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Shahinnia F, Geyer M, Schürmann F, Rudolphi S, Holzapfel J, Kempf H, Stadlmeier M, Löschenberger F, Morales L, Buerstmayr H, Sánchez JIY, Akdemir D, Mohler V, Lillemo M, Hartl L. Genome-wide association study and genomic prediction of resistance to stripe rust in current Central and Northern European winter wheat germplasm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3583-3595. [PMID: 36018343 PMCID: PMC9519682 DOI: 10.1007/s00122-022-04202-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/17/2022] [Indexed: 05/03/2023]
Abstract
We found two loci on chromosomes 2BS and 6AL that significantly contribute to stripe rust resistance in current European winter wheat germplasm. Stripe or yellow rust, caused by the fungus Puccinia striiformis Westend f. sp. tritici, is one of the most destructive wheat diseases. Sustainable management of wheat stripe rust can be achieved through the deployment of rust resistant cultivars. To detect effective resistance loci for use in breeding programs, an association mapping panel of 230 winter wheat cultivars and breeding lines from Northern and Central Europe was employed. Genotyping with the Illumina® iSelect® 25 K Infinium® single nucleotide polymorphism (SNP) genotyping array yielded 8812 polymorphic markers. Structure analysis revealed two subpopulations with 92 Austrian breeding lines and cultivars, which were separated from the other 138 genotypes from Germany, Norway, Sweden, Denmark, Poland, and Switzerland. Genome-wide association study for adult plant stripe rust resistance identified 12 SNP markers on six wheat chromosomes which showed consistent effects over several testing environments. Among these, two marker loci on chromosomes 2BS (RAC875_c1226_652) and 6AL (Tdurum_contig29607_413) were highly predictive in three independent validation populations of 1065, 1001, and 175 breeding lines. Lines with the resistant haplotype at both loci were nearly free of stipe rust symptoms. By using mixed linear models with those markers as fixed effects, we could increase predictive ability in the three populations by 0.13-0.46 compared to a standard genomic best linear unbiased prediction approach. The obtained results facilitate an efficient selection for stripe rust resistance against the current pathogen population in the Northern and Central European winter wheat gene pool.
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Affiliation(s)
- Fahimeh Shahinnia
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany.
| | - Manuel Geyer
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany
| | | | - Sabine Rudolphi
- SECOBRA Saatzucht GmbH, Lagesche Str. 250, 32657, Lemgo, Germany
| | - Josef Holzapfel
- SECOBRA Saatzucht GmbH, Feldkirchen 3, 85368, Moosburg, Germany
| | - Hubert Kempf
- SECOBRA Saatzucht GmbH, Feldkirchen 3, 85368, Moosburg, Germany
| | | | | | - Laura Morales
- Department of Agrobiotechnology, Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Straße 20, 3430, Tulln an der Donau, Austria
| | - Hermann Buerstmayr
- Department of Agrobiotechnology, Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Straße 20, 3430, Tulln an der Donau, Austria
| | - Julio Isidro Y Sánchez
- Centro de Biotecnologia y Genómica de Plantas, Instituto Nacional de Investigación y Tecnologia Agraria y Alimentaria, Universidad Politécnica de Madrid, Campus de Montegancedo, Madrid, Spain
| | - Deniz Akdemir
- Center for International Blood and Marrow Transplant Research (CIBMTR), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Volker Mohler
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany
| | - Morten Lillemo
- Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | - Lorenz Hartl
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany.
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Jambuthenne DT, Riaz A, Athiyannan N, Alahmad S, Ng WL, Ziems L, Afanasenko O, Periyannan SK, Aitken E, Platz G, Godwin I, Voss-Fels KP, Dinglasan E, Hickey LT. Mining the Vavilov wheat diversity panel for new sources of adult plant resistance to stripe rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1355-1373. [PMID: 35113190 PMCID: PMC9033734 DOI: 10.1007/s00122-022-04037-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Multi-year evaluation of the Vavilov wheat diversity panel identified new sources of adult plant resistance to stripe rust. Genome-wide association studies revealed the key genomic regions influencing resistance, including seven novel loci. Wheat stripe rust (YR) caused by Puccinia striiformis f. sp. tritici (Pst) poses a significant threat to global food security. Resistance genes commonly found in many wheat varieties have been rendered ineffective due to the rapid evolution of the pathogen. To identify novel sources of adult plant resistance (APR), 292 accessions from the N.I. Vavilov Institute of Plant Genetic Resources, Saint Petersburg, Russia, were screened for known APR genes (i.e. Yr18, Yr29, Yr46, Yr33, Yr39 and Yr59) using linked polymerase chain reaction (PCR) molecular markers. Accessions were evaluated against Pst (pathotype 134 E16 A + Yr17 + Yr27) at seedling and adult plant stages across multiple years (2014, 2015 and 2016) in Australia. Phenotypic analyses identified 132 lines that potentially carry novel sources of APR to YR. Genome-wide association studies (GWAS) identified 68 significant marker-trait associations (P < 0.001) for YR resistance, representing 47 independent quantitative trait loci (QTL) regions. Fourteen genomic regions overlapped with previously reported Yr genes, including Yr29, Yr56, Yr5, Yr43, Yr57, Yr30, Yr46, Yr47, Yr35, Yr36, Yrxy1, Yr59, Yr52 and YrYL. In total, seven QTL (positioned on chromosomes 1D, 2A, 3A, 3D, 5D, 7B and 7D) did not collocate with previously reported genes or QTL, indicating the presence of promising novel resistance factors. Overall, the Vavilov diversity panel provides a rich source of new alleles which could be used to broaden the genetic bases of YR resistance in modern wheat varieties.
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Affiliation(s)
- Dilani T Jambuthenne
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Adnan Riaz
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Naveenkumar Athiyannan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food,, Canberra, ACT, Australia
| | - Samir Alahmad
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Wei Ling Ng
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Laura Ziems
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Olga Afanasenko
- Department of Plant Resistance To Diseases, All Russian Research Institute for Plant Protection, St Petersburg, Russia, 196608
| | - Sambasivam K Periyannan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food,, Canberra, ACT, Australia
| | - Elizabeth Aitken
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Greg Platz
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, Australia
| | - Ian Godwin
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Eric Dinglasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia.
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia.
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Bouvet L, Holdgate S, James L, Thomas J, Mackay IJ, Cockram J. The evolving battle between yellow rust and wheat: implications for global food security. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:741-753. [PMID: 34821981 PMCID: PMC8942934 DOI: 10.1007/s00122-021-03983-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 10/21/2021] [Indexed: 05/04/2023]
Abstract
Wheat (Triticum aestivum L.) is a global commodity, and its production is a key component underpinning worldwide food security. Yellow rust, also known as stripe rust, is a wheat disease caused by the fungus Puccinia striiformis Westend f. sp. tritici (Pst), and results in yield losses in most wheat growing areas. Recently, the rapid global spread of genetically diverse sexually derived Pst races, which have now largely replaced the previous clonally propagated slowly evolving endemic populations, has resulted in further challenges for the protection of global wheat yields. However, advances in the application of genomics approaches, in both the host and pathogen, combined with classical genetic approaches, pathogen and disease monitoring, provide resources to help increase the rate of genetic gain for yellow rust resistance via wheat breeding while reducing the carbon footprint of the crop. Here we review key elements in the evolving battle between the pathogen and host, with a focus on solutions to help protect future wheat production from this globally important disease.
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Affiliation(s)
- Laura Bouvet
- John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Sarah Holdgate
- John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Lucy James
- John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Jane Thomas
- John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Ian J Mackay
- John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
- Scotland's Rural College (SRUC), The King's Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - James Cockram
- John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
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Rollar S, Geyer M, Hartl L, Mohler V, Ordon F, Serfling A. Quantitative Trait Loci Mapping of Adult Plant and Seedling Resistance to Stripe Rust ( Puccinia striiformis Westend.) in a Multiparent Advanced Generation Intercross Wheat Population. FRONTIERS IN PLANT SCIENCE 2021; 12:684671. [PMID: 35003147 PMCID: PMC8733622 DOI: 10.3389/fpls.2021.684671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 11/19/2021] [Indexed: 05/20/2023]
Abstract
Stripe rust caused by the biotrophic fungus Puccinia striiformis Westend. is one of the most important diseases of wheat worldwide, causing high yield and quality losses. Growing resistant cultivars is the most efficient way to control stripe rust, both economically and ecologically. Known resistance genes are already present in numerous cultivars worldwide. However, their effectiveness is limited to certain races within a rust population and the emergence of stripe rust races being virulent against common resistance genes forces the demand for new sources of resistance. Multiparent advanced generation intercross (MAGIC) populations have proven to be a powerful tool to carry out genetic studies on economically important traits. In this study, interval mapping was performed to map quantitative trait loci (QTL) for stripe rust resistance in the Bavarian MAGIC wheat population, comprising 394 F6 : 8 recombinant inbred lines (RILs). Phenotypic evaluation of the RILs was carried out for adult plant resistance in field trials at three locations across three years and for seedling resistance in a growth chamber. In total, 21 QTL for stripe rust resistance corresponding to 13 distinct chromosomal regions were detected, of which two may represent putatively new QTL located on wheat chromosomes 3D and 7D.
