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Lehnert H, Berner T, Lang D, Beier S, Stein N, Himmelbach A, Kilian B, Keilwagen J. Insights into breeding history, hotspot regions of selection, and untapped allelic diversity for bread wheat breeding. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:897-918. [PMID: 36073999 DOI: 10.1111/tpj.15952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Breeding has increasingly altered the genetics of crop plants since the domestication of their wild progenitors. It is postulated that the genetic diversity of elite wheat breeding pools is too narrow to cope with future challenges. In contrast, plant genetic resources (PGRs) of wheat stored in genebanks are valuable sources of unexploited genetic diversity. Therefore, to ensure breeding progress in the future, it is of prime importance to identify the useful allelic diversity available in PGRs and to transfer it into elite breeding pools. Here, a diverse collection consisting of modern winter wheat cultivars and genebank accessions was investigated based on reduced-representation genomic sequencing and an iSelect single nucleotide polymorphism (SNP) chip array. Analyses of these datasets provided detailed insights into population structure, levels of genetic diversity, sources of new allelic diversity, and genomic regions affected by breeding activities. We identified 57 regions representing genomic signatures of selection and 827 regions representing private alleles associated exclusively with genebank accessions. The presence of known functional wheat genes, quantitative trait loci, and large chromosomal modifications, i.e., introgressions from wheat wild relatives, provided initial evidence for putative traits associated within these identified regions. These findings were supported by the results of ontology enrichment analyses. The results reported here will stimulate further research and promote breeding in the future by allowing for the targeted introduction of novel allelic diversity into elite wheat breeding pools.
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Affiliation(s)
- Heike Lehnert
- Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, Germany
| | - Thomas Berner
- Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, Germany
| | - Daniel Lang
- PGSB, Helmholtz Center Munich, German Research Center for Environmental Health, Plant Genome and Systems Biology, Neuherberg, Germany
| | - Sebastian Beier
- Research Group Bioinformatics and Information Technology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nils Stein
- Research Group Genomics of Genetic Resources, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Center of integrated Breeding Research (CiBreed), Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Axel Himmelbach
- Research Group Genomics of Genetic Resources, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, Germany
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Postulation of Specific Disease Resistance Genes in Cereals: A Widely Used Method and Its Detailed Description. Pathogens 2022; 11:pathogens11030284. [PMID: 35335608 PMCID: PMC8954282 DOI: 10.3390/pathogens11030284] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 02/06/2023] Open
Abstract
Cultivation of resistant varieties is an environmentally friendly and inexpensive method of crop protection. Numerous alleles of specific disease resistance occur in cereals and other crops, and knowledge of their presence in individual varieties has wide utilization in research and practice. Postulation based on phenotyping host—pathogen interactions and the gene-for-gene model is a common way of identifying these genes. The same technique and design of tests are used for postulating virulence when pathogen populations are studied. Powdery mildews caused by different formae speciales of Blumeria graminis (Bg) are important cereal diseases. In this contribution, experimental methods are described that use a model organism Bg f. sp. hordei, which can be employed for other cereal mildews and possibly rusts. It includes illustrations and a summary of our long-term practical experience. It also critically evaluates the benefits of leaf segment tests compared with screening whole plants.
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Wu H, Kang Z, Li X, Li Y, Li Y, Wang S, Liu D. Identification of Wheat Leaf Rust Resistance Genes in Chinese Wheat Cultivars and the Improved Germplasms. PLANT DISEASE 2020; 104:2669-2680. [PMID: 32729796 DOI: 10.1094/pdis-12-19-2619-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Leaf rust is an important wheat disease that is a significant hindrance for wheat production in most areas of the world. Breeding resistant cultivars can effectively and economically control the disease. In the present study, a wheat collection consisting of 100 cultivars from China and 18 improved germplasms from global landrace donors together with 36 known single Lr gene lines were tested with 20 strains of Puccinia triticina Eriks. in the seedling stage to postulate the Lr gene in the cultivars and germplasms. In addition, 12 diagnostic molecular markers specific to 10 Lr genes were used to detect the presence of the Lr genes in the wheat collection. Resistance to leaf rust of these cultivars at the adult plant stage was tested in fields under natural infection during the 2016 to 2018 cropping seasons in Baoding, Hebei Province. The gene postulation combined with molecular marker detection showed that six Lr genes (Lr1, Lr26, Lr33, Lr34, Lr45, and Lr46) were identified in 44 wheat accessions, including 37 cultivars and seven improved germplasms. Among the 44 wheat accessions postulated with Lr genes, Lr1 was present in four accessions, Lr26 in 12 accessions, Lr33 in two accessions, Lr34 in 14 accessions, Lr45 in three accessions, and Lr46 in 16 accessions. In the collection of 118 cultivars/germplasms, 34 wheat lines displayed adult-plant resistance carrying Lr34, Lr46, and/or underdetermined genes. Therefore, a high level of leaf rust resistance can be achieved through the combination of all-stage resistance and adult-plant resistance genes together in wheat cultivars.
