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ARS Home » Midwest Area » Madison, Wisconsin » Cereal Crops Research » Research » Publications at this Location » Publication #421379
Research Project: Harnessing Multi-omics for Augmenting Seed Quality and Stress Tolerance in Barley

Location: Cereal Crops Research

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

Author
item HAYES, PATRICK - Oregon State University
item HEISEL, SCOTT - American Malting Barley Association
item KILIAN, BENJAMIN - Global Crop Diversity Trust
item KOMATSUDA, TAKAO - Shandong Academy Of Agricultural Sciences
item LEE, YOONJUNG - University Of Minnesota
item LI, CHENGDAO - Murdoch University
item LIU, CHENG - Shandong Academy Of Agricultural Sciences
item Mahalingam, Ramamurthy
item MATNY, OADI - University Of Minnesota
item MAURER, ANDREAS - Martin Luther University
item MORRELL, PETER - University Of Minnesota
item Moscou, Matthew
item MUEHLBAUER, GARY - University Of Minnesota
item OONO, YOUKO - National Agriculture And Food Research Organization (NARO), Agricultrual Research Center
item ORDON, FRANK - Cukurova University
item PECINKA, ALES - Institute Of Experimental Botany
item POURKHEIRANDISH, MOHAMMAD - University Of Melbourne
item PEROVIC, DRAGAN - Julius Kuhn Institute
item RUSSELL, JOANNE - The James Hutton Institute
item RUTH, HAMILTON - The James Hutton Institute
item SAFAR, JAN - Institute Of Experimental Botany
item SALVI, SILVIO - University Of Bologna
item SANCHEZ-GARCIA, MIGUEL - The International Center For Agricultural Research In The Dry Areas(ICARDA)
item SATO, KAZUHIRO - Okayama University
item SCHMUTZER, THOMAS - Martin Luther University
item SCHOLZ, UWE - Leibniz Institute
item SCOTT, JENESS - Oregon State University
item SIMMONS, JAMIE - University Of Minnesota
item SMITH, KEVIN - University Of Minnesota
item SORRELLS, MARK - Cornell University
item SPANNAGL, MANUEL - German Research Center For Environmental Health
item STEIN, NILS - Leibniz Institute Of Plant Genetics And Crop Plant Research
item TONDELLI, ALESSANDRO - Crea - Research Centre For Genomics And Bioinformatics
item TUBEROSA, ROBERTO - University Of Bologna
item TUCKER, JAMES - Brandon Research Center
item TURKINGTON, KELLY - Agriculture And Agri-Food Canada
item VALKOUN, JAN - The International Center For Agricultural Research In The Dry Areas(ICARDA)
item VERMA, RAMESH - The International Center For Agricultural Research In The Dry Areas(ICARDA)
item Vinje, Marcus
item Walling, Jason
item WAUGH, ROBBIE - The James Hutton Institute
item Wise, Roger
item WULFF, BRANDE - King Abdullah University Of Science And Technology
item Yang, Shengming
item ZHANG, GUOPING - Zhejiang University
item MASCHER, MARTIN - Leibniz Institute
item STEFFENSON, BRIAN - University Of Minnesota
item LUIS WILLIAM, PACHECO ARGE - University Of Minnesota
item YINJIE, QUI - University Of Minnesota
item LIOR, GLICK - Tel Aviv University
item Henson, Cynthia
item MARUSCHEWSKI, MAREN - Leibniz Institute Of Plant Biochemistry
item MAYER, KLAUS FX - Helmholtz Centre For Environmental Research
item MAYROSE, ITAY - Tel Aviv University
item PILLEN, KLAUS - Institute Of Plant Nutrition - Germany
item KORFF VON, MARI - Institute Of Plant Nutrition - Germany
item GREINER, STEPHAN - Roche
item SALLAM, AHMAD - University Of Minnesota
item GUO, YU - Leibniz Institute
item JAYAKODI, MURUKARTHICK - Leibniz Institute
item HIMMELBACH, AXEL - Leibniz Institute
item FIEBIG, ANNE - Leibniz Institute
item BADEA, ANA - Brandon Research Center
item BAUM, MICHAEL - The International Center For Agricultural Research In The Dry Areas(ICARDA)
item BELZILE, FRANCOIS - University Of Laval
item BEN-DAVID, ROI - Agricultural Research Organization - Volcani Center
item BETHKE, GERIT - University Of Minnesota
item BRAR, GURCHARN - University Of Alberta
item SPANNER, REBECCA - University Of Minnesota
item BRUEGGEMAN, ROBERT - Washington State University
item CASE, AUSTIN - Anheuser-Busch
item CATTIVELLI, LUIGI - Crea - Research Centre For Genomics And Bioinformatics
item DAVIS, MICHAEL - American Malting Barley Association
item DOCKTER, CHRISTOPH - Carlsberg Research Laboratory
item DOLEZEL, JAROSLAV - Institute Of Experimental Botany
item DREISEITL, ANTONIN - Agricultural Research Institute Kromeríž, Ltd
item GAVIN, RYAN - University Of Minnesota