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Affiliation(s)
- Sandra Rollar
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Manuel Geyer
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Freising, Germany
| | - Lorenz Hartl
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Freising, Germany
| | - Volker Mohler
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Freising, Germany
| | - Frank Ordon
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Albrecht Serfling
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
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Dyda M, Tyrka M, Gołębiowska G, Rapacz M, Wędzony M. Genetic mapping of adult-plant resistance genes to powdery mildew in triticale. J Appl Genet 2021; 63:73-86. [PMID: 34561842 PMCID: PMC8755695 DOI: 10.1007/s13353-021-00664-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/03/2021] [Accepted: 09/13/2021] [Indexed: 11/21/2022]
Abstract
Triticale is a cereal of high economic importance; however, along with the increase in the area of this cereal, it is more often infected by the fungal pathogen Blumeria graminis, which causes powdery mildew. The rapid development of molecular biology techniques, in particular methods based on molecular markers may be an important tool used in modern plant breeding. Development of genetic maps, location of the QTLs defining the region of the genome associated with resistance and selection of markers linked to particular trait can be used to select resistant genotypes as well as to pyramidize several resistance genes in one variety. In this paper, we present a new, high-density genetic map of triticale doubled haploids (DH) population “Grenado” × “Zorro” composed of DArT, silicoDArT, and SNP markers. Composite interval mapping method was used to detect eight QTL regions associated with the area under disease progress curve (AUDPC) and 15 regions with the average value of powdery mildew infection (avPM) based on observation conducted in 3-year period in three different locations across the Poland. Two regions on rye chromosome 4R, and single loci on 5R and 6R were reported for the first time as regions associated with powdery mildew resistance. Among all QTLs, 14 candidate genes were identified coded cyclin-dependent kinase, serine/threonine-protein kinase-like protein as well as AMEIOTIC 1 homolog DYAD-like protein, DETOXIFICATION 16-like protein, and putative disease resistance protein RGA3. Three of identified candidate genes were found among newly described QTL regions associated with powdery mildew resistance in triticale.
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Affiliation(s)
- Mateusz Dyda
- Chair of Genetics, Institute of Biology, Pedagogical University of Cracow, Podchorążych 2, 30-084, Kraków, Poland.
| | - Mirosław Tyrka
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszów University of Technology, Rzeszów, Poland
| | - Gabriela Gołębiowska
- Chair of Genetics, Institute of Biology, Pedagogical University of Cracow, Podchorążych 2, 30-084, Kraków, Poland
| | - Marcin Rapacz
- Department of Plant Breeding, Physiology and Seed Science, University of Agriculture in Kraków, Podłużna 3, 30-239, Krakow, Poland
| | - Maria Wędzony
- Chair of Genetics, Institute of Biology, Pedagogical University of Cracow, Podchorążych 2, 30-084, Kraków, Poland
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Wang Y, Yu C, Cheng Y, Yao F, Long L, Wu Y, Li J, Li H, Wang J, Jiang Q, Li W, Pu Z, Qi P, Ma J, Deng M, Wei Y, Chen X, Chen G, Kang H, Jiang Y, Zheng Y. Genome-wide association mapping reveals potential novel loci controlling stripe rust resistance in a Chinese wheat landrace diversity panel from the southern autumn-sown spring wheat zone. BMC Genomics 2021; 22:34. [PMID: 33413106 PMCID: PMC7791647 DOI: 10.1186/s12864-020-07331-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 12/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is a serious foliar disease of wheat. Identification of novel stripe rust resistance genes and cultivation of resistant cultivars are considered to be the most effective approaches to control this disease. In this study, we evaluated the infection type (IT), disease severity (DS) and area under the disease progress curve (AUDPC) of 143 Chinese wheat landrace accessions for stripe rust resistance. Assessments were undertaken in five environments at the adult-plant stage with Pst mixture races under field conditions. In addition, IT was assessed at the seedling stage with two prevalent Pst races (CYR32 and CYR34) under a controlled greenhouse environment. RESULTS Seventeen accessions showed stable high-level resistance to stripe rust across all environments in the field tests. Four accessions showed resistance to the Pst races CYR32 and CYR34 at the seedling stage. Combining phenotypic data from the field and greenhouse trials with 6404 markers that covered the entire genome, we detected 17 quantitative trait loci (QTL) on 11 chromosomes for IT associated with seedling resistance and 15 QTL on seven chromosomes for IT, final disease severity (FDS) or AUDPC associated with adult-plant resistance. Four stable QTL detected on four chromosomes, which explained 9.99-23.30% of the phenotypic variation, were simultaneously associated with seedling and adult-plant resistance. Integrating a linkage map of stripe rust resistance in wheat, 27 QTL overlapped with previously reported genes or QTL, whereas four and one QTL conferring seedling and adult-plant resistance, respectively, were mapped distantly from previously reported stripe rust resistance genes or QTL and thus may be novel resistance loci. CONCLUSIONS Our results provided an integrated overview of stripe rust resistance resources in a wheat landrace diversity panel from the southern autumn-sown spring wheat zone of China. The identified resistant accessions and resistance loci will be useful in the ongoing effort to develop new wheat cultivars with strong resistance to stripe rust.
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Affiliation(s)
- Yuqi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Can Yu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Yukun Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Fangjie Yao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Li Long
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Yu Wu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Jing Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Hao Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Pengfei Qi
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Xianming Chen
- US Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit; and Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China
| | - Houyang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China.
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China.
| | - Yunfeng Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China.
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, P. R. China.
- State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan, 611130, P. R. China.
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7
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Yao F, Long L, Wang Y, Duan L, Zhao X, Jiang Y, Li H, Pu Z, Li W, Jiang Q, Wang J, Wei Y, Ma J, Kang H, Dai S, Qi P, Zheng Y, Chen X, Chen G. Population structure and genetic basis of the stripe rust resistance of 140 Chinese wheat landraces revealed by a genome-wide association study. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110688. [PMID: 33218646 DOI: 10.1016/j.plantsci.2020.110688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is one of the most devastating foliar diseases in wheat. Host resistance is the most effective strategy for the management of the disease. To screen for accessions with stable resistance and identify effective stripe rust resistance loci, a genome-wide association study (GWAS) was conducted using a panel of 140 Chinese wheat landraces. The panel was evaluated for stripe rust response at the adult-plant stage at six field-year environments with mixed races and at the seedling stage with two separate predominant races of the pathogen, and genotyped with the genome-wide Diversity Arrays Technology markers. The panel displayed abundant phenotypic variation in stripe rust responses, with 9 landraces showing stable resistance to the mixture of Pst races at the adult-plant stage in the field and 10 landraces showing resistance to individual races at the seedling stage in the greenhouse. GWAS identified 12 quantitative trait loci (QTL) significantly (P ≤ 0.001) associated to stripe rust resistance using the field data of at least two environments and 18 QTL using the seedling data with two races. Among these QTL, 10 were presumably novel, including 4 for adult-plant resistance mapped to chromosomes 1B (QYrcl.sicau-1B.3), 4A (QYrcl.sicau-4A.3), 6A (QYrcl.sicau-6A.2) and 7B (QYrcl.sicau-7B.2) and 6 for all-stage resistance mapped to chromosomes 2D (QYrcl.sicau-2D.1), 3B (QYrcl.sicau-3B.3), 3D (QYrcl.sicau-3D), 4B (QYrcl.sicau-4B), 6A (QYrcl.sicau-6A.1) and 6D (QYrcl.sicau-6D). The landraces with stable resistance can be used for developing wheat cultivars with effective resistance to stripe rust.
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Affiliation(s)
- Fangjie Yao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Li Long
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Yuqi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Luyao Duan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Xuyang Zhao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Yunfeng Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Hao Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Houyang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Shoufen Dai
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Pengfei Qi
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China
| | - Xianming Chen
- US Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, PR China; State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China, Wenjiang, Chengdu, Sichuan 611130, PR China.
