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

Jayakodi Murukarthick; Padmarasu Sudharsan; Haberer Georg; Bonthala Venkata Suresh; Gundlach Heidrun; Monat Ceecile; Lux Thomas; Kamal Nadia; Lang Daniel; Himmelbach Axel; Ens Jennifer; Zhang Xiao-Qi; Angessa Tefera T.; Zhou Gaofeng; Tan Cong; Hill Camilla; Wang Penghao; Schreiber Miriam; Boston Lori B.; Plott Christopher; Jenkins Jerry; Guo Yu; Fiebig Anne; Budak Hikmet; Xu Dongdong; Zhang Jing; Wang Chunchao; Grimwood Jane; Schmutz Jeremy; Guo Ganggang; Zhang Guoping; Mochida Keiichi; Hirayama Takashi; Sato Kazuhiro; Chalmers Kenneth J.; Langridge Peter; Waugh Robbie; Pozniak Curtis J.; Scholz Uwe; Mayer Klaus F. X.; Spannagl Manuel; Li Chengdao; Mascher Martin; Stein Nils

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

机译：大麦泛基因组揭示了突变育种的隐藏遗产

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Chromosome-scale sequence assemblies of 20 diverse varieties of barley are used to construct a first-generation pan-genome, revealing previously hidden genetic variation that can be used by studies aimed at crop improvementGenetic 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 conditions(2). 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.

机译：染色体级序列组件为20种不同品种的大麦，用于构建第一代泛基因组，揭示了先前隐藏的遗传变异，这些遗传变异可以通过针对作物改善的研究来使用的是作物改善的关键。由于基因组结构变异，单一参考基因组组件不能捕获作物物种的序列多样性的完全补充（称为“泛基因组”（1））。多种高质量的序列组件是泛基因组基础设施的不可或缺的组成部分。大麦（Hordeum Vulgare L.）是一种重要的谷物作物，历史悠久的栽培历史，适应广泛的农业气候条件（2）。在这里，我们报告了染色体级序列组件的构建，用于含有20种大麦的体重体，品种和野生大麦的基因型 - 被选为全球大麦多样性的代表。我们编目的基因组存在/缺失变体，并探讨了通过300基因堤防的全基因组霰弹枪测序使用结构变体进行定量遗传分析。我们发现了丰富的大型反转多态性，并详细分析了当前精英大麦种质中经常发现的两种反转;一个可能是突变育种的产物，另一个是与涉及地理范围扩展的基因座紧密相关。该第一代大麦泛基因组使得先前隐藏的遗传变异可用于遗传研究和繁殖。

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《Nature》 |2020年第7837期|284-289|共6页
作者
Jayakodi Murukarthick; Padmarasu Sudharsan; Haberer Georg; Bonthala Venkata Suresh; Gundlach Heidrun; Monat Ceecile; Lux Thomas; Kamal Nadia; Lang Daniel; Himmelbach Axel; Ens Jennifer; Zhang Xiao-Qi; Angessa Tefera T.; Zhou Gaofeng; Tan Cong; Hill Camilla; Wang Penghao; Schreiber Miriam; Boston Lori B.; Plott Christopher; Jenkins Jerry; Guo Yu; Fiebig Anne; Budak Hikmet; Xu Dongdong; Zhang Jing; Wang Chunchao; Grimwood Jane; Schmutz Jeremy; Guo Ganggang; Zhang Guoping; Mochida Keiichi; Hirayama Takashi; Sato Kazuhiro; Chalmers Kenneth J.; Langridge Peter; Waugh Robbie; Pozniak Curtis J.; Scholz Uwe; Mayer Klaus F. X.; Spannagl Manuel; Li Chengdao; Mascher Martin; Stein Nils;
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作者单位

Leibniz Inst Plant Genet & Crop Plant Res IPK Gat Seeland Germany;

Leibniz Inst Plant Genet & Crop Plant Res IPK Gat Seeland Germany;

German Res Ctr Environm Hlth Helmholtz Ctr Munich Plant Genome & Syst Biol PGSB Neuherberg Germany;

German Res Ctr Environm Hlth Helmholtz Ctr Munich Plant Genome & Syst Biol PGSB Neuherberg Germany;

German Res Ctr Environm Hlth Helmholtz Ctr Munich Plant Genome & Syst Biol PGSB Neuherberg Germany;

