The barley pan-genome reveals the hidden legacy of mutation breeding

Murukarthick Jayakodi; Sudharsan Padmarasu; Georg Haberer; Venkata Suresh Bonthala; Heidrun Gundlach; Cécile 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

doi:10.1038/s41586-020-2947-8

The barley pan-genome reveals the hidden legacy of mutation breeding

Murukarthick Jayakodi, Sudharsan Padmarasu, Georg Haberer, Venkata Suresh Bonthala, Heidrun Gundlach, Cécile 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 PlottJerry 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 (Lead / Corresponding author), Martin Mascher (Lead / Corresponding author), Nils Stein (Lead / Corresponding author)

Plant Sciences

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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'1). 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 conditions2. 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.

Original language	English
Pages (from-to)	284-289
Number of pages	6
Journal	Nature
Volume	588
Early online date	25 Nov 2020
DOIs	https://doi.org/10.1038/s41586-020-2947-8
Publication status	Published - 10 Dec 2020

Keywords

Genomics
lant genetics
Structural variation

ASJC Scopus subject areas

General

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Final Published VersionFinal published version, 21.6 MBLicence: CC BY

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Jayakodi, M., Padmarasu, S., Haberer, G., Bonthala, V. S., Gundlach, H., Monat, C., Lux, T., Kamal, N., Lang, D., Himmelbach, A., Ens, J., Zhang, X.-Q., Angessa, T. T., Zhou, G., Tan, C., Hill, C., Wang, P., Schreiber, M., Boston, L. B., ... Stein, N. (2020). The barley pan-genome reveals the hidden legacy of mutation breeding. Nature, 588, 284-289. https://doi.org/10.1038/s41586-020-2947-8

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title = "The barley pan-genome reveals the hidden legacy of mutation breeding",

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'1). 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 conditions2. 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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author = "Murukarthick Jayakodi and Sudharsan Padmarasu and Georg Haberer and Bonthala, {Venkata Suresh} and Heidrun Gundlach and C{\'e}cile Monat and Thomas Lux and Nadia Kamal and Daniel Lang and Axel Himmelbach and Jennifer Ens and Xiao-Qi Zhang and Angessa, {Tefera T.} and Gaofeng Zhou and Cong Tan and Camilla Hill and Penghao Wang and Miriam Schreiber and Boston, {Lori B.} and Christopher Plott and Jerry Jenkins and Yu Guo and Anne Fiebig and Hikmet Budak and Dongdong Xu and Jing Zhang and Chunchao Wang and Jane Grimwood and Jeremy Schmutz and Ganggang Guo and Guoping Zhang and Keiichi Mochida and Takashi Hirayama and Kazuhiro Sato and Chalmers, {Kenneth J.} and Peter Langridge and Robbie Waugh and Pozniak, {Curtis J.} and Uwe Scholz and Mayer, {Klaus F. X.} and Manuel Spannagl and Chengdao Li and Martin Mascher and Nils Stein",

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Jayakodi, M, Padmarasu, S, Haberer, G, Bonthala, VS, Gundlach, H, Monat, C, Lux, T, Kamal, N, Lang, D, Himmelbach, A, Ens, J, Zhang, X-Q, Angessa, TT, Zhou, G, Tan, C, Hill, C, Wang, P, Schreiber, M, Boston, LB, Plott, C, Jenkins, J, Guo, Y, Fiebig, A, Budak, H, Xu, D, Zhang, J, Wang, C, Grimwood, J, Schmutz, J, Guo, G, Zhang, G, Mochida, K, Hirayama, T, Sato, K, Chalmers, KJ, Langridge, P, Waugh, R, Pozniak, CJ, Scholz, U, Mayer, KFX, Spannagl, M, Li, C, Mascher, M & Stein, N 2020, 'The barley pan-genome reveals the hidden legacy of mutation breeding', Nature, vol. 588, pp. 284-289. https://doi.org/10.1038/s41586-020-2947-8

TY - JOUR

T1 - The barley pan-genome reveals the hidden legacy of mutation breeding

AU - Jayakodi, Murukarthick

AU - Padmarasu, Sudharsan

AU - Haberer, Georg

AU - Bonthala, Venkata Suresh

AU - Gundlach, Heidrun

AU - Monat, Cécile

AU - Lux, Thomas

AU - Kamal, Nadia

AU - Lang, Daniel

AU - Himmelbach, Axel

AU - Ens, Jennifer

AU - Zhang, Xiao-Qi

AU - Angessa, Tefera T.

AU - Zhou, Gaofeng

AU - Tan, Cong

AU - Hill, Camilla

AU - Wang, Penghao

AU - Schreiber, Miriam

AU - Boston, Lori B.

AU - Plott, Christopher

AU - Jenkins, Jerry

AU - Guo, Yu

AU - Fiebig, Anne

AU - Budak, Hikmet

AU - Xu, Dongdong

AU - Zhang, Jing

AU - Wang, Chunchao

AU - Grimwood, Jane

AU - Schmutz, Jeremy

AU - Guo, Ganggang

AU - Zhang, Guoping

AU - Mochida, Keiichi

AU - Hirayama, Takashi

AU - Sato, Kazuhiro

AU - Chalmers, Kenneth J.

AU - Langridge, Peter

AU - Waugh, Robbie

AU - Pozniak, Curtis J.

AU - Scholz, Uwe

AU - Mayer, Klaus F. X.

AU - Spannagl, Manuel

AU - Li, Chengdao

AU - Mascher, Martin

AU - Stein, Nils

PY - 2020/12/10

Y1 - 2020/12/10

N2 - 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'1). 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 conditions2. 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.

AB - 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'1). 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 conditions2. 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.

KW - Genomics

KW - lant genetics

KW - Structural variation

U2 - 10.1038/s41586-020-2947-8

DO - 10.1038/s41586-020-2947-8

M3 - Article

C2 - 33239781

SN - 0028-0836

VL - 588

SP - 284

EP - 289

JO - Nature

JF - Nature

ER -

The barley pan-genome reveals the hidden legacy of mutation breeding

Abstract

Keywords

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