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Ijaz U, Zhao C, Shahbala S, Zhou M. Genome-Wide Association Study for Identification of Marker-Trait Associations Conferring Resistance to Scald from Globally Collected Barley Germplasm. PHYTOPATHOLOGY 2024; 114:1637-1645. [PMID: 38451589 DOI: 10.1094/phyto-01-24-0043-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Scald is one of the major economically important foliar diseases in barley, causing up to 40% yield loss in susceptible varieties. The identification of quantitative trait loci and elite alleles that confer resistance to scald is imperative in reducing the threats to barley production. In this study, genome-wide association studies were conducted using a panel of 697 barley genotypes to identify quantitative trait loci for scald resistance. Field experiments were conducted over three consecutive years. Among different models used for genome-wide association studies analysis, FarmCPU was shown to be the best-suited model. Nineteen significant marker-trait associations related to scald resistance were identified across six different chromosomes. Eleven of these marker-trait associations correspond to previously reported scald resistance genes Rrs1, Rrs4, and Rrs2, respectively. Eight novel marker-trait associations were identified in this study, with the candidate genes encoding a diverse class of proteins, including region leucine-rich repeats, AP2/ERF transcription factor, homeodomain-leucine zipper, and protein kinase family proteins. The combination of identified superior alleles significantly reduces disease severity scores. The results will be valuable for marker-assisted breeding for developing scald-resistant varieties.
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Affiliation(s)
- Usman Ijaz
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia
| | - Sergey Shahbala
- School of Biological Science, University of Western Australia, Crawley, WA 6009, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia
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Ijaz U, Zhao C, Shabala S, Zhou M. Molecular Basis of Plant-Pathogen Interactions in the Agricultural Context. BIOLOGY 2024; 13:421. [PMID: 38927301 PMCID: PMC11200688 DOI: 10.3390/biology13060421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
Biotic stressors pose significant threats to crop yield, jeopardizing food security and resulting in losses of over USD 220 billion per year by the agriculture industry. Plants activate innate defense mechanisms upon pathogen perception and invasion. The plant immune response comprises numerous concerted steps, including the recognition of invading pathogens, signal transduction, and activation of defensive pathways. However, pathogens have evolved various structures to evade plant immunity. Given these facts, genetic improvements to plants are required for sustainable disease management to ensure global food security. Advanced genetic technologies have offered new opportunities to revolutionize and boost plant disease resistance against devastating pathogens. Furthermore, targeting susceptibility (S) genes, such as OsERF922 and BnWRKY70, through CRISPR methodologies offers novel avenues for disrupting the molecular compatibility of pathogens and for introducing durable resistance against them in plants. Here, we provide a critical overview of advances in understanding disease resistance mechanisms. The review also critically examines management strategies under challenging environmental conditions and R-gene-based plant genome-engineering systems intending to enhance plant responses against emerging pathogens. This work underscores the transformative potential of modern genetic engineering practices in revolutionizing plant health and crop disease management while emphasizing the importance of responsible application to ensure sustainable and resilient agricultural systems.
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Affiliation(s)
- Usman Ijaz
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (U.I.); (C.Z.)
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (U.I.); (C.Z.)
| | - Sergey Shabala
- School of Biological Science, University of Western Australia, Crawley, WA 6009, Australia;
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (U.I.); (C.Z.)
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Ababa G, Kesho A, Tadesse Y, Amare D. Reviews of taxonomy, epidemiology, and management practices of the barley scald ( Rhynchosporium graminicola) disease. Heliyon 2023; 9:e14315. [PMID: 36938428 PMCID: PMC10018571 DOI: 10.1016/j.heliyon.2023.e14315] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023] Open
Abstract
Barley scald is very important in temperate and wet regions worldwide and has become one of the most important foliar diseases. Before the development of recent technologies, several scientists had argued that Rhynchosporium secalis is the causal agent of scald disease. However, the causal agent of this disease was revised and recognized as Rhynchosporium commune. Again recently, Rhynchosporium graminicola was suggested to be replaced as the causal agent of R. commune. The disease outbreak is depending on cool and frequent rainfall. Because of scald disease significance, numerous management practices have been advocated. Then, resistance materials, and mixing of resistant and susceptible cultivars have been used as the best management methods. Several studies have demonstrated that some cultivars and landraces of barley are resistant to scald disease during the seedling and adult growth stages. The first cultivar is "Atlas 46″ which was created from the cultivar "Turk". From biological method: Bacillus polymyxa, Paenibacillus polymyxa KaI245, and Bacillus subtilis are very effective in treating this disease. Finally, as a last option, different fungicides have been suggested. Pathogenicity testing, seed treatments, tillage, cultivar mixtures, and biological control are all commonly overlooked in developing countries. Cultural practices such as times of fungicide application, appropriate time of sowing to scape disease, and tillage practices which are adopted for other diseases are greatly missed for scald disease. Then, we are intended to assess the various findings available on barley scald biology, taxonomy, and management.