Leibniz Inst Plant Genet & Crop Plant Res IPK Gat Seeland Germany;

German Res Ctr Environm Hlth Helmholtz Ctr Munich Plant Genome & Syst Biol PGSB Neuherberg Germany;

German Res Ctr Environm Hlth Helmholtz Ctr Munich Plant Genome & Syst Biol PGSB Neuherberg Germany;

German Res Ctr Environm Hlth Helmholtz Ctr Munich Plant Genome & Syst Biol PGSB Neuherberg Germany;

Leibniz Inst Plant Genet & Crop Plant Res IPK Gat Seeland Germany;

Univ Saskatchewan Dept Plant Sci Saskatoon SK Canada;

Murdoch Univ Coll Sci Hlth Engn & Educ State Agr Biotechnol Ctr Western Barley Genet Alliance Murdoch WA Australia;

Murdoch Univ Coll Sci Hlth Engn & Educ State Agr Biotechnol Ctr Western Barley Genet Alliance Murdoch WA Australia;

Murdoch Univ Coll Sci Hlth Engn & Educ State Agr Biotechnol Ctr Western Barley Genet Alliance Murdoch WA Australia|Dept Primary Ind & Reg Dev Agr & Food S Perth WA Australia;

Murdoch Univ Coll Sci Hlth Engn & Educ State Agr Biotechnol Ctr Western Barley Genet Alliance Murdoch WA Australia;

Murdoch Univ Coll Sci Hlth Engn & Educ State Agr Biotechnol Ctr Western Barley Genet Alliance Murdoch WA Australia;

Murdoch Univ Coll Sci Hlth Engn & Educ State Agr Biotechnol Ctr Western Barley Genet Alliance Murdoch WA Australia;

James Hutton Inst Dundee Scotland;

HudsonAlpha Inst Biotechnol Huntsville AL USA;

HudsonAlpha Inst Biotechnol Huntsville AL USA;

HudsonAlpha Inst Biotechnol Huntsville AL USA;

Leibniz Inst Plant Genet & Crop Plant Res IPK Gat Seeland Germany;

Leibniz Inst Plant Genet & Crop Plant Res IPK Gat Seeland Germany;

Montana BioAg Inc Missoula MT USA;

Chinese Acad Agr Sci ICS CAAS Inst Crop Sci Beijing Peoples R China;

Chinese Acad Agr Sci ICS CAAS Inst Crop Sci Beijing Peoples R China;

Chinese Acad Agr Sci ICS CAAS Inst Crop Sci Beijing Peoples R China;

HudsonAlpha Inst Biotechnol Huntsville AL USA;

HudsonAlpha Inst Biotechnol Huntsville AL USA;

Chinese Acad Agr Sci ICS CAAS Inst Crop Sci Beijing Peoples R China;

Zhejiang Univ Coll Agr & Biotechnol Hangzhou Peoples R China;

RIKEN Ctr Sustainable Resource Sci Bioprod Informat Res Team Yokohama Kanagawa Japan|Yokohama City Univ Kihara Inst Biol Res Yokohama Kanagawa Japan|Okayama Univ Inst Plant Sci & Resources Kurashiki Okayama Japan;

Okayama Univ Inst Plant Sci & Resources Kurashiki Okayama Japan;

Okayama Univ Inst Plant Sci & Resources Kurashiki Okayama Japan;

Univ Adelaide Sch Agr Food & Wine Glen Osmond SA Australia;

Univ Adelaide Sch Agr Food & Wine Glen Osmond SA Australia;

James Hutton Inst Dundee Scotland|Univ Adelaide Sch Agr Food & Wine Glen Osmond SA Australia|Univ Dundee Sch Life Sci Dundee Scotland;

Univ Saskatchewan Dept Plant Sci Saskatoon SK Canada;

Leibniz Inst Plant Genet & Crop Plant Res IPK Gat Seeland Germany;

German Res Ctr Environm Hlth Helmholtz Ctr Munich Plant Genome & Syst Biol PGSB Neuherberg Germany|Tech Univ Munich Sch Life Sci Weihenstephan Freising Weihenstephan Germany;

German Res Ctr Environm Hlth Helmholtz Ctr Munich Plant Genome & Syst Biol PGSB Neuherberg Germany;

