Structural variation in the pangenome of wild and domesticated barley - Institut des sciences des plantes de Montpellier
Article Dans Une Revue Nature Année : 2024

Structural variation in the pangenome of wild and domesticated barley

Murukarthick Jayakodi (1) , Qiongxian Lu (2) , Hélène Pidon (3, 1) , M Timothy Rabanus-Wallace (1) , Micha Bayer (4) , Thomas Lux , Yu Guo (1) , Benjamin Jaegle (5) , Ana Badea (6) , Wubishet Bekele (7) , Gurcharn S Brar (8) , Katarzyna Braune (2) , Boyke Bunk (9) , Kenneth J Chalmers (10) , Brett Chapman (11) , Morten Egevang Jørgensen (2) , Jia-Wu Feng (1) , Manuel Feser (1) , Anne Fiebig (1) , Heidrun Gundlach (12) , Wenbin Guo (4) , Georg Haberer (12) , Mats Hansson (13) , Axel Himmelbach (1) , Iris Hoffie (1) , Robert E Hoffie (1) , Haifei Hu (11, 14) , Sachiko Isobe (15) , Patrick König (1) , Sandip M Kale (2) , Nadia Kamal (12) , Gabriel Keeble-Gagnère (16) , Beat Keller (5) , Manuela Knauft (1) , Ravi Koppolu (1) , Simon G Krattinger (17) , Jochen Kumlehn (1) , Peter Langridge (18) , Chengdao Li (11, 19, 20) , Marina P Marone (1) , Andreas Maurer (21) , Klaus F X Mayer (12, 22) , Michael Melzer (1) , Gary J Muehlbauer (23) , Emiko Murozuka (2) , Sudharsan Padmarasu (1) , Dragan Perovic (24) , Klaus Pillen (21) , Pierre A Pin (25) , Curtis J Pozniak (26) , Luke Ramsay (4) , Pai Rosager Pedas (2) , Twan Rutten (1) , Shun Sakuma (27) , Kazuhiro Sato (15, 28) , Danuta Schüler (1) , Thomas Schmutzer (21) , Uwe Scholz (1) , Miriam Schreiber (4) , Kenta Shirasawa (15) , Craig Simpson (4) , Birgitte Skadhauge (2) , Manuel Spannagl (12) , Brian J Steffenson (23) , Hanne C Thomsen (2) , Josquin F Tibbits (16) , Martin Toft Simmelsgaard Nielsen (2) , Corinna Trautewig (1) , Dominique Vequaud (25) , Cynthia Voss (2) , Penghao Wang (11) , Robbie Waugh (29) , Sharon Westcott (11) , Magnus Wohlfahrt Rasmussen (2) , Runxuan Zhang (4) , Xiao-Qi Zhang (11) , Thomas Wicker (5) , Christoph Dockter (2) , Martin Mascher (1, 30) , Nils Stein (21, 1)
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 UZH - Universität Zürich [Zürich] = University of Zurich
6 Agriculture and Agri-Food Canada, Saskatoon Research Centre
7 Agriculture and Agri-Food Canada
8 UBC - University of British Columbia [Canada]
9 DSMZ - Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
10 School of Agriculture, Food and Wine
11 Murdoch University [Perth]
12 HMGU - Helmholtz Zentrum München = German Research Center for Environmental Health
13 Lund University
14 GDAAS - Guangdong Academy of Agricultural Sciences
15 KDRI - Kazusa DNA Research Institute
16 La Trobe University
17 KAUST - King Abdullah University of Science and Technology [Saudi Arabia]
18 University of Adelaide
19 Government of Western Australia
20 Yangtze University
21 Martin-Luther-University Halle-Wittenberg
22 TUM - Technische Universität Munchen - Technical University Munich - Université Technique de Munich
23 UMN - University of Minnesota [Twin Cities]
24 JKI - Julius Kühn-Institut - Federal Research Centre for Cultivated Plants
25 Secobra Recherches
26 U of S - University of Saskatchewan [Saskatoon, Canada]
27 Tottori University
28 Okayama University
29 University of Dundee
30 iDiv - German Centre for Integrative Biodiversity Research
Murukarthick Jayakodi
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Qiongxian Lu
Carlsberg Research Laboratory
Hélène Pidon
Institut des Sciences des Plantes de Montpellier
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
CV
M Timothy Rabanus-Wallace
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Micha Bayer
The James Hutton Institute
Thomas Lux
Yu Guo
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Benjamin Jaegle
  • Fonction : Auteur
Universität Zürich [Zürich] = University of Zurich
Ana Badea
  • Fonction : Auteur
Agriculture and Agri-Food Canada, Saskatoon Research Centre
Wubishet Bekele
  • Fonction : Auteur
Agriculture and Agri-Food Canada
Gurcharn S Brar
  • Fonction : Auteur
University of British Columbia [Canada]
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 J Chalmers
  • Fonction : Auteur