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Hautsalo J, Novakazi F, Jalli M, Göransson M, Manninen O, Isolahti M, Reitan L, Bergersen S, Krusell L, Damsgård Robertsen C, Orabi J, Due Jensen J, Jahoor A, Bengtsson T. Pyramiding of scald resistance genes in four spring barley MAGIC populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3829-3843. [PMID: 34350474 PMCID: PMC8580920 DOI: 10.1007/s00122-021-03930-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Genome-Wide Association Studies (GWAS) of four Multi-parent Advanced Generation Inter-Cross (MAGIC) populations identified nine regions on chromosomes 1H, 3H, 4H, 5H, 6H and 7H associated with resistance against barley scald disease. Three of these regions are putatively novel resistance Quantitative Trait Loci (QTL). Barley scald is caused by Rhynchosporium commune, one of the most important barley leaf diseases that are prevalent in most barley-growing regions. Up to 40% yield losses can occur in susceptible barley cultivars. Four MAGIC populations were generated in a Nordic Public-Private Pre-breeding of spring barley project (PPP Barley) to introduce resistance to several important diseases. Here, these MAGIC populations consisting of six to eight founders each were tested for scald resistance in field trials in Finland and Iceland. Eight different model covariate combinations were compared for GWAS studies, and the models that deviated the least from the expected p-values were selected. For all QTL, candidate genes were identified that are predicted to be involved in pathogen defence. The MAGIC progenies contained new haplotypes of significant SNP-markers with high resistance levels. The lines with successfully pyramided resistance against scald and mildew and the significant markers are now distributed among Nordic plant breeders and will benefit development of disease-resistant cultivars.
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Affiliation(s)
- Juho Hautsalo
- Natural Resources Institute Finland (Luke), Survontie 9, 40500, Jyväskylä, Finland
| | - Fluturë Novakazi
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, 234 22, Lomma, Sweden
| | - Marja Jalli
- Natural Resources Institute Finland (Luke), Tietotie 4, 31600, Jokioinen, Finland
| | - Magnus Göransson
- Faculty of Land and Animal Resources, The Agricultural University of Iceland, Hvanneyri, 311, Borgarnes, Iceland
| | - Outi Manninen
- Boreal Plant Breeding Ltd., Myllytie 10, 31600, Jokioinen, Norway
| | - Mika Isolahti
- Boreal Plant Breeding Ltd., Myllytie 10, 31600, Jokioinen, Norway
| | - Lars Reitan
- Graminor Ltd. Hommelstadvegen 60, 2322, Ridabu, Norway
| | | | - Lene Krusell
- Sejet Plant Breeding, Nørremarksvej 67, 8700, Horsens, Norway
| | | | - Jihad Orabi
- Nordic Seed A/S, Kornmarken 1, 8464, Galten, Denmark
| | | | - Ahmed Jahoor
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, 234 22, Lomma, Sweden
- Nordic Seed A/S, Kornmarken 1, 8464, Galten, Denmark
| | - Therése Bengtsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, 234 22, Lomma, Sweden.
