new race group, Ug99, then capable of infecting over 80% of the world’s wheat germplasm (Singh et al., 2008), was discovered in Uganda. Ug99 has since migrated as far north as Iran, and has evolved to overcome an even larger set of major-effect resistance genes, increasing the susceptibility of commercially grown cultivars to about 90% (Jin et al., 2008, 2009). The emergence and continued evolution of Ug99 has prompted efforts to rapidly develop Published in The Plant Genome 8 doi: 10.3835/plantgenome2014.10.0074 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. J. Rutkoski, International Programs in the College of Agriculture and Life Sciences, and Plant Breeding and Genetics Section in the School of Integrative Plant Science, 240 Emerson Hall, Cornell University, Ithaca, NY 14853, USA, and International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600 El Batan, Mexico; R.P. Singh and J. Huerta-Espino, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600 El Batan, Mexico; J. Huerta-Espino, Campo Experimental Valle de Mexico INIFAP, Apdo. Postal 10, 56230 Chapingo, Edo de Mexico, Mexico; S. Bhavani, CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market-00621, Nairobi, Kenya; J. Poland, Wheat Genetics Resource Center, Dep. of Plant Pathology and Dep. of Agronomy; Kansas State Univ. (KSU); 4011 Throckmorton Hall, Manhattan KS, 66506, USA; J.L. Jannink, USDA–ARS and Plant Breeding and Genetics Section in the School of Integrative Plant Science, 240 Emerson Hall, Cornell Univ., Ithaca, NY 14853, USA; M.E. Sorrells, Plant Breeding and Genetics Section in the School of Integrative Plant Science, 240 Emerson Hall, Cornell Univ., Ithaca, NY 14853, USA. Received 23 Oct. 2014. Accepted 26 Jan. 2015. *Corresponding author (mes12@cornell.edu). Abbreviations: BLUP, best linear unbiased prediction; C0, cycle zero population; C1, cycle one population; C2, cycle two population; G-BLUP, genomic best linear unbiased prediction; GBS, genotypingby-sequencing; GS, genomic selection; PBC, pseudo-black chaff; PS, phenotypic selection; QSRR, quantitative stem rust resistance; TP, training population. Published July 10, 2015
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emergence and spread of new races of wheat stem rust fungus continued threat to food security and prospects of genetic control
Phytopathology, 2015Co-Authors: Ravi P Singh, Matthew N Rouse, Evans Lagudah, Yue Jin, Sridhar Bhavani, Zacharias A Pretorius, David Hodson, Les J Szabo, Michael Ayliffe, Julio HuertaespinoAbstract:Race Ug99 (TTKSK) of Puccinia graminis f. sp. tritici, detected in Uganda in 1998, has been recognized as a serious threat to food security because it possesses combined virulence to a large number of resistance genes found in current widely grown wheat (Triticum aestivum) varieties and germplasm, leading to its potential for rapid spread and evolution. Since its initial detection, variants of the Ug99 lineage of stem rust have been discovered in Eastern and Southern African countries, Yemen, Iran, and Egypt. To date, eight races belonging to the Ug99 lineage are known. Increased pathogen monitoring activities have led to the identification of other races in Africa and Asia with additional virulence to commercially important resistance genes. This has led to localized but severe stem rust epidemics becoming common once again in East Africa due to the breakdown of race-specific resistance gene SrTmp, which was deployed recently in the ‘Digalu’ and ‘Robin’ varieties in Ethiopia and Kenya, respectively. Enha...
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emergence and spread of new races of wheat stem rust fungus continued threat to food security and prospects of genetic control
Phytopathology, 2015Co-Authors: Ravi P Singh, Matthew N Rouse, Evans Lagudah, Yue Jin, Sridhar Bhavani, Zacharias A Pretorius, David Hodson, Les J Szabo, Michael Ayliffe, Julio HuertaespinoAbstract:Race Ug99 (TTKSK) of Puccinia graminis f. sp. tritici, detected in Uganda in 1998, has been recognized as a serious threat to food security because it possesses combined virulence to a large number of resistance genes found in current widely grown wheat (Triticum aestivum) varieties and germplasm, leading to its potential for rapid spread and evolution. Since its initial detection, variants of the Ug99 lineage of stem rust have been discovered in Eastern and Southern African countries, Yemen, Iran, and Egypt. To date, eight races belonging to the Ug99 lineage are known. Increased pathogen monitoring activities have led to the identification of other races in Africa and Asia with additional virulence to commercially important resistance genes. This has led to localized but severe stem rust epidemics becoming common once again in East Africa due to the breakdown of race-specific resistance gene SrTmp, which was deployed recently in the 'Digalu' and 'Robin' varieties in Ethiopia and Kenya, respectively. Enhanced research in the last decade under the umbrella of the Borlaug Global Rust Initiative has identified various race-specific resistance genes that can be utilized, preferably in combinations, to develop resistant varieties. Research and development of improved wheat germplasm with complex adult plant resistance (APR) based on multiple slow-rusting genes has also progressed. Once only the Sr2 gene was known to confer slow rusting APR; now, four more genes-Sr55, Sr56, Sr57, and Sr58-have been characterized and additional quantitative trait loci identified. Cloning of some rust resistance genes opens new perspectives on rust control in the future through the development of multiple resistance gene cassettes. However, at present, disease-surveillance-based chemical control, large-scale deployment of new varieties with multiple race-specific genes or adequate levels of APR, and reducing the cultivation of susceptible varieties in rust hot-spot areas remains the best stem rust management strategy.