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8
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Habib M, Awan FS, Sadia B, Zia MA. Genome-Wide Association Mapping for Stripe Rust Resistance in Pakistani Spring Wheat Genotypes. PLANTS 2020; 9:plants9091056. [PMID: 32824927 PMCID: PMC7570266 DOI: 10.3390/plants9091056] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/13/2020] [Accepted: 06/15/2020] [Indexed: 11/16/2022]
Abstract
Stripe rust caused by the pathogen Puccinia striiformis f. sp. tritici (Pst) is a major threat for wheat, resulting in low yield and grain quality loss in many countries. Genetic resistance is a prevalent method to combat the disease. Mapping the resistant loci and their association with traits is highly exploited in this era. A panel of 465 Pakistani spring wheat genotypes were evaluated for their phenotypic response to stripe rust at the seedling and adult plant stages. A total of 765 single nucleotide polymorphism (SNP) markers were applied on 465 wheat genotypes to evaluate their stripe rust response against nine races during the seedling test and in three locations for the field test. Currently, twenty SNPs dispersed on twelve chromosomal regions (1A, 1B, 1D, 2A, 2B, 4A, 4B, 5B, 6A, 6B, 6D and 7B) have been identified that were associated with rust race-specific resistance at the seedling stage. Thirty SNPs dispersed on eighteen chromosomal regions (1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4B, 5A, 5B, 6A, 6B, 6D, 7A, 7B and 7D) are associated with adult plant resistance. SNP loci IWB3662 was linked with all three Pakistani races, and likewise IWA2344 and IWA4096 were found to be linked with three different USA races. The present research findings can be applied by wheat breeders to increase their resistant capability and yield potential of their cultivars, through marker-assisted selection.
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Affiliation(s)
- Madiha Habib
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38000, Pakistan; (M.H.); (B.S.)
| | - Faisal Saeed Awan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38000, Pakistan; (M.H.); (B.S.)
- Correspondence: ; Tel.: +92-41-9201087
| | - Bushra Sadia
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38000, Pakistan; (M.H.); (B.S.)
| | - Muhammad Anjum Zia
- Department of Biochemistry, University of Agriculture, Faisalabad 38000, Pakistan;
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9
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Revealing Differentially Expressed Genes and Identifying Effector Proteins of Puccinia striiformis f. sp.
tritici
in Response to High-Temperature Seedling Plant Resistance of Wheat Based on Transcriptome Sequencing. mSphere 2020. [PMCID: PMC7316484 DOI: 10.1128/msphere.00096-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the present study, we performed transcriptomic analysis to identify differentially expressed genes and effector proteins of
Puccinia striiformis
f. sp.
tritici
(
Pst
) in response to the high-temperature seedling-plant (HTSP) resistance in wheat. Experimental validation confirmed the function of the highest upregulated effector protein, PstCEP1. This study provides a key resource for understanding the biology and molecular basis of
Pst
responses to wheat HTSP resistance, and PstCEP1 may be used in future studies to understand pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity processes in the
Pst
-wheat interaction system.
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10
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Genome-wide association analysis of stripe rust resistance loci in wheat accessions from southwestern China. J Appl Genet 2020; 61:37-50. [PMID: 31912452 PMCID: PMC6969011 DOI: 10.1007/s13353-019-00533-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 12/01/2019] [Accepted: 12/11/2019] [Indexed: 11/17/2022]
Abstract
Wheat stripe rust can cause considerable yield losses, and genetic resistance is the most effective approach for controlling the disease. To identify the genomic regions responsible for Puccinia striiformis f. sp. tritici (Pst) resistance in a set of winter wheat strains mainly from southwestern China, and to identify DNA markers in these regions, we carried out a genome-wide association study (GWAS) of 120 China winter wheat accessions using single nucleotide polymorphism (SNP) markers from 90K wheat SNP arrays. In total, 16 SNP loci were significantly associated with wheat stripe rust in field and greenhouse trials. Of these, three distinctive SNPs on chromosomes 1B, 4A, and 6A were identified at a site in Mianyang in 2014, where the most prevalent wheat stripe rust races since 2009 have been V26 (G22-9, G22-14). This suggests that the three SNP loci were linked to the new quantitative trait loci (QTL)/genes resistant to the V26 races. Germplasm with immunity to Pst is a good source of stripe rust resistance for breeding, and after further validation, SNPs closely linked to resistance QTLs/genes could be converted into user-friendly markers and facilitate marker-assisted selection to improve wheat stripe rust resistance.
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11
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Mu J, Liu L, Liu Y, Wang M, See DR, Han D, Chen X. Genome-Wide Association Study and Gene Specific Markers Identified 51 Genes or QTL for Resistance to Stripe Rust in U.S. Winter Wheat Cultivars and Breeding Lines. FRONTIERS IN PLANT SCIENCE 2020; 11:998. [PMID: 32719705 PMCID: PMC7350909 DOI: 10.3389/fpls.2020.00998] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/17/2020] [Indexed: 05/06/2023]
Abstract
Stripe (yellow) rust, caused by fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is a serious disease of wheat in the United States and many other countries. Growing resistant cultivars has been approved to be the best approach for control of stripe rust. To determine stripe rust resistance genes in U.S. winter wheat cultivars and breeding lines, we analyzed a winter wheat panel of 857 cultivars and breeding lines in a genome-wide association study (GWAS) using genotyping by multiplexed sequencing (GMS) and by genotyping with molecular markers of 18 important stripe rust resistance genes or quantitative trait loci (QTL). The accessions were phenotyped for stripe rust response at adult-plant stage under natural infection in Pullman and Mount Vernon, Washington in 2018 and 2019, and in the seedling stage with six predominant or most virulent races of Pst. A total of 51 loci were identified to be related to stripe rust resistance, and at least 10 of them (QYrww.wgp.1D-3, QYrww.wgp.2B-2, QYrww.wgp.2B-3, QYrww.wgp.2B-4, QYrww.wgp.3A, QYrww.wgp.5A, QYrww.wgp.5B, QYrww.wgp.5D, QYrww.wgp.6A-2 and QYrww.wgp.7B-3) were previously reported. These genes or QTL were found to be present at different frequencies in breeding lines and cultivars developed by breeding programs in various winter wheat growing regions. Both Yr5 and Yr15, which are highly resistant to all races identified thus far in the U.S., as well as Yr46 providing resistance to many races, were found absent in the breeding lines and commercially grown cultivars. The identified genes or QTL and their markers are useful in breeding programs to improve the level and durability of resistance to stripe rust.
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Affiliation(s)
- Jingmei Mu
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- College of Life Science and Food Engineering, Hebei University of Engineering, Handan, China
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Lu Liu
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Yan Liu
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Deven R. See
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- Wheat Health, Genetics and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA, United States
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- Wheat Health, Genetics and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA, United States
- *Correspondence: Xianming Chen,
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12
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Liu L, Wang M, Feng J, See DR, Chen X. Whole-Genome Mapping of Stripe Rust Resistance Quantitative Trait Loci and Race Specificity Related to Resistance Reduction in Winter Wheat Cultivar Eltan. PHYTOPATHOLOGY 2019; 109:1226-1235. [PMID: 30730788 DOI: 10.1094/phyto-10-18-0385-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Winter wheat cultivar Eltan has been one of the most widely grown cultivars in the U.S. Pacific Northwest. It has shown variable levels of resistance to stripe rust in different years since it was released in 1990. To map all currently effective and defeated resistance genes in Eltan and understand the factors causing the resistance changes, 112 F2:5 recombinant inbred lines (RILs) were developed from a cross of Eltan with cultivar Avocet S. The RILs were evaluated in fields of Pullman, Washington in 2015, 2016, 2017, and 2018 and Mount Vernon, Washington in 2016 and 2017 under natural infections; they were also evaluated in the greenhouse with races PSTv-4 and PSTv-40 of Puccinia striiformis f. sp. tritici. The RILs were genotyped with the 90K Illumina iSelect wheat single-nucleotide polymorphism chip. A total of five quantitative trait loci (QTLs) were identified in Eltan. Two major QTLs on chromosome arms 2BS and 4AL were detected in the greenhouse tests, explaining up to 28.0 and 42.0% of phenotypic variation, respectively. The two race-specific QTLs were also detected in some field experiments but with reduced effects. A minor QTL on 5BS was detected in the greenhouse and field tests, explaining 10.0 to 14.8% of the phenotypic variation. The other two minor QTLs were mapped on 6AS and 7BL and detected only in field experiments, explaining up to 20.5 and 13.5% of phenotypic variation, respectively. All stripe rust samples collected in the experimental fields in 2015 and 2016 were identified as P. striiformis f. sp. tritici races virulent on seedlings of Eltan. The resistance reduction of Eltan was caused by changes of the P. striiformis f. sp. tritici population from avirulent to virulent, overcoming the race-specific all-stage resistance in Eltan.
