Gene sequencing uncovers differences in wild and domesticated crops
Can understanding these differences help researchers breed better crops suited for a changing climate?
Hiroshima University
image:
This diagram illustrates the methodology of a meta-analysis comparing gene expression data between wild relatives and domesticated species. Using public gene expression databases and computer-based methods, researchers analyzed data from rice, tomato, and soybean to identify differentially expressed genes and common expression changes associated with domestication.
view moreCredit: Makoto Yumiya, Hiroshima University
With climate change and more frequent extreme weather events, researchers predict that global yields of important crops like maize, rice, and soybeans could decline by 12 to 20% by the end of the century. To prepare, plant scientists are hoping to find ways to improve yields and grow hardier varieties of these crops. New insights into the genetic makeup of wild varieties of common crops show how domestication has changed crop traits over time and propose a new cultivation method to improve genetic diversity. The research was shared in a paper published in Life on July 11.
“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 used RNA sequencing data from public databases, including the National Center for Biotechnology Information Gene Expression Omnibus and published studies online. They focused on crops with wild relatives that had widely available RNA sequencing data: tomatoes, rice, and soybeans. The gene expression data of the wild varieties was then compared to the domesticated varieties. To evaluate the data, researchers classified all genes into three groups: upregulated, unchanged, and downregulated.
By understanding the gene expression comparison between the wild varieties and the domesticated varieties, researchers could understand differences in how the plants respond to stressors. “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 found 18 genes that were upregulated in the wild relatives and 36 genes that were upregulated in the domesticated species. Wild species were found to have genes related to environmental stress responses while domesticated species had more genes related to the hormone regulation and chemical compound export and detoxification. For example, a gene called HKT1 affects salt stress response and salt tolerance was found to be upregulated in wild varieties. This could be an opportunity to develop crops that can grow in soil with more saline. Researchers also found genes that were upregulated in wild varieties that helped with drought stress (RD22), water stress (HB-12), leaf development and photosynthesis promotion (HB-7), and osmotic stress response and wound signaling (MYB102).
In domesticated plants, researchers also found beneficial genes that were upregulated compared to wild varieties. Several genes help detox the plants and remove chemicals found in soil. One gene (ALF5) improves the plant’s resistance to tetramethylammonium, and another (DTX1) manages cadmium and toxic compounds. These genes and others can help plants grow in soils that have been contaminated by chemicals. Researchers suspect this may have become beneficial for plants because of increased pesticide and chemical fertilizer use.
“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.
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The other contributor to this research was Makoto Yumiya of the Graduate School of Integrated Sciences for Life at Hiroshima University.
The Center for Bio-Digital Transformation (BioDX), COI-NEXT, and the Japan Science and Technology Agency (JST) supported this research.
This paper received funding from Hiroshima University to cover open access fees.
About Hiroshima University
Since its foundation in 1949, Hiroshima University has striven to become one of the most prominent and comprehensive universities in Japan for the promotion and development of scholarship and education. Consisting of 12 schools for undergraduate level and 5 graduate schools, ranging from natural sciences to humanities and social sciences, the university has grown into one of the most distinguished comprehensive research universities in Japan. English website: https://www.hiroshima-u.ac.jp/en
Journal
Life
Article Title
Meta-Analysis of Wild Relatives and Domesticated Species of Rice, Tomato, and Soybean Using Publicly Available Transcriptome Data
How amino acids are transported in plants
Biology: Publication in Nature Plants
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Different forms of seven-week-old Arabidopsis thaliana plants: the wild type (left) compared with a plant lacking RE1 (right). The characteristic “reticulated” leaf form is clearly visible in the right-hand plant – the leaf tissue is lighter due to a lack of mesophyll cells, while the leaf veins appear greener due to a greater number of chloroplasts. (Image: HHU/Franziska Kuhnert)
view moreCredit: HHU/Franziska Kuhnert
Plants produce all amino acids essential for human life. This commonly occurs in specialised cell organelles, so-called plastids. A research team headed by Heinrich Heine University Düsseldorf (HHU) has now decoded the mechanism by which the plants distribute these amino acids within their organisms. In the scientific journal Nature Plants, the researchers describe the mechanism and the class of transport proteins used for this process. The findings could potentially contribute to breeding crop plants with a higher content of essential amino acids and thus improved nutritional quality.
Proteins – the fundamental building blocks of every organism – are large molecules, which are made up of many so-called amino acids. Humans can produce some of these amino acids themselves, but others – the “essential amino acids” – must be obtained from food. Plants synthesise all 20 “proteinogenic” amino acids – from which proteins are comprised – themselves, making plants the ideal supplier of amino acids for the human diet.
However, plants do not produce the amino acids in all areas. Nine of these molecules, including important building blocks such as lysine and arginine, are only produced in the plastids. “Chloroplasts”, in which photosynthesis takes place, are also plastids. Until now, it was unknown how the amino acids are transported from the plastids to other parts of the plant.
The research group headed by Professor Dr Andreas P. M. Weber from the Institute of Plant Biochemistry at HHU has now attributed the function of transporting amino acids through chloroplast membranes to a class of transport proteins called RETICULATA1 (for short: RE1). This enables them to be exchanged within the plant.
Professor Weber, corresponding author of the study, which has now appeared in Nature Plants: “The molecular function of RE1 has been a mystery for decades, even though it was known that mutations in this gene cause conspicuous leaf shapes in the model plant Arabidopsis thaliana (thale cress). We now show that RE1 is a specialised transporter for basic amino acids such as arginine, citrulline, ornithine and lysine.”
Plants lacking RE1 not only have a characteristic “reticulated” leaf shape, but also only contain small amounts of basic amino acids in their leaves and chloroplasts. Lead author Dr Franziska Kuhnert: “This indicates a disrupted amino acid distribution in the plant. A complete loss of RE1 and its closest relative RER1 (RETICULATA-RELATED1) is even lethal to the plant, underscoring the essential role of these proteins.”
The research team was also able to demonstrate that the loss of RE1 reduces the biosynthesis of basic amino acids and impairs the balance of amino acid pools between plastids and cytosol – the fluid within the cells.
Kuhnert: “RE1 and related proteins are found exclusively in organisms that contain plastids. Since all plants and photosynthetic algae possess RE proteins, these proteins must be old in evolutionary terms and have originated from an era when plastids were formed through ‘endosymbiosis’ – the absorption of previously independent cells into other cells. RE1 may have made an important contribution to this evolutionary development of plants.”
“Our results provide crucial insights into the complex connection between the transport of amino acids into plastids and leaf development, as well as nutrient distribution in plants,” summarises Weber, adding: “The discovery opens up new perspectives for plant breeding and enables the development of crops with a higher content of essential amino acids. This can contribute to global food security.”
The research work was carried out at HHU within the framework of the CEPLAS Cluster of Excellence and the collaborative research centres CRC1208/2 and 1535/1. All projects received funding from the German Research Foundation (DFG). In addition, co-author Dr Peter K. Lundquist received an Alexander von Humboldt Postdoctoral Fellowship.
Original publication
Franziska Kuhnert, Philipp Westhoff, Vanessa Valencia, Stephan Krüger, Karolina Vogel, Peter K. Lundquist, Christian Rosar, Tatjana Goss and Andreas P. M. Weber. RETICULATA1 is a Plastid-Localized Basic Amino Acid Transporter. Nature Plants XXX (2025).
DOI: 10.1038/s41477-025-02080-z
Journal
Nature Plants
Article Title
RETICULATA1 is a Plastid-Localized Basic Amino Acid Transporter
Article Publication Date
22-Aug-2025
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