Murdoch Univ Coll Sci Hlth Engn & Educ State Agr Biotechnol Ctr Western Barley Genet Alliance Murdoch WA Australia|Dept Primary Ind & Reg Dev Agr & Food S Perth WA Australia|Yangtze Univ Hubei Collaborat Innovat Ctr Grain Ind Jingzhou Peoples R China;

Leibniz Inst Plant Genet & Crop Plant Res IPK Gat Seeland Germany|German Ctr Integrat Biodivers Res iDiv Leipzig Germany;

Leibniz Inst Plant Genet & Crop Plant Res IPK Gat Seeland Germany|Georg August Univ Gottingen Ctr Integrated Breeding Res CiBreed Gottingen Germany;

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收录信息美国《科学引文索引》(SCI);美国《工程索引》(EI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
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1. Interregional Training Course on Mutation Induction and Breeding for Cereal (Wheat and Barley) Rust Resistance and Climate Hardening/Harsh Environment Adaptation Part I Responding to the Transboundary Threat to Wheat Black Stem Rust (Ug99) and Mutation Induction and Supportive Breeding and Biotechnologies for Improving Crop Productivity (ARASIA), INT/5/150 & RAS/5/048, Seib-ersdorf, Austria, 7-11 June 2010 [J] . Plant breeding & genetics newsletter . 2010,第25期

机译：谷物（小麦和大麦）抗锈性突变诱导和育种与气候硬化/恶劣环境适应的区域间培训课程第一部分，应对小麦黑茎锈病（Ug99）的跨界威胁以及诱变和支持性育种以及改善作物的生物技术生产力（ARASIA），INT / 5/150和RAS / 5/048，奥地利塞伯斯多夫，2010年6月7日至11日
2. HorTILLUS—A Rich and Renewable Source of Induced Mutations for Forward/Reverse Genetics and Pre-breeding Programs in Barley ( Hordeum vulgare L.) [J] . Miriam E. Szurman-Zubrzycka, Justyna Zbieszczyk, Marek Marzec, Frontiers in Plant Science . 2018,第4期

机译： Hor TILLUS-大麦正向/反向遗传和预育程序的诱变诱变的丰富且可更新的来源（ Hordeum vulgare L.）
3. Mutations in the gene of the Gα subunit of the heterotrimeric G protein are the cause for the brachytic1 semi-dwarf phenotype in barley and applicable for practical breeding [J] . Ilka Braumann, Christoph Dockter, Sebastian Beier, Hereditas . 2018,第1期

机译：三聚体G蛋白的Gα亚基基因突变是大麦brachytic1半矮表型的原因，可用于实际育种
4. Genome-Wide Association Mapping Reveals Genetic Architecture of DurAble Spot Blotch Resistance in US Barley Breeding Germplasm [C] . Hao Zhou, Brian J. Steffenson Advance in barley sciences : proceedings of 11th international barley genetics symposium . 2012

机译：全基因组关联图谱揭示了美国大麦育种种种对持久性斑点病的抗性遗传结构
5. Point Mutational Examination of Eukaryotic Initiation Factor 4E (eIF4E), Inclusion Bodies Analysis, and Barley yellow dwarf virus (BYDV) Exonuclease Resistant RNA Structure Mapping and Prediction [D] . Sheber, Melissa. 2018

机译：真核生物起始因子4E（eIF4E）的点突变检查，包涵体分析和大麦黄矮病毒（BYDV）核酸外切酶抗性RNA结构定位和预测
6. Mutations in the gene of the Gα subunit of the heterotrimeric G protein are the cause for the brachytic1 semi-dwarf phenotype in barley and applicable for practical breeding [O] . Ilka Braumann, Christoph Dockter, Sebastian Beier, 2018

机译：三聚体G蛋白的Gα亚基基因突变是大麦brachytic1半矮表型的原因可用于实际育种
7. The barley pan-genome reveals the hidden legacy of mutation breeding [O] . Murukarthick Jayakodi, Sudharsan Padmarasu, Georg Haberer, 2020

机译：大麦泛基因组揭示了突变育种的隐藏遗产
8. Ontogeny of the Barley Plant as Related to Mutation Expression and Detection of Pollen Mutations [R] . Hodgdon, A. L., Marcus, A. H., Arenaz, P., 1980

机译：与突变表达和花粉突变检测有关的大麦植物的发育

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

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