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Affiliation(s)
- Lu Liu
- 1 Department of Plant Pathology, Washington State University, Pullman 99164-6430, WA, U.S.A
| | - Meinan Wang
- 1 Department of Plant Pathology, Washington State University, Pullman 99164-6430, WA, U.S.A
| | - Junyan Feng
- 1 Department of Plant Pathology, Washington State University, Pullman 99164-6430, WA, U.S.A
- 2 Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China; and
| | - Deven R See
- 1 Department of Plant Pathology, Washington State University, Pullman 99164-6430, WA, U.S.A
- 3 Wheat Health, Genetics and Quality Research Unit, U.S. Department of Agriculture Agricultural Research Service, Pullman 99164-6430, WA, U.S.A
| | - Xianming Chen
- 1 Department of Plant Pathology, Washington State University, Pullman 99164-6430, WA, U.S.A
- 3 Wheat Health, Genetics and Quality Research Unit, U.S. Department of Agriculture Agricultural Research Service, Pullman 99164-6430, WA, U.S.A
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13
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Zeng Q, Wu J, Liu S, Huang S, Wang Q, Mu J, Yu S, Han D, Kang Z. A major QTL co-localized on chromosome 6BL and its epistatic interaction for enhanced wheat stripe rust resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1409-1424. [PMID: 30707240 DOI: 10.1007/s00122-019-03288-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 01/16/2019] [Indexed: 05/27/2023]
Abstract
Co-localization of a major QTL for wheat stripe rust resistance to a 3.9-cM interval on chromosome 6BL across both populations and another QTL on chromosome 2B with epistatic interaction. Cultivars with diverse resistance are the optimal strategy to minimize yield losses caused by wheat stripe rust (Puccinia striiformis f. sp. tritici). Two wheat populations involving resistant wheat lines P10078 and Snb"S" from CIMMYT were evaluated for stripe rust response in multiple environments. Pool analysis by Wheat660K SNP array showed that the overlapping interval on chromosome 6B likely harbored a major QTL between two populations. Then, linkage maps were constructed using KASP markers, and a co-localized locus with large effect on chromosome 6BL was detected using QTL analysis in both populations. The coincident QTL, named QYr.nwafu-6BL.2, explained 59.7% of the phenotypic maximum variation in the Mingxian 169 × P10078 and 52.5% in the Zhengmai 9023 × Snb"S" populations, respectively. This co-localization interval spanning 3.9 cM corresponds to ~ 30.5-Mb genomic region of the newest common wheat reference genome (IWGSC RefSeq v.1.0). In addition, another QTL was also detected on chromosome 2B in Zhengmai 9023 × Snb"S" population and it can accelerate expression of QYr.nwafu-6BL.2 to enhance resistance with epistatic interaction. Allowing for Pst response, marker genotypes, pedigree analysis and relative genetic distance, QYr.nwafu-6BL.2 is likely to be a distinct adult plant resistance QTL. Haplotype analysis of QYr.nwafu-6BL.2 revealed specific SNPs or alleles in the target region from a diversity panel of 176 unrelated wheat accessions. This QTL region provides opportunity for further map-based cloning, and haplotypes analysis enables pyramiding favorable alleles into commercial cultivars by marker-assisted selection.
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Affiliation(s)
- Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jingmei Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shizhou Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
- College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
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14
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Zeng Q, Wu J, Liu S, Chen X, Yuan F, Su P, Wang Q, Huang S, Mu J, Han D, Kang Z, Chen XM. Genome-wide Mapping for Stripe Rust Resistance Loci in Common Wheat Cultivar Qinnong 142. PLANT DISEASE 2019; 103:439-447. [PMID: 30648483 DOI: 10.1094/pdis-05-18-0846-re] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Stripe rust caused by Puccinia striiformis f. sp. tritici threatens worldwide wheat production. Growing resistant cultivars is the best way to control this disease. Chinese wheat cultivar Qinnong 142 (QN142) has a high level of adult-plant resistance to stripe rust. To identify quantitative trait loci (QTLs) related to stripe rust resistance, we developed a recombinant inbred line (RIL) population from a cross between QN142 and susceptible cultivar Avocet S. The parents and 165 F6 RILs were evaluated in terms of their stripe rust infection type and disease severity in replicated field tests with six site-year environments. The parents and RILs were genotyped with single-nucleotide polymorphism (SNP) markers. Four stable QTLs were identified in QN142 and mapped to chromosome arms 1BL, 2AL, 2BL, and 6BS. The 1BL QTL was probably the known resistance gene Yr29, the 2BL QTL was in a resistance gene-rich region, and the 2AL and 6BS QTLs might be new. Kompetitive allele specific polymerase chain reaction markers developed from the SNP markers flanking these QTLs were highly polymorphic in a panel of 150 wheat cultivars and breeding lines. These markers could be used in marker-assisted selection for incorporating the stripe rust resistance QTL into new wheat cultivars.
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Affiliation(s)
- Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Xianming Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Fengping Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Pingping Su
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Jingmei Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - X M Chen
- Wheat Health, Genetics, and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA 99164; and Department of Plant Pathology, Washington State University, Pullman, WA 99164, U.S.A
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15
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Wang Z, Ren J, Du Z, Che M, Zhang Y, Quan W, Jiang X, Ma Y, Zhao Y, Zhang Z. Identification of a major QTL on chromosome arm 2AL for reducing yellow rust severity from a Chinese wheat landrace with evidence for durable resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:457-471. [PMID: 30426175 DOI: 10.1007/s00122-018-3232-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
A QTL on 2AL for reducing yellow rust severity was identified from a Chinese wheat landrace, being more effective than Yr18, with evidence for durable resistance from field observations. Utilization of wheat resistance is an important strategy to control yellow rust. The Chinese wheat landrace Hong Qimai (HQM) and the advanced breeding line AQ24788-83 (AQ; a progeny of HQM) can significantly reduce disease severity at the adult-plant growth stage. HQM has maintained adult-plant resistance for a prolonged period of time. To study the inheritance of the resistance, 126 recombinant inbred lines (RILs) derived from the cross Thatcher (TC) × HQM and 138 RILs from Luke × AQ were assessed for disease severity in six field trials. A genetic map of TC × HQM was constructed by genotyping these RILs using the 90 K wheat single-nucleotide polymorphism chip. Luke × AQ map was previously constructed for another disease study and also utilized here. Based on these maps and disease data, a quantitative trait locus (QTL) was detected on the chromosome arm 2AL from both TC × HQM and Luke × AQ and designated as QYr.cau-2AL. The resistance allele at QYr.cau-2AL came from HQM and AQ. QYr.cau-2AL was significantly effective across all the test environments and different genetic backgrounds, with its effect magnitude being higher than that of Yr18. QYr.cau-2AL synergistically acted with Yr18 and a QTL for high-temperature adult-plant resistance on 2BS, resulting in an elevated resistance from the juvenile plant growth stage onward, although QYr.cau-2AL alone displayed no substantial resistance at juvenile stage. Evidence indicates that QYr.cau-2AL is novel and confers durable resistance, and thus, should have high potential value for practical breeding.
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Affiliation(s)
- Zhen Wang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Junda Ren
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Ziyi Du
- Open University of China, Beijing, 100039, People's Republic of China
| | - Mingzhe Che
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yibin Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Wei Quan
- Beijing Engineering and Technique Research Center for Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Xu Jiang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yuan Ma
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yin Zhao
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Zhongjun Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China.
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16
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Long L, Yao F, Yu C, Ye X, Cheng Y, Wang Y, Wu Y, Li J, Wang J, Jiang Q, Li W, Ma J, Liu Y, Deng M, Wei Y, Zheng Y, Chen G. Genome-Wide Association Study for Adult-Plant Resistance to Stripe Rust in Chinese Wheat Landraces ( Triticum aestivum L.) From the Yellow and Huai River Valleys. FRONTIERS IN PLANT SCIENCE 2019; 10:596. [PMID: 31156668 PMCID: PMC6532019 DOI: 10.3389/fpls.2019.00596] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/24/2019] [Indexed: 05/21/2023]
Abstract
Stripe rust (also known as yellow rust), caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), is a common and serious fungal disease of wheat (Triticum aestivum L.) worldwide. To identify effective stripe rust resistance loci, a genome-wide association study was performed using 152 wheat landraces from the Yellow and Huai River Valleys in China based on Diversity Arrays Technology and simple sequence repeat markers. Phenotypic evaluation of the degree of resistance to stripe rust at the adult-plant stage under field conditions was carried out in five environments. In total, 19 accessions displayed stable, high degrees of resistance to stripe rust development when exposed to mixed races of Pst at the adult-plant stage in multi-environment field assessments. A marker-trait association analysis indicated that 51 loci were significantly associated with adult-plant resistance to stripe rust. These loci included 40 quantitative trait loci (QTL) regions for adult-plant resistance. Twenty identified resistance QTL were linked closely to previously reported yellow rust resistance genes or QTL regions, which were distributed across chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4A, 4B, 5B, 6B, 7A, 7B, and 7D. Six multi-trait QTL were detected on chromosomes 1B, 1D, 2B, 3A, 3B, and 7D. Twenty QTL were mapped to chromosomes 1D, 2A, 2D, 4B, 5B, 6A, 6B, 6D, 7A, 7B, and 7D, distant from previously identified yellow rust resistance genes. Consequently, these QTL are potentially novel loci for stripe rust resistance. Among the 20 potentially novel QTL, five (QDS.sicau-2A, QIT.sicau-4B, QDS.sicau-4B.2, QDS.sicau-6A.3, and QYr.sicau-7D) were associated with field responses at the adult-plant stage in at least two environments, and may have large effects on stripe rust resistance. The novel effective QTL for adult-plant resistance to stripe rust will improve understanding of the genetic mechanisms that control the spread of stripe rust, and will aid in the molecular marker-assisted selection-based breeding of wheat for stripe rust resistance.