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Büttner B, Draba V, Pillen K, Schweizer G, Maurer A. Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25. BMC Genomics 2020; 21:837. [PMID: 33246416 PMCID: PMC7694317 DOI: 10.1186/s12864-020-07258-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Barley scald, caused by the fungus Rhynchosporium commune, is distributed worldwide to all barley growing areas especially in cool and humid climates. Scald is an economically important leaf disease resulting in yield losses of up to 40%. To breed resistant cultivars the identification of quantitative trait loci (QTLs) conferring resistance to scald is necessary. Introgressing promising resistance alleles of wild barley is a way to broaden the genetic basis of scald resistance in cultivated barley. Here, we apply nested association mapping (NAM) to map resistance QTLs in the barley NAM population HEB-25, comprising 1420 lines in BC1S3 generation, derived from crosses of 25 wild barley accessions with cv. Barke. RESULTS In scald infection trials in the greenhouse variability of resistance across and within HEB-25 families was found. NAM based on 33,005 informative SNPs resulted in the identification of eight reliable QTLs for resistance against scald with most wild alleles increasing resistance as compared to cv. Barke. Three of them are located in the region of known resistance genes and two in the regions of QTLs, respectively. The most promising wild allele was found at Rrs17 in one specific wild donor. Also, novel QTLs with beneficial wild allele effects on scald resistance were detected. CONCLUSIONS To sum up, wild barley represents a rich resource for scald resistance. As the QTLs were linked to the physical map the identified candidate genes will facilitate cloning of the scald resistance genes. The closely linked flanking molecular markers can be used for marker-assisted selection of the respective resistance genes to integrate them in elite cultivars.
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Affiliation(s)
- Bianca Büttner
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Freising, Germany
| | - Vera Draba
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Halle, Germany
| | - Klaus Pillen
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Halle, Germany
| | - Günther Schweizer
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Freising, Germany
| | - Andreas Maurer
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Halle, Germany.
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Zhang X, Ovenden B, Milgate A. Recent insights into barley and Rhynchosporium commune interactions. MOLECULAR PLANT PATHOLOGY 2020; 21:1111-1128. [PMID: 32537933 PMCID: PMC7368125 DOI: 10.1111/mpp.12945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/18/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
Rhynchosporium commune is the causal pathogen of scald in barley (Hordeum vulgare), a foliar disease that can reduce yield by up to 40% in susceptible cultivars. R. commune is found worldwide in all temperate growing regions and is regarded as one of the most economically important barley pathogens. It is a polycyclic pathogen with the ability to rapidly evolve new virulent strains in response to resistance genes deployed in commercial cultivars. Hence, introgression and pyramiding of different loci for resistance (qualitative or quantitative) through marker-assisted selection is an effective way to improve scald resistance in barley. This review summarizes all 148 resistance quantitative trait loci reported at the date of submission of this review and projects them onto the barley physical map, where it is clear many loci co-locate on chromosomes 3H and 7H. We have summarized the major named resistance loci and reiterated the renaming of Rrs15 (CI8288) to Rrs17. This review provides a comprehensive resource for future discovery and breeding efforts of qualitative and quantitative scald resistance loci.
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Affiliation(s)
- Xuechen Zhang
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNSWAustralia
| | - Ben Ovenden
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNSWAustralia
| | - Andrew Milgate
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNSWAustralia
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Wang Y, Xu Y, Gupta S, Zhou Y, Wallwork H, Zhou G, Broughton S, Zhang XQ, Tan C, Westcott S, Moody D, Sun D, Loughman R, Zhang W, Li C. Fine mapping QSc.VR4, an effective and stable scald resistance locus in barley (Hordeum vulgare L.), to a 0.38-Mb region enriched with LRR-RLK and GLP genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2307-2321. [PMID: 32405768 DOI: 10.1007/s00122-020-03599-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 05/01/2020] [Indexed: 06/11/2023]
Abstract
An effective and stable quantitative resistance locus, QSc.VR4, was fine mapped, characterized and physically anchored to the short arm of 4H, conferring adult plant resistance to the fungus Rhynchosporium commune in barley. Scald caused by Rhynchosporium commune is one of the most destructive barley diseases worldwide. Accumulation of adult plant resistance (APR) governed by multiple resistance alleles is predicted to be effective and long-lasting against a broad spectrum of pathotypes. However, the molecular mechanisms that control APR remain poorly understood. Here, quantitative trait loci (QTL) analysis of APR and fine mapping were performed on five barley populations derived from a common parent Vlamingh, which expresses APR to scald. Two QTLs, designated QSc.VR4 and QSc.BR7, were detected from a cross between Vlamingh and Buloke. Our data confirmed that QSc.VR4 is an effective and stable APR locus, residing on the short arm of chromosome 4H, and QSc.BR7 derived from Buloke may be an allele of reported Rrs2. High-resolution fine mapping revealed that QSc.VR4 is located in a 0.38 Mb genomic region between InDel markers 4H2282169 and 4H2665106. The gene annotation analysis and sequence comparison suggested that a gene cluster containing two adjacent multigene families encoding leucine-rich repeat receptor kinase-like proteins (LRR-RLKs) and germin-like proteins (GLPs), respectively, is likely contributing to scald resistance. Adult plant resistance (APR) governed by QSc.VR4 may confer partial levels of resistance to the fungus Rhynchosporium commune and, furthermore, be an important resource for gene pyramiding that may contribute broad-based and more durable resistance.
