ArticleG3 (Bethesda, Md.)2026
Whole-genome resequencing of the wild barley diversity collection: a resource for identifying and exploiting genetic variation for cultivated barley improvement.
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6citing papers in PubMed
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6 citing papers in PubMed.
- Spatial Regulation of Silicon Accumulation in Peduncle Confers Sheathed Spike in Barley.Plant biotechnology journal · 2026Article
- Molecular Labelling Tool for Cereal Genetic Resources Management Derived from Barley and Tetraploid Wheat Genebank-Genomics Projects.Plants (Basel, Switzerland) · 2026Article
- Dormancy Versus Germination: 3D Protein Modeling and Evolutionary Analyses Define the Roles of Genetic Variants in the Barley MKK3 Enzyme.International journal of molecular sciences · 2026Article
- Extensive photophysiological variation in wild barley is linked to environmental origin.The New phytologist · 2026Article
- Article
- Effects of using deep learning to predict the geographic origin of barley genebank accessions on genome-environment association studies.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
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Authors and funding
78 authors.
Rebecca SpannerDepartment of Plant Pathology, University of Minnesota Twin Cities, Saint Paul, MN 55108, United States.ORCID 0000-0002-4735-9649
Ahmad H SallamDepartment of Plant Pathology, University of Minnesota Twin Cities, Saint Paul, MN 55108, United States.
Yu GuoLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Saxony-Anhalt 06466, Germany.
Murukarthick JayakodiLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Saxony-Anhalt 06466, Germany.ORCID 0000-0003-2951-0541
Axel HimmelbachLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Saxony-Anhalt 06466, Germany.
Anne FiebigBioinformatics and Information Technology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Saxony-Anhalt 06466, Germany.
Jamie SimmonsDepartment of Plant Pathology, University of Minnesota Twin Cities, Saint Paul, MN 55108, United States.
Gerit BethkeDepartment of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN 55108, United States.ORCID 0009-0009-8431-6419
Yoonjung LeeDepartment of Plant Pathology, University of Minnesota Twin Cities, Saint Paul, MN 55108, United States.
Luis Willian Pacheco ArgeDepartment of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN 55108, United States.
Yinjie QiuMinnesota Supercomputing Institute, University of Minnesota Twin Cities, Minneapolis, MN 55455, United States.ORCID 0000-0002-0584-0688
Ana BadeaBrandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, Manitoba R7A 5Y3, Canada.
Michael BaumBiodiversity and Crop Improvement, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat BP6299, Morocco.
François BelzileDépartement de Phytologie, Université Laval, Québec G1V 0A6, Canada.ORCID 0000-0001-6893-4529
Roi Ben-DavidDepartment of Vegetables and Field Crops, ARO-Volcani Center, Rishon LeZion 7505101, Israel.
Robert BrueggemanDepartment of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, United States.ORCID 0000-0002-1777-1624
Austin CaseAnheuser-Busch InBev, Fort Collins, CO 80524, United States.
Luigi CattivelliResearch Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Fiorenzuola d'Arda, Piacenza 29017, Italy.
Michael DavisAmerican Malting Barley Association, Inc., Brookfield, WI 53005, United States.
Christoph DockterRaw Materials, Carlsberg Research Laboratory, Copenhagen DK-1799, Denmark.ORCID 0000-0001-5923-3667
Jaroslav DoleželCentre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, Olomouc CZ-77900, Czech Republic.ORCID 0000-0002-6263-0492
Antonin DreiseitlDepartment of Integrated Plant Protection, Agrotest Fyto Ltd., Kroměříž CZ-767 01, Czech Republic.ORCID 0000-0002-9137-3210
Ryan GavinDepartment of Plant Pathology, University of Minnesota Twin Cities, Saint Paul, MN 55108, United States.
Lior GlickSchool of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel.ORCID 0000-0002-9286-3094
Stephan GreinerRoche Information Solutions (RIS), Data, Analytics & Research (DA&R), Roche Diagnostics GmbH, Penzberg, Bavaria 82377, Germany.
