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Xianming Chen - One of the best experts on this subject based on the ideXlab platform.
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Pathogens which threaten food security: Puccinia striiformis, the wheat Stripe Rust pathogen
Food Security, 2020Co-Authors: Xianming ChenAbstract:Stripe Rust, caused by Puccinia striiformis , is an important disease of wheat worldwide. The disease is old, but often appears as a re-emerging problem and also expands to new areas. Large-scale Stripe Rust epidemics occur when new races overcoming specific resistance genes develop in the pathogen population and/or when extreme disease-favourable weather conditions occur. Research progress has been made in the understanding of the biology, genomics, and evolution of the pathogen; host-pathogen interaction; and epidemiology and management of the disease. Despite its importance, the complete life cycle of this important pathogen was not known until very recently. The pathogen is now known to have a heteroecious macrocyclic lifecycle, but whether sexual reproduction on alternate hosts plays an important role in generating diverse races and increasing epidemics on crops is largely unknown. The pathogen has a large number of host species in the grass family, but the role of grass hosts in crop epidemics is not clear in many regions of the world. The disease can be controlled by growing resistant cultivars, appropriate use of fungicide, and suitable cultural practices. However, greater effort are needed to develop more cultivars with durable, high level resistance, develop accurate forecast models, and monitor the disease and pathogen virulence for more effective, profitable, and sustainable control of Stripe Rust.
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characterization of molecular diversity and genome wide mapping of loci associated with resistance to Stripe Rust and stem Rust in ethiopian bread wheat accessions
BMC Plant Biology, 2017Co-Authors: Kebede T Muleta, Xianming Chen, Matthew N Rouse, Sheri Rynearson, Bedada G Buta, Michael O PumphreyAbstract: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. 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. 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.
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genome wide association mapping reveals a rich genetic architecture of Stripe Rust resistance loci in emmer wheat triticum turgidum ssp dicoccum
Theoretical and Applied Genetics, 2017Co-Authors: Weizhen Liu, Xianming Chen, Marco Maccaferri, Gaetano Laghetti, Domenico Pignone, Michael O Pumphrey, Roberto TuberosaAbstract:SNP-based genome scanning in worldwide domesticated emmer germplasm showed high genetic diversity, rapid linkage disequilibrium decay and 51 loci for Stripe Rust resistance, a large proportion of which were novel. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum), one of the oldest domesticated crops in the world, is a potentially rich reservoir of variation for improvement of resistance/tolerance to biotic and abiotic stresses in wheat. Resistance to Stripe Rust (Puccinia striiformis f. sp. tritici) in emmer wheat has been under-investigated. Here, we employed genome-wide association (GWAS) mapping with a mixed linear model to dissect effective Stripe Rust resistance loci in a worldwide collection of 176 cultivated emmer wheat accessions. Adult plants were tested in six environments and seedlings were evaluated with five races from the United States and one from Italy under greenhouse conditions. Five accessions were resistant across all experiments. The panel was genotyped with the wheat 90,000 Illumina iSelect single nucleotide polymorphism (SNP) array and 5106 polymorphic SNP markers with mapped positions were obtained. A high level of genetic diversity and fast linkage disequilibrium decay were observed. In total, we identified 14 loci associated with field resistance in multiple environments. Thirty-seven loci were significantly associated with all-stage (seedling) resistance and six of them were effective against multiple races. Of the 51 total loci, 29 were mapped distantly from previously reported Stripe Rust resistance genes or quantitative trait loci and represent newly discovered resistance loci. Our results suggest that GWAS is an effective method for characterizing genes in cultivated emmer wheat and confirm that emmer wheat is a rich source of Stripe Rust resistance loci that can be used for wheat improvement.
