A research group led by Visiting Professor Kentaro K. Shimizu at the Kihara Institute for Biological Research, Yokohama City University (Professor at the University of Zurich, Switzerland); Assistant Professor Moeko Okada at the Faculty of Agriculture, Niigata University; Professor Shuhei Nasuda at the Graduate School of Agriculture, Kyoto University; and Professor Hirokazu Handa at the Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, conducted a comprehensive gene expression analysis of nine varieties of wheat, including Norin 61 that is representative of Japan, in a joint study with the International 10+ Wheat Genomes Project. They announced that Norin 61 has distinct chromosomal regions not found in other varieties. Many novel genes that function in a tissue-specific manner and genes related to disease resistance were found in these regions. The findings are expected to be useful for developing new varieties for stable wheat production. The results were published in Nature Communications on October 6.
(B) Overview of transcriptome data generated for this study of wheat cultivars. 1 and 2: whole aerial organs sampled at dawn and dusk, 3: root, 4: complete spike at heading (GS59), 5: flag leaf 7 days post anthesis (GS71), 6: whole grains 15 days post anthesis (GS77).
(C) Network fragment from Julius module significantly enriched for cloud genes. Labelled nodes refer to cloud genes annotated as histones. The top five highly connected genes for each cloud gene are coloured according to core or shell genome membership. Node size is scaled to the log2 average expression +1 of each gene across tissues and edge width reflects the weight of the connection between nodes.
Provided by Yokohama City University
Japan's wheat self-sufficiency rate is approximately 15% based on production value, with over 80% dependency on imports. International wheat prices are highly volatile due to the effects of global warming, natural disasters, and the international situation. In Japan, the price at which the government sells imported wheat to the private sector has risen approximately 1.5 times over the past decade.
Stabilizing wheat production and prices is closely related to human life, and strategic genome breeding that effectively utilizes the diversity of genetic resources is required for this stable production.
The research group had previously worked on decoding the genome sequences of nine modern varieties of wheat, including Norin 61 that is representative of Japan, with the International 10+ Wheat Genomes Project in 2020, and had established an analytical platform. However, at that time, data for gene prediction was limited, and it was not possible to search for variety-specific genes or novel genes.
The International 10+ Wheat Genomes Project is an international project launched with the aim of establishing a foundation for wheat genome variation analysis, with participation from various countries including Japan, Canada, the United States, the United Kingdom, Germany, and Israel.
In this study, the gene composition of nine wheat varieties whose genome sequences have been decoded was comprehensively identified through cross-varietal pan-transcriptome analysis.
As a result, it was found that the number and sequences of prolamin gene families, which are involved in stress response, growth, and seed quality and can also be allergens that lead to gluten-related diseases, clearly differed among the nine varieties.
It was found that differences in gene composition and gene expression patterns between wheat varieties represent genetic differences (inter-varietal differences) that are greater than individual differences in humans.
Norin 61 has distinct chromosomal regions not found in other varieties, and, in particular, many disease resistance genes were found in these distinct chromosomal regions. Furthermore, a catalog of genetic information such as "which genes function in which tissues of which varieties and how" can be created. "Genome breeding" that strategically breeds varieties less susceptible to climate change and international situations becomes possible.
Analyzing unused genetic resources such as Japanese and Asian landraces is expected to lead to the discovery of novel genes important for breeding.
Shimizu commented: "At a time when steeply rising rice prices and food security are topics of discussion, isn't this a good opportunity to reconsider wheat, a traditional grain that has been cultivated since the Yayoi period, even in Japan? I am very pleased that Japanese wheat researchers have joined forces and achieved the genome analysis of Japanese varieties, which differ greatly from Western varieties, as one of the nine varieties in the international project. In the future, by advancing the genome analysis of valuable Asian landraces collected by Japanese researchers since Hitoshi Kihara, we hope to accelerate the breeding of varieties adapted to climate change and also contribute to elucidating the history of how wheat spread to Japan through routes such as the Silk Road."
Journal Information
Publication: Nature Communications
Title: De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome
DOI: 10.1038/s41467-025-64046-1
This article has been translated by JST with permission from The Science News Ltd. (https://sci-news.co.jp/). Unauthorized reproduction of the article and photographs is prohibited.