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Affiliation(s)
- Li Long
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Fangjie Yao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Can Yu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Xueling Ye
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Yukun Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Yuqi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Yu Wu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Jing Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - YaXi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Guoyue Chen,
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Ando K, Rynearson S, Muleta KT, Gedamu J, Girma B, Bosque-Pérez NA, Chen MS, Pumphrey MO. Genome-wide associations for multiple pest resistances in a Northwestern United States elite spring wheat panel. PLoS One 2018; 13:e0191305. [PMID: 29415008 PMCID: PMC5802848 DOI: 10.1371/journal.pone.0191305] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/01/2018] [Indexed: 12/01/2022] Open
Abstract
Northern areas of the western United States are one of the most productive wheat growing regions in the United States. Increasing productivity through breeding is hindered by several biotic stresses which slow and constrain targeted yield improvement. In order to understand genetic variation for stripe rust (Puccinia striiformis f. sp. tritici), Septoria tritici blotch (Mycosphaerella graminicola), and Hessian fly (Mayetiola destructor) in regional germplasm, a panel of 408 elite spring wheat lines was characterized and genotyped with an Illumina 9K wheat single nucleotide polymorphism (SNP) chip to enable genome-wide association study (GWAS) analyses. Significant marker-trait associations were identified for stripe rust (38 loci), Septoria tritici blotch (8) and Hessian fly (9) resistance. Many of the QTL corresponded with previously reported gene locations or QTL, but we also discovered new resistance loci for each trait. We validated one of the stripe rust resistance loci detected by GWAS in a bi-parental mapping population, which confirmed the detection of Yr15 in the panel. This study elucidated well-defined chromosome regions for multiple pest resistances in elite Northwest germplasm. Newly identified resistance loci, along with SNPs more tightly linked to previously reported genes or QTL will help future breeding and marker assisted selection efforts.
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Affiliation(s)
- Kaori Ando
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Sheri Rynearson
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Kebede T. Muleta
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Jhonatan Gedamu
- Ethiopian Institute of Agricultural Research, Holeta Agricultural Research Center, Holeta, Ethiopia
| | - Bedada Girma
- Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, Assela, Ethiopia
| | - Nilsa A. Bosque-Pérez
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, Idaho, United States of America
| | - Ming-Shun Chen
- United States Department of Agriculture–Agricultural Research Service and Department of Entomology, Kansas State University, Manhattan, Kansas, United States of America
| | - Mike O. Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
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Godoy JG, Rynearson S, Chen X, Pumphrey M. Genome-Wide Association Mapping of Loci for Resistance to Stripe Rust in North American Elite Spring Wheat Germplasm. PHYTOPATHOLOGY 2018; 108:234-245. [PMID: 28952421 DOI: 10.1094/phyto-06-17-0195-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a major yield-limiting foliar disease of wheat (Triticum aestivum) worldwide. In this study, the genetic variability of elite spring wheat germplasm from North America was investigated to characterize the genetic basis of effective all-stage and adult plant resistance (APR) to stripe rust. A genome-wide association study was conducted using 237 elite spring wheat lines genotyped with an Illumina Infinium 90K single-nucleotide polymorphism array. All-stage resistance was evaluated at seedling stage in controlled conditions and field evaluations were conducted under natural disease pressure in eight environments across Washington State. High heritability estimates and correlations between infection type and severity were observed. Ten loci for race-specific all-stage resistance were confirmed from previous mapping studies. Three potentially new loci associated with race-specific all-stage resistance were identified on chromosomes 1D, 2A, and 5A. For APR, 11 highly significant quantitative trait loci (QTL) (false discovery rate < 0.01) were identified, of which 3 QTL on chromosomes 3A, 5D, and 7A are reported for the first time. The QTL identified in this study can be used to enrich the current gene pool and improve the diversity of resistance to stripe rust disease.
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Affiliation(s)
- Jayfred Gaham Godoy
- First, second, and fourth authors: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420; and third author: United States Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, Washington State University, Pullman 99164-6430
| | - Sheri Rynearson
- First, second, and fourth authors: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420; and third author: United States Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, Washington State University, Pullman 99164-6430
| | - Xianming Chen
- First, second, and fourth authors: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420; and third author: United States Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, Washington State University, Pullman 99164-6430
| | - Michael Pumphrey
- First, second, and fourth authors: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420; and third author: United States Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, Washington State University, Pullman 99164-6430
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Wu J, Wang Q, Kang Z, Liu S, Li H, Mu J, Dai M, Han D, Zeng Q, Chen X. Development and Validation of KASP-SNP Markers for QTL Underlying Resistance to Stripe Rust in Common Wheat Cultivar P10057. PLANT DISEASE 2017; 101:2079-2087. [PMID: 30677371 DOI: 10.1094/pdis-04-17-0468-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Stripe rust (Puccinia striiformis f. sp. tritici) is among the most important diseases of wheat (Triticum aestivum L.) globally. Utilization of adult plant resistance (APR) constitutes a key tool for maintaining protection against this disease. The CIMMYT wheat cultivar P10057 displayed a high level of APR to stripe rust in germplasm evaluation in field environments. To clarify the genetic basis and identify quantitative trait loci (QTLs) involved in stripe rust resistance in P10057, three wheat populations were used: 150 F5:6 recombinant inbred lines (RILs) derived from the cross Mingxian 169 × P10057, and 161 and 140 F2:3 lines from Avocet S × P10057 and Zhengmai 9023 × P10057, respectively. These three populations were evaluated for infection type (IT) and disease severity (DS) in Shaanxi, Gansu, and Sichuan during the 2014-15 and 2015-16 cropping seasons. Genotyping was performed with Kompetitive Allelic Specific PCR (KASP) and simple sequence repeat (SSR) markers linked to the resistance loci. Using QTL analysis, two genomic regions associated with resistance were found on chromosome arms 2BS and 3BS, respectively. These two stable QTLs, designated Qyrlov.nwafu-2BS and Qyrlov.nwafu-3BS, were detected across all environments and explained average 22.6 to 31.6% and 21.3 to 32.3% of stripe rust severity phenotypic variation, respectively. Qyrlov.nwafu-2BS may be the resistance allele derived from CIMMYT germplasm and Qyrlov.nwafu-3BS likely corresponds to the locus Sr2/Lr27/Yr30/Pbc. The KASP markers IWA5377, IWA2674, and IWA5830 linked to QYrlov.nwafu-2BS and IWB57990 and IWB6491 linked to Qyrlov.nwafu-3BS were reliable for marker-assisted selection (MAS) in the Zhengmai 9023 × P10057 population. These QTLs with KASP markers are expected to contribute in developing wheat cultivars with improved stripe rust resistance.
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Affiliation(s)
- Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Haiyang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Jingmei Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Miaofei Dai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Xianming Chen
- Wheat Health, Genetics, and Quality Research Unit, Agricultural Research Service, United States Department of Agriculture, and Department of Plant Pathology, Washington State University, Pullman, WA
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20
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Muleta KT, Bulli P, Rynearson S, Chen X, Pumphrey M. Loci associated with resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a core collection of spring wheat (Triticum aestivum). PLoS One 2017; 12:e0179087. [PMID: 28591221 PMCID: PMC5462451 DOI: 10.1371/journal.pone.0179087] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/23/2017] [Indexed: 11/21/2022] Open
Abstract
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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Affiliation(s)
- Kebede T. Muleta
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Peter Bulli
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Sheri Rynearson
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Xianming Chen
- USDA-ARS, Wheat Health, Genetics, and Quality Research Unit, and Department of Plant Pathology, Washington State University, Pullman, Washington, United States of America
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
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21
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Wu J, Wang Q, Liu S, Huang S, Mu J, Zeng Q, Huang L, Han D, Kang Z. Saturation Mapping of a Major Effect QTL for Stripe Rust Resistance on Wheat Chromosome 2B in Cultivar Napo 63 Using SNP Genotyping Arrays. FRONTIERS IN PLANT SCIENCE 2017; 8:653. [PMID: 28491075 PMCID: PMC5405077 DOI: 10.3389/fpls.2017.00653] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/10/2017] [Indexed: 05/18/2023]
Abstract
Stripe rust or yellow rust (YR), caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat (Triticum aestivum L.). Widespread deployment of resistant cultivars is the best means of achieving durable disease control. The red grain, spring wheat cultivar Napo 63 produced by CIMMYT in the 1960s shows a high level of adult-plant resistance to stripe rust in the field. To elucidate the genetic basis of resistance in this cultivar we evaluated 224 F2:3 lines and 175 F2:6 recombinant inbred lines (RILs) derived from a cross between Napo 63 and the Pst-susceptible line Avocet S. The maximum disease severity (MDS) data of F2:3 lines and the relative area under the disease progress curve (rAUDPC) data of RILs were collected during the 2014-2015 and 2015-2016 wheat growing seasons, respectively. Combined bulked segregant analysis and 90K single nucleotide polymorphism (SNP) arrays placed 275 of 511 polymorphic SNPs on chromosome 2B. Sixty four KASP markers selected from the 275 SNPs and 76 SSR markers on 2B were used to identify a chromosome region associated with rust response. A major effect QTL, named Qyrnap.nwafu-2BS, was identified by inclusive composite interval mapping and was preliminarily mapped to a 5.46 cM interval flanked by KASP markers 90K-AN34 and 90K-AN36 in chromosome 2BS. Fourteen KASP markers more closely linked to the locus were developed following a 660K SNP array analysis. The QTL region was finally narrowed to a 0.9 cM interval flanked by KASP markers 660K-AN21 and 660K-AN57 in bin region 2BS-1-0.53. The resistance of Napo 63 was stable across all environments, and as a QTL, explained an average 66.1% of the phenotypic variance in MDS of F2:3 lines and 55.7% of the phenotypic variance in rAUDPC of F5:6 RILs. The short genetic interval and flanking KASP markers developed in the study will facilitate marker-assisted selection, gene pyramiding, and eventual positional cloning of Qyrnap.nwafu-2BS.