Submitted to: Genes, Genomes, and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/2/2025
Publication Date: 11/8/2025
Citation: Hayes, P., Heisel, S., Kilian, B., Komatsuda, T., Lee, Y., Li, C., Liu, C., Mahalingam, R., Matny, O., Maurer, A., Morrell, P., Moscou, M.J., Muehlbauer, G., Oono, Y., Ordon, F., Pecinka, A., Pourkheirandish, M., Perovic, D., Russell, J., Ruth, H., Safar, J., Salvi, S., Sanchez-Garcia, M., Sato, K., Schmutzer, T., Scholz, U., Scott, J., Simmons, J., Smith, K., Sorrells, M., Spannagl, M., Stein, N., Tondelli, A., Tuberosa, R., Tucker, J., Turkington, K., Valkoun, J., Verma, R.P., Vinje, M.A., Walling, J.G., Waugh, R., Wise, R.P., Wulff, B., Yang, S., Zhang, G., Mascher, M., Steffenson, B.J., Luis William, P., Yinjie, Q., Lior, G., Henson, C.A., Maruschewski, M., Mayer, K., Mayrose, I., Pillen, K., Korff Von, M., Greiner, S., Sallam, A.H., Guo, Y., Jayakodi, M., Himmelbach, A., Fiebig, A., Badea, A., Baum, M., Belzile, F., Ben-David, R., Bethke, G., Brar, G.S., Spanner, R., Brueggeman, R., Case, A., Cattivelli, L., Davis, M., Dockter, C., Dolezel, J., Dreiseitl, A., Gavin, R. 2025. Whole-genome resequencing of the wild barley diversity collection: a resource for identifying and exploiting genetic variation for cultivated barley improvement. Genes, Genomes, and Genomics. https://doi.org/10.1093/g3journal/jkaf261.
DOI: https://doi.org/10.1093/g3journal/jkaf261

Interpretive Summary: Wild barley plants are a very useful resources for identifying novel genes that can be exploited for improving agronomic traits such as flowering time , seed morphology. It can also be useful for identifying genes that confer tolerance to pathogens, pests, and also environmental stresses such as heat, cold, drought, salinity. In order to identify these useful genetic variants, the DNA sequence of the genome of 300 wild barley lines were determined in this study. The utility of this sequence information data was demonstrated by identifying a DNA marker associated with black lemma phenotype. Four markers were identified for stem rust resistance. The sequence information from these wild barley lines will be a valuable resource for identifying novel genetic variants that can be exploited by breeders for improving barley resiliency.

Technical Abstract: To exploit allelic variation in Hordeum vulgare subsp. spontaneum, the Wild Barley Diversity Collection was evaluated for several agronomic traits and subjected to paired-end Illumina sequencing at ~9X depth, generating 109.5 million single nucleotide polymorphisms after alignment to the Morex v3 assembly. A genome-wide association study of lemma color identified one marker-trait association (MTA) on chromosome 1HL close to HvBlp, the cloned gene controlling black lemma. Four MTAs were identified for stem rust resistance: one co-locating to the complex RMRL1-RMRL2 locus on 5HL, and three novel loci on 1HS, 1HL, and 5HL. Six MTAs for days to heading (DTH) on vernalized plants were identified on all chromosomes except 1H and 6H. Two MTAs for DTH on non-vernalized plants were identified on chromosomes 1HL and 2HS. All MTAs for DTH were novel. The whole genome sequence data described herein will facilitate the identification and utilization of many new alleles for barley improvement.