Preprints, Working Papers, ... Year : 2024

Adaptive diversification through structural variation in barley

Murukarthick Jayakodi (1) , Qiongxian Lu (2) , Helene Pidon (1, 3) , M. Timothy Rabanus-Wallace (1) , Micha Bayer (4) , Thomas Lux (5) , Yu Guo (1) , Benjamin Jaegle (6) , Ana Badea (7) , Wubishet Bekele (8) , Gurcharn Brar (9) , Katarzyna Braune (2) , Boyke Bunk (10) , Kenneth Chalmers (11) , Brett Chapman (12) , Morten Egevang Jorgensen (2) , Jia-Wu Feng (1) , Manuel Feser (1) , Anne Fiebig (1) , Heidrun Gundlach (5) , Wenbin Guo (4) , Georg Haberer (5) , Mats Hansson (13) , Axel Himmelbach (1) , Iris Hoffie (1) , Robert Hoffie (1) , Haifei Hu (12, 14) , Sachiko Isobe (15) , Patrick Koenig (1) , Sandip Kale (2) , Nadia Kamal (16) , Gabriel Keeble-Gagnere (17) , Beat Keller (6) , Manuela Knauft (1) , Ravi Koppolu (1) , Simon Krattinger (18) , Jochen Kumlehn (1) , Peter Langridge (11) , Chengdao Li (12, 19) , Marina Marone (1) , Andreas Maurer (20) , Klaus Mayer (16, 21) , Michael Melzer (1) , Gary Muehlbauer (22) , Emiko Murozuka (2) , Sudharsan Padmarasu (23) , Dragan Perovic (24) , Klaus Pillen (25) , Pierre Pin (26) , Curtis Pozniak (27) , Luke Ramsay (4) , Pai Rosager Pedas (2) , Twan Rutten (1) , Shun Sakuma (28) , Kazuhiro Sato (29, 15) , Danuta Schueler (1) , Thomas Schmutzer (25) , Uwe Scholz (1) , Miriam Schreiber (4) , Kenta Shirasawa (15) , Craig Simpson (4) , Birgitte Skadhauge (2) , Manuel Spannagl (5) , Brian Steffenson (30) , Hanne Thomsen (2) , Josquin Tibbits (31) , Martin Toft Simmelsgaard Nielsen (2) , Corinna Trautewig (1) , Dominique Vequaud (26) , Cynthia Voss (2) , Penghao Wang (12) , Robbie Waugh (4, 32) , Sharon Westcott (12) , Magnus Wohlfahrt Rasmussen (2) , Runxuan Zhang (4) , Xiao-Qi Zhang (12) , Thomas Wicker (33) , Christoph Dockter (2) , Martin Mascher (1, 34) , Nils Stein (1, 35)
1 IPK-Gatersleben - Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
2 Carlsberg Research Laboratory
3 IPSIM - Institut des Sciences des Plantes de Montpellier
4 The James Hutton Institute
5 PGSB - Plant Genome and Systems Biology
6 UZH - Universität Zürich [Zürich] = University of Zurich
7 Agriculture and Agri-Food Canada, Saskatoon Research Centre
8 Ottawa Research and Development Centre
9 Faculty of Land and Food Systems
10 DSMZ - Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
11 School of Agriculture, Food and Wine
12 Murdoch University [Perth]
13 Lund University
14 GDAAS - Guangdong Academy of Agricultural Sciences
15 KDRI - Kazusa DNA Research Institute
16 PGSB
17 AgriBio - Agriculture Victoria
18 Biological and Environmental Science & Engineering Division (BESE)
19 Department of Primary Industry and Regional Development
20 Martin-Luther-University Halle-Wittenberg
21 TUM - Technische Universität Munchen - Technical University Munich - Université Technique de Munich
22 Department of Agronomy and Plant Genetics
23 Fraunhofer IPK - Fraunhofer Institute for Production Systems and Design Technology
24 JKI - Julius Kühn-Institut - Federal Research Centre for Cultivated Plants
25 Institute of Agricultural and Nutritional Sciences
26 Secobra Recherches
27 University of perpetuity
28 Tottori University
29 Okayama University
30 UMN - University of Minnesota [Twin Cities]
31 La Trobe University
32 University of Dundee
33 Department of Plant and Microbial Biology
34 iDiv - German Centre for Integrative Biodiversity Research
35 Georg-August-University = Georg-August-Universität Göttingen
Murukarthick Jayakodi
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Qiongxian Lu
Carlsberg Research Laboratory
Helene Pidon
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Institut des Sciences des Plantes de Montpellier
CV
M. Timothy Rabanus-Wallace
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Micha Bayer
The James Hutton Institute
Thomas Lux
Plant Genome and Systems Biology
Yu Guo
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Benjamin Jaegle
Universität Zürich [Zürich] = University of Zurich
Ana Badea
Agriculture and Agri-Food Canada, Saskatoon Research Centre
Wubishet Bekele
Ottawa Research and Development Centre
Gurcharn Brar
Faculty of Land and Food Systems
Katarzyna Braune
Carlsberg Research Laboratory
Boyke Bunk
Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
Kenneth Chalmers
School of Agriculture, Food and Wine
Brett Chapman
Murdoch University [Perth]
Morten Egevang Jorgensen
Carlsberg Research Laboratory
Jia-Wu Feng
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Manuel Feser
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Anne Fiebig
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Heidrun Gundlach
Plant Genome and Systems Biology
Wenbin Guo
The James Hutton Institute
Georg Haberer
Plant Genome and Systems Biology
Mats Hansson
Lund University
Axel Himmelbach
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Iris Hoffie
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Robert Hoffie
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Haifei Hu
Murdoch University [Perth]
Guangdong Academy of Agricultural Sciences
Sachiko Isobe
Kazusa DNA Research Institute
Patrick Koenig
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Sandip Kale
Carlsberg Research Laboratory
Nadia Kamal
PGSB
Gabriel Keeble-Gagnere
Agriculture Victoria
Beat Keller
Universität Zürich [Zürich] = University of Zurich
Manuela Knauft
  • Function : Author
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Ravi Koppolu
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Simon Krattinger
Biological and Environmental Science & Engineering Division (BESE)
Jochen Kumlehn
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Peter Langridge
School of Agriculture, Food and Wine
Chengdao Li
Murdoch University [Perth]
Department of Primary Industry and Regional Development
Marina Marone
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Andreas Maurer
Martin-Luther-University Halle-Wittenberg
Klaus Mayer
PGSB
Technische Universität Munchen - Technical University Munich - Université Technique de Munich
Michael Melzer
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Gary Muehlbauer
Department of Agronomy and Plant Genetics
Emiko Murozuka
Carlsberg Research Laboratory
Sudharsan Padmarasu
Fraunhofer Institute for Production Systems and Design Technology
Dragan Perovic
Julius Kühn-Institut - Federal Research Centre for Cultivated Plants
Klaus Pillen
Institute of Agricultural and Nutritional Sciences
Pierre Pin
Secobra Recherches
Curtis Pozniak
University of perpetuity
Luke Ramsay
The James Hutton Institute
Pai Rosager Pedas
Carlsberg Research Laboratory
Twan Rutten
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Shun Sakuma
Tottori University
Kazuhiro Sato
Okayama University
Kazusa DNA Research Institute
Danuta Schueler
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Thomas Schmutzer
Institute of Agricultural and Nutritional Sciences
Uwe Scholz
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Miriam Schreiber
The James Hutton Institute
Kenta Shirasawa
Kazusa DNA Research Institute
Craig Simpson
The James Hutton Institute
Birgitte Skadhauge
Carlsberg Research Laboratory
Manuel Spannagl
Plant Genome and Systems Biology
Brian Steffenson
University of Minnesota [Twin Cities]
Hanne Thomsen
Carlsberg Research Laboratory
Josquin Tibbits
  • Function : Author
La Trobe University
Martin Toft Simmelsgaard Nielsen
Carlsberg Research Laboratory
Corinna Trautewig
  • Function : Author
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Dominique Vequaud
Secobra Recherches
Cynthia Voss
Carlsberg Research Laboratory
Penghao Wang
Murdoch University [Perth]
Robbie Waugh
The James Hutton Institute
University of Dundee
Sharon Westcott
  • Function : Author
Murdoch University [Perth]
Magnus Wohlfahrt Rasmussen
Carlsberg Research Laboratory
Runxuan Zhang
The James Hutton Institute
Xiao-Qi Zhang
  • Function : Author
Murdoch University [Perth]
Thomas Wicker
  • Function : Correspondent author
  • PersonId : 1109064

