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Schreiber M, Chen YY, Ramsay L, Waugh R. Measuring the frequency and distribution of meiotic crossovers in homozygous barley inbred lines. FRONTIERS IN PLANT SCIENCE 2022; 13:965217. [PMID: 36035701 PMCID: PMC9403744 DOI: 10.3389/fpls.2022.965217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
We report a novel approach for establishing the number and position of CO events in individual homozygous inbred plants by combining low level EMS mutagenesis, speed breeding, whole genome shotgun sequencing and sliding window analysis of the induced molecular variant data. We demonstrate the approach by exploring CO frequency and distribution in self-fertilised progeny of the inbred barley cultivar Bowman and compare these observations to similar data obtained from a Bowman nearly isogenic line (BW230 Hvmlh3) containing a mutation in the DNA mismatch repair gene HvMLH3. We have previously shown that Hvmlh3 decreases both plant fertility and recombination by ~50%. We compare our results to those from previously published traditional genetic analysis of F3 families derived from multiple F2 lines containing WT or mutant alleles of HvMLH3, revealing a high level of correspondence between analyses. We discuss possible applications of the approach in streamlining the assessment of recombination in plant meiosis research.
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Affiliation(s)
- Miriam Schreiber
- Informational and Computational Sciences, James Hutton Institute, Dundee, United Kingdom
| | - Yun-Yu Chen
- Cell and Molecular Sciences, James Hutton Institute, Dundee, United Kingdom
| | - Luke Ramsay
- Cell and Molecular Sciences, James Hutton Institute, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, James Hutton Institute, Dundee, United Kingdom
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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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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Schreiber M, Mascher M, Wright J, Padmarasu S, Himmelbach A, Heavens D, Milne L, Clavijo BJ, Stein N, Waugh R. A Genome Assembly of the Barley 'Transformation Reference' Cultivar Golden Promise. G3 (BETHESDA, MD.) 2020; 10:1823-1827. [PMID: 32241919 DOI: 10.1101/2020.02.12.945550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Barley (Hordeum vulgare) is one of the most important crops worldwide and is also considered a research model for the large-genome small grain temperate cereals. Despite genomic resources improving all the time, they are limited for the cv Golden Promise, the most efficient genotype for genetic transformation. We have developed a barley cv Golden Promise reference assembly integrating Illumina paired-end reads, long mate-pair reads, Dovetail Chicago in vitro proximity ligation libraries and chromosome conformation capture sequencing (Hi-C) libraries into a contiguous reference assembly. The assembled genome of 7 chromosomes and 4.13Gb in size, has a super-scaffold N50 after Chicago libraries of 4.14Mb and contains only 2.2% gaps. Using BUSCO (benchmarking universal single copy orthologous genes) as evaluation the genome assembly contains 95.2% of complete and single copy genes from the plant database. A high-quality Golden Promise reference assembly will be useful and utilized by the whole barley research community but will prove particularly useful for CRISPR-Cas9 experiments.
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Affiliation(s)
- Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Jonathan Wright
- Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK
| | - Sudharasan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Darren Heavens
- Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK
| | - Linda Milne
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
| | | | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- CiBreed - Center for Integrated Breeding Research, Georg-August University Göttingen, Department of Crop Sciences, Von Siebold Straße 8, 37075 Göttingen, Germany
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- School of Agriculture and Wine, University of Adelaide, Plant Genome Building, Waite Campus, Urrbrae, Adelaide, South Australia
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Schreiber M, Mascher M, Wright J, Padmarasu S, Himmelbach A, Heavens D, Milne L, Clavijo BJ, Stein N, Waugh R. A Genome Assembly of the Barley 'Transformation Reference' Cultivar Golden Promise. G3 (BETHESDA, MD.) 2020; 10:1823-1827. [PMID: 32241919 PMCID: PMC7263683 DOI: 10.1534/g3.119.401010] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/27/2020] [Indexed: 01/02/2023]
Abstract
Barley (Hordeum vulgare) is one of the most important crops worldwide and is also considered a research model for the large-genome small grain temperate cereals. Despite genomic resources improving all the time, they are limited for the cv Golden Promise, the most efficient genotype for genetic transformation. We have developed a barley cv Golden Promise reference assembly integrating Illumina paired-end reads, long mate-pair reads, Dovetail Chicago in vitro proximity ligation libraries and chromosome conformation capture sequencing (Hi-C) libraries into a contiguous reference assembly. The assembled genome of 7 chromosomes and 4.13Gb in size, has a super-scaffold N50 after Chicago libraries of 4.14Mb and contains only 2.2% gaps. Using BUSCO (benchmarking universal single copy orthologous genes) as evaluation the genome assembly contains 95.2% of complete and single copy genes from the plant database. A high-quality Golden Promise reference assembly will be useful and utilized by the whole barley research community but will prove particularly useful for CRISPR-Cas9 experiments.