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Affiliation(s)
- Yonggang Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Yanhao Xu
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, China
| | - Sanjiv Gupta
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Yi Zhou
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, China
| | - Hugh Wallwork
- South Australian Research and Development Institute, Hartley Grove, Urrbrae, SA, Australia
| | - Gaofeng Zhou
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Sue Broughton
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Cong Tan
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Sharon Westcott
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - David Moody
- InterGrain Pty Ltd, South Perth, WA, Australia
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, China
| | - Robert Loughman
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Wenying Zhang
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, China.
| | - Chengdao Li
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia.
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, China.
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia.
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Looseley ME, Griffe LL, Büttner B, Wright KM, Bayer MM, Coulter M, Thauvin JN, Middlefell-Williams J, Maluk M, Okpo A, Kettles N, Werner P, Byrne E, Avrova A. Characterisation of barley landraces from Syria and Jordan for resistance to rhynchosporium and identification of diagnostic markers for Rrs1 Rh4. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1243-1264. [PMID: 31965232 DOI: 10.1007/s00122-020-03545-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 01/13/2020] [Indexed: 06/10/2023]
Abstract
Diagnostic markers for Rrs1Rh4 have been identified by testing for associations between SNPs within the Rrs1 interval in 150 barley genotypes and their resistance to Rhynchosporium commune isolates recognised by lines containing Rrs1. Rhynchosporium or barley scald, caused by the destructive fungal pathogen Rhynchosporium commune, is one of the most economically important diseases of barley in the world. Barley landraces from Syria and Jordan demonstrated high resistance to rhynchosporium in the field. Genotyping of a wide range of barley cultivars and landraces, including known sources of different Rrs1 genes/alleles, across the Rrs1 interval, followed by association analysis of this genotypic data with resistance phenotypes to R. commune isolates recognised by Rrs1, allowed the identification of diagnostic markers for Rrs1Rh4. These markers are specific to Rrs1Rh4 and do not detect other Rrs1 genes/alleles. The Rrs1Rh4 diagnostic markers represent a resource that can be exploited by breeders for the sustainable deployment of varietal resistance in new cultivars. Thirteen out of the 55 most resistant Syrian and Jordanian landraces were shown to contain markers specific to Rrs1Rh4. One of these lines came from Jordan, with the remaining 12 lines from different locations in Syria. One of the Syrian landraces containing Rrs1Rh4 was also shown to have Rrs2. The remaining landraces that performed well against rhynchosporium in the field are likely to contain other resistance genes and represent an important novel resource yet to be exploited by European breeders.
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Affiliation(s)
- Mark E Looseley
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Lucie L Griffe
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- RAGT Seeds Ltd, Grange Road, Ickleton, Saffron Walden, Essex, CB10 1TA, UK
| | - Bianca Büttner
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 2, 85354, Freising, Germany
| | - Kathryn M Wright
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Micha M Bayer
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Max Coulter
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Jean-Noël Thauvin
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | | | - Marta Maluk
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Aleksandra Okpo
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | | | - Peter Werner
- KWS UK Limited, Thriplow, Royston, Herts, SG8 7RE, UK
| | - Ed Byrne
- KWS UK Limited, Thriplow, Royston, Herts, SG8 7RE, UK
| | - Anna Avrova
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK.
