The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

First author: Lei Gao; Affiliations: Cornell University (康奈尔大学): Ithaca, USA

Corresponding author: Zhangjun Fei

Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in the TomLoxC promoter selected against during domestication. Quantitative trait locus mapping and analysis of transgenic plants reveal a role for TomLoxC in apocarotenoid production, which contributes to desirable tomato flavor. In orange-stage fruit, accessions harboring both the rare and common TomLoxC alleles (heterozygotes) have higher TomLoxC expression than those homozygous for either and are resurgent in modern tomatoes. The tomato pan-genome adds depth and completeness to the reference genome, and is useful for future biological discovery and breeding.

现代番茄的遗传多样性比较狭窄，限制了番茄的遗传改良前景。作者利用725份系统演化和地理上具有代表性的试验材料构建了番茄的泛基因组，鉴定了番茄参考基因组中缺失了的4873个基因。存在/缺失变异PAV分析显示番茄驯化过程中多个基因丢失、并且多个基因和启动子遭受了强烈的负选择压。这些丢失或者被负选择的基因显著富集与重要性状相关条目，尤其是疾病抗性。作者在启动子上鉴定到了一个罕见的等位基因在驯化过程中受到选择。数量性状位点作图和对转基因植株的分析显示TomLoxC在番茄类胡萝卜素的产量方面发挥作用，从而作用于番茄果实的风味。具有橙色果实的试验材料同时包含罕见和正常的TomLoxC等位基因，即该位点为杂合子，这些试验材料中TomLoxC基因的表达量要高于该位点为纯合子的现代番茄材料。本文所报道的番茄泛基因组在很大程度上使得番茄的参考基因组更加完整，对于将来番茄的遗传育种改良具有促进作用。

通讯：Zhangjun Fei（https://btiscience.org/zhangjun-fei/）

研究方向：多组学大数据的生物信息学分析工具开发。

doi: https://doi.org/10.1038/s41588-019-0410-2

Journal: Nature Genetics

Published date: May 13, 2019