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Affiliation(s)
- Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Jingmei Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, China
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22
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Du Z, Che M, Li G, Chen J, Quan W, Guo Y, Wang Z, Ren J, Zhang H, Zhang Z. A QTL with major effect on reducing leaf rust severity on the short arm of chromosome 1A of wheat detected across different genetic backgrounds and diverse environments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1579-94. [PMID: 25982130 DOI: 10.1007/s00122-015-2533-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 05/02/2015] [Indexed: 05/02/2023]
Abstract
Selection for QLr.cau - 1AS (a major QTL detected in wheat for reducing leaf rust severity) based on the DNA marker gpw2246 was as effective as selection for Lr34 based on cssfr5. Leaf rust is an important disease of wheat worldwide. Utilization of slow-rusting resistance constitutes a strategy to sustainably control this disease. The American wheat cultivar Luke exhibits slow leaf-rusting resistance at the adult plant stage. The objectives of this study were to detect and validate QTL for the resistance in Luke. Three winter wheat populations were used, namely, 149 recombinant inbred lines (RILs) derived from the cross Luke × Aquileja, 307 RILs from Luke × AQ24788-83, and 80 F2:3 families selected from Lingxing66 × KA298. Aquileja and Lingxing66 are highly susceptible to leaf rust. AQ24788-83 shows high (susceptible) infection type but contains the slow-rusting gene Lr34 as diagnosed by the gene-specific marker cssfr5. KA298, an F9 RIL selected from Luke × AQ24788-83, contains Lr34 and QLr.cau-1AS (a major QTL originated from Luke, this study). These wheats were evaluated for leaf rust in 12 field and greenhouse environments involving four locations and five seasons. Genotyping was done using simple sequence repeat (SSR) and diversity arrays technology markers. Of the detected QTLs, QLr.cau-1AS was significant consistently across all the genetic backgrounds, test environments, and likely a wide range of pathogen races. QLr.cau-1AS explained 22.3-55.2% of leaf rust phenotypic variation, being comparable to Lr34 in effect size. A co-dominant SSR marker (gpw2246, http://wheat.pw.usda.gov/GG2/index.shtml ) was identified to be tightly linked to QLr.cau-1AS. Selection based on gpw2246 for QLr.cau-1AS was as effective as the selection based on cssfr5 for Lr34. QLr.cau-1AS will be helpful for increasing the genetic diversity of slow leaf-rusting resistance in wheat breeding programs.
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Affiliation(s)
- Ziyi Du
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, People's Republic of China
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23
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Hou L, Chen X, Wang M, See DR, Chao S, Bulli P, Jing J. Mapping a Large Number of QTL for Durable Resistance to Stripe Rust in Winter Wheat Druchamp Using SSR and SNP Markers. PLoS One 2015; 10:e0126794. [PMID: 25970329 PMCID: PMC4430513 DOI: 10.1371/journal.pone.0126794] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 04/07/2015] [Indexed: 11/22/2022] Open
Abstract
Winter wheat Druchamp has both high-temperature adult-plant (HTAP) resistance and all-stage resistance to stripe rust caused by Puccinia striiformis f. sp. tritici (Pst). The HTAP resistance in Druchamp is durable as the variety has been resistant in adult-plant stage since it was introduced from France to the United States in late 1940s. To map the quantitative trait loci (QTL) for stripe rust resistance, an F8 recombinant inbred line (RIL) population from cross Druchamp × Michigan Amber was phenotyped for stripe rust response in multiple years in fields under natural infection and with selected Pst races under controlled greenhouse conditions, and genotyped with simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. Composite interval mapping (CIM) identified eight HTAP resistance QTL and three all-stage resistance QTL. Among the eight HTAP resistance QTL, QYrdr.wgp-1BL.2 (explaining 2.36-31.04% variation), QYrdr.wgp-2BL (2.81-15.65%), QYrdr.wgp-5AL (2.27-17.22%) and QYrdr.wgp-5BL.2 (2.42-15.13%) were significant in all tests; and QYrdr.wgp-1BL.1 (1.94-10.19%), QYrdr.wgp-1DS (2.04-27.24%), QYrdr.wgp-3AL (1.78-13.85%) and QYrdr.wgp-6BL.2 (1.69-33.71%) were significant in some of the tests. The three all-stage resistance QTL, QYrdr.wgp-5BL.1 (5.47-36.04%), QYrdr.wgp-5DL (9.27-11.94%) and QYrdr.wgp-6BL.1 (13.07-20.36%), were detected based on reactions in the seedlings tested with certain Pst races. Among the eleven QTL detected in Druchamp, at least three (QYrdr.wgp-5DL for race-specific all-stage resistance and QYrdr.wgp-3AL and QYrdr.wgp-6BL.2 for race non-specific HTAP resistance) are new. All these QTL, especially those for durable HTAP resistance, and their closely linked molecular markers could be useful for developing wheat cultivars with durable resistance to stripe rust.
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Affiliation(s)
- Lu Hou
- Key Laboratory of Agricultural Integrated Pest Management, Institute of Plant Protection, Qinghai Academy of Agriculture and Forestry Sciences, Xining, Qinghai, China
- Department of Plant Pathology, Washington State University, Pullman, Washington, United States of America
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, Washington, United States of America
- US Department of Agriculture, Agricultural Research Service, Wheat Genetics, Quality, Physiology and Disease Research Unit, Pullman, Washington, United States of America
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, Washington, United States of America
| | - Deven R. See
- Department of Plant Pathology, Washington State University, Pullman, Washington, United States of America
- US Department of Agriculture, Agricultural Research Service, Wheat Genetics, Quality, Physiology and Disease Research Unit, Pullman, Washington, United States of America
| | - Shiaoman Chao
- US Department of Agriculture, Agricultural Research Service, Cereal Crops Research, Fargo, North Dakota, United States of America
| | - Peter Bulli
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Jinxue Jing
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
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Rosewarne GM, Herrera-Foessel SA, Singh RP, Huerta-Espino J, Lan CX, He ZH. Quantitative trait loci of stripe rust resistance in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2427-49. [PMID: 23955314 PMCID: PMC3782644 DOI: 10.1007/s00122-013-2159-9] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 07/12/2013] [Indexed: 05/18/2023]
Abstract
Over thirty publications during the last 10 years have identified more than 140 QTLs for stripe rust resistance in wheat. It is likely that many of these QTLs are identical genes that have been spread through plant breeding into diverse backgrounds through phenotypic selection under stripe rust epidemics. Allelism testing can be used to differentiate genes in similar locations but in different genetic backgrounds; however, this is problematic for QTL studies where multiple loci segregate from any one parent. This review utilizes consensus maps to illustrate important genomic regions that have had effects against stripe rust in wheat, and although this methodology cannot distinguish alleles from closely linked genes, it does highlight the extent of genetic diversity for this trait and identifies the most valuable loci and the parents possessing them for utilization in breeding programs. With the advent of cheaper, high throughput genotyping technologies, it is envisioned that there will be many more publications in the near future describing ever more QTLs. This review sets the scene for the coming influx of data and will quickly enable researchers to identify new loci in their given populations.