Ruth HamiltonCell and Molecular Sciences, The James Hutton Institute, Dundee, Scotland DD2 5DA, UK.
Patrick M HayesDepartment of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, United States.
Scott HeiselAmerican Malting Barley Association, Inc., Brookfield, WI 53005, United States.
Cynthia HensonCereal Crops Research Unit, USDA-ARS, Madison, WI 53726, United States.
Benjamin KilianGlobal Crop Diversity Trust, Bonn, North Rhine-Westphalia 53113, Germany.
Takao KomatsudaShandong Academy of Agricultural Sciences (SAAS), Crop Research Institute, Jinan, Shandong 250100, China.
Chengdao LiWestern Crop Genetics Alliance, Food Futures Institute/School of Agriculture, Murdoch University, Murdock, WA 6150, Australia.ORCID 0000-0002-9653-2700
Cheng LiuShandong Academy of Agricultural Sciences (SAAS), Crop Research Institute, Jinan, Shandong 250100, China.ORCID 0000-0003-3354-8817
Ramamurthy MahalingamCereal Crops Research Unit, USDA-ARS, Madison, WI 53726, United States.
Maren MaruschewskiBioinformatics and Information Technology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Saxony-Anhalt 06466, Germany.
Oadi MatnyDepartment of Plant Pathology, University of Minnesota Twin Cities, Saint Paul, MN 55108, United States.ORCID 0000-0002-8447-2886
Andreas MaurerInstitute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Saxony-Anhalt 06120, Germany.ORCID 0000-0002-2916-7475
Klaus F X MayerPlant Genome and Systems Biology (PGSB), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Bavaria 85764, Germany.
Itay MayroseSchool of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel.ORCID 0000-0002-8460-1502
Matthew MoscouCereal Disease Laboratory, USDA-ARS, Saint Paul, MN 55108, United States.ORCID 0000-0003-2098-6818
Gary J MuehlbauerDepartment of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN 55108, United States.
Youko OonoInstitute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8602, Japan.ORCID 0000-0003-3575-4059
Frank OrdonInstitute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI), Quedlinburg, Saxony-Anhalt 06484, Germany.
Hakan ÖzkanDepartment of Field Crops, Faculty of Agriculture, University of Çukurova, Sarıçam, Adana 1250, Turkey.
Ales PecinkaCentre of Plant Structural and Functional Genomics, Institute of Experimental Botany, Czech Academy of Sciences, Olomouc CZ-77900, Czech Republic.ORCID 0000-0001-9277-1766
Dragan PerovicInstitute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI), Quedlinburg, Saxony-Anhalt 06484, Germany.ORCID 0000-0002-0292-1693
Klaus PillenInstitute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Saxony-Anhalt 06120, Germany.ORCID 0000-0003-4646-6351
Mohammad PourkheirandishSchool of Agriculture, Food, and Ecosystem Sciences (SAFES), University of Melbourne, Melbourne, Victoria 3010, Australia.ORCID 0000-0003-4337-3600
Joanne RussellCell and Molecular Sciences, The James Hutton Institute, Dundee, Scotland DD2 5DA, UK.
Jan ŠafářInstitute of Experimental Botany, Centre of Plant Structural and Functional Genomics, Olomouc 779 00, Czech Republic.
Silvio SalviDepartment of Agricultural and Food Sciences, University of Bologna, Bologna 40127, Italy.ORCID 0000-0002-0338-8894
Miguel Sanchez-GarciaBiodiversity and Crop Improvement, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat BP6299, Morocco.
Kazuhiro SatoInstitute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan.ORCID 0000-0001-8818-5203
Thomas SchmutzerInstitute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Saxony-Anhalt 06120, Germany.ORCID 0000-0003-1073-6719
Uwe ScholzBioinformatics and Information Technology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Saxony-Anhalt 06466, Germany.ORCID 0000-0001-6113-3518
Jeness ScottDepartment of Plant Pathology, University of Minnesota Twin Cities, Saint Paul, MN 55108, United States.
Gurcharn Singh BrarDepartment of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB T6G 2P5, Canada.
