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 () and Ray Ming ()
Additional contact information
Jishan Lin: Fujian Agriculture and Forestry University
Wenping Zhang: Fujian Agriculture and Forestry University
Xingtan Zhang: Fujian Agriculture and Forestry University
Xiaokai Ma: Fujian Agriculture and Forestry University
Shengcheng Zhang: Fujian Agriculture and Forestry University
Shuai Chen: Fujian Agriculture and Forestry University
Yibin Wang: Fujian Agriculture and Forestry University
Haifeng Jia: Fujian Agriculture and Forestry University
Zhenyang Liao: Fujian Agriculture and Forestry University
Jing Lin: Fujian Agriculture and Forestry University
Mengting Zhu: Fujian Agriculture and Forestry University
Xiuming Xu: Fujian Agriculture and Forestry University
Mingxing Cai: Fujian Agriculture and Forestry University
Hui Zeng: China Academy of Tropical Agricultural Sciences
Jifeng Wan: China Academy of Tropical Agricultural Sciences
Weihai Yang: China Academy of Tropical Agricultural Sciences
Tracie Matsumoto: Pacific Basin Agricultural Research Center
Craig Hardner: The University of Queensland
Catherine J. Nock: Southern Cross University
Ray Ming: University of Illinois at Urbana-Champaign

Nature Communications, 2022, vol. 13, issue 1, 1-12

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-021-27937-7

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