biostudies-literatureSpanner RGerman Research FoundationTowArds Next GENeration CropsARSCarlsberg FoundationGovernment of NorwayU.S. Department of AgricultureKing Abdullah University of Science and TechnologyAmerican Malting Barley AssociationUSDA-Agricultural Research ServicePlant Genome Research ProgramHatch projectExploiting Wild Relatives for Cultivated Wheat and Barley ImprovementNational Institute of Food and AgricultureBinational Agriculture Research and Development FundGerman Ministry of Research and EducationERDF Programme Johannes Amos ComeniusUniversity of MinnesotaBiodiversity for Opportunities, Livelihoods and DevelopmentRecovering and Exploiting Old and New Barley Diversity for Future-Ready AgricultureUnited States Department of Agriculture-Agricultural Research ServiceNational Science Foundationjkaf261https://www.ebi.ac.uk/biostudies/studies/S-EPMC12774595biostudies-literatureUnknown16(1)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 aG3 (Bethesda, Md.)Whole-genome resequencing of the wild barley diversity collection: a resource for identifying and exploiting genetic variation for cultivated barley improvement.PMC12774595031B01905030-21220-068-000-DUS-5089-183625-21000-067-00DCF15-0236#MIN-22-0855090-21430-011-000D5090-43440-007-000DCRIS #5062-21220-025-000D460265804QZA-20/015413-39348Jayakodi MZhang GSpanner RHenson CGlick LGuo YMayer KFXHimmelbach ABaum MPourkheirandish MSmith KPSchmutzer TDavis MFiebig AQiu YCase ADockter CCattivelli LDolezel JOzkan HSallam AHMuehlbauer GJTuberosa RLi COono YPecinka ASafar JTondelli AMatny OSimmons JRussell JKilian BMayrose ISalvi SVinje MABadea Avon Korff MPerovic DSingh Brar GYang SGavin RHamilton RWalling JGSorrells MEMaurer AOrdon FDreiseitl AVerma RPSScott JStein NSteffenson BJBrueggeman RWulff BBHKomatsuda TMascher MSpannagl MMahalingam RPillen KMorrell PLMoscou MBethke GHayes PMScholz UPacheco Arge LWBen-David RValkoun JBelzile FMaruschewski MSanchez-Garcia MWise RPLee YHeisel SLiu CSato KWaugh RTucker JTurkington TGreiner SfalseWhole-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 a2026-01-01T00:00:00Z2026 Jan2026-05-29T03:17:07.284Z2026-05-29T03:11:27.439ZS-EPMC127745954120669410.1093/g3journal/jkaf261