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loci associated with resistance to Stripe Rust puccinia striiformis f sp tritici in a core collection of spring wheat triticum aestivum
PLOS ONE, 2017Co-Authors: Kebede T Muleta, Xianming Chen, Sheri Rynearson, Peter Bulli, Michael O PumphreyAbstract:Stripe Rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst) remains one of the most significant diseases of wheat worldwide. We investigated Stripe Rust resistance by genome-wide association analysis (GWAS) in 959 spring wheat accessions from the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection, representing major global production environments. The panel was characterized for field resistance in multi-environment field trials and seedling resistance under greenhouse conditions. A genome-wide set of 5,619 informative SNP markers were used to examine the population structure, linkage disequilibrium and marker-trait associations in the germplasm panel. Based on model-based analysis of population structure and hierarchical Ward clustering algorithm, the accessions were clustered into two major subgroups. These subgroups were largely separated according to geographic origin and improvement status of the accessions. A significant correlation was observed between the population sub-clusters and response to Stripe Rust infection. We identified 11 and 7 genomic regions with significant associations with Stripe Rust resistance at adult plant and seedling stages, respectively, based on a false discovery rate multiple correction method. The regions harboring all, except three, of the QTL identified from the field and greenhouse studies overlap with positions of previously reported QTL. Further work should aim at validating the identified QTL using proper germplasm and populations to enhance their utility in marker assisted breeding.
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mapping genes for resistance to Stripe Rust in spring wheat landrace pi 480035
PLOS ONE, 2017Co-Authors: Xianming Chen, Jinita Sthapit Kandel, Vandhana Krishnan, Derick Jiwan, Daniel Z SkinnerAbstract:: Stripe Rust caused by Puccinia striiformis Westend. f. sp. tritici Erikks. is an economically important disease of wheat (Triticum aestivum L.). Hexaploid spring wheat landrace PI 480035 was highly resistant to Stripe Rust in the field in Washington during 2011 and 2012. The objective of this research was to identify quantitative trait loci (QTL) for Stripe Rust resistance in PI 480035. A spring wheat, "Avocet Susceptible" (AvS), was crossed with PI 480035 to develop a biparental population of 110 recombinant inbred lines (RIL). The population was evaluated in the field in 2013 and 2014 and seedling reactions were examined against three races (PSTv-14, PSTv-37, and PSTv-40) of the pathogen under controlled conditions. The population was genotyped with genotyping-by-sequencing and microsatellite markers across the whole wheat genome. A major QTL, QYr.wrsggl1-1BS was identified on chromosome 1B. The closest flanking markers were Xgwm273, Xgwm11, and Xbarc187 1.01 cM distal to QYr.wrsggl1-1BS, Xcfd59 0.59 cM proximal and XA365 3.19 cM proximal to QYr.wrsggl1-1BS. Another QTL, QYr.wrsggl1-3B, was identified on 3B, which was significant only for PSTv-40 and was not significant in the field, indicating it confers a race-specific resistance. Comparison with markers associated with previously reported Yr genes on 1B (Yr64, Yr65, and YrH52) indicated that QYr.wrsggl1-1BS is potentially a novel Stripe Rust resistance gene that can be incorporated into modern breeding materials, along with other all-stage and adult-plant resistance genes to develop cultivars that can provide durable resistance.
Julio Huertaespino - One of the best experts on this subject based on the ideXlab platform.
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genetic analysis of resistance to Stripe Rust in durum wheat triticum turgidum l var durum
PLOS ONE, 2018Co-Authors: Xue Lin, Amidou Ndiaye, Sean Walkowiak, Kirby T Nilsen, Aron T Cory, Jemanesh K Haile, Hadley R Kutcher, Karim Ammar, Alexander Loladze, Julio HuertaespinoAbstract:Stripe Rust, caused by the fungal pathogen Puccinia striiformis Westend. f. sp. tritici Eriks, is an important disease of bread wheat (Triticum aestivum L.) worldwide and there is an indication that it may also become a serious disease of durum wheat (T. turgidum L. var. durum). Therefore, we investigated the genetic architecture underlying resistance to Stripe Rust in adapted durum wheat germplasm. Wheat infection assays were conducted under controlled conditions in Canada and under field conditions in Mexico. Disease assessments were performed on a population of 155 doubled haploid (DH) lines derived from the cross of Kofa (susceptible) and W9262-260D3 (moderately resistant) and on a breeding panel that consisted of 92 diverse cultivars and breeding lines. Both populations were genotyped using the 90K single-nucleotide polymorphism (SNP) iSelect assay. In the DH population, QTL for Stripe Rust resistance were identified on chromosome 7B (LOD 6.87–11.47) and chromosome 5B (LOD 3.88–9.17). The QTL for Stripe Rust resistance on chromosome 7B was supported in the breeding panel. Both QTL were anchored to the genome sequence of wild emmer wheat, which identified gene candidates involved in disease resistance. Exome capture sequencing identified variation in the candidate genes between Kofa and W9262-260D3. These genetic insights will be useful in durum breeding to enhance resistance to Stripe Rust.