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Affiliation(s)
- Hui Wu
- College of Plant Protection, Hebei Agricultural University/Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, Hebei 071001, China
| | - Zhanhai Kang
- College of Plant Protection, Hebei Agricultural University/Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, Hebei 071001, China
| | - Xing Li
- College of Plant Protection, Hebei Agricultural University/Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, Hebei 071001, China
| | - Yanyan Li
- College of Plant Protection, Hebei Agricultural University/Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, Hebei 071001, China
| | - Yi Li
- College of Plant Protection, Hebei Agricultural University/Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, Hebei 071001, China
| | - Shuo Wang
- College of Plant Protection, Hebei Agricultural University/Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, Hebei 071001, China
| | - Daqun Liu
- College of Plant Protection, Hebei Agricultural University/Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, Hebei 071001, China
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Miedaner T, Akel W, Flath K, Jacobi A, Taylor M, Longin F, Würschum T. Molecular tracking of multiple disease resistance in a winter wheat diversity panel. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:419-431. [PMID: 31720693 DOI: 10.1007/s00122-019-03472-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 11/04/2019] [Indexed: 05/20/2023]
Abstract
About 10% of cultivars possessed superior resistance to four fungal diseases and association mapping for multiple disease resistance identified loci which are not detected by analyzing individual disease resistances. Multiple disease resistance (MDR) aims for cultivars that are resistant to more than one disease which is an important prerequisite for the registration of commercial cultivars. We analyzed a European winter wheat diversity panel of 158 old and new cultivars for four diseases by natural (powdery mildew) and artificial inoculation (yellow rust, stem rust, Fusarium head blight) observed on the same plot in a multilocation trial. Genotypic analyses were based on 21,543 genotype-by-sequencing markers. By association mapping, eight to 18 quantitative-trait loci (QTL) were detected for individual disease resistances, explaining in total 67-90% of the total genotypic variation. For MDR, nine QTL could be found explaining 62% of the total genotypic variation. Only three of them were also found as QTL for a single disease resistance illustrating that mapping of MDR-associated QTL can be regarded as a complementary approach. The high prediction ability obtained for MDR (> 0.9) implies that genomic prediction could be used in future, thereby eliminating the necessity to separately screen large numbers of lines in breeding programs for several diseases.
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Affiliation(s)
- Thomas Miedaner
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany.
| | - Wessam Akel
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany
- Strube Research GmbH & Co. KG, Hauptstraße 1, 38387, Söllingen, Germany
| | - Kerstin Flath
- Institute for Plant Protection in Field Crops and Grassland, Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Stahnsdorfer Damm 81, 14532, Kleinmachnow, Germany
| | - Andreas Jacobi
- Strube Research GmbH & Co. KG, Hauptstraße 1, 38387, Söllingen, Germany
| | - Mike Taylor
- LIMAGRAIN GMBH - Zuchtstation Rosenthal, Salder Str. 4, 31226, Peine, Germany
| | - Friedrich Longin
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany
| | - Tobias Würschum
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany
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Odilbekov F, Armoniené R, Koc A, Svensson J, Chawade A. GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage. Front Genet 2019; 10:1224. [PMID: 31850073 PMCID: PMC6901976 DOI: 10.3389/fgene.2019.01224] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 11/05/2019] [Indexed: 02/01/2023] Open
Abstract
Septoria tritici blotch (STB) disease caused by Zymoseptoria tritici is one of the most damaging diseases of wheat causing significant yield losses worldwide. Identification and employment of resistant germplasm is the most cost-effective method to control STB. In this study, we characterized seedling stage resistance to STB in 175 winter wheat landraces and old cultivars of Nordic origin. The study revealed significant (p < 0.05) phenotypic differences in STB severity in the germplasm. Genome-wide association analysis (GWAS) using five different algorithms identified ten significant markers on five chromosomes. Six markers were localized within a region of 2 cM that contained seven candidate genes on chromosome 1B. Genomic prediction (GP) analysis resulted in a model with an accuracy of 0.47. To further improve the prediction efficiency, significant markers identified by GWAS were included as fixed effects in the GP model. Depending on the number of fixed effect markers, the prediction accuracy improved from 0.47 (without fixed effects) to 0.62 (all non-redundant GWAS markers as fixed effects), respectively. The resistant genotypes and single-nucleotide polymorphism (SNP) markers identified in the present study will serve as a valuable resource for future breeding for STB resistance in wheat. The results also highlight the benefits of integrating GWAS with GP to further improve the accuracy of GP.
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Affiliation(s)
- Firuz Odilbekov
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Rita Armoniené
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.,Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry (LAMMC), Akademija, Lithuania
| | - Alexander Koc
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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