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      A consensus map for Ug99 stem rust resistance loci in wheat

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          Abstract

          Key message

          This consensus map of stem rust genes, QTLs, and molecular markers will facilitate the identification of new resistance genes and provide a resource of in formation for development of new markers for breeding wheat varieties resistant to Ug99.

          Abstract

          The global effort to identify new sources of resistance to wheat stem rust, caused by Puccinia graminis f. sp. tritici race group Ug99 has resulted in numerous studies reporting both qualitative genes and quantitative trait loci. The purpose of our study was to assemble all available information on loci associated with stem rust resistance from 21 recent studies on Triticum aestivum L. (bread wheat) and Triticum turgidum subsp. durum desf. (durum wheat). The software LPmerge was used to construct a stem rust resistance loci consensus wheat map with 1,433 markers incorporating Single Nucleotide Polymorphism, Diversity Arrays Technology, Genotyping-by-Sequencing as well as Simple Sequence Repeat marker information. Most of the markers associated with stem rust resistance have been identified in more than one population. Several loci identified in these populations map to the same regions with known Sr genes including Sr2, SrND643, Sr25 and Sr57 ( Lr34/ Yr18/ Pm38), while other significant markers were located in chromosome regions where no Sr genes have been previously reported. This consensus map provides a comprehensive source of information on 141 stem rust resistance loci conferring resistance to stem rust Ug99 as well as linked markers for use in marker-assisted selection.

          Electronic supplementary material

          The online version of this article (doi:10.1007/s00122-014-2326-7) contains supplementary material, which is available to authorized users.

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          Most cited references 53

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          Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure.

          Linkage disequilibrium can be used for identifying associations between traits of interest and genetic markers. This study used mapped diversity array technology (DArT) markers to find associations with resistance to stem rust, leaf rust, yellow rust, and powdery mildew, plus grain yield in five historical wheat international multienvironment trials from the International Maize and Wheat Improvement Center (CIMMYT). Two linear mixed models were used to assess marker-trait associations incorporating information on population structure and covariance between relatives. An integrated map containing 813 DArT markers and 831 other markers was constructed. Several linkage disequilibrium clusters bearing multiple host plant resistance genes were found. Most of the associated markers were found in genomic regions where previous reports had found genes or quantitative trait loci (QTL) influencing the same traits, providing an independent validation of this approach. In addition, many new chromosome regions for disease resistance and grain yield were identified in the wheat genome. Phenotyping across up to 60 environments and years allowed modeling of genotype x environment interaction, thereby making possible the identification of markers contributing to both additive and additive x additive interaction effects of traits.
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            The emergence of Ug99 races of the stem rust fungus is a threat to world wheat production.

            Race Ug99 of the fungus Puccinia graminis tritici that causes stem or black rust disease on wheat was first detected in Uganda in 1998. Seven races belonging to the Ug99 lineage are now known and have spread to various wheat-growing countries in the eastern African highlands, as well as Zimbabwe, South Africa, Sudan, Yemen, and Iran. Because of the susceptibility of 90% of the wheat varieties grown worldwide, the Ug99 group of races was recognized as a major threat to wheat production and food security. Its spread, either wind-mediated or human-aided, to other countries in Africa, Asia, and beyond is evident. Screening in Kenya and Ethiopia has identified a low frequency of resistant wheat varieties and breeding materials. Identification and transfer of new sources of race-specific resistance from various wheat relatives is underway to enhance the diversity of resistance. Although new Ug99-resistant varieties that yield more than current popular varieties are being released and promoted, major efforts are required to displace current Ug99 susceptible varieties with varieties that have diverse race-specific or durable resistance and mitigate the Ug99 threat. Copyright © 2011 by Annual Reviews. All rights reserved.
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              Detection of Virulence to Resistance GeneSr24Within Race TTKS ofPuccinia graminisf. sp.tritici

              The stem rust resistance gene Sr24 is effective against most races of Puccinia graminis f. sp. tritici, including race TTKS (syn. Ug99), and is used widely in commercial wheat cultivars worldwide. In 2006, susceptible infection responses were observed on wheat lines and cultivars carrying Sr24 in a field stem rust screening nursery at Njoro, Kenya. We derived 28 single-pustule isolates from stem rust samples collected from the 2006 Njoro nursery. The isolates were evaluated for virulence on 16 North American stem rust differential lines; on wheat lines carrying Sr24, Sr31, Sr38, and SrMcN; and on a wheat cultivar with a combination of Sr24 and Sr31. All isolates were identified as race TTKS with additional virulence on Sr31 and Sr38. These isolates were divided into two groups: group A (seven isolates and the two control isolates), producing a low infection type, and group B (21 isolates), producing a high infection type on Sr24, respectively. Isolates of group B represented a new variant of race TTKS with virulence to Sr24. Eighteen simple sequence repeat (SSR) markers were used to examine the genetic relationship between these two groups of isolates in race TTKS and five North American races (MCCF, QCCQ, RCRS, RTHS, and TPMK) that are representative of distinct lineage groups. All isolates of race TTKS shared an identical SSR genotype and were clearly different from North American races. The virulence and SSR data indicated that the new variant of race TTKS with Sr24 virulence likely has arisen via mutation within the TTKS genetic lineage. We propose to revise the North American stem rust nomenclature system by the addition of four genes (Sr24, Sr31, Sr38, and SrMcN) as the fifth set. This revision recognizes the virulence on Sr31 and differentiates isolates within race TTKS into two separate races: TTKSK and TTKST, with avirulence and virulence on Sr24, respectively. The occurrence of race TTKST with combined virulence on Sr24 and Sr31 has substantially increased the vulnerability of wheat to stem rust worldwide.
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                Author and article information

                Contributors
                mes12@cornell.edu
                Journal
                Theor Appl Genet
                Theor. Appl. Genet
                TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik
                Springer Berlin Heidelberg (Berlin/Heidelberg )
                0040-5752
                1432-2242
                6 June 2014
                6 June 2014
                2014
                : 127
                : 1561-1581
                Affiliations
                [ ]Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853 USA
                [ ]International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600 Texcoco, Mexico
                [ ]Campo Experimental Valle de México INIFAP, Apdo. Postal 10, 56230 Chapingo, Edo de México Mexico
                [ ]United States Department of Agriculture, Agricultural Research Service, Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, Minneapolis, MN 55108 USA
                [ ]United States Department of Agriculture, Agricultural Research Service, Vegetable and Forage Crops Research Unit, 24106 N. Bunn Road, Prosser, WA 99350–9687 USA
                Author notes

                Communicated by Beat Keller.

                Article
                2326
                10.1007/s00122-014-2326-7
                4072096
                24903979
                © The Author(s) 2014

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.

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                Original Paper
                Custom metadata
                © Springer-Verlag Berlin Heidelberg 2014

                Genetics

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