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qtl characterization of resistance to leaf Rust and Stripe Rust in the spring wheat line francolin 1
Molecular Breeding, 2014Co-Authors: Caixia Lan, S A Herrerafoessel, Garry M Rosewarne, Julio Huertaespino, Ravi P Singh, Bhoja R Basnet, Yelun Zhang, Ennian YangAbstract:Growing resistant wheat varieties is a key method of controlling two important wheat diseases, leaf Rust and Stripe Rust. We analyzed quantitative trait loci (QTL) to investigate adult plant resistance (APR) to these Rusts, using 141 F5 RILs derived from the cross ‘Avocet-YrA/Francolin#1’. Phenotyping of leaf Rust resistance was conducted during two seasons at Ciudad Obregon, Mexico, whereas Stripe Rust was evaluated for two seasons in Toluca, Mexico, and one season in Chengdu, China. The genetic map was constructed with 581 markers, including diversity arrays technology and simple sequence repeat. Significant loci for reducing leaf Rust severity were designated QLr.cim-1BL, QLr.cim-3BS.1, QLr.cim-3DC, and QLr.cim-7DS. The six QTL that reduced Stripe Rust severity were designated QYr.cim-1BL, QYr.cim-2BS, QYr.cim-2DS, QYr.cim-3BS.2, QYr.cim-5AL, and QYr.cim-6AL. All loci were conferred by Francolin#1, with the exception of QYr.cim-2DS, QYr.cim-5AL, and QYr.cim-6AL, which were derived from Avocet-YrA. Closely linked markers indicated that the 1BL locus was the pleiotropic APR gene Lr46/Yr29. QYr.cim-2BS was a seedling resistance gene designated as YrF that conferred intermediate seedling reactions and moderate resistance at the adult plant stage in both Mexican and Chinese environments. Significant additive interactions were detected between the six QTL for Stripe Rust, but not between the four QTL for leaf Rust. Furthermore, we detected two new APR loci for leaf Rust in common wheat: QLr.cim-3BS.1 and QLr.cim-7DS.
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quantitative trait loci of Stripe Rust resistance in wheat
Theoretical and Applied Genetics, 2013Co-Authors: Garry M Rosewarne, S A Herrerafoessel, Julio Huertaespino, Ravi P Singh, Caixia LanAbstract:Key message Over 140 QTLs for resistance to Stripe Rust in wheat have been published and through mapping flanking markers on consensus maps, 49 chromosomal regions are identified.
