Adaptive diversification through structural variation in barley

Murukarthick Jayakodi; Qiongxian Lu; Helene Pidon; M. Timothy Rabanus-Wallace; Micha Bayer; Thomas Lux; Yu Guo; Benjamin Jaegle; Ana Badea; Wubishet Bekele; Gurcharn Brar; Katarzyna Braune; Boyke Bunk; Kenneth Chalmers; Brett Chapman; Morten Egevang Jorgensen; Jia-Wu Feng; Manuel Feser; Anne Fiebig; Heidrun Gundlach; Wenbin Guo; Georg Haberer; Mats Hansson; Axel Himmelbach; Iris Hoffie; Robert Hoffie; Haifei Hu; Sachiko Isobe; Patrick Koenig; Sandip Kale; Nadia Kamal; Gabriel Keeble-Gagnere; Beat Keller; Manuela Knauft; Ravi Koppolu; Simon Krattinger; Jochen Kumlehn; Peter Langridge; Chengdao Li; Marina Marone; Andreas Maurer; Klaus Mayer; Michael Melzer; Gary Muehlbauer; Emiko Murozuka; Sudharsan Padmarasu; Dragan Perovic; Klaus Pillen; Pierre Pin; Curtis Pozniak; Luke Ramsay; Pai Rosager Pedas; Twan Rutten; Shun Sakuma; Kazuhiro Sato; Danuta Schueler; Thomas Schmutzer; Uwe Scholz; Miriam Schreiber; Kenta Shirasawa; Craig Simpson; Birgitte Skadhauge; Manuel Spannagl; Brian Steffenson; Hanne Thomsen; Josquin Tibbits; Martin Toft Simmelsgaard Nielsen; Corinna Trautewig; Dominique Vequaud; Cynthia Voss; Penghao Wang; Robbie Waugh; Sharon Westcott; Magnus Wohlfahrt Rasmussen; Runxuan Zhang; Xiao-Qi Zhang; Thomas Wicker; Christoph Dockter; Martin Mascher; Nils Stein

doi:10.1101/2024.02.14.580266

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Adaptive diversification through structural variation in barley

Working paper

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Adaptive diversification through structural variation in barley

Murukarthick Jayakodi, Qiongxian Lu, Helene Pidon, M. Timothy Rabanus-Wallace, Micha Bayer, Thomas Lux, Yu Guo, Benjamin Jaegle, Ana Badea, Wubishet Bekele, …

18/02/2024

DOI: https://doi.org/10.1101/2024.02.14.580266

Abstract

Pangenomes are collections of annotated genome sequences of multiple individuals of a species. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants. Here, we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that have become hot spots of gene copy number variation in evolutionarily recent times. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release, and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that rapid evolution at structurally complex loci may have helped crop plants adapt to new selective regimes in agricultural ecosystems.

