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

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

doi:10.1093/g3journal/jkaf261

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

Rebecca Spanner
, Ahmad H. Sallam
, Yu Guo
, Murukarthick Jayakodi
, Axel Himmelbach
, Anne Fiebig
, Jamie Simmons
, Gerit Bethke
, Yoonjung Lee
, Luis Willian Pacheco Arge
, Yinjie Qiu
, Ana Badea
, Michael Baum
, François Belzile
, Roi Ben-David
, Robert Brueggeman
, Austin Case
, Luigi Cattivelli
, Michael Davis
, Christoph Dockter

Jaroslav Doležel, Antonin Dreiseitl, Ryan Gavin, Lior Glick, Stephan Greiner, Ruth Hamilton, Patrick M. Hayes, Scott Heisel, Cynthia Henson, Benjamin Kilian, Takao Komatsuda, Chengdao Li, Cheng Liu, Ramamurthy Mahalingam, Maren Maruschewski, Oadi Matny, Andreas Maurer, Klaus F.X. Mayer, Itay Mayrose, Matthew Moscou, Gary J. Muehlbauer, Youko Oono, Frank Ordon, Hakan Özkan, Ales Pecinka, Dragan Perovic, Klaus Pillen, Mohammad Pourkheirandish, Joanne Russell, Jan Šafář, Silvio Salvi, Miguel Sanchez-Garcia, Kazuhiro Sato, Thomas Schmutzer, Uwe Scholz, Jeness Scott, Gurcharn Singh Brar, Kevin P. Smith, Mark E. Sorrells, Manuel Spannagl, Nils Stein, Alessandro Tondelli, Roberto Tuberosa, James Tucker, Thomas Turkington, Jan Valkoun, Ramesh Pal Singh Verma, Marcus A. Vinje, Maria von Korff, Jason G. Walling, Robbie Waugh, Roger P. Wise, Brande B.H. Wulff, Shengming Yang, Guoping Zhang, Peter L. Morrell, Martin Mascher (Lead / Corresponding author), Brian J. Steffenson (Lead / Corresponding author)

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

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.

Original language	English
Article number	jkaf261
Number of pages	10
Journal	G3 (Bethesda, Md.)
Volume	16
Issue number	1
Early online date	8 Nov 2025
DOIs	https://doi.org/10.1093/g3journal/jkaf261
Publication status	Published - Jan 2026

Keywords

Hordeum vulgare subsp. spontaneum
agronomic traits
genome-wide association study
whole genome sequence data

ASJC Scopus subject areas

Molecular Biology
Genetics
Genetics(clinical)

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10.1093/g3journal/jkaf261Licence: Other

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Spanner, R., Sallam, A. H., Guo, Y., Jayakodi, M., Himmelbach, A., Fiebig, A., Simmons, J., Bethke, G., Lee, Y., Pacheco Arge, L. W., Qiu, Y., Badea, A., Baum, M., Belzile, F., Ben-David, R., Brueggeman, R., Case, A., Cattivelli, L., Davis, M., ... Steffenson, B. J. (2026). Whole-genome resequencing of the wild barley diversity collection: a resource for identifying and exploiting genetic variation for cultivated barley improvement. G3 (Bethesda, Md.), 16(1), Article jkaf261. https://doi.org/10.1093/g3journal/jkaf261

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

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.",

keywords = "Hordeum vulgare subsp. spontaneum, agronomic traits, genome-wide association study, whole genome sequence data",

author = "Rebecca Spanner and Sallam, \{Ahmad H.\} and Yu Guo and Murukarthick Jayakodi and Axel Himmelbach and Anne Fiebig and Jamie Simmons and Gerit Bethke and Yoonjung Lee and \{Pacheco Arge\}, \{Luis Willian\} and Yinjie Qiu and Ana Badea and Michael Baum and Fran{\c c}ois Belzile and Roi Ben-David and Robert Brueggeman and Austin Case and Luigi Cattivelli and Michael Davis and Christoph Dockter and Jaroslav Dole{\v z}el and Antonin Dreiseitl and Ryan Gavin and Lior Glick and Stephan Greiner and Ruth Hamilton and Hayes, \{Patrick M.\} and Scott Heisel and Cynthia Henson and Benjamin Kilian and Takao Komatsuda and Chengdao Li and Cheng Liu and Ramamurthy Mahalingam and Maren Maruschewski and Oadi Matny and Andreas Maurer and Mayer, \{Klaus F.X.\} and Itay Mayrose and Matthew Moscou and Muehlbauer, \{Gary J.\} and Youko Oono and Frank Ordon and Hakan {\"O}zkan and Ales Pecinka and Dragan Perovic and Klaus Pillen and Mohammad Pourkheirandish and Joanne Russell and Jan {\v S}af{\'a}{\v r} and Silvio Salvi and Miguel Sanchez-Garcia and Kazuhiro Sato and Thomas Schmutzer and Uwe Scholz and Jeness Scott and \{Singh Brar\}, Gurcharn and Smith, \{Kevin P.\} and Sorrells, \{Mark E.\} and Manuel Spannagl and Nils Stein and Alessandro Tondelli and Roberto Tuberosa and James Tucker and Thomas Turkington and Jan Valkoun and Verma, \{Ramesh Pal Singh\} and Vinje, \{Marcus A.\} and \{von Korff\}, Maria and Walling, \{Jason G.\} and Robbie Waugh and Wise, \{Roger P.\} and Wulff, \{Brande B.H.\} and Shengming Yang and Guoping Zhang and Morrell, \{Peter L.\} and Martin Mascher and Steffenson, \{Brian J.\}",

note = "Publisher Copyright: Published by Oxford University Press on behalf of The Genetics Society of America 2025.",

