With climate change and more frequent extreme weather, researchers project that global yields of key crops such as maize, rice, and soybeans could decline by 12–20% by the end of the century. To address this, plant scientists are exploring ways to increase yields and develop more resilient crop varieties. A recent study published in Life on July 11 highlights how the genetic analysis of wild crop relatives reveals changes in traits caused by domestication and suggests new cultivation approaches to enhance genetic diversity.
“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 introduction of useful traits, especially those found in wild relatives, may provide hints for the development of new useful varieties,” said Hidemasa Bono, a professor at Hiroshima University’s Graduate School of Integrated Sciences for Life in Hiroshima, Japan.
The researchers analyzed RNA sequencing data from public sources, including the National Center for Biotechnology Information Gene Expression Omnibus and other published studies. They focused on crops with wild relatives that had extensive RNA sequencing data, specifically tomatoes, rice, and soybeans. Gene expression in the wild varieties was compared with that of domesticated varieties. For analysis, genes were categorized into three groups: upregulated, unchanged, or downregulated, according to a press release.
Comparing gene expression between wild and domesticated varieties allowed the researchers to identify differences in how the plants respond to stress.
“Wild relatives have high environmental stress tolerance with the potential to respond to climate change and severe changes in the natural environment, which has been an issue in recent years,” said Bono.
The researchers identified 18 genes that were upregulated in wild relatives and 36 genes upregulated in domesticated species. Wild varieties tended to have genes associated with environmental stress responses, while domesticated species showed more genes linked to hormone regulation and chemical detoxification.
For example, the gene HKT1, which influences salt stress response and tolerance, was upregulated in wild varieties, suggesting potential for developing crops that can grow in saline soils. Other genes upregulated in wild species included RD22 (drought stress), HB-12 (water stress), HB-7 (leaf development and photosynthesis), and MYB102 (osmotic stress response and wound signaling).
Domesticated plants also showed upregulated genes that could be beneficial. Some genes assist in detoxifying the plant and removing harmful compounds from the soil. For instance, ALF5 enhances resistance to tetramethylammonium, and DTX1 helps manage cadmium and other toxic substances. Researchers suggest these traits may have become advantageous due to increased use of pesticides and chemical fertilizers.
“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, such as drought, osmotic pressure, and wound stress. The high expression levels of genes that contribute to stress tolerance that these three less closely related species have in common suggest that wild species of other species are likely to have useful traits as well,” said Bono.
Looking ahead, researchers hope to learn even more about these essential differences between wild relatives and domesticated species to improve breeding. “In addition, we would like to collect and reanalyze data used in crop breeding research to construct a database that will contribute to the promotion of digital breeding of crops,” said Bono.