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Bivariate analysis of barley scald resistance with relative maturity reveals a new major QTL on chromosome 3H. Sci Rep 2019; 9:20263. [PMID: 31889102 PMCID: PMC6937342 DOI: 10.1038/s41598-019-56742-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/13/2019] [Indexed: 12/02/2022] Open
Abstract
The disease scald of barley is caused by the pathogen Rhynchosporium commune and can cause up to 30–40% yield loss in susceptible cultivars. In this study, the Australian barley cultivar ‘Yerong’ was demonstrated to have resistance that differed from Turk (Rrs1 (Rh3 type)) based on seedling tests with 11 R. commune isolates. A doubled haploid population with 177 lines derived from a cross between ‘Yerong’ and the susceptible Australian cultivar ‘Franklin’ was used to identify quantitative trait loci (QTL) for scald resistance. A QTL on chromosome 3H was identified with large effect, consistent with a major gene conferring scald resistance at the seedling stage. Under field conditions, a bivariate analysis was used to model scald percentage of infected leaf area and relative maturity, the residuals from the regression were used as our phenotype for QTL analysis. This analysis identified one major QTL on chromosome 3H, which mapped to the same position as the QTL at seedling stage. The identified QTL on 3H is proposed to be different from the Rrs1 on the basis of seedling resistance against different R. commune isolates and physical map position. This study increases the current understanding of scald resistance and identifies genetic material possessing QTLs useful for the marker-assisted selection of scald resistance in barley breeding programs.
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10
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Daba SD, Horsley R, Brueggeman R, Chao S, Mohammadi M. Genome-wide Association Studies and Candidate Gene Identification for Leaf Scald and Net Blotch in Barley ( Hordeum vulgare L.). PLANT DISEASE 2019; 103:880-889. [PMID: 30806577 DOI: 10.1094/pdis-07-18-1190-re] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We report genomic regions that significantly control resistance to scald, net form (NFNB) and spot form net blotch (SFNB) in barley. Barley genotypes from Ethiopia, ICARDA, and the United States were evaluated in Ethiopia and North Dakota State University (NDSU). Genome-wide association studies (GWAS) were conducted using 23,549 single nucleotide polymorphism (SNP) markers for disease resistance in five environments in Ethiopia. For NFNB and SFNB, we assessed seedling resistance in a glasshouse at NDSU. A large proportion of the Ethiopian landraces and breeding genotypes were resistant to scald and NFNB. Most of genotypes resistant to SFNB were from NDSU. We identified 17, 26, 7, and 1 marker-trait associations (MTAs) for field-scored scald, field-scored net blotch, greenhouse-scored NFNB, and greenhouse-scored SFNB diseases, respectively. Using the genome sequence and the existing literature, we compared the MTAs with previously reported loci and genes for these diseases. For leaf scald, only a few of our MTAs overlap with previous reports. However, the MTAs found for field-scored net blotch as well as NFNB and SFNB mostly overlap with previous reports. We scanned the barley genome for identification of candidate genes within 250 kb of the MTAs, resulting in the identification of 307 barley genes for the 51 MTAs. Some of these genes are related to plant defense responses such as subtilisin-like protease, chalcone synthase, lipoxygenase, and defensin-like proteins.
