Signatures of selection in recently domesticated macadamia

Jishan Lin; Wenping Zhang; Xingtan Zhang; Xiaokai Ma; Shengcheng Zhang; Shuai Chen; Yibin Wang; Haifeng Jia; Zhenyang Liao; Jing Lin; Mengting Zhu; Xiuming Xu; Mingxing Cai; Hui Zeng; Jifeng Wan; Weihai Yang; Tracie Matsumoto; Craig Hardner; Catherine J. Nock; Ray Ming

doi:10.1038/s41467-021-27937-7

Signatures of selection in recently domesticated macadamia

Jishan Lin, Wenping Zhang, Xingtan Zhang, Xiaokai Ma, Shengcheng Zhang, Shuai Chen, Yibin Wang, Haifeng Jia, Zhenyang Liao, Jing Lin, Mengting Zhu, Xiuming Xu, Mingxing Cai, Hui Zeng, Jifeng Wan, Weihai Yang, Tracie Matsumoto, Craig Hardner, Catherine J. Nock, Ray Ming

Plant Biology

Research output: Contribution to journal › Article › peer-review

Abstract

Macadamia is a high value nut crop that is recently domesticated, ideal for testing the effect of artificial selection. Here, we sequence the genome of Hawaiian cultivar ‘Kau’ and assemble into 794 Mb in 14 pseudo-chromosomes with 37,728 genes. Genome analysis reveals a whole-genome duplication event, occurred 46.8 million years ago. Gene expansions occurred in gene families involves in fatty acid biosynthesis. Gene duplication of MADS-Box transcription factors in proanthocyanidin biosynthesis are relevant for seed coat development. Genome re-sequencing of 112 accessions reveals the origin of Hawaiian cultivars from Mount Bauple in southeast Queensland in Australia. Selective sweeps are detected in macadamia cultivars, including genes involved in fatty acid biosynthesis, seed coat development, and heat stress response. Such strong effects of artificial selection in few generations reveals the genomic basis for ‘one-step operation’ for clonal crop domestication. The knowledge gained could accelerate domestication of new crops from wild species.

Original language	English (US)
Article number	242
Journal	Nature communications
Volume	13
Issue number	1
Early online date	Jan 11 2022
DOIs	https://doi.org/10.1038/s41467-021-27937-7
State	Published - Dec 2022

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General
General Physics and Astronomy

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10.1038/s41467-021-27937-7License: CC BY

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title = "Signatures of selection in recently domesticated macadamia",

abstract = "Macadamia is a high value nut crop that is recently domesticated, ideal for testing the effect of artificial selection. Here, we sequence the genome of Hawaiian cultivar {\textquoteleft}Kau{\textquoteright} and assemble into 794 Mb in 14 pseudo-chromosomes with 37,728 genes. Genome analysis reveals a whole-genome duplication event, occurred 46.8 million years ago. Gene expansions occurred in gene families involves in fatty acid biosynthesis. Gene duplication of MADS-Box transcription factors in proanthocyanidin biosynthesis are relevant for seed coat development. Genome re-sequencing of 112 accessions reveals the origin of Hawaiian cultivars from Mount Bauple in southeast Queensland in Australia. Selective sweeps are detected in macadamia cultivars, including genes involved in fatty acid biosynthesis, seed coat development, and heat stress response. Such strong effects of artificial selection in few generations reveals the genomic basis for {\textquoteleft}one-step operation{\textquoteright} for clonal crop domestication. The knowledge gained could accelerate domestication of new crops from wild species.",

author = "Jishan Lin and Wenping Zhang and Xingtan Zhang and Xiaokai Ma and Shengcheng Zhang and Shuai Chen and Yibin Wang and Haifeng Jia and Zhenyang Liao and Jing Lin and Mengting Zhu and Xiuming Xu and Mingxing Cai and Hui Zeng and Jifeng Wan and Weihai Yang and Tracie Matsumoto and Craig Hardner and Nock, {Catherine J.} and Ray Ming",

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doi = "10.1038/s41467-021-27937-7",

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AU - Lin, Jishan

AU - Zhang, Wenping

AU - Zhang, Xingtan

AU - Ma, Xiaokai

AU - Zhang, Shengcheng

AU - Chen, Shuai

AU - Wang, Yibin

AU - Jia, Haifeng

AU - Liao, Zhenyang

AU - Lin, Jing

AU - Zhu, Mengting

AU - Xu, Xiuming

AU - Cai, Mingxing

AU - Zeng, Hui

AU - Wan, Jifeng

AU - Yang, Weihai

AU - Matsumoto, Tracie

AU - Hardner, Craig

AU - Nock, Catherine J.

AU - Ming, Ray

N1 - This work was supported by startup fund from Fujian Agriculture and Forestry University.

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Signatures of selection in recently domesticated macadamia

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