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analysis of leaf and Stripe Rust severities reveals pathotype changes and multiple minor qtls associated with resistance in an avocet pastor wheat population
Theoretical and Applied Genetics, 2012Co-Authors: Garry M Rosewarne, R. P. Singh, S A Herrerafoessel, Julio Huertaespino, Kerrie Forrest, Matthew Hayden, G J RebetzkeAbstract:Leaf Rust and Stripe Rust are important diseases of wheat world-wide and deployment of cultivars with genetic resistance is an effective and environmentally sound control method. The use of minor, additive genes conferring adult plant resistance (APR) has been shown to provide resistance that is durable. The wheat cultivar ‘Pastor’ originated from the CIMMYT breeding program that focuses on minor gene-based APR to both diseases by selecting and advancing generations alternately under leaf Rust and Stripe Rust pressures. As a consequence, Pastor has good resistance to both Rusts and was used as the resistant parent to develop a mapping population by crossing with the susceptible ‘Avocet’. All 148 F5 recombinant inbred lines were evaluated under artificially inoculated epidemic environments for leaf Rust (3 environments) and Stripe Rust (4 environments, 2 of which represent two evaluation dates in final year due to the late build-up of a new race virulent to Yr31) in Mexico. Map construction and QTL analysis were completed with 223 polymorphic markers on 84 randomly selected lines in the population. Pastor contributed Yr31, a moderately effective race-specific gene for Stripe Rust resistance, which was overcome during this study, and this was clearly shown in the statistical analysis. Linked or pleiotropic chromosomal regions contributing to resistance against both pathogens included Lr46/Yr29 on 1BL, the Yr31 region on 2BS, and additional minor genes on 5A, 6B and 7BL. Other minor genes for leaf Rust resistance were located on 1B, 2A and 2D and for Stripe Rust on 1AL, 1B, 3A, 3B, 4D, 6A, 7AS and 7AL. The 1AL, 1BS and 7AL QTLs are in regions that were not identified previously as having QTLs for Stripe Rust resistance. The development of uniform and severe epidemics facilitated excellent phenotyping, and when combined with multi-environment analysis, resulted in the relatively large number of QTLs identified in this study.
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new slow Rusting leaf Rust and Stripe Rust resistance genes lr67 and yr46 in wheat are pleiotropic or closely linked
Theoretical and Applied Genetics, 2011Co-Authors: S A Herrerafoessel, E S Lagudah, H S Bariana, Matthew J Hayden, Davinder Singh, Julio Huertaespino, Ravi P SinghAbstract:The common wheat genotype ‘RL6077’ was believed to carry the gene Lr34/Yr18 that confers slow-Rusting adult plant resistance (APR) to leaf Rust and Stripe Rust but located to a different chromosome through inter-chromosomal reciprocal translocation. However, haplotyping using the cloned Lr34/Yr18 diagnostic marker and the complete sequencing of the gene indicated Lr34/Yr18 is absent in RL6077. We crossed RL6077 with the susceptible parent ‘Avocet’ and developed F3, F4 and F6 populations from photoperiod-insensitive F3 lines that were segregating for resistance to leaf Rust and Stripe Rust. The populations were characterized for leaf Rust resistance at two Mexican sites, Cd. Obregon during the 2008–2009 and 2009–2010 crop seasons, and El Batan during 2009, and for Stripe Rust resistance at Toluca, a third Mexican site, during 2009. The F3 population was also evaluated for Stripe Rust resistance at Cobbitty, Australia, during 2009. Most lines had correlated responses to leaf Rust and Stripe Rust, indicating that either the same gene, or closely linked genes, confers resistance to both diseases. Molecular mapping using microsatellites led to the identification of five markers (Xgwm165, Xgwm192, Xcfd71, Xbarc98 and Xcfd23) on chromosome 4DL that are associated with this gene(s), with the closest markers being located at 0.4 cM. In a parallel study in Canada using a Thatcher × RL6077 F3 population, the same leaf Rust resistance gene was designated as Lr67 and mapped to the same chromosomal region. The pleiotropic, or closely linked, gene derived from RL6077 that conferred Stripe Rust resistance in this study was designated as Yr46. The slow-Rusting gene(s) Lr67/Yr46 can be utilized in combination with other slow-Rusting genes to develop high levels of durable APR to leaf Rust and Stripe Rust in wheat.
Ravi P Singh - One of the best experts on this subject based on the ideXlab platform.