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Affiliation(s)
- Sintayehu D Daba
- 1 Purdue University, Department of Agronomy, West Lafayette, IN 47907-2053
| | - Richard Horsley
- 2 North Dakota State University, Department of Plant Sciences, Fargo, ND 58108-6050
| | - Robert Brueggeman
- 3 North Dakota State University, Department of Plant Pathology, Fargo, ND 58102-2765; and
| | | | - Mohsen Mohammadi
- 1 Purdue University, Department of Agronomy, West Lafayette, IN 47907-2053
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11
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Coulter M, Büttner B, Hofmann K, Bayer M, Ramsay L, Schweizer G, Waugh R, Looseley ME, Avrova A. Characterisation of barley resistance to rhynchosporium on chromosome 6HS. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1089-1107. [PMID: 30547184 DOI: 10.1007/s00122-018-3262-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/07/2018] [Indexed: 06/09/2023]
Abstract
Major resistance gene to rhynchosporium, Rrs18, maps close to the telomere on the short arm of chromosome 6H in barley. Rhynchosporium or barley scald caused by a fungal pathogen Rhynchosporium commune is one of the most destructive and economically important diseases of barley in the world. Testing of Steptoe × Morex and CIho 3515 × Alexis doubled haploid populations has revealed a large effect QTL for resistance to R. commune close to the telomere on the short arm of chromosome 6H, present in both populations. Mapping markers flanking the QTL from both populations onto the 2017 Morex genome assembly revealed a rhynchosporium resistance locus independent of Rrs13 that we named Rrs18. The causal gene was fine mapped to an interval of 660 Kb using Steptoe × Morex backcross 1 S2 and S3 lines with molecular markers developed from Steptoe exome capture variant calling. Sequencing RNA from CIho 3515 and Alexis revealed that only 4 genes within the Rrs18 interval were transcribed in leaf tissue with a serine/threonine protein kinase being the most likely candidate for Rrs18.
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Affiliation(s)
- Max Coulter
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Bianca Büttner
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture, Am Gereuth 2, 85354, Freising, Germany
| | - Kerstin Hofmann
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture, Am Gereuth 2, 85354, Freising, Germany
| | - Micha Bayer
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Luke Ramsay
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Günther Schweizer
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture, Am Gereuth 2, 85354, Freising, Germany
| | - Robbie Waugh
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Mark E Looseley
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Anna Avrova
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK.
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12
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Looseley ME, Griffe LL, Büttner B, Wright KM, Middlefell-Williams J, Bull H, Shaw PD, Macaulay M, Booth A, Schweizer G, Russell JR, Waugh R, Thomas WTB, Avrova A. Resistance to Rhynchosporium commune in a collection of European spring barley germplasm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2513-2528. [PMID: 30151748 DOI: 10.1007/s00122-018-3168-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/17/2018] [Indexed: 05/02/2023]
Abstract
Association analyses of resistance to Rhynchosporium commune in a collection of European spring barley germplasm detected 17 significant resistance quantitative trait loci. The most significant association was confirmed as Rrs1. Rhynchosporium commune is a fungal pathogen of barley which causes a highly destructive and economically important disease known as rhynchosporium. Genome-wide association mapping was used to investigate the genetic control of host resistance to R. commune in a collection of predominantly European spring barley accessions. Multi-year disease nursery field trials revealed 8 significant resistance quantitative trait loci (QTL), whilst a separate association mapping analysis using historical data from UK national and recommended list trials identified 9 significant associations. The most significant association identified in both current and historical data sources, collocated with the known position of the major resistance gene Rrs1. Seedling assays with R. commune single-spore isolates expressing the corresponding avirulence protein NIP1 confirmed that this locus is Rrs1. These results highlight the significant and continuing contribution of Rrs1 to host resistance in current elite spring barley germplasm. Varietal height was shown to be negatively correlated with disease severity, and a resistance QTL was identified that co-localised with the semi-dwarfing gene sdw1, previously shown to contribute to disease escape. The remaining QTL represent novel resistances that are present within European spring barley accessions. Associated markers to Rrs1 and other resistance loci, identified in this study, represent a set of tools that can be exploited by breeders for the sustainable deployment of varietal resistance in new cultivars.
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Affiliation(s)
- Mark E Looseley
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK.
