Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits

First author: Shaogui Guo; Affiliations: Beijing Academy of Agricultural and Forestry Sciences (北京市农林科学院): Beijing, China

Corresponding author: Yong Xu 

Fruit characteristics of sweet watermelon are largely the result of human selection. Here we report an improved watermelon reference genome and whole-genome resequencing of 414 accessions representing all extant species in the Citrullus genus. Population genomic analyses reveal the evolutionary history of Citrullus, suggesting independent evolutions in Citrullus amarus and the lineage containing Citrullus lanatus and Citrullus mucosospermus. Our findings indicate that different loci affecting watermelon fruit size have been under selection during speciation, domestication and improvement. A non-bitter allele, arising in the progenitor of sweet watermelon, is largely fixed in C. lanatus. Selection for flesh sweetness started in the progenitor of C. lanatus and continues through modern breeding on loci controlling raffinose catabolism and sugar transport. Fruit flesh coloration and sugar accumulation might have co-evolved through shared genetic components including a sugar transporter gene. This study provides valuable genomic resources and sheds light on watermelon speciation and breeding history.

甜西瓜的水果特性在很大程度上是人类选择的结果。本文中，作者报告了一个改良版的西瓜参考基因组和414份西瓜属所有现存物种代表材料的全基因组重测序。群体基因组学分析揭示了西瓜属的演化历史，说明了阿玛鲁西瓜（Citrullus amarus）和包含西瓜（Citrullus lanatus）和黏籽西瓜（Citrullus mucosospermus）支系的独立演化。本文的发现表明，在物种形成、驯化和改良过程中，影响西瓜果实大小的基因组上不同位点都受到了选择。起源于甜西瓜的非苦味等位基因在西瓜群体中很大程度上被固定下来。果肉甜度的选择起始于西瓜的祖先，并通过控制棉子糖分解代谢和糖运输基因座的现代育种持续选择。果肉着色和糖分积累可能通过包括糖转运蛋白基因在内的共有遗传成分共同演化。本文的研究提供了宝贵的基因组资源，并为西瓜的物种形成和育种历史提供了新的视野。

通讯：徐勇

研究方向：葫芦科蔬菜的遗传育种与基因组学研究。

doi: https://doi.org/10.1038/s41588-019-0518-4

Journal: Nature Genetics

Published date: November 01, 2019