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Affiliation(s)
- G M Rosewarne
- Crop Research Institute, Key Laboratory of Biology and Genetic Breeding in Wheat (Southwest), Sichuan Academy of Agricultural Science, #4 Shizishan Rd, Jinjiang, 610066, Chengdu, Sichuan Province, People's Republic of China,
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25
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Yang EN, Rosewarne GM, Herrera-Foessel SA, Huerta-Espino J, Tang ZX, Sun CF, Ren ZL, Singh RP. QTL analysis of the spring wheat "Chapio" identifies stable stripe rust resistance despite inter-continental genotype × environment interactions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1721-32. [PMID: 23558982 DOI: 10.1007/s00122-013-2087-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 03/19/2013] [Indexed: 05/13/2023]
Abstract
Chapio is a spring wheat developed by CIMMYT in Mexico by a breeding program that focused on multigenic resistances to leaf rust and stripe rust. A population consisting of 277 recombinant inbred lines (RILs) was developed by crossing Chapio with Avocet. The RILs were genotyped with DArT markers (137 randomly selected RILs) and bulked segregant analysis conducted to supplement the map with informative SSR markers. The final map consisted of 264 markers. Phenotyping against stripe rust was conducted for three seasons in Toluca, Mexico and at three sites over two seasons (total of four environments) in Sichuan Province, China. Significant loci across the two inter-continental regions included Lr34/Yr18 on 7DS, Sr2/Yr30 on 3BS, and a QTL on 3D. There were significant genotype × environment interactions with resistance gene Yr31 on 2BS being effective in most of the Toluca environments; however, a late incursion of a virulent pathotype in 2009 rendered this gene ineffective. This locus also had no effect in China. Conversely, a 5BL locus was only effective in the Chinese environments. There were also complex additive interactions. In the Mexican environments, Yr31 suppressed the additive effect of Yr30 and the 3D locus, but not of Lr34/Yr18, while in China, the 3D and 5BL loci were generally not additive with each other, but were additive when combined with other loci. These results indicate the importance of maintaining diverse, multi-genic resistances as Chapio had stable inter-continental resistance despite the fact that there were QTLs that were not effective in either one or the other region.
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Affiliation(s)
- E-N Yang
- Key Laboratory of Biology and Genetic Breeding in Wheat (Southwest), Crop Research Institute, Sichuan Academy of Agricultural Science, #4 Shizishan Rd, Jinjiang, Chengdu, Sichuan 610066, People's Republic of China
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Basnet BR, Singh RP, Herrera-Foessel SA, Ibrahim AMH, Huerta-Espino J, Calvo-Salazar V, Rudd JC. Genetic Analysis of Adult Plant Resistance to Yellow Rust and Leaf Rust in Common Spring Wheat Quaiu 3. PLANT DISEASE 2013; 97:728-736. [PMID: 30722591 DOI: 10.1094/pdis-02-12-0141-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Identifying and utilizing rust resistance genes in wheat has been hampered by the continuous and rapid emergence of new pathogen races. A major focus of many wheat breeding programs is achieving durable adult plant resistance (APR) to yellow (stripe) rust (YR) and leaf (brown) rust (LR), caused by Puccinia striiformis and P. triticina, respectively. This study aimed to determine the genetic basis of resistance to YR and LR in the common spring wheat 'Quaiu 3'. To that end, we evaluated 198 F5 recombinant inbred lines (RILs), derived from a cross of susceptible 'Avocet-YrA' with Quaiu 3, for APR to LR and YR in artificially inoculated field trials conducted in Mexico during the 2009 and 2010 growing seasons. High narrow-sense heritability (h2) estimates, ranging between 0.91 and 0.95, were obtained for both LR and YR disease severities for both years. The quantitative and qualitative approaches used to estimate gene numbers showed that, in addition to known resistance genes, there are at least two to three APR genes associated with LR and YR resistance in the RIL population. The moderately effective race-specific resistance gene Lr42 and the pleiotropic slow-rusting APR gene Lr46/Yr29 were found to interact with additional unidentified APR genes. The unidentified APR genes should be of particular interest for further characterization through molecular mapping, and for utilization by wheat breeding programs.
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Affiliation(s)
- B R Basnet
- International Maize and Wheat Improvement Center (CIMMYT) Apdo. Postal 6-641, C.P. 06600, D.F., Mexico and Department of Soil and Crop Sciences, Texas A&M University, College Station 77843
| | | | | | - A M H Ibrahim
- Department of Soil and Crop Sciences, Texas A&M University
| | - J Huerta-Espino
- Campo Experimental Valle de Mexico INIFAP, Apdo. Postal 10, 56230 Chapingo, Edo. de Mexico, Mexico
| | | | - J C Rudd
- Department of Soil and Crop Sciences, Texas A&M University
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Chen X. Review Article: High-Temperature Adult-Plant Resistance, Key for Sustainable Control of Stripe Rust. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ajps.2013.43080] [Citation(s) in RCA: 219] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Ren Y, He Z, Li J, Lillemo M, Wu L, Bai B, Lu Q, Zhu H, Zhou G, Du J, Lu Q, Xia X. QTL mapping of adult-plant resistance to stripe rust in a population derived from common wheat cultivars Naxos and Shanghai 3/Catbird. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1211-21. [PMID: 22798057 DOI: 10.1007/s00122-012-1907-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Accepted: 05/25/2012] [Indexed: 05/20/2023]
Abstract
Stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss., is a severe foliar disease of common wheat (Triticum aestivum L.) worldwide. Use of adult-plant resistance (APR) is an efficient approach to provide long-term protection of crops from the disease. The German spring wheat cultivar Naxos showed a high level of APR to stripe rust in the field. To identify the APR genes in this cultivar, a mapping population of 166 recombinant inbred lines (RILs) was developed from a cross between Naxos and Shanghai 3/Catbird (SHA3/CBRD), a moderately susceptible line developed by CIMMYT. The RILs were evaluated for maximum disease severity (MDS) in Sichuan and Gansu in the 2009-2010 and 2010-2011 cropping seasons. Composite interval mapping (CIM) identified four QTL, QYr.caas-1BL.1RS, QYr.caas-1DS, QYr.caas-5BL.3 and QYr.caas-7BL.1, conferring stable resistance to stripe rust across all environments, each explaining 1.9-27.6, 2.1-5.8, 2.5-7.8 and 3.7-9.1 % of the phenotypic variance, respectively. QYr.caas-1DS flanked by molecular markers XUgwm353-Xgdm33b was likely a new QTL for APR to stripe rust. Because the interval between flanking markers for each QTL was less than 6.5 cM, these QTL and their closely linked markers are potentially useful for improving resistance to stripe rust in wheat breeding.
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Affiliation(s)
- Yan Ren
- Institute of Crop Science, National Wheat Improvement Center/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
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29
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Dolores Vazquez M, James Peterson C, Riera-Lizarazu O, Chen X, Heesacker A, Ammar K, Crossa J, Mundt CC. Genetic analysis of adult plant, quantitative resistance to stripe rust in wheat cultivar 'Stephens' in multi-environment trials. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1-11. [PMID: 21912857 DOI: 10.1007/s00122-011-1681-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 08/04/2011] [Indexed: 05/20/2023]
Abstract
The wheat (Triticum aestivum L.) cultivar 'Stephens' has been grown commercially in the USA Pacific Northwest for 30 years. The durable resistance of 'Stephens' to stripe rust (Puccinia striiformis f. sp. tritici) was believed to be due to a combination of seedling and adult plant resistance genes. Multilocation field trials, diversity array technology (DArT), and simple sequence repeat (SSR) markers were used to identify quantitative trait loci (QTL) for resistance. Recombinant inbred lines were assessed for stripe rust response in eight locations/years, five in 2008 and three in 2009. The data from Mt. Vernon, WA, differed from all other environments, and composite interval mapping (CIM) identified three QTL, QYrst.orr-1AL, QYrst.orr-4BS, and QYrpl.orr-6AL, which accounted for 12, 11, and 6% of the phenotypic variance, respectively. CIM across the remaining six environments identified four main QTL. Two QTL, QYrst.orr-2BS.2 and QYrst.orr-7AS, were detected in five of six environments and explained 11 and 15% of the phenotypic variance, respectively. Two other QTL, QYrst.orr-2AS and QYrpl.orr-4BL, were detected across four and three of six environments, and explained 19 and 9% of the phenotypic variance, respectively. The susceptible parent 'Platte' contributed QYrpl.orr-4BL and QYrpl.orr-6AL, with the remaining QTL originating from 'Stephens'. For each environment, additional minor QTL were detected, each accounting for 6-10% of the phenotypic variance. Different QTL with moderate effects were identified in both 'Stephens' and 'Platte'. Significant QTL × environment interactions were evident, suggesting that specificity to plant stage, pathogen genotype, and/or temperature was important.
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Affiliation(s)
- M Dolores Vazquez
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA.
