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ARS Home » Pacific West Area » Hilo, Hawaii » Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center » Tropical Plant Genetic Resources and Disease Research » Research » Publications at this Location » Publication #384761

Research Project: Management, Characterization, and Evaluation of Pacific Tropical and Subtropical Fruit and Nut Genetic Resources and Associated Information

Location: Tropical Plant Genetic Resources and Disease Research

Title: Rambutan genome revealed gene networks for spine formation and aril development

Author
item ZHANG, WENPING - Fujian Agricultural & Forestry University
item LIN, JISHAN - Fujian Agricultural & Forestry University
item LI, JIANGUO - Fujian Fruit Breeding Engineering Technology Research Center For Longan And Loquat
item ZHEN, SHAOQUAN - Fujian Agricultural & Forestry University
item ZHANG, XINGTAN - Fujian Agricultural & Forestry University
item CHEN, SHUAI - Fujian Agricultural & Forestry University
item MA, XIAOKAI - Fujian Agricultural & Forestry University
item DONG, FEI - Fujian Agricultural & Forestry University
item JIA, HAIFENG - Fujian Agricultural & Forestry University
item XU, XIUMING - Fujian Agricultural & Forestry University
item YANG, ZIQIN - Chinese Academy Of Tropical Agricultural Sciences
item MA, PANPAN - Fujian Agricultural & Forestry University
item DENG, FANG - Fujian Agricultural & Forestry University
item DENG, BAN - Fujian Agricultural & Forestry University
item HUANG, YONGJI - Fujian Agricultural & Forestry University
item LI, ZHANJIE - Fujian Agricultural & Forestry University
item LV, XIAOZHOU - Tropical Crop Institute (ICT)
item MA, YAYING - Fujian Agricultural & Forestry University
item LIAO, ZHENYANG - Fujian Agricultural & Forestry University
item LIN, ZHICONG - Fujian Agricultural & Forestry University
item LIN, JING - Fujian Agricultural & Forestry University
item ZHANG, SHENGCHENG - Fujian Agricultural & Forestry University
item Matsumoto Brower, Tracie
item XIA, RUI - Tropical Crop Institute (ICT)
item ZHANG, JISEN - Fujian Agricultural & Forestry University
item RAY, MING - University Of Illinois

Submitted to: The Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/6/2021
Publication Date: 9/13/2021
Citation: Zhang, W., Lin, J., Li, J., Zhen, S., Zhang, X., Chen, S., Ma, X., Dong, F., Jia, H., Xu, X., Yang, Z., Ma, P., Deng, F., Deng, B., Huang, Y., Li, Z., Lv, X., Ma, Y., Liao, Z., Lin, Z., Lin, J., Zhang, S., Matsumoto Brower, T.K., Xia, R., Zhang, J., Ray, M. 2021. Rambutan genome revealed gene networks for spine formation and aril development. The Plant Journal. 108:1037-1052. https://doi.org/10.1111/tpj.15491.
DOI: https://doi.org/10.1111/tpj.15491

Interpretive Summary: Rambutan is a popular tropical fruit with exotic appearance with long flexible spines on shells, extraordinary aril growth, desirable nutrition and favorable taste. The genome of the cultivar Baoyan 7 was sequences and assembled. Comparing the rambutan genome to the lychee genome, showed that the chromosomes fused together after the two species had evolved from a common ancestor,15.7 million years ago. Genes were found that are thought to be responsible for the spine like structures on the outer skin of the fruit, as well as the sweet flesh of the fruit or aril. Other genes associated with root development and other plant hormones were also found. These findings enhanced our understanding of spine and aril development and provide genomic resources for rambutan improvement.

Technical Abstract: Rambutan is a popular tropical fruit with exotic appearance with long flexible spines on shells, extraordinary aril growth, desirable nutrition and favorable taste. The genome of an elite rambutan cultivar Baoyan 7 was assembled into 328 Mb in 16 pseudo-chromosomes. Comparative genomics analysis between rambutan and lychee revealed a chromosome fusion event after divergence of these two species from their common ancestor 15.7 million years ago. Genomic and transcriptomic analyses revealed candidate genes and gene networks controlling spine formation, fleshy aril development, and sex differentiation. Root development and plant hormone response genes regulate spine development, including endoplasmic reticulum pathway genes, jasmonic acid response genes, vascular bundle development genes, and potassium ion transport genes. Aril development were regulated by D-class gene (NlSTK and NlSHP1), plant hormone and phenylpropanoid biosynthesis genes, and sugar related metabolism genes. Population genomic analyses revealed that varieties from Hawaii and Hainan province can be grouped into three distinct clusters. Genes in selective sweeps during domestication are related to fruit morphology and environment stress response. These findings enhanced our understanding of spine and aril development and provide genomic resources for rambutan improvement.