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a consensus map for Ug99 stem rust resistance loci in wheat
Theoretical and Applied Genetics, 2014Co-Authors: Hugues Barbier, Matthew N Rouse, Sridhar Bhavani, Ravi P Singh, Julio Huertaespino, Sukhwinder Singh, Mark E SorrellsAbstract:Key message This consensus map of stem rust genes, QTLs, and molecular markers will facilitate the identi‑ fication of new resistance genes and provide a resource of information for development of new markers for breeding wheat varieties resistant to Ug99.
Jorge Dubcovsky - One of the best experts on this subject based on the ideXlab platform.
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identification and characterization of sr22b a new allele of the wheat stem rust resistance gene sr22 effective against the Ug99 race group
Plant Biotechnology Journal, 2021Co-Authors: Jing Luo, Matthew N Rouse, Jorge Dubcovsky, Wenjun Zhang, Lei Hua, Caixia Gao, Yanpeng Wang, Shisheng ChenAbstract: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 a ~112-kb circular BAC 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 programs. Sr22b can be a valuable component of gene pyramids or transgenic cassettes combining different resistance genes to control this devastating disease.
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identification and characterization of wheat stem rust resistance gene sr21 effective against the Ug99 race group at high temperature
PLOS Genetics, 2018Co-Authors: Shisheng Chen, Matthew N Rouse, Jorge Dubcovsky, Wenjun Zhang, Stephen BolusAbstract: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.
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mapping and characterization of wheat stem rust resistance genes srtm5 and sr60 from triticum monococcum
Theoretical and Applied Genetics, 2018Co-Authors: Shisheng Chen, Shiaoman Chao, Matthew N Rouse, Wenjun Zhang, Yan Guo, Jordan Briggs, Felix Dubach, Jorge DubcovskyAbstract:The new stem rust resistance gene Sr60 was fine-mapped to the distal region of chromosome arm 5AmS, 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 7AmL, 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 5AmS 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.
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identification and characterization of sr13 a tetraploid wheat gene that confers resistance to the Ug99 stem rust race group
Proceedings of the National Academy of Sciences of the United States of America, 2017Co-Authors: Wenjun Zhang, Matthew N Rouse, Shisheng Chen, Zewdie Abate, Jayaveeramuthu Nirmala, Jorge DubcovskyAbstract: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 Sr13CNL13 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.
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fine mapping and characterization of sr21 a temperature sensitive diploid wheat resistance gene effective against the puccinia graminis f sp tritici Ug99 race group
Theoretical and Applied Genetics, 2015Co-Authors: Matthew N Rouse, Yue Jin, Jorge Dubcovsky, Wenjun Zhang, Shisheng Chen, Eduard Akhunov, Yuming WeiAbstract:Key message The diploid wheat stem rust resistance gene Sr21 confers temperature‑sensitive resistance to isolates of the Ug99 group and maps to the middle of the long arm of chromosome 2A m .
Sridhar Bhavani - One of the best experts on this subject based on the ideXlab platform.
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vulnerability of barley to african pathotypes of puccinia graminis f sp tritici and sources of resistance
Phytopathology, 2017Co-Authors: Brian J Steffenson, Austin J Case, Zacharias A Pretorius, Vicky Coetzee, Frederik Kloppers, Hao Zhou, Yuan Chai, R Wanyera, Godwin Macharia, Sridhar BhavaniAbstract:The emergence of widely virulent pathotypes (e.g., TTKSK in the Ug99 race group) of the stem rust pathogen (Puccinia graminis f. sp. tritici) in Africa threatens wheat production on a global scale. Although intensive research efforts have been advanced to address this threat in wheat, few studies have been conducted on barley, even though pathotypes such as TTKSK are known to attack the crop. The main objectives of this study were to assess the vulnerability of barley to pathotype TTKSK and identify possible sources of resistance. From seedling evaluations of more than 1,924 diverse cultivated barley accessions to pathotype TTKSK, more than 95% (1,844) were found susceptible. A similar high frequency (910 of 934 = 97.4%) of susceptibility was found for the wild progenitor (Hordeum vulgare subsp. spontaneum) of cultivated barley. Additionally, 55 barley lines with characterized or putative introgressions from various wild Hordeum spp. were also tested against pathotype TTKSK but none was found resistant. I...