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qtl characterization of resistance to leaf Rust and Stripe Rust in the spring wheat line francolin 1
Molecular Breeding, 2014Co-Authors: Caixia Lan, S A Herrerafoessel, Garry M Rosewarne, Julio Huertaespino, Ravi P Singh, Bhoja R Basnet, Yelun Zhang, Ennian YangAbstract:Growing resistant wheat varieties is a key method of controlling two important wheat diseases, leaf Rust and Stripe Rust. We analyzed quantitative trait loci (QTL) to investigate adult plant resistance (APR) to these Rusts, using 141 F5 RILs derived from the cross ‘Avocet-YrA/Francolin#1’. Phenotyping of leaf Rust resistance was conducted during two seasons at Ciudad Obregon, Mexico, whereas Stripe Rust was evaluated for two seasons in Toluca, Mexico, and one season in Chengdu, China. The genetic map was constructed with 581 markers, including diversity arrays technology and simple sequence repeat. Significant loci for reducing leaf Rust severity were designated QLr.cim-1BL, QLr.cim-3BS.1, QLr.cim-3DC, and QLr.cim-7DS. The six QTL that reduced Stripe Rust severity were designated QYr.cim-1BL, QYr.cim-2BS, QYr.cim-2DS, QYr.cim-3BS.2, QYr.cim-5AL, and QYr.cim-6AL. All loci were conferred by Francolin#1, with the exception of QYr.cim-2DS, QYr.cim-5AL, and QYr.cim-6AL, which were derived from Avocet-YrA. Closely linked markers indicated that the 1BL locus was the pleiotropic APR gene Lr46/Yr29. QYr.cim-2BS was a seedling resistance gene designated as YrF that conferred intermediate seedling reactions and moderate resistance at the adult plant stage in both Mexican and Chinese environments. Significant additive interactions were detected between the six QTL for Stripe Rust, but not between the four QTL for leaf Rust. Furthermore, we detected two new APR loci for leaf Rust in common wheat: QLr.cim-3BS.1 and QLr.cim-7DS.
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quantitative trait loci of Stripe Rust resistance in wheat
Theoretical and Applied Genetics, 2013Co-Authors: Garry M Rosewarne, S A Herrerafoessel, Julio Huertaespino, Ravi P Singh, Caixia LanAbstract:Key message Over 140 QTLs for resistance to Stripe Rust in wheat have been published and through mapping flanking markers on consensus maps, 49 chromosomal regions are identified.
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identification and mapping of leaf stem and Stripe Rust resistance quantitative trait loci and their interactions in durum wheat
Molecular Breeding, 2013Co-Authors: Ashutosh Singh, R E Knox, Ravi P Singh, Karim Ammar, Madhav Pandey, Atul Singh, J M Clarke, F R Clarke, Curtis J Pozniak, R M DepauwAbstract:Leaf Rust (Puccinia triticina Eriks.), Stripe Rust (Puccinia striiformis f. tritici Eriks.) and stem Rust (Puccinia graminis f. sp. tritici) cause major production losses in durum wheat (Triticum turgidum L. var. durum). The objective of this research was to identify and map leaf, Stripe and stem Rust resistance loci from the French cultivar Sachem and Canadian cultivar Strongfield. A doubled haploid population from Sachem/Strongfield and parents were phenotyped for seedling reaction to leaf Rust races BBG/BN and BBG/BP and adult plant response was determined in three field Rust nurseries near El Batan, Obregon and Toluca, Mexico. Stripe Rust response was recorded in 2009 and 2011 nurseries near Toluca and near Njoro, Kenya in 2010. Response to stem Rust was recorded in field nurseries near Njoro, Kenya, in 2010 and 2011. Sachem was resistant to leaf, Stripe and stem Rust. A major leaf Rust quantitative trait locus (QTL) was identified on chromosome 7B at Xgwm146 in Sachem. In the same region on 7B, a Stripe Rust QTL was identified in Strongfield. Leaf and Stripe Rust QTL around DArT marker wPt3451 were identified on chromosome 1B. On chromosome 2B, a significant leaf Rust QTL was detected conferred by Strongfield, and at the same QTL, a Yr gene derived from Sachem conferred resistance. Significant stem Rust resistance QTL were detected on chromosome 4B. Consistent interactions among loci for resistance to each Rust type across nurseries were detected, especially for leaf Rust QTL on 7B. Sachem and Strongfield offer useful sources of Rust resistance genes for durum Rust breeding.
