2018年1月11日，Cell发表了题为“Rewiring of the Fruit Metabolome in Tomato Breeding”的文章。该文章为中国农业科学院深圳农业基因组研究所黄三文研究员、华中农业大学罗杰教授合作完成。

本研究利用多重组学，揭示了番茄在驯化和育种过程中，其果实的营养和风味物质发生的变化，并发现了调控这些物质的重要遗传位点。该研究为番茄果实风味和营养物质的遗传调控和全基因组设计育种提供了思路。

人类严重依赖数十种驯化植物物种，它们可以通过密集育种得到进一步改良。为了评估育种是如何改变番茄果实代谢组的，我们产生并分析了包含来自数百种番茄基因型的基因组，转录组和代谢组的数据集。综合结果说明了育种是如何广泛的改变果实代谢物含量的。与较大果实相关基因的等位基因的选择，由于与附近基因的连锁而改变代谢模式。五个主要基因座的选择减少了成熟果实中抗营养型甾体生物碱的积累，使果实更加可食。粉红番茄的选育改变了超过100种代谢物的含量。野生亲缘抗性基因的渗入也导致了主要和意料之外的代谢变化。该研究揭示了番茄代谢育种历史的多元组学观点，并提供了代谢组辅助育种和植物生物学的见解。

Humans heavily rely on dozens of domesticated plant species that have been further improved through intensive breeding. To evaluate how breeding changed the tomato fruit metabolome, we have generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes from hundreds of tomato genotypes. The combined results illustrate how breeding globally altered fruit metabolite content. Selection for alleles of genes associated with larger fruits altered metabolite profiles as a consequence of linkage with nearby genes. Selection of five major loci reduced the accumulation of anti-nutritional steroidal glycoalkaloids in ripened fruits, rendering the fruit more edible. Breeding for pink tomatoes modified the content of over 100 metabolites. The introgression of resistance genes from wild relatives in cultivars also resulted in major and unexpected metabolic changes. The study reveals a multi-omics view of the metabolic breeding history of tomato, as well as provides insights into metabolome-assisted breeding and plant biology.