| | - Lucie L Griffe
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- RAGT Seeds Ltd, Grange Road, Ickleton, Saffron Walden, Essex, CB10 1TA, UK
| | - Bianca Büttner
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 2, 85354, Freising, Germany
| | - Kathryn M Wright
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | | | - Hazel Bull
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- Syngenta UK Ltd, Market Stainton, Market Rasen, Lincolnshire, LN8 5LJ, UK
| | - Paul D Shaw
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Malcolm Macaulay
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Allan Booth
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Günther Schweizer
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 2, 85354, Freising, Germany
| | - Joanne R Russell
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Robbie Waugh
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | | | - Anna Avrova
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
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13
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Marzin S, Hanemann A, Sharma S, Hensel G, Kumlehn J, Schweizer G, Röder MS. Are PECTIN ESTERASE INHIBITOR Genes Involved in Mediating Resistance to Rhynchosporium commune in Barley? PLoS One 2016; 11:e0150485. [PMID: 26937960 PMCID: PMC4777559 DOI: 10.1371/journal.pone.0150485] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/15/2016] [Indexed: 11/25/2022] Open
Abstract
A family of putative PECTIN ESTERASE INHIBITOR (PEI) genes, which were detected in the genomic region co-segregating with the resistance gene Rrs2 against scald caused by Rhynchosporium commune in barley, were characterized and tested for their possible involvement in mediating resistance to the pathogen by complementation and overexpression analysis. The sequences of the respective genes were derived from two BAC contigs originating from the susceptible cultivar ‘Morex’. For the genes HvPEI2, HvPEI3, HvPEI4 and HvPEI6, specific haplotypes for 18 resistant and 23 susceptible cultivars were detected after PCR-amplification and haplotype-specific CAPS-markers were developed. None of the tested candidate genes HvPEI2, HvPEI3 and HvPEI4 alone conferred a high resistance level in transgenic over-expression plants, though an improvement of the resistance level was observed especially with OE-lines for gene HvPEI4. These results do not confirm but also do not exclude an involvement of the PEI gene family in the response to the pathogen. A candidate for the resistance gene Rrs2 could not be identified yet. It is possible that Rrs2 is a PEI gene or another type of gene which has not been detected in the susceptible cultivar ‘Morex’ or the full resistance reaction requires the presence of several PEI genes.
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Affiliation(s)
- Stephan Marzin
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Anja Hanemann
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Shailendra Sharma
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | | | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- * E-mail:
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14
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Schmidt M, Kollers S, Maasberg-Prelle A, Großer J, Schinkel B, Tomerius A, Graner A, Korzun V. Prediction of malting quality traits in barley based on genome-wide marker data to assess the potential of genomic selection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:203-13. [PMID: 26649866 DOI: 10.1007/s00122-015-2639-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/11/2015] [Indexed: 05/02/2023]
Abstract
KEY MESSAGE Genomic prediction of malting quality traits in barley shows the potential of applying genomic selection to improve selection for malting quality and speed up the breeding process. ABSTRACT Genomic selection has been applied to various plant species, mostly for yield or yield-related traits such as grain dry matter yield or thousand kernel weight, and improvement of resistances against diseases. Quality traits have not been the main scope of analysis for genomic selection, but have rather been addressed by marker-assisted selection. In this study, the potential to apply genomic selection to twelve malting quality traits in two commercial breeding programs of spring and winter barley (Hordeum vulgare L.) was assessed. Phenotypic means were calculated combining multilocational field trial data from 3 or 4 years, depending on the trait investigated. Three to five locations were available in each of these years. Heritabilities for malting traits ranged between 0.50 and 0.98. Predictive abilities (PA), as derived from cross validation, ranged between 0.14 to 0.58 for spring barley and 0.40-0.80 for winter barley. Small training sets were shown to be sufficient to obtain useful PAs, possibly due to the narrow genetic base in this breeding material. Deployment of genomic selection in malting barley breeding clearly has the potential to reduce cost intensive phenotyping for quality traits, increase selection intensity and to shorten breeding cycles.
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Affiliation(s)
- Malthe Schmidt
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Straße 5, 29303, Bergen, Germany
| | - Sonja Kollers
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Straße 5, 29303, Bergen, Germany
| | | | - Jörg Großer
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Straße 5, 29303, Bergen, Germany
| | - Burkhard Schinkel
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Straße 5, 29303, Bergen, Germany
| | - Alexandra Tomerius
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Straße 5, 29303, Bergen, Germany
- AIB Dr. Alexandra Tomerius, Saffeweg 32, 38304, Wolfenbüttel, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany
| | - Viktor Korzun
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Straße 5, 29303, Bergen, Germany.