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Title: Adaptive diversification through structural variation in barley
Creators - without role: Murukarthick Jayakodi - Leibniz Institute of Plant Genetics and Crop Plant Research
Qiongxian Lu - Carlsberg Laboratory
Helene Pidon - Leibniz Institute of Plant Genetics and Crop Plant Research
M. Timothy Rabanus-Wallace - Leibniz Institute of Plant Genetics and Crop Plant Research
Micha Bayer - James Hutton Institute
Thomas Lux - Center for Systems Biology Dresden
Yu Guo - Leibniz Institute of Plant Genetics and Crop Plant Research
Benjamin Jaegle - University of Zurich
Ana Badea - Agriculture and Agri-Food Canada
Wubishet Bekele - International Development Research Centre
Gurcharn Brar - University of British Columbia
Katarzyna Braune - Carlsberg Laboratory
Boyke Bunk - Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures
Kenneth Chalmers - School of Agriculture, Food and Wine
Brett Chapman - Murdoch University
Morten Egevang Jorgensen - Carlsberg Research Laboratory
Jia-Wu Feng - Leibniz Institute of Plant Genetics and Crop Plant Research
Manuel Feser - Leibniz Institute of Plant Genetics and Crop Plant Research
Anne Fiebig - Leibniz Institute of Plant Genetics and Crop Plant Research
Heidrun Gundlach - Center for Systems Biology Dresden
Wenbin Guo - James Hutton Institute
Georg Haberer - Center for Systems Biology Dresden
Mats Hansson - Lund University
Axel Himmelbach - Leibniz Institute of Plant Genetics and Crop Plant Research
Iris Hoffie - Leibniz Institute of Plant Genetics and Crop Plant Research
Robert Hoffie - Leibniz Institute of Plant Genetics and Crop Plant Research
Haifei Hu - Guangdong Academy of Agricultural Sciences
Sachiko Isobe - Kazusa DNA Research Institute
Patrick Koenig - Leibniz Institute of Plant Genetics and Crop Plant Research
Sandip Kale - Carlsberg Laboratory
Nadia Kamal - PGSB
Gabriel Keeble-Gagnere - AgriBio
Beat Keller - University of Zurich
Manuela Knauft - Leibniz Institute of Plant Genetics and Crop Plant Research
Ravi Koppolu - Leibniz Institute of Plant Genetics and Crop Plant Research
Simon Krattinger - Biological and Environmental Science & Engineering Division (BESE)
Jochen Kumlehn - Leibniz Institute of Plant Genetics and Crop Plant Research
Peter Langridge - School of Agriculture, Food and Wine
Chengdao Li - Murdoch University
Marina Marone - Leibniz Institute of Plant Genetics and Crop Plant Research
Andreas Maurer - Martin Luther University Halle-Wittenberg
Klaus Mayer - Technical University of Munich
Michael Melzer - Leibniz Institute of Plant Genetics and Crop Plant Research
Gary Muehlbauer - Plant
Emiko Murozuka - Carlsberg Laboratory
Sudharsan Padmarasu - Fraunhofer Institute for Production Systems and Design Technology
Dragan Perovic - Julius Kühn-Institut
Klaus Pillen - Institute of Agricultural and Nutritional Sciences
Pierre Pin - Secobra Recherches
Curtis Pozniak - University of perpetuity
Luke Ramsay - James Hutton Institute
Pai Rosager Pedas - Carlsberg Laboratory
Twan Rutten - Leibniz Institute of Plant Genetics and Crop Plant Research
Shun Sakuma - Tottori University
Kazuhiro Sato - Kazusa DNA Research Institute
Danuta Schueler - Leibniz Institute of Plant Genetics and Crop Plant Research
Thomas Schmutzer - Institute of Agricultural and Nutritional Sciences
Uwe Scholz - Leibniz Institute of Plant Genetics and Crop Plant Research
Miriam Schreiber - James Hutton Institute
Kenta Shirasawa - Kazusa DNA Research Institute
Craig Simpson - James Hutton Institute
Birgitte Skadhauge - Carlsberg Laboratory
Manuel Spannagl - Center for Systems Biology Dresden
Brian Steffenson - Twin Cities Orthopedics
Hanne Thomsen - Carlsberg Laboratory
Josquin Tibbits - La Trobe University
Martin Toft Simmelsgaard Nielsen - Carlsberg Laboratory
Corinna Trautewig - Leibniz Institute of Plant Genetics and Crop Plant Research
Dominique Vequaud - Secobra Recherches
Cynthia Voss - Carlsberg Laboratory
Penghao Wang - Murdoch University
Robbie Waugh - James Hutton Institute
Sharon Westcott - Murdoch University
Magnus Wohlfahrt Rasmussen - Carlsberg Laboratory
Runxuan Zhang - James Hutton Institute
Xiao-Qi Zhang - Murdoch University
Thomas Wicker - Plant
Christoph Dockter - Carlsberg Laboratory
Martin Mascher - Leibniz Institute of Plant Genetics and Crop Plant Research
Nils Stein - University of Göttingen
Identifiers: 9937646509311
Academic Unit: Institut des Sciences des Plantes de Montpellier - IPSiM
Language: English
Resource Type: Working paper
Local Fields: hal-04493576