Kevin P SmithDepartment of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN 55108, United States.ORCID 0000-0001-8253-3326
Mark E SorrellsPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853-1902, United States.
Manuel SpannaglPlant Genome and Systems Biology (PGSB), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Bavaria 85764, Germany.ORCID 0000-0003-0701-7035
Nils SteinGenebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Saxony-Anhalt 06466, Germany.ORCID 0000-0003-3011-8731
Alessandro TondelliResearch Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Fiorenzuola d'Arda, Piacenza 29017, Italy.
Roberto TuberosaDepartment of Agricultural and Food Sciences, University of Bologna, Bologna 40127, Italy.ORCID 0000-0001-9143-9569
James TuckerBrandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, Manitoba R7A 5Y3, Canada.
Thomas TurkingtonAgriculture and Agri-Food Canada, Lacombe Research and Development Centre, Lacombe, Alberta T4L 1W1, Canada.
Jan ValkounGenetic Resources Unit, International Center for Agricultural Research in the Dry Areas (ICARDA), Praha 15000, Czech Republic.
Ramesh Pal Singh VermaBiodiversity and Crop Improvement, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat BP6299, Morocco.
Marcus A VinjeCereal Crops Research Unit, USDA-ARS, Madison, WI 53726, United States.
Maria von KorffInstitute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, North Rhine-Westphalia 40225, Germany.ORCID 0000-0002-6816-586X
Jason G WallingCereal Crops Research Unit, USDA-ARS, Madison, WI 53726, United States.ORCID 0000-0001-7897-6896
Robbie WaughCell and Molecular Sciences, The James Hutton Institute, Dundee, Scotland DD2 5DA, UK.ORCID 0000-0003-1045-3065
Roger P WiseCorn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, United States.ORCID 0000-0001-7786-1528
Brande B H WulffPlant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.ORCID 0000-0003-4044-4346
Shengming YangCereal Crops Improvement Research Unit, USDA-ARS, Fargo, ND 58102, United States.ORCID 0000-0002-4558-8448
Guoping ZhangDepartment of Agronomy, Zhejiang University, Hangzhou, Zhejiang 310029, China.ORCID 0000-0002-9042-2607
Peter L MorrellDepartment of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN 55108, United States.ORCID 0000-0001-6282-1582
Martin MascherLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Saxony-Anhalt 06466, Germany.ORCID 0000-0001-6373-6013
Brian J SteffensonDepartment of Plant Pathology, University of Minnesota Twin Cities, Saint Paul, MN 55108, United States.ORCID 0000-0001-7961-5363
Funding
American Malting Barley AssociationARSBinational Agriculture Research and Development Fund US-5089-18Biodiversity for Opportunities, Livelihoods and DevelopmentCarlsberg Foundation CF15-0236ERDF Programme Johannes Amos ComeniusExploiting Wild Relatives for Cultivated Wheat and Barley ImprovementGerman Ministry of Research and Education 031B0190German Research Foundation 460265804Government of Norway QZA-20/0154Hatch project #MIN-22-085King Abdullah University of Science and TechnologyNational Institute of Food and AgricultureNational Science FoundationPlant Genome Research Program 13-39348Recovering and Exploiting Old and New Barley Diversity for Future-Ready AgricultureTowArds Next GENeration CropsUnited States Department of Agriculture-Agricultural Research Service CRIS #5062-21220-025-000DUniversity of MinnesotaUSDA-Agricultural Research Service 3625-21000-067-00DUSDA-Agricultural Research Service 5030-21220-068-000-DUSDA-Agricultural Research Service 5090-21430-011-000DUSDA-Agricultural Research Service 5090-43440-007-000DU.S. Department of Agriculture
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.
Indexed as
Genetic VariationGenome, PlantHordeumWhole Genome SequencingAllelesChromosome MappingGenome-Wide Association StudyPhenotypePolymorphism, Single NucleotideQuantitative Trait Lociagronomic traitsgenome-wide association studyHordeum vulgare subsp. spontaneumwhole genome sequence data
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