Whole-genome resequencing of the wild barley diversity collection: a resource for identifying and exploiting genetic variation for cultivated barley improvement

To exploit allelic variation in Hordeum vulgare subsp. spontaneum, the Wild Barley Diversity Collection was subjected to paired-end Illumina sequencing at ∼9 × depth and evaluated for several agronomic traits. We discovered 240.2 million single nucleotide polymorphisms (SNPs) after alignment to the Morex V3 assembly and 24.4 million short (1 to 50 bp) insertions and deletions. A genome-wide association study of lemma color identified one marker-trait association (MTA) on chromosome 1H close to HvBlp, the cloned gene controlling black lemma. Four MTAs were identified for seedling stem rust resistance, including 2 novel loci on chromosomes 1H and 6H and one co-locating to the complex RMRL1-RMRL2 locus on 5H. The whole-genome sequence data described herein will facilitate the identification and utilization of new alleles for barley improvement.

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Journal
G3 Genes Genomes Genetics
Published
2025-11-08
DOI
https://doi.org/10.1093/g3journal/jkaf261
Citations
1
Primary Topic
Wheat and Barley Genetics and Pathology
Type
article
Field-Weighted Citation Impact
1.75

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article

Whole-genome resequencing of the wild barley diversity collection: a resource for identifying and exploiting genetic variation for cultivated barley improvement

Ahmad H. Sallam, Frank Ordon, Silvio Salvi, Patrick M. Hayes et al.
1 citations
G3 Genes Genomes Genetics
Wheat and Barley Genetics and Pathology
1.75
article

Whole-genome resequencing of the wild barley diversity collection: a resource for identifying and exploiting genetic variation for cultivated barley improvement

Ahmad H. Sallam, Frank Ordon, Silvio Salvi, Patrick M. Hayes, Klaus Pillen, Brande B. H. Wulff, Murukarthick Jayakodi, Cheng Liu, Andreas Maurer, Gerit Bethke, Kevin P. Smith, J. Valkoun, Alessandro Tondelli, Thomas Schmutzer, Benjamin Kilian, Youko Oono, Rebecca Spanner, Martin Mascher, Stephan Greiner, Marcus A. Vinje, Itay Mayrose, Ruth Hamilton, Y. C. Lee, Gary J. Muehlbauer, Jeness C. Scott, Ana Badea, Robert Brueggeman, Jan Šafář, Jamie Simmons, Roger P. Wise, Roi Ben‐David, Antonín Dreiseitl, Shengming Yang, Yinjie Qiu, T. Kelly Turkington, Klaus Mayer, Takao Komatsuda, François Belzile, Lior Glick, Nils Stein, Roberto Tuberosa, Christoph Dockter, Aleš Pečinka, Oadi Matny, Dragan Perović, Miguel Sanchez‐Garcia, Uwe Scholz, Jaroslav Doležel, Anne Fiebig, Mohammad Pourkheirandish, Chengdao Li, Yu Guo, Jason G. Walling, Michaël Baum, Ramamurthy Mahalingam, Luigi Cattivelli, Gurcharn S. Brar, Peter L. Morrell, Hakan Özkan, James R. Tucker, Robbie Waugh, Kazuhiro Sato, Maria von Korff, Luis Willian Pacheco Arge, Axel Himmelbach, M. Spannagl, Mark E. Sorrells, Brian J. Steffenson, Matthew Moscou, Austin J. Case, Maren Maruschewski, Guoping Zhang, Ryan Gavin, Ramesh Pal Singh Verma, Cynthia A. Henson, Joanne Russell, Michael H. Davis, Scott Heisel
article en
1 citations

Abstract

To exploit allelic variation in Hordeum vulgare subsp. spontaneum, the Wild Barley Diversity Collection was subjected to paired-end Illumina sequencing at ∼9 × depth and evaluated for several agronomic traits. We discovered 240.2 million single nucleotide polymorphisms (SNPs) after alignment to the Morex V3 assembly and 24.4 million short (1 to 50 bp) insertions and deletions. A genome-wide association study of lemma color identified one marker-trait association (MTA) on chromosome 1H close to HvBlp, the cloned gene controlling black lemma. Four MTAs were identified for seedling stem rust resistance, including 2 novel loci on chromosomes 1H and 6H and one co-locating to the complex RMRL1-RMRL2 locus on 5H. The whole-genome sequence data described herein will facilitate the identification and utilization of new alleles for barley improvement.

G3 Genes Genomes GeneticsVol. 16(1)
Setsunan University (JP), Roche (Switzerland) (CH), American Bar Association (US), University of Minnesota (US), Agricultural Research Service (US), Oregon State University (US), National Agriculture and Food Research Organization (JP), Julius Kühn-Institut (DE), Agriculture and Agri-Food Canada (CA), University of Bonn (DE), University of Alberta (CA), James Hutton Institute (GB), Okayama University (JP), Tel Aviv University (IL), The University of Melbourne (AU), Texas A&M University System (US), Iowa State University (US), Murdoch University (AU), University of Dundee (GB), International Center for Agricultural Research in the Dry Areas (LB), Cornell University (US), Carlsberg Laboratory (DK), German Centre for Integrative Biodiversity Research (DE), Twin Cities Public Television (US), Helmholtz Zentrum München (DE), Agricultural Research Organization (IL), Alberta Crop Industry Development Fund (CA), Twin Cities Orthopedics (US), Department of Primary Industries and Regional Development (AU), Shandong Academy of Agricultural Sciences (CN), Leibniz Institute of Plant Biochemistry (DE), Agricultural Research Institute Kromeriz (CZ), Anheuser-Busch InBev (Belgium) (BE), Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (IT), Cluster of Excellence on Plant Sciences (DE), Anheuser-Busch InBev (United States) (US), Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) (DE), U.S. Arid Land Agricultural Research Center (US), Kazusa DNA Research Institute (JP), Czech Academy of Sciences, Institute of Experimental Botany (CZ), Institute of Crop Science (JP), Cereal Disease Laboratory (US), Edward T. Schafer Agricultural Research Center (US), Université Laval (CA), Heinrich Heine University Düsseldorf (DE), Brandon University (CA), Cukurova University (TR), The University of Adelaide (AU), North Dakota State University (US), Technical University of Munich (DE), Martin Luther University Halle-Wittenberg (DE), King Abdullah University of Science and Technology (SA), Washington State University (US), Zhejiang University (CN), University of Bologna (IT)
National Science Foundation, U.S. Department of Agriculture, University of Minnesota, American Malting Barley Association, Deutsche Forschungsgemeinschaft, Bundesministerium für Bildung und Forschung, King Abdullah University of Science and Technology, National Institute of Food and Agriculture, Agricultural Research Service, European Regional Development Fund
Openalex Percentile: Top 11%
Wheat and Barley Genetics and Pathology
1.75
DOIOpen Access PDFOpenAlex
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