Meta-Analysis of Wild Relatives and Domesticated Species of Rice, Tomato, and Soybean Using Publicly Available Transcriptome Data

The domesticated species currently available in the market have been developed through the breeding of wild relatives. Breeding strategies using wild relatives with high genetic diversity are attracting attention as an important approach for addressing climate change and ensuring sustainable food supply. However, studies examining gene expression variation in multiple wild and domesticated species are limited. Therefore, we aimed to investigate the changes in gene expression associated with domestication. We performed a meta-analysis of public gene expression data of domesticated species of rice, tomato, and soybean and their presumed ancestral species using 21 pairs for rice, 36 pairs for tomato, and 56 pairs for soybean. In wild relatives, the expression of genes involved in osmotic, drought, and wound stress tolerance was upregulated, with 18 genes included in the top 5% of DW scores. In domesticated species, upregulated expression was observed in genes related to auxin and those involved in the efflux of heavy metals and harmful substances, with 36 genes included in the top 5% of DW scores. These findings provide insights into how domestication influences changes in crop traits. Thus, our findings may contribute to rapid breeding and the development of new varieties capable of growing in harsh natural environments. Hence, 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.