As climate change threatens global harvests of rice, maize, and soybeans, scientists are turning to wild relatives of domesticated crops for answers. A study published in Life highlights genetic traits in wild varieties that could help improve stress tolerance and yield stability in future cultivars.
Hidemasa Bono, professor at Hiroshima University’s Graduate School of Integrated Sciences for Life, explained the motivation behind the work: “While domesticated species have originally been bred by cultivating wild species, the resulting reduction in genetic diversity can damage all individuals by exposing them to diseases and environmental stresses. To solve this problem, we set out to identify differences in crop traits between wild relatives and domesticated species and to contribute to the selection of new breeding candidate genes.”
The team analyzed RNA sequencing data from public repositories such as the NCBI Gene Expression Omnibus, focusing on rice, tomatoes, and soybeans. Gene expression patterns were grouped as upregulated, unchanged, or downregulated, allowing comparisons between wild and cultivated varieties.
Wild species showed strong expression of stress-response genes, including HKT1 for salt tolerance, RD22 for drought response, HB-12 for water stress, HB-7 for leaf development and photosynthesis, and MYB102 for osmotic stress and wound signaling. Bono noted that “wild relatives have high environmental stress tolerance with the potential to respond to climate change and severe changes in the natural environment.”
In contrast, domesticated species exhibited higher expression of genes involved in hormone signaling and detoxification. Genes such as ALF5 and DTX1 help plants resist soil contaminants like tetramethylammonium and cadmium, which may reflect adaptation to modern agricultural conditions.
The findings underscore the value of reintroducing genetic diversity into breeding programs. “The three wild species used in this analysis—rice, tomato, and soybean—had in common high expression levels of genes that contribute to stress responses,” said Bono. He added that expanding data collection and building digital breeding databases could accelerate the development of improved crop varieties.
Publication Details
Yumiya, M.; Bono, H. Meta-Analysis of Wild Relatives and Domesticated Species of Rice, Tomato, and Soybean Using Publicly Available Transcriptome Data. Life 2025, 15, 1088. https://doi.org/10.3390/life15071088
Hidemasa Bono, professor at Hiroshima University’s Graduate School of Integrated Sciences for Life, explained the motivation behind the work: “While domesticated species have originally been bred by cultivating wild species, the resulting reduction in genetic diversity can damage all individuals by exposing them to diseases and environmental stresses. To solve this problem, we set out to identify differences in crop traits between wild relatives and domesticated species and to contribute to the selection of new breeding candidate genes.”
The team analyzed RNA sequencing data from public repositories such as the NCBI Gene Expression Omnibus, focusing on rice, tomatoes, and soybeans. Gene expression patterns were grouped as upregulated, unchanged, or downregulated, allowing comparisons between wild and cultivated varieties.
Wild species showed strong expression of stress-response genes, including HKT1 for salt tolerance, RD22 for drought response, HB-12 for water stress, HB-7 for leaf development and photosynthesis, and MYB102 for osmotic stress and wound signaling. Bono noted that “wild relatives have high environmental stress tolerance with the potential to respond to climate change and severe changes in the natural environment.”
In contrast, domesticated species exhibited higher expression of genes involved in hormone signaling and detoxification. Genes such as ALF5 and DTX1 help plants resist soil contaminants like tetramethylammonium and cadmium, which may reflect adaptation to modern agricultural conditions.
The findings underscore the value of reintroducing genetic diversity into breeding programs. “The three wild species used in this analysis—rice, tomato, and soybean—had in common high expression levels of genes that contribute to stress responses,” said Bono. He added that expanding data collection and building digital breeding databases could accelerate the development of improved crop varieties.
Publication Details
Yumiya, M.; Bono, H. Meta-Analysis of Wild Relatives and Domesticated Species of Rice, Tomato, and Soybean Using Publicly Available Transcriptome Data. Life 2025, 15, 1088. https://doi.org/10.3390/life15071088