Supplementary Table10 Gene List Oryza sativa rufipogon Enrichment analysis.csv

Currently, domesticated species available on the market have been developed through the breeding of wild relatives. We collected gene expression data of domesticated species of rice, tomato, and soybean, along with their presumed ancestral species, and conducted a meta-analysis to investigate differentially expressed genes during domestication. In wild relatives, the expression of gene groups involved in osmotic, drought, and wound stress tolerance was upregulated. In contrast, in domesticated species, upregulated ex-pression was observed in gene groups related to auxin and those involved in the efflux of heavy metals and harmful substances. By identifying these genes with differential ex-pression levels, we can gain insights into how domestication has influenced changes in crop traits. In particular, breeding strategies that make use of wild relatives with high genetic diversity are attracting attention as an important approach for addressing climate change and ensuring a sustainable food supply. The findings obtained in this study are expected to contribute to the realization of rapid breeding and the development of new varieties capable of growing in harsh natural environments. To address this issue, a new cultivation method called "De novo domestication" has been proposed, which combines the genetic diversity of currently unused wild relatives and wild relatives with genome editing technologies that enable rapid breeding.

目前市面流通的驯化作物，均通过与其野生近缘种杂交育种培育获得。本研究收集了水稻、番茄、大豆及其推定祖先野生种的基因表达数据，并开展荟萃分析，以探究驯化过程中的差异表达基因。在野生近缘种中，参与渗透胁迫、干旱胁迫与创伤胁迫耐受的基因群表达量呈上调趋势；与之相反，驯化作物中与生长素相关、以及参与重金属与有害物质外排过程的基因群表达量显著上调。通过鉴定这类差异表达基因，可深入解析驯化过程如何影响作物性状的变化。尤为值得关注的是，利用高遗传多样性野生近缘种的育种策略，已成为应对气候变化、保障粮食可持续供应的重要途径。本研究所得成果有望助力快速育种的实现，并培育出可在恶劣自然环境中生长的作物新品种。为解决上述问题，学界提出了一种名为“从头驯化（De novo domestication）”的新型栽培方法，该方法将尚未被开发利用的野生近缘种的遗传多样性，与可实现快速育种的基因组编辑技术相结合。