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Graph pangenome captures missing heritability and empowers tomato breeding

Zhou, Yao and Zhang, Zhiyang and Bao, Zhigui and Li, Hongbo and Lyu, Yaqing and Zan, Yanjun and Wu, Yaoyao and Cheng, Lin and Fang, Yuhan and Wu, Kun and Zhang, Jinzhe and Lyu, Hongjun and Lin, Tao and Saha, Surya and Mueller, Lukas and Fei, Zhangjun and Fei, Zhangjun and Stadler, Thomas and Xu, Shizhong and Zhang, Zhiwu and Speed, Doug and Huang, Sanwen (2022). Graph pangenome captures missing heritability and empowers tomato breeding. Nature. 606 :7914 , 527-534
[Research article]

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Abstract

Missing heritability in genome-wide association studies defines a major problem in genetic analyses of complex biological traits(1,2). The solution to this problem is to identify all causal genetic variants and to measure their individual contributions(3,4). Here we report a graph pangenome of tomato constructed by precisely cataloguing more than 19 million variants from 838 genomes, including 32 new reference-level genome assemblies. This graph pangenome was used forgenome-wide association study analyses and heritability estimation of 20,323 gene-expression and metabolite traits. The average estimated trait heritability is 0.41 compared with 0.33 when using the single linear reference genome. This 24% increase in estimated heritability is largely due to resolving incomplete linkage disequilibrium through the inclusion of additional causal structural variants identified using the graph pangenome. Moreover, by resolving allelic and locus heterogeneity, structural variants improve the power to identify genetic factors underlying agronomically important traits leading to, for example, the identification of two new genes potentially contributing to soluble solid content. The newly identified structural variants will facilitate genetic improvement of tomato through both marker-assisted selection and genomic selection. Our study advances the understanding of the heritability of complex traits and demonstrates the power of the graph pangenome in crop breeding.

Authors/Creators:Zhou, Yao and Zhang, Zhiyang and Bao, Zhigui and Li, Hongbo and Lyu, Yaqing and Zan, Yanjun and Wu, Yaoyao and Cheng, Lin and Fang, Yuhan and Wu, Kun and Zhang, Jinzhe and Lyu, Hongjun and Lin, Tao and Saha, Surya and Mueller, Lukas and Fei, Zhangjun and Fei, Zhangjun and Stadler, Thomas and Xu, Shizhong and Zhang, Zhiwu and Speed, Doug and Huang, Sanwen
Title:Graph pangenome captures missing heritability and empowers tomato breeding
Series Name/Journal:Nature
Year of publishing :2022
Volume:606
Number:7914
Page range:527-534
Number of Pages:8
Publisher:NATURE PORTFOLIO
ISSN:0028-0836
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
URN:NBN:urn:nbn:se:slu:epsilon-p-118029
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-118029
Additional ID:
Type of IDID
DOI10.1038/s41586-022-04808-9
Web of Science (WoS)000808011000004
ID Code:28677
Faculty:S - Faculty of Forest Sciences
Department:(S) > Dept. of Forest Genetics and Plant Physiology
Deposited By: SLUpub Connector
Deposited On:30 Aug 2022 14:34
Metadata Last Modified:30 Aug 2022 14:41

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