Whole genomes and transcriptomes reveal adaptation and domestication of pistachio.
Lin Zeng, Xiao-Long Tu, He Dai, Feng-Ming Han, Bing-She Lu, Ming-Shan Wang, Hojjat Asadollahpour Nanaei, Ali Tajabadipour, Mehdi Mansouri, Xiao-Long Li, Li-Li Ji, David M Irwin, Hong Zhou, Min Liu, Hong-Kun Zheng, Ali Esmailizadeh, Dong-Dong Wu
Author Information
Lin Zeng: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
Bing-She Lu: College of Landscape Architecture and Tourism, Agricultural University of Hebei, Baoding, 071000, China.
Ming-Shan Wang: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
Hojjat Asadollahpour Nanaei: Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran.
Ali Tajabadipour: Pistachio Research Center, Horticultural Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Rafsanjan, Iran.
Mehdi Mansouri: Department of Agricultural Biotechnology, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.
David M Irwin: Department of Laboratory Medicine and Pathobiology, Banting and Best Diabetes Centre, University of Toronto, Toronto, ON, M5S 1A8, Canada.
Hong Zhou: Chinese Academy of Forestry Sciences, Beijing, China.
Min Liu: Biomarker Technologies Corporation, Beijing, China.
Ali Esmailizadeh: Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran. aliesmaili@uk.ac.ir.
Dong-Dong Wu: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. wudongdong@mail.kiz.ac.cn.
BACKGROUND: Pistachio (Pistacia vera), one of the most important commercial nut crops worldwide, is highly adaptable to abiotic stresses and is tolerant to drought and salt stresses. RESULTS: Here, we provide a draft de novo genome of pistachio as well as large-scale genome resequencing. Comparative genomic analyses reveal stress adaptation of pistachio is likely attributable to the expanded cytochrome P450 and chitinase gene families. Particularly, a comparative transcriptomic analysis shows that the jasmonic acid (JA) biosynthetic pathway plays an important role in salt tolerance in pistachio. Moreover, we resequence 93 cultivars and 14 wild P. vera genomes and 35 closely related wild Pistacia genomes, to provide insights into population structure, genetic diversity, and domestication. We find that frequent genetic admixture occurred among the different wild Pistacia species. Comparative population genomic analyses reveal that pistachio was domesticated about 8000 years ago and suggest that key genes for domestication related to tree and seed size experienced artificial selection. CONCLUSIONS: Our study provides insight into genetic underpinning of local adaptation and domestication of pistachio. The Pistacia genome sequences should facilitate future studies to understand the genetic basis of agronomically and environmentally related traits of desert crops.