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15
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Shavrukov Y. Comparison of SNP and CAPS markers application in genetic research in wheat and barley. BMC PLANT BIOLOGY 2016; 16 Suppl 1:11. [PMID: 26821936 PMCID: PMC4895257 DOI: 10.1186/s12870-015-0689-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
BACKGROUND Barley and bread wheat show large differences in frequencies of Single Nucleotide Polymorphism (SNP) as determined from genome-wide studies. These frequencies have been estimated as 2.4-3 times higher in the entire barley genome than within each diploid genomes of wheat (A, B or D). However, barley SNPs within individual genes occur significantly more frequently than quoted. Differences between wheat and barley are based on the origin and evolutionary history of the species. Bread wheat contains rarer SNPs due to the double genetic 'bottle-neck' created by natural hybridisation and spontaneous polyploidisation. Furthermore, wheat has the lowest level of useful SNP-derived markers while barley is estimated to have the highest level of polymorphism. RESULTS Different strategies are required for the development of suitable molecular markers in these cereal species. For example, SNP markers based on high-throughput technology (Infinium or KASP) are very effective and useful in both barley and bread wheat. In contrast, Cleaved Amplified Polymorphic Sequences (CAPS) are more widely and successfully employed in small-scale experiments with highly polymorphic genetic regions containing multiple SNPs in barley, but not in wheat. However, preliminary 'in silico' search databases for assessing the potential value of SNPs have yet to be developed. CONCLUSIONS This mini-review summarises results supporting the development of different strategies for the application of effective SNP and CAPS markers in wheat and barley.
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Affiliation(s)
- Yuri Shavrukov
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia.
- Department of Biological Sciences, Flinders University, Adelaide, Australia.
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Loscos J, Igartua E, Contreras-Moreira B, Gracia MP, Casas AM. HvFT1 polymorphism and effect-survey of barley germplasm and expression analysis. FRONTIERS IN PLANT SCIENCE 2014; 5:251. [PMID: 24936204 PMCID: PMC4047512 DOI: 10.3389/fpls.2014.00251] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/16/2014] [Indexed: 05/05/2023]
Abstract
Flowering time in plants is a tightly regulated process. In barley (Hordeum vulgare L.), HvFT1, ortholog of FLOWERING LOCUS T, is the main integrator of the photoperiod and vernalization signals leading to the transition from vegetative to reproductive state of the plant. This gene presents sequence polymorphisms affecting flowering time in the first intron and in the promoter. Recently, copy number variation (CNV) has been described for this gene. An allele with more than one copy was linked to higher gene expression, earlier flowering, and an overriding effect of the vernalization mechanism. This study aims at (1) surveying the distribution of HvFT1 polymorphisms across barley germplasm and (2) assessing gene expression and phenotypic effects of HvFT1 alleles. We analyzed HvFT1 CNV in 109 winter, spring, and facultative barley lines. There was more than one copy of the gene (2-5) only in spring or facultative barleys without a functional vernalization VrnH2 allele. CNV was investigated in several regions inside and around HvFT1. Two models of the gene were found: one with the same number of promoters and transcribed regions, and another with one promoter and variable number of transcribed regions. This last model was found in Nordic barleys only. Analysis of HvFT1 expression showed that association between known polymorphisms at the HvFT1 locus and the expression of the gene was highly dependent on the genetic background. Under long day conditions the earliest flowering lines carried a sensitive PpdH1 allele. Among spring cultivars with different number of copies, no clear relation was found between CNV, gene expression and flowering time. This was confirmed in a set of doubled haploid lines of a population segregating for HvFT1 CNV. Earlier flowering in the presence of several copies of HvFT1 was only seen in cultivar Tammi, which carries one promoter, suggesting a relation of gene structure with its regulation. HvCEN also affected to a large extent flowering time.
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Affiliation(s)
- Jorge Loscos
- Department of Genetics and Plant Production, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
| | - Ernesto Igartua
- Department of Genetics and Plant Production, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
| | - Bruno Contreras-Moreira
- Department of Genetics and Plant Production, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
- Fundación ARAIDZaragoza, Spain
| | - M. Pilar Gracia
- Department of Genetics and Plant Production, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
| | - Ana M. Casas
- Department of Genetics and Plant Production, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones CientíficasZaragoza, Spain
- *Correspondence: Ana M. Casas, Department of Genetics and Plant Production, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Avda. Montañana 1005, 50059 Zaragoza, Spain e-mail:
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