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Lowe I, Cantu D, Dubcovsky J. Durable resistance to the wheat rusts: Integrating systems biology and traditional phenotype-based research methods to guide the deployment of resistance genes. EUPHYTICA: NETHERLANDS JOURNAL OF PLANT BREEDING 2011. [PMID: 26900170 DOI: 10.1007/s10681‐010‐0311‐z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Genes which confer partial resistance to the rusts in wheat figure prominently in discussions of potential durable resistance strategies. The positional cloning of the first of these genes, Lr34/Yr18 and Yr36, has revealed different protein structures, suggesting that the category of partial resistance genes, as defined by phenotype, likely groups together suites of functionally heterogenous genes. With the number of mapped partial rust resistance genes increasing rapidly as a result of ongoing advances in marker and sequencing technologies, breeding programs needing to select and prioritize genes for deployment confront a fundamental question: which genes or gene combinations are more likely to provide durable protection against these evolving pathogens? We argue that a refined classification of partial rust resistance genes is required to start answering this question, one based not merely on disease phenotype but also on gene cloning, molecular functional characterization, and interactions with other host and pathogen proteins. Combined with accurate and detailed disease phenotyping and standard genetic studies, an integrated wheat-rust interactome promises to provide the basis for a functional classification of partial resistance genes and thus a conceptual framework for their rational deployment.
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Affiliation(s)
- Iago Lowe
- Department of Plant Sciences, University of California, Davis, One Shields Ave, Davis CA 95616, U.S.A
| | - Dario Cantu
- Department of Plant Sciences, University of California, Davis, One Shields Ave, Davis CA 95616, U.S.A
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, One Shields Ave, Davis CA 95616, U.S.A
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Lowe I, Cantu D, Dubcovsky J. Durable resistance to the wheat rusts: Integrating systems biology and traditional phenotype-based research methods to guide the deployment of resistance genes. EUPHYTICA: NETHERLANDS JOURNAL OF PLANT BREEDING 2011; 179:69-79. [PMID: 26900170 PMCID: PMC4756431 DOI: 10.1007/s10681-010-0311-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 11/11/2010] [Indexed: 05/18/2023]
Abstract
Genes which confer partial resistance to the rusts in wheat figure prominently in discussions of potential durable resistance strategies. The positional cloning of the first of these genes, Lr34/Yr18 and Yr36, has revealed different protein structures, suggesting that the category of partial resistance genes, as defined by phenotype, likely groups together suites of functionally heterogenous genes. With the number of mapped partial rust resistance genes increasing rapidly as a result of ongoing advances in marker and sequencing technologies, breeding programs needing to select and prioritize genes for deployment confront a fundamental question: which genes or gene combinations are more likely to provide durable protection against these evolving pathogens? We argue that a refined classification of partial rust resistance genes is required to start answering this question, one based not merely on disease phenotype but also on gene cloning, molecular functional characterization, and interactions with other host and pathogen proteins. Combined with accurate and detailed disease phenotyping and standard genetic studies, an integrated wheat-rust interactome promises to provide the basis for a functional classification of partial resistance genes and thus a conceptual framework for their rational deployment.
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Affiliation(s)
- Iago Lowe
- Department of Plant Sciences, University of California, Davis, One Shields Ave, Davis CA 95616, U.S.A
| | - Dario Cantu
- Department of Plant Sciences, University of California, Davis, One Shields Ave, Davis CA 95616, U.S.A
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, One Shields Ave, Davis CA 95616, U.S.A
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Lan C, Liang S, Zhou X, Zhou G, Lu Q, Xia X, He Z. Identification of genomic regions controlling adult-plant stripe rust resistance in Chinese landrace Pingyuan 50 through bulked segregant analysis. PHYTOPATHOLOGY 2010; 100:313-8. [PMID: 20205534 DOI: 10.1094/phyto-100-4-0313] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
ABSTRACT Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most widespread and destructive wheat diseases worldwide. Growing resistant cultivars with adult-plant resistance (APR) is an effective approach for the control of the disease. In this study, 540 simple sequence repeat markers were screened to map quantitative trait loci (QTL) for APR to stripe rust in a doubled haploid (DH) population of 137 lines derived from the cross Pingyuan 50 x Mingxian 169. The DH lines were planted in randomized complete blocks with three replicates in Gansu and Sichuan provinces during the 2005-06, 2006-07, and 2007-08 cropping seasons, providing data for four environments. Artificial inoculations were carried out in Gansu and Sichuan with the prevalent Chinese race CYR32. Broad-sense heritability of resistance to stripe rust for maximum disease severity was 0.91, based on the mean value averaged across four environments. Inclusive composite interval mapping detected three QTL for APR to stripe rust on chromosomes 2BS, 5AL, and 6BS, designated QYr.caas-2BS, QYr.caas-5AL, and QYr.caas-6BS, respectively, separately explaining from 4.5 to 19.9% of the phenotypic variation. QYr.caas-5AL, different from QTL previously reported, was flanked by microsatellite markers Xwmc410 and Xbarc261, and accounted for 5.0 to 19.9% of phenotypic variance. Molecular markers closely linked to the QTL could be used in marker-assisted selection for APR to stripe rust in wheat breeding programs.
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Affiliation(s)
- Caixia Lan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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33
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Carter AH, Chen XM, Garland-Campbell K, Kidwell KK. Identifying QTL for high-temperature adult-plant resistance to stripe rust (Puccinia striiformis f. sp. tritici) in the spring wheat (Triticum aestivum L.) cultivar 'Louise'. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:1119-28. [PMID: 19644666 DOI: 10.1007/s00122-009-1114-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Accepted: 07/12/2009] [Indexed: 05/06/2023]
Abstract
Over time, many single, all-stage resistance genes to stripe rust (Puccinia striiformis f. sp. tritici) in wheat (Triticum aestivum L.) are circumvented by race changes in the pathogen. In contrast, high-temperature, adult-plant resistance (HTAP), which only is expressed during the adult-plant stage and when air temperatures are warm, provides durable protection against stripe rust. Our objective was to identify major quantitative trait loci (QTL) for HTAP resistance to stripe rust in the spring wheat cultivar 'Louise'. The mapping population consisted of 188 recombinant inbred lines (RIL) from a Louise (resistant) by 'Penawawa' (susceptible) cross. F(5:6) lines were evaluated for stripe rust reaction under natural infection in replicated field trials at five locations in the US Pacific Northwest in 2007 and 2008. Infection type (IT) and disease severity were recorded for each RIL 2-4 times per location. In all environments, Penawawa, the susceptible parent, was rated with an IT ranging from 6 to 8 at all growth stages evaluated. In contrast, Louise, the resistant parent, was rated with an IT of 2 or 3 across growth stages. Distribution of IT values was bimodal, indicating a single major gene was affecting the trait. The parents and RIL population were evaluated with 295 polymorphic simple sequence repeat and one single nucleotide polymorphism markers. One major QTL, designated QYrlo.wpg-2BS, associated with HTAP resistance in Louise, was detected on chromosome 2BS (LOD scores ranging from 5.5 to 62.3 across locations and years) within a 16.9 cM region flanked by Xwmc474 and Xgwm148. SSR markers associated with QYrlo.wpg-2BS are currently being used in marker-based forward breeding strategies to transfer the target region into adapted germplasm to improve the durability of resistance in resulting cultivars.
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Affiliation(s)
- Arron Hyrum Carter
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
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34
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Fredua-Agyeman R, Adamski D, Liao RJ, Morden C, Borthakur D. Development and characterization of microsatellite markers for analysis of population differentiation in the tree legume Acacia koa (Fabaceae: Mimosoideae) in the Hawaiian Islands. Genome 2009; 51:1001-15. [PMID: 19088813 DOI: 10.1139/g08-087] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The aim of this research was to develop and use microsatellite markers to characterize the high-value timber tree Acacia koa (koa), which is endemic to the Hawaiian Islands. Genomic DNA fragments of 300-1000 bp were cloned and sequenced following enrichment for microsatellite motifs by PCR using 7 oligonucleotide repeat primers in separate reactions. Among 96 sequences analyzed, 63 contained unique microsatellite motifs flanked by variable sequences. A dual PCR method involving a primer walking step was used to develop 15 primer pairs. Another 16 primer pairs were developed directly from the variable sequences on both sides of the microsatellite motifs. These 31 primer pairs were tested on 172 koa plants representing 11 populations collected from 4 of the major Hawaiian Islands. Nine of the primers that identified polymorphic microsatellite loci and 3 that detected unique alleles exclusively in some populations were used for genetic diversity studies of koa. Cluster analysis and multidimensional scaling of the allelic phenotype data revealed that koa from Kauai formed a distinct group separate from koa of the neighboring islands of Oahu, Maui, and Hawaii. The oldest of the four islands, Kauai, also had the most diverse populations of koa.
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Affiliation(s)
- Rudolph Fredua-Agyeman
- Department of Molecular Biosciences & Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Agricultural Science 218, Honolulu, HI 96822, USA
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