Connectez-vous pour contacter l'auteur
Department of Plant and Microbial Biology
Christoph Dockter
Connectez-vous pour contacter l'auteur
Carlsberg Research Laboratory
Martin Mascher
  • Function : Correspondent author
  • PersonId : 956041

Connectez-vous pour contacter l'auteur
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
German Centre for Integrative Biodiversity Research
Nils Stein
  • Function : Correspondent author
  • PersonId : 956047

Connectez-vous pour contacter l'auteur
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Georg-August-University = Georg-August-Universität Göttingen

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.

Domains

Vegetal Biology Life Sciences [q-bio]
Fichier principal
Vignette du fichier
JayakodiM.-et al-bioRxiv-2024.pdf (10.66 Mo) Télécharger le fichier
Origin Files produced by the author(s)
Licence
Attribution - NonCommercial

Chantal Baracco  : Connect in order to contact the contributor

https://hal.inrae.fr/hal-04493576

Submitted on : Thursday, March 7, 2024-11:04:24 AM

Last modification on : Tuesday, December 17, 2024-1:46:02 PM

Download

Dates and versions

hal-04493576 , version 1 (07-03-2024)

Licence

Attribution - NonCommercial

Identifiers

Cite

Murukarthick Jayakodi, Qiongxian Lu, Helene Pidon, M. Timothy Rabanus-Wallace, Micha Bayer, et al.. Adaptive diversification through structural variation in barley. 2024. ⟨hal-04493576⟩

Export

BibTeX XML-TEI Dublin Core DC Terms EndNote DataCite

Collections

CNRS UNIV-MONTPELLIER INSTITUT-AGRO-MONTPELLIER INRAE INRAEOCCITANIEMONTPELLIER IPSIM RESEAU-EAU BIOLOGIE_ET_AMELIORATION_DES_PLANTES
76 View
28 Download

Altmetric

Share

More