The Barley Pan-genome Reveals the Hidden Legacy of Mutation Breeding

Overview

Journal Nature

Specialty Science

Date 2020 Nov 26

PMID 33239781

Citations 205

Authors

Murukarthick Jayakodi

Sudharsan Padmarasu

Georg Haberer

Venkata Suresh Bonthala

Heidrun Gundlach

Cecile Monat

Thomas Lux

Nadia Kamal

Daniel Lang

Axel Himmelbach

Jennifer Ens

Xiao-Qi Zhang

Tefera T Angessa

Gaofeng Zhou

Cong Tan

Camilla Hill

Penghao Wang

Miriam Schreiber

Lori B Boston

Christopher Plott

Jerry Jenkins

Yu Guo

Anne Fiebig

Hikmet Budak

Dongdong Xu

Jing Zhang

Chunchao Wang

Jane Grimwood

Jeremy Schmutz

Ganggang Guo

Guoping Zhang

Keiichi Mochida

Takashi Hirayama

Kazuhiro Sato

Kenneth J Chalmers

Peter Langridge

Robbie Waugh

Curtis J Pozniak

Uwe Scholz

Klaus F X Mayer

Manuel Spannagl

Chengdao Li

Martin Mascher

Nils Stein

Affiliations

Soon will be listed here.

Abstract

Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the 'pan-genome'). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley-comprising landraces, cultivars and a wild barley-that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.

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