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Affiliation(s)
- Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Jonathan Wright
- Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK
| | - Sudharasan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Darren Heavens
- Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK
| | - Linda Milne
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
| | | | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- CiBreed - Center for Integrated Breeding Research, Georg-August University Göttingen, Department of Crop Sciences, Von Siebold Straße 8, 37075 Göttingen, Germany
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, Scotland DD2 5DA, UK
- School of Agriculture and Wine, University of Adelaide, Plant Genome Building, Waite Campus, Urrbrae, Adelaide, South Australia
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Hoseinzadeh P, Ruge-Wehling B, Schweizer P, Stein N, Pidon H. High Resolution Mapping of a Hordeum bulbosum-Derived Powdery Mildew Resistance Locus in Barley Using Distinct Homologous Introgression Lines. FRONTIERS IN PLANT SCIENCE 2020; 11:225. [PMID: 32194602 PMCID: PMC7063055 DOI: 10.3389/fpls.2020.00225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/13/2020] [Indexed: 05/17/2023]
Abstract
Powdery mildew caused by Blumeria graminis f. sp. hordei (Bgh) is one of the main foliar diseases in barley (Hordeum vulgare L.; Hv). Naturally occurring resistance genes used in barley breeding are a cost effective and environmentally sustainable strategy to minimize the impact of pathogens, however, the primary gene pool of H. vulgare contains limited diversity owing to recent domestication bottlenecks. To ensure durable resistance against this pathogen, more genes are required that could be unraveled by investigation of secondary barley gene-pool. A large set of Hordeum bulbosum (Hb) introgression lines (ILs) harboring a diverse set of desirable resistance traits have been developed and are being routinely used as source of novel diversity in gene mapping studies. Nevertheless, this strategy is often compromised by a lack of recombination between the introgressed fragment and the orthologous chromosome of the barley genome. In this study, we fine-mapped a Hb gene conferring resistance to barley powdery mildew. The initial genotyping of two Hb ILs mapping populations with differently sized 2HS introgressions revealed severely reduced interspecific recombination in the region of the introgressed segment, preventing precise localization of the gene. To overcome this difficulty, we developed an alternative strategy, exploiting intraspecific recombination by crossing two Hv/Hb ILs with collinear Hb introgressions, one of which carries a powdery mildew resistance gene, while the other doesn't. The intraspecific recombination rate in the Hb-introgressed fragment of 2HS was approximately 20 times higher than it was in the initial simple ILs mapping populations. Using high-throughput genotyping-by-sequencing (GBS), we allocated the resistance gene to a 1.4 Mb interval, based on an estimate using the Hv genome as reference, in populations of only 103 and 146 individuals, respectively, similar to what is expected at this locus in barley. The most likely candidate resistance gene within this interval is part of the coiled-coil nucleotide-binding-site leucine-rich-repeat (CC-NBS-LLR) gene family, which is over-represented among genes conferring strong dominant resistance to pathogens. The reported strategy can be applied as a general strategic approach for identifying genes underlying traits of interest in crop wild relatives.
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Affiliation(s)
- Parastoo Hoseinzadeh
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Brigitte Ruge-Wehling
- Institute for Breeding Research on Agricultural Crops, Julius Kühn Institute (JKI), Sanitz, Germany
| | - Patrick Schweizer
- Pathogen-Stress Genomics, Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nils Stein
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Hélène Pidon
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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