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new slow Rusting leaf Rust and Stripe Rust resistance genes lr67 and yr46 in wheat are pleiotropic or closely linked
Theoretical and Applied Genetics, 2011Co-Authors: S A Herrerafoessel, E S Lagudah, H S Bariana, Matthew J Hayden, Davinder Singh, Julio Huertaespino, Ravi P SinghAbstract:The common wheat genotype ‘RL6077’ was believed to carry the gene Lr34/Yr18 that confers slow-Rusting adult plant resistance (APR) to leaf Rust and Stripe Rust but located to a different chromosome through inter-chromosomal reciprocal translocation. However, haplotyping using the cloned Lr34/Yr18 diagnostic marker and the complete sequencing of the gene indicated Lr34/Yr18 is absent in RL6077. We crossed RL6077 with the susceptible parent ‘Avocet’ and developed F3, F4 and F6 populations from photoperiod-insensitive F3 lines that were segregating for resistance to leaf Rust and Stripe Rust. The populations were characterized for leaf Rust resistance at two Mexican sites, Cd. Obregon during the 2008–2009 and 2009–2010 crop seasons, and El Batan during 2009, and for Stripe Rust resistance at Toluca, a third Mexican site, during 2009. The F3 population was also evaluated for Stripe Rust resistance at Cobbitty, Australia, during 2009. Most lines had correlated responses to leaf Rust and Stripe Rust, indicating that either the same gene, or closely linked genes, confers resistance to both diseases. Molecular mapping using microsatellites led to the identification of five markers (Xgwm165, Xgwm192, Xcfd71, Xbarc98 and Xcfd23) on chromosome 4DL that are associated with this gene(s), with the closest markers being located at 0.4 cM. In a parallel study in Canada using a Thatcher × RL6077 F3 population, the same leaf Rust resistance gene was designated as Lr67 and mapped to the same chromosomal region. The pleiotropic, or closely linked, gene derived from RL6077 that conferred Stripe Rust resistance in this study was designated as Yr46. The slow-Rusting gene(s) Lr67/Yr46 can be utilized in combination with other slow-Rusting genes to develop high levels of durable APR to leaf Rust and Stripe Rust in wheat.
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microsatellite markers for genes lr34 yr18 and other quantitative trait loci for leaf Rust and Stripe Rust resistance in bread wheat
Phytopathology, 2003Co-Authors: K Suenaga, Julio Huertaespino, Ravi P Singh, H M WilliamAbstract:ABSTRACT Leaf Rust and Stripe Rust, caused by Puccinia triticina and P. striiformis, respectively, are important diseases of wheat in many countries. In this study we sought to identify molecular markers for adult plant resistance genes that could aid in incorporating such durable resistance into wheat. We used a doubled haploid population from a Japanese cv. Fukuho-komugi × Israeli wheat Oligoculm cross that had segregated for resistance to leaf Rust and Stripe Rust in field trials. Joint and/or single-year analyses by composite interval mapping identified two quantitative trait loci (QTL) that reduced leaf Rust severity and up to 11 and 7 QTLs that might have influenced Stripe Rust severity and infection type, respectively. Four common QTLs reduced Stripe Rust severity and infection type. Except for a QTL on chromosome 7DS, no common QTL for leaf Rust and Stripe Rust was detected. QTL-7DS derived from ‘Fukuho-komugi’ had the largest effect on both leaf Rust and Stripe Rust severities, possibly due to li...
Abraham B Korol - One of the best experts on this subject based on the ideXlab platform.
