Signatures of selection in recently domesticated macadamia

Authors: LIN, JISHAN - Fujian Agricultural & Forestry University; ZHANG, WENPING - Fujian Agricultural & Forestry University; ZHANG, XINGTAN - Fujian Agricultural & Forestry University; MA, XIAOKAI - Fujian Agricultural & Forestry University; ZHANG, SHENGCHENG - Fujian Agricultural & Forestry University; CHEN, S - Fujian Agricultural & Forestry University; WANG, YIBIN - Fujian Agricultural & Forestry University; JIA, HAIFENG - Fujian Agricultural & Forestry University; LIAO, ZHENYANG - Fujian Agricultural & Forestry University; LIN, JING - Fujian Agricultural & Forestry University; ZHU, MENGTING - Fujian Agricultural & Forestry University; XU, XIUMING - Fujian Agricultural & Forestry University; CAI, MINGXING - Fujian Agricultural & Forestry University; ZENG, HUI - Chinese Academy Of Tropical Agricultural Sciences; WAN, JIFENG - Chinese Academy Of Tropical Agricultural Sciences; YANG, WEIHAI - Chinese Academy Of Tropical Agricultural Sciences; Matsumoto Brower, Tracie; HARDNER, CRAIG - University Of Queensland; NOCK, CATHERINE - Southern Cross University; MING, RAY - University Of Illinois

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/21/2021
Publication Date: 1/11/2022
Citation: Lin, J., Zhang, W., Zhang, X., Ma, X., Zhang, S., Chen, S., Wang, Y., Jia, H., Liao, Z., Lin, J., Zhu, M., Xu, X., Cai, M., Zeng, H., Wan, J., Yang, W., Matsumoto Brower, T.K., Hardner, C., Nock, C.J., Ming, R. 2022. Signatures of selection in recently domesticated macadamia. Nature Communications. 13. Article 242. https://doi.org/10.1038/s41467-021-27937-7.
DOI: https://doi.org/10.1038/s41467-021-27937-7

Interpretive Summary: Macadamia is a high value nut crop grown for the edible fruit that is clonally propagated. The genome of the Hawaiian macadamia cultivar 'Kau' was sequence and genome assembled. Analysis of this genome showed the genome was duplicated over 46.8 million years ago. Many of the genes that were duplicated were those involved in fatty acid biosynthesis, seed coat development and heat stress response. This cultivar represents the first step in domestication is only a few generations from their wild ancestors. With this in depth knowledge of the genome, relationships between domesticated Hawaiian macadamia cultivars and wild germplasm can be achieved. This knowledge could accelerate domestication of new crops from wild species.

Technical Abstract: Macadamia is a high value nut crop that is recently domesticated, ideal for testing the effect of artificial selection. The genome of Hawaiian cultivar ‘KAU’ was sequenced and assembled into 794 Mb in 14 pseudo-chromosomes with 37,742 genes. Genome analysis revealed a whole-genome duplication event, occurred 46.8 million years ago. Gene expansions occurred in gene families involved 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 in south-east Queensland in Australia. Selective sweeps were 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 revealed the genomic basis for “one-step operation” for clonal crop domestication. The knowledge gained could accelerate domestication of new crops from wild species.