School of Agriculture, Food and Wine
Brett Chapman
Murdoch University [Perth]
Morten Egevang Jørgensen
Carlsberg Research Laboratory
Jia-Wu Feng
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Manuel Feser
  • Fonction : Auteur
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Anne Fiebig
  • Fonction : Auteur
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Heidrun Gundlach
Helmholtz Zentrum München = German Research Center for Environmental Health
Wenbin Guo
The James Hutton Institute
Georg Haberer
Helmholtz Zentrum München = German Research Center for Environmental Health
Mats Hansson
Lund University
Axel Himmelbach
  • Fonction : Auteur
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Iris Hoffie
  • Fonction : Auteur
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Robert E Hoffie
  • Fonction : Auteur
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Haifei Hu
  • Fonction : Auteur
Murdoch University [Perth]
Guangdong Academy of Agricultural Sciences
Sachiko Isobe
Kazusa DNA Research Institute
Patrick König
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Sandip M Kale
Carlsberg Research Laboratory
Nadia Kamal
  • Fonction : Auteur
Helmholtz Zentrum München = German Research Center for Environmental Health
Gabriel Keeble-Gagnère
  • Fonction : Auteur
La Trobe University
Beat Keller
Universität Zürich [Zürich] = University of Zurich
Manuela Knauft
  • Fonction : Auteur
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Ravi Koppolu
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Simon G Krattinger
King Abdullah University of Science and Technology [Saudi Arabia]
Jochen Kumlehn
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Peter Langridge
University of Adelaide
Chengdao Li
Murdoch University [Perth]
Government of Western Australia
Yangtze University
Marina P Marone
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Andreas Maurer
  • Fonction : Auteur
Martin-Luther-University Halle-Wittenberg
Klaus F X Mayer
Helmholtz Zentrum München = German Research Center for Environmental Health
Technische Universität Munchen - Technical University Munich - Université Technique de Munich
Michael Melzer
  • Fonction : Auteur
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Gary J Muehlbauer
University of Minnesota [Twin Cities]
Emiko Murozuka
  • Fonction : Auteur
Carlsberg Research Laboratory
Sudharsan Padmarasu
  • Fonction : Auteur
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Dragan Perovic
  • Fonction : Auteur
Julius Kühn-Institut - Federal Research Centre for Cultivated Plants
Klaus Pillen
Martin-Luther-University Halle-Wittenberg
Pierre A Pin
  • Fonction : Auteur
Secobra Recherches
Curtis J Pozniak
University of Saskatchewan [Saskatoon, Canada]
Luke Ramsay
The James Hutton Institute
Pai Rosager Pedas
  • Fonction : Auteur
Carlsberg Research Laboratory
Twan Rutten
  • Fonction : Auteur
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Shun Sakuma
Tottori University
Kazuhiro Sato
Kazusa DNA Research Institute
Okayama University
Danuta Schüler
  • Fonction : Auteur
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Thomas Schmutzer
Martin-Luther-University Halle-Wittenberg
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
Helmholtz Zentrum München = German Research Center for Environmental Health
Brian J Steffenson
University of Minnesota [Twin Cities]
Hanne C Thomsen
  • Fonction : Auteur
Carlsberg Research Laboratory
Josquin F Tibbits
La Trobe University
Martin Toft Simmelsgaard Nielsen
Carlsberg Research Laboratory
Corinna Trautewig
  • Fonction : Auteur
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]
Dominique Vequaud
Secobra Recherches
Cynthia Voss
  • Fonction : Auteur
Carlsberg Research Laboratory
Penghao Wang
Murdoch University [Perth]
Robbie Waugh
University of Dundee
Sharon Westcott
  • Fonction : Auteur
Murdoch University [Perth]
Magnus Wohlfahrt Rasmussen
Carlsberg Research Laboratory
Runxuan Zhang
The James Hutton Institute
Xiao-Qi Zhang
  • Fonction : Auteur
Murdoch University [Perth]
Thomas Wicker
  • Fonction : Auteur correspondant
  • PersonId : 1109064