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evaluation of marker assisted selection for the Stripe Rust resistance gene yr15 introgressed from wild emmer wheat
Molecular Breeding, 2015Co-Authors: H S Bariana, Elitsur Yaniv, Dina Raats, Y I Ronin, Abraham B Korol, Adriana Grama, Jorge Dubcovsky, Alan H SchulmanAbstract:Stripe Rust disease is caused by the fungus Puccinia striiformis f. sp. tritici and severely threatens wheat worldwide, repeatedly breaking resistance conferred by resistance genes and evolving more aggressive strains. Wild emmer wheat, Triticum dicoccoides, is an important source for novel Stripe Rust resistance (Yr) genes. Yr15, a major gene located on chromosome 1BS of T. dicoccoides, was previously reported to confer resistance to a broad spectrum of Stripe Rust isolates, at both seedling and adult plant stages. Introgressions of Yr15 into cultivated T. aestivum bread wheat and T. durum pasta wheat that began in the 1980s are widely used. In the present study, we aimed to validate SSR markers from the Yr15 region as efficient tools for marker-assisted selection (MAS) for introgression of Yr15 into wheat and to compare the outcome of gene introgression by MAS and by conventional phenotypic selection. Our findings establish the validity of MAS for introgression of Yr15 into wheat. We show that the size of the introgressed segment, defined by flanking markers, varies for both phenotypic selection and MAS. The genetic distance of the MAS marker from Yr15 and the number of backcross steps were the main factors affecting the length of the introgressed donor segments. Markers Xbarc8 and Xgwm493, which are the nearest flanking markers studied, were consistent and polymorphic in all 34 introgressions reported here and are therefore the most recommended markers for the introgression of Yr15 into wheat cultivars. Introgression directed by markers, rather than by phenotype, will facilitate simultaneous selection for multiple Stripe Rust resistant genes and will help to avoid escapees during the selection process.
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linkage disequilibrium and association analysis of Stripe Rust resistance in wild emmer wheat triticum turgidum ssp dicoccoides population in israel
Theoretical and Applied Genetics, 2014Co-Authors: Hanan Sela, J Manisterski, Pnina Benyehuda, Smadar Ezrati, Eduard Akhunov, Jan Dvorak, Adina Breiman, Abraham B KorolAbstract:Key Message Rapid LD decay in wild emmer population from Israel allows high-resolution association mapping. Known and putative new Stripe Rust resistance genes were found.
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microsatellite tagging of the Stripe Rust resistance gene yrh52 derived from wild emmer wheat triticum dicoccoides and suggestive negative crossover interference on chromosome 1b
Theoretical and Applied Genetics, 1999Co-Authors: Junhua Peng, Tzion Fahima, Y I Ronin, Abraham B Korol, Adriana Grama, M S Roder, A Dahan, E NevoAbstract:Stripe Rust caused by Puccinia striifomis West. is one of the most devastating diseases relating to wheat production. Wild emmer wheat, Triticum dicoccoides, the tetraploid progenitor of cultivated wheat, has proven to be a valuable source of novel Stripe-Rust resistance genes for wheat breeding. For example, T. dicoccoides accessions from Mt. Hermon, Israel, are uniformly and highly resistant to Stripe-Rust. The main objective of the present study is to map a Stripe-Rust resistance gene, derived from the unique Mt. Hermon population of wild emmer, using microsatellite markers. An F2 mapping population was established by crossing Stripe-Rust resistant T. dicoccoides accession H52 from Mt. Hermon with the Triticum durum cultivar Langdon. The Stripe-Rust resistance derived from accession H52 was found to be controlled by a single dominant gene which was temporarily designated as YrH52. Out of 120 microsatellite markers tested, 109 (91%) showed polymorphism between the parental lines. Among 79 segregating microsatellite loci generated from 56 microsatellite primer pairs, nine were linked to YrH52 with recombination frequencies of 0.02–0.35, and LOD scores of 3.56–54.22. A genetic map of chromosome 1B, consisting of ten microsatellite loci and the Stripe-Rust resistance gene YrH52, was constructed with a total map length of 101.5 cM. YrH52 is also closely linked to RFLP marker Nor1 with a map distance of 1.4 cM and a LOD value of 29.62. Apparent negative crossover interference was observed in chromosome 1B, especially in the region spanning the centromere. Negative crossover interference may be a common characteristic of gene-rich regions or gene clusters in specific chromosomes.
