The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor
The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor
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DOI：
10.1038/s41588-019-0410-2
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发表时间：
2019-06-01
期刊：
影响因子：
30.8
通讯作者：
Fei, Zhangjun
中科院分区：
文献类型：
--
作者：
Gao, Lei;Gonda, Itay;Fei, Zhangjun
现代番茄的遗传多样性狭窄，限制了其改良潜力。我们提出了使用 725 个系统发育和地理代表性种质的基因组序列构建的番茄泛基因组，揭示了参考基因组中缺失的 4,873 个基因。存在/不存在变异分析揭示了番茄驯化和改良过程中基因的大量丢失以及基因和启动子的强烈负选择。丢失或负选择的基因会丰富重要的性状，尤其是抗病性。我们在驯化过程中选择的 TomLoxC 启动子中发现了一个罕见的等位基因。转基因植物的数量性状基因座作图和分析揭示了 TomLoxC 在类胡萝卜素生产中的作用，这有助于产生理想的番茄风味。在橙色阶段的果实中，同时含有稀有和常见 TomLoxC 等位基因（杂合子）的材料比纯合子的 TomLoxC 表达更高，并且在现代番茄中复活。番茄泛基因组增加了参考基因组的深度和完整性，对于未来的生物发现和育种很有用。
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.