Whole genomes and transcriptomes reveal adaptation and domestication of pistachio

First author: Lin Zeng; Affiliations: CAS Kunming Institute of Zoology (中国科学院昆明动物研究所): Kunming, China

Corresponding author: Dong-Dong Wu

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. 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. 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.

开心果（Pistacia vera）是最具商业价值的坚果作物之一，对于非生物胁迫具有较高的适应能力，能够抵御干旱和盐胁迫。本文中，作者报道了开心果的基因组组装结果，同时还有大范围的基因组重测序结果。比较基因组的结果显示开心果的抗性很有可能与细胞色素P450基因家族和几丁质酶基因家族的扩张有关。比较转录组显示茉莉酸的生物合成通路在开心果的高耐盐能力方面发挥重要作用。此外，作者还对93个栽培种、14个野生种以及35个与野生开心果近缘物种进行了重测序，揭示了开心果的群体结构特征、遗传多样性以及驯化。作者发现在不同的野生开心果物种之间存在频繁的遗传物质交流。比较群体基因组分析显示开心果大概在距今8000年前开始被驯化，作者鉴定了驯化过程中受到人工选择的、与树体和种子大小相关的关键基因。本文的研究结果为开心果的区域适应性和驯化提供了遗传基础。本文所报道的开心果基因组将有利于加速研究沙漠作物农艺和环境相关性状的遗传基础。

通讯：吴东东（http://sourcedb.kiz.cas.cn/zw/zjrc/201512/t20151230_4505492.html）

个人简介：2002-2006年，复旦大学生科院，学士；2006-2011年，中国科学院昆明动物研究所，遗传学博士。

研究方向：灵长类动物基因组进化；家养动物环境适应的遗传机制。

doi: https://doi.org/10.1186/s13059-019-1686-3

Journal: Genome Biology

Published date: April 18, 2019