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kenyan isolates of puccinia graminis f sp tritici from 2008 to 2014 virulence to srtmp in the Ug99 race group and implications for breeding programs
Phytopathology, 2016Co-Authors: Maria Newcomb, Matthew N Rouse, R Wanyera, Godwin Macharia, Les J Szabo, Pablo D Olivera, Jerry L Johnson, S Gale, Douglas G Luster, Sridhar BhavaniAbstract:Frequent emergence of new variants in the Puccinia graminis f. sp. tritici Ug99 race group in Kenya has made pathogen survey a priority. We analyzed 140 isolates from 78 P. graminis f. sp. tritici samples collected in Kenya between 2008 and 2014 and identified six races, including three not detected prior to 2013. Genotypic analysis of 20 isolates from 2013 and 2014 collections showed that the new races TTHST, TTKTK, and TTKTT belong to the Ug99 race group. International advanced breeding lines were evaluated against an isolate of TTKTT (Sr31, Sr24, and SrTmp virulence) at the seedling stage. From 169 advanced lines from Kenya, 23% of lines with resistance to races TTKSK and TTKST were susceptible to TTKTT and, from two North American regional nurseries, 44 and 91% of resistant lines were susceptible. Three lines with combined resistance genes were developed to facilitate pathogen monitoring and race identification. These results indicate the increasing virulence and variability in the Kenyan P. graminis f. sp. tritici population and reveal vulnerabilities of elite germplasm to new races.
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association mapping of north american spring wheat breeding germplasm reveals loci conferring resistance to Ug99 and other african stem rust races
BMC Plant Biology, 2015Co-Authors: Matthew N Rouse, Sridhar Bhavani, P Njau, R Wanyera, Prabin Bajgain, Peter Bulli, T Gordon, W LegesseAbstract:The recently identified Puccinia graminis f. sp. tritici (Pgt) race TTKSK (Ug99) poses a severe threat to global wheat production because of its broad virulence on several widely deployed resistance genes. Additional virulences have been detected in the Ug99 group of races, and the spread of this race group has been documented across wheat growing regions in Africa, the Middle East (Yemen), and West Asia (Iran). Other broadly virulent Pgt races, such as TRTTF and TKTTF, present further difficulties in maintaining abundant genetic resistance for their effective use in wheat breeding against this destructive fungal disease of wheat. In an effort to identify loci conferring resistance to these races, a genome-wide association study was carried out on a panel of 250 spring wheat breeding lines from the International Maize and Wheat Improvement Center (CIMMYT), six wheat breeding programs in the United States and three wheat breeding programs in Canada. The lines included in this study were grouped into two major clusters, based on the results of principal component analysis using 23,976 SNP markers. Upon screening for adult plant resistance (APR) to Ug99 during 2013 and 2014 in artificial stem rust screening nurseries at Njoro, Kenya and at Debre Zeit, Ethiopia, several wheat lines were found to exhibit APR. The lines were also screened for resistance at the seedling stage against races TTKSK, TRTTF, and TKTTF at USDA-ARS Cereal Disease Laboratory in St. Paul, Minnesota; and only 9 of the 250 lines displayed seedling resistance to all the races. Using a mixed linear model, 27 SNP markers associated with APR against Ug99 were detected, including markers linked with the known APR gene Sr2. Using the same model, 23, 86, and 111 SNP markers associated with seedling resistance against races TTKSK, TRTTF, and TKTTF were identified, respectively. These included markers linked to the genes Sr8a and Sr11 providing seedling resistance to races TRTTF and TKTTF, respectively. We also identified putatively novel Sr resistance genes on chromosomes 3B, 4D, 5A, 5B, 6A, 7A, and 7B. Our results demonstrate that the North American wheat breeding lines have several resistance loci that provide APR and seedling resistance to highly virulent Pgt races. Using the resistant lines and the SNP markers identified in this study, marker-assisted resistance breeding can assist in development of varieties with elevated levels of resistance to virulent stem rust races including TTKSK.