year = "2026",

month = jan,

doi = "10.1093/g3journal/jkaf261",

language = "English",

volume = "16",

journal = "G3 (Bethesda, Md.)",

issn = "2160-1836",

publisher = "Genetics Society of America",

number = "1",

}

Spanner, R, Sallam, AH, Guo, Y, Jayakodi, M, Himmelbach, A, Fiebig, A, Simmons, J, Bethke, G, Lee, Y, Pacheco Arge, LW, Qiu, Y, Badea, A, Baum, M, Belzile, F, Ben-David, R, Brueggeman, R, Case, A, Cattivelli, L, Davis, M, Dockter, C, Doležel, J, Dreiseitl, A, Gavin, R, Glick, L, Greiner, S, Hamilton, R, Hayes, PM, Heisel, S, Henson, C, Kilian, B, Komatsuda, T, Li, C, Liu, C, Mahalingam, R, Maruschewski, M, Matny, O, Maurer, A, Mayer, KFX, Mayrose, I, Moscou, M, Muehlbauer, GJ, Oono, Y, Ordon, F, Özkan, H, Pecinka, A, Perovic, D, Pillen, K, Pourkheirandish, M, Russell, J, Šafář, J, Salvi, S, Sanchez-Garcia, M, Sato, K, Schmutzer, T, Scholz, U, Scott, J, Singh Brar, G, Smith, KP, Sorrells, ME, Spannagl, M, Stein, N, Tondelli, A, Tuberosa, R, Tucker, J, Turkington, T, Valkoun, J, Verma, RPS, Vinje, MA, von Korff, M, Walling, JG, Waugh, R, Wise, RP, Wulff, BBH, Yang, S, Zhang, G, Morrell, PL, Mascher, M & Steffenson, BJ 2026, 'Whole-genome resequencing of the wild barley diversity collection: a resource for identifying and exploiting genetic variation for cultivated barley improvement', G3 (Bethesda, Md.), vol. 16, no. 1, jkaf261. https://doi.org/10.1093/g3journal/jkaf261

TY - JOUR

T1 - Whole-genome resequencing of the wild barley diversity collection

T2 - a resource for identifying and exploiting genetic variation for cultivated barley improvement

AU - Spanner, Rebecca

AU - Sallam, Ahmad H.

AU - Guo, Yu

AU - Jayakodi, Murukarthick

AU - Himmelbach, Axel

AU - Fiebig, Anne

AU - Simmons, Jamie

AU - Bethke, Gerit

AU - Lee, Yoonjung

AU - Pacheco Arge, Luis Willian

AU - Qiu, Yinjie

AU - Badea, Ana

AU - Baum, Michael

AU - Belzile, François

AU - Ben-David, Roi

AU - Brueggeman, Robert

AU - Case, Austin

AU - Cattivelli, Luigi

AU - Davis, Michael

AU - Dockter, Christoph

AU - Doležel, Jaroslav

AU - Dreiseitl, Antonin

AU - Gavin, Ryan

AU - Glick, Lior

AU - Greiner, Stephan

AU - Hamilton, Ruth

AU - Hayes, Patrick M.

AU - Heisel, Scott

AU - Henson, Cynthia

AU - Kilian, Benjamin

AU - Komatsuda, Takao

AU - Li, Chengdao

AU - Liu, Cheng

AU - Mahalingam, Ramamurthy

AU - Maruschewski, Maren

AU - Matny, Oadi

AU - Maurer, Andreas

AU - Mayer, Klaus F.X.

AU - Mayrose, Itay

AU - Moscou, Matthew

AU - Muehlbauer, Gary J.

AU - Oono, Youko

AU - Ordon, Frank

AU - Özkan, Hakan

AU - Pecinka, Ales

AU - Perovic, Dragan

AU - Pillen, Klaus

AU - Pourkheirandish, Mohammad

AU - Russell, Joanne

AU - Šafář, Jan

AU - Salvi, Silvio

AU - Sanchez-Garcia, Miguel

AU - Sato, Kazuhiro

AU - Schmutzer, Thomas

AU - Scholz, Uwe

AU - Scott, Jeness

AU - Singh Brar, Gurcharn

AU - Smith, Kevin P.

AU - Sorrells, Mark E.

AU - Spannagl, Manuel

AU - Stein, Nils

AU - Tondelli, Alessandro

AU - Tuberosa, Roberto

AU - Tucker, James

AU - Turkington, Thomas

AU - Valkoun, Jan

AU - Verma, Ramesh Pal Singh

AU - Vinje, Marcus A.

AU - von Korff, Maria

AU - Walling, Jason G.

AU - Waugh, Robbie

AU - Wise, Roger P.

AU - Wulff, Brande B.H.

AU - Yang, Shengming

AU - Zhang, Guoping

AU - Morrell, Peter L.

AU - Mascher, Martin

AU - Steffenson, Brian J.

N1 - Publisher Copyright: Published by Oxford University Press on behalf of The Genetics Society of America 2025.

PY - 2026/1

Y1 - 2026/1

N2 - 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.

AB - 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.

KW - Hordeum vulgare subsp. spontaneum

KW - agronomic traits

KW - genome-wide association study

KW - whole genome sequence data

UR - https://www.scopus.com/pages/publications/105026870761

U2 - 10.1093/g3journal/jkaf261

DO - 10.1093/g3journal/jkaf261

M3 - Article

C2 - 41206694

AN - SCOPUS:105026870761

SN - 2160-1836

VL - 16

JO - G3 (Bethesda, Md.)

JF - G3 (Bethesda, Md.)

IS - 1

M1 - jkaf261

ER -

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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