Supplementary Table6 TPM Data of Glycine soja and Glycine max.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.目前市场上的驯化作物，均通过其野生近缘种的选育培育而来。本研究收集了水稻、番茄、大豆三类驯化作物及其推定祖先物种的基因表达数据，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、干旱胁迫及创伤胁迫耐受的基因簇表达量显著上调；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簇表达量显著上调。通过鉴定此类差异表达基因，我们可明晰驯化作用如何影响作物性状的改变。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，作为应对气候变化、保障粮食可持续供应的重要手段，正受到学界广泛关注。本研究所得成果有望助力快速育种的实现，并推动可在恶劣自然环境中生长的作物新品种的培育。为解决上述问题，学界提出了一种名为‘从头驯化（De novo domestication）’的新型培育方法，该方法整合当前未被利用的野生近缘种的遗传多样性，并结合可实现快速育种的基因组编辑技术。