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genetic gain from phenotypic and genomic selection for quantitative resistance to stem rust of wheat
The Plant Genome, 2015Co-Authors: Jessica Rutkoski, Sridhar Bhavani, Ravi P Singh, Julio Huertaespino, Jesse Poland, Jeanluc Jannink, Mark E SorrellsAbstract:Stem rust of wheat (Triticum aestivum L.) caused by Puccinia graminis f. sp. tritici Eriks. and E. Henn. is a globally important disease that can cause severe yield loss. Breeding for quantitative stem rust resistance (QSRR) is important for developing cultivars with durable resistance. Genomic selection (GS) could increase rates of genetic gain for quantitative traits, but few experiments comparing GS and phenotypic selection (PS) have been conducted. Our objectives were to (i) compare realized gain from GS based on markers only with that of PS for QSRR in spring wheat using equal selection intensities; (ii) determine if gains agree with theoretical expectations; and (iii) compare the impact of GS and PS on inbreeding, genetic variance, and correlated response for pseudo-black chaff (PBC), a correlated trait. Over 2 yr, two cycles of GS were performed in parallel with one cycle of PS, with each method replicated twice. For GS, markers were generated using genotyping-by-sequencing, the prediction model was initially trained using historical data, and the model was updated before the second GS cycle. Overall, GS and PS led to a 31 11 and 42 12% increase in QSRR and a 138 22 and 180 70% increase in PBC, respectively. Genetic gains were not significant but were in agreement with expectations. Per year, gains from GS and PS were equal, but GS led to significantly lower genetic variance. This shows that while GS and PS can lead to equal rates of short-term gains, GS can reduce genetic variance more rapidly. Further work to develop efficient GS implementation strategies in spring wheat is warranted. Stem rust of wheat caused by the fungal pathogen P. graminis is a globally widespread and highly damaging disease capable of causing severe yield losses in susceptible cultivars (Park, 2007). In 1998, a new race group, Ug99, then capable of infecting over 80% of the world’s wheat germplasm (Singh et al., 2008), was discovered in Uganda. Ug99 has since migrated as far north as Iran, and has evolved to overcome an even larger set of major-effect resistance genes, increasing the susceptibility of commercially grown cultivars to about 90% (Jin et al., 2008, 2009). The emergence and continued evolution of Ug99 has prompted efforts to rapidly develop Published in The Plant Genome 8 doi: 10.3835/plantgenome2014.10.0074 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. J. Rutkoski, International Programs in the College of Agriculture and Life Sciences, and Plant Breeding and Genetics Section in the School of Integrative Plant Science, 240 Emerson Hall, Cornell University, Ithaca, NY 14853, USA, and International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600 El Batan, Mexico; R.P. Singh and J. Huerta-Espino, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600 El Batan, Mexico; J. Huerta-Espino, Campo Experimental Valle de Mexico INIFAP, Apdo. Postal 10, 56230 Chapingo, Edo de Mexico, Mexico; S. Bhavani, CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market-00621, Nairobi, Kenya; J. Poland, Wheat Genetics Resource Center, Dep. of Plant Pathology and Dep. of Agronomy; Kansas State Univ. (KSU); 4011 Throckmorton Hall, Manhattan KS, 66506, USA; J.L. Jannink, USDA–ARS and Plant Breeding and Genetics Section in the School of Integrative Plant Science, 240 Emerson Hall, Cornell Univ., Ithaca, NY 14853, USA; M.E. Sorrells, Plant Breeding and Genetics Section in the School of Integrative Plant Science, 240 Emerson Hall, Cornell Univ., Ithaca, NY 14853, USA. Received 23 Oct. 2014. Accepted 26 Jan. 2015. *Corresponding author (mes12@cornell.edu). Abbreviations: BLUP, best linear unbiased prediction; C0, cycle zero population; C1, cycle one population; C2, cycle two population; G-BLUP, genomic best linear unbiased prediction; GBS, genotypingby-sequencing; GS, genomic selection; PBC, pseudo-black chaff; PS, phenotypic selection; QSRR, quantitative stem rust resistance; TP, training population. Published July 10, 2015
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emergence and spread of new races of wheat stem rust fungus continued threat to food security and prospects of genetic control
Phytopathology, 2015Co-Authors: Ravi P Singh, Matthew N Rouse, Evans Lagudah, Yue Jin, Sridhar Bhavani, Zacharias A Pretorius, David Hodson, Les J Szabo, Michael Ayliffe, Julio HuertaespinoAbstract:Race Ug99 (TTKSK) of Puccinia graminis f. sp. tritici, detected in Uganda in 1998, has been recognized as a serious threat to food security because it possesses combined virulence to a large number of resistance genes found in current widely grown wheat (Triticum aestivum) varieties and germplasm, leading to its potential for rapid spread and evolution. Since its initial detection, variants of the Ug99 lineage of stem rust have been discovered in Eastern and Southern African countries, Yemen, Iran, and Egypt. To date, eight races belonging to the Ug99 lineage are known. Increased pathogen monitoring activities have led to the identification of other races in Africa and Asia with additional virulence to commercially important resistance genes. This has led to localized but severe stem rust epidemics becoming common once again in East Africa due to the breakdown of race-specific resistance gene SrTmp, which was deployed recently in the ‘Digalu’ and ‘Robin’ varieties in Ethiopia and Kenya, respectively. Enha...