Connectez-vous pour contacter l'auteur
Universität Zürich [Zürich] = University of Zurich
Christoph Dockter
Connectez-vous pour contacter l'auteur
Carlsberg Research Laboratory
Martin Mascher
  • Fonction : Auteur correspondant
  • 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
  • Fonction : Auteur correspondant
  • PersonId : 956047

Connectez-vous pour contacter l'auteur
Martin-Luther-University Halle-Wittenberg
Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben]

Résumé

P an genomes are collections of annotated genome sequences of multiple individuals of a species 1 . The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants 2 . 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 are rich in gene copy number variation. 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 allelic diversity at structurally complex loci may have helped crop plants to adapt to new selective regimes in agricultural ecosystems.

Reliable crop yields fuelled the rise of human civilizations. As people embraced a new way of life, cultivated plants, too, had to adapt to the needs of their domesticators. There are different adaptive requirements in a wild compared with an arable habitat. Crop plants and their wild progenitors differ in how many vegetative branches they initiate or how many seeds or fruits they produce and when. A case in point is barley (Hordeum vulgare): in six-rowed forms of the crops, thrice as many grains set as in the ancestral two-rowed forms. This change was brought about by knockout mutations 3 of a recently evolved regulator 4 of inflorescence development. Consequently, six-rowed barleys came to predominate in most barley-growing regions 5 . Taking a broader view of the environment as a set of exogeneous factors that drive natural selection, barley provides another fascinating, and economically important, example. The process of malting involves the sprouting of moist barley grains, driving the release of enzymes that break down starch into fermentable sugars. In the wild, various environmental cues can trigger germination to improve the odds of the emerging seedling encountering favourable weather conditions for subsequent growth 6 . In the malt house, by contrast, germination has to be fast and uniform in modern cultivars to satisfy the desired specifications of the industry. In addition to these examples, traits such as disease resistance, plant architecture and nutrient use have been a focus for plant breeders and studied intensively by barley geneticists 7 . Although barley genetic analysis flourished during a 'classical' period 8 in the first half of the 20th century, it started to lag behind small-genome models because of difficulties in adapting molecular biology techniques to a large genome rich in repeats 9 . However, interest in barley as a diploid model for temperate cereals has surged again as DNA sequencing became more powerful. High-quality sequences of several barley genomes have been recently assembled 10 . New sequencing technologies have shifted the focus of

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Génomique, Transcriptomique et Protéomique [q-bio.GN]
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Dominique Fournier  : Connectez-vous pour contacter le contributeur

https://hal.inrae.fr/hal-04837447

Soumis le : vendredi 13 décembre 2024-17:40:20

Dernière modification le : mardi 17 décembre 2024-13:46:02

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hal-04837447 , version 1 (13-12-2024)

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Paternité - Pas d'utilisation commerciale - Pas de modification

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Murukarthick Jayakodi, Qiongxian Lu, Hélène Pidon, M Timothy Rabanus-Wallace, Micha Bayer, et al.. Structural variation in the pangenome of wild and domesticated barley. Nature, inPress, ⟨10.1038/s41586-024-08187-1⟩. ⟨hal-04837447⟩

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