Michael O Pumphrey - One of the best experts on this subject based on the ideXlab platform.
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characterization of molecular diversity and genome wide mapping of loci associated with resistance to Stripe Rust and stem Rust in ethiopian bread wheat accessions
BMC Plant Biology, 2017Co-Authors: Kebede T Muleta, Xianming Chen, Matthew N Rouse, Sheri Rynearson, Bedada G Buta, Michael O PumphreyAbstract: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. 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. 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.
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genome wide association mapping reveals a rich genetic architecture of Stripe Rust resistance loci in emmer wheat triticum turgidum ssp dicoccum
Theoretical and Applied Genetics, 2017Co-Authors: Weizhen Liu, Xianming Chen, Marco Maccaferri, Gaetano Laghetti, Domenico Pignone, Michael O Pumphrey, Roberto TuberosaAbstract:SNP-based genome scanning in worldwide domesticated emmer germplasm showed high genetic diversity, rapid linkage disequilibrium decay and 51 loci for Stripe Rust resistance, a large proportion of which were novel. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum), one of the oldest domesticated crops in the world, is a potentially rich reservoir of variation for improvement of resistance/tolerance to biotic and abiotic stresses in wheat. Resistance to Stripe Rust (Puccinia striiformis f. sp. tritici) in emmer wheat has been under-investigated. Here, we employed genome-wide association (GWAS) mapping with a mixed linear model to dissect effective Stripe Rust resistance loci in a worldwide collection of 176 cultivated emmer wheat accessions. Adult plants were tested in six environments and seedlings were evaluated with five races from the United States and one from Italy under greenhouse conditions. Five accessions were resistant across all experiments. The panel was genotyped with the wheat 90,000 Illumina iSelect single nucleotide polymorphism (SNP) array and 5106 polymorphic SNP markers with mapped positions were obtained. A high level of genetic diversity and fast linkage disequilibrium decay were observed. In total, we identified 14 loci associated with field resistance in multiple environments. Thirty-seven loci were significantly associated with all-stage (seedling) resistance and six of them were effective against multiple races. Of the 51 total loci, 29 were mapped distantly from previously reported Stripe Rust resistance genes or quantitative trait loci and represent newly discovered resistance loci. Our results suggest that GWAS is an effective method for characterizing genes in cultivated emmer wheat and confirm that emmer wheat is a rich source of Stripe Rust resistance loci that can be used for wheat improvement.
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loci associated with resistance to Stripe Rust puccinia striiformis f sp tritici in a core collection of spring wheat triticum aestivum
PLOS ONE, 2017Co-Authors: Kebede T Muleta, Xianming Chen, Sheri Rynearson, Peter Bulli, Michael O PumphreyAbstract:Stripe Rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst) remains one of the most significant diseases of wheat worldwide. We investigated Stripe Rust resistance by genome-wide association analysis (GWAS) in 959 spring wheat accessions from the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection, representing major global production environments. The panel was characterized for field resistance in multi-environment field trials and seedling resistance under greenhouse conditions. A genome-wide set of 5,619 informative SNP markers were used to examine the population structure, linkage disequilibrium and marker-trait associations in the germplasm panel. Based on model-based analysis of population structure and hierarchical Ward clustering algorithm, the accessions were clustered into two major subgroups. These subgroups were largely separated according to geographic origin and improvement status of the accessions. A significant correlation was observed between the population sub-clusters and response to Stripe Rust infection. We identified 11 and 7 genomic regions with significant associations with Stripe Rust resistance at adult plant and seedling stages, respectively, based on a false discovery rate multiple correction method. The regions harboring all, except three, of the QTL identified from the field and greenhouse studies overlap with positions of previously reported QTL. Further work should aim at validating the identified QTL using proper germplasm and populations to enhance their utility in marker assisted breeding.
