Plant Genome Dynamics Analysis
•Screening of the active retrotransposon families
•DNA genotyping based on retrotransposon insertion sites by NGS
Staff
- Assoc. Prof. MONDEN Yuki
- E-mail：y_monden (please add @okayama-u.ac.jp)
- Specialty: Plant genetics and breeding
Research Topics
In our laboratory, we are conducting genetic and breeding research on several crop species such as sweetpotato. Utilizing a next generation sequencer (NGS) that outputs a huge amount of DNA sequence data, we are working on the development of DNA markers and gene identification for important agricultural traits such as disease, pest resistance and yield. We are also conducting gene expression analysis (Iso-Seq, RNA-seq analysis, etc.) to elucidate the mechanism of disease resistance and developing a new genotyping system that can be applied to polyploid crop species. For the purpose of protecting valuable crop cultivars/varieties, we are working on the development of DNA markers to discriminate crop cultivars/varieties.
Identification of genetic regions involved in agricultural traits using genome-wide analysis
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Since sweetpotato is a polyploid species (2n = 6x =90), the mode of inheritance is complicated and genetic analysis is extremely difficult. We are conducting a large-scale genetic analysis of this genetically complex sweetpotato crop species using NGS. In recent research, we have succeeded in finding gene regions related to nematode and weevil resistance. Using the information on the detected genetic regions, we are also working on the development of DNA markers that can select resistant plants at an early stage. |
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Gene expression analysis for elucidation of disease resistance mechanism
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The mechanism by which sweet potato resists harmful nematodes and weevil is unknown. Therefore, we are conducting transcriptome analysis to comprehensively investigate gene expression using resistant and susceptible cultivars. The purpose is to identify the genes that control resistance or to gain insight into the resistance mechanism. It is expected that resistant cultivars can be developed efficiently. |
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Development of crop cultivar discrimination technology using retrotransposon insertion site
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Crop cultivar identification is an important test for the protection of valuable cultivars. In recent years, excellent cultivars cultivated in Japan have been taken overseas without permission, plagiarism of varieties, false labeling, and even reimportation to Japan have occurred. Therefore, we are working on the development of crop cultivar identification technology to prevent such a situation and protect valuable crop cultivars. Through the joint research, we have been developing technology for various crop species such as apples, strawberries, citrus fruits, grapes, and wheat, in addition to sweet potatoes. We are developing a technology that enables easy and accurate identification of crop cultivars by utilizing retrotransposon insertion sites. |
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Publication List
- Developing Transposable Element Marker System for Molecular Breeding. Bhat, R.S., Shirasawa, K., Monden, Y., Yamashita, H. and Tahara, M. In: Jain M., Garg R. (eds) Legume Genomics. Methods in Molecular Biology, vol 2107. Humana, New York, NY Springer US, pp 233-251 (2020).
- Genetic Mapping in Autohexaploid Sweet Potato with Low-coverage NGS-based Genotyping Data. Yamamoto, E., Shirasawa, K., Kimura, T., Monden, Y., Tanaka, M. and Isobe, S. G3, 10, 2661-2670 (2020).
- QTL analysis and GWAS of agronomic traits in sweetpotato (Ipomoea batata) using genome wide SNPs. Haque, E., Tabuchi, H., Monden, Y., Suematsu, K., Shirasawa, K., Isobe, S. and Tanaka, M. Breed. Sci., 70, 283-291 (2020).
- DNA markers based on retrotransposon insertion polymorphisms can detect short DNA fragments for strawberry cultivar identification. Hirata, C., Waki, T., Shimomura, K., Wada, T., Tanaka, S., Ikegami, H., Uchimura, Y., Hirashima, K., Nakazawa, Y., Okada, K., Namai, K., Tahara, M. and Monden, Y. Breed. Sci., 70, 231-240 (2020).
- レトロトランスポゾンを用いた4倍体ブドウ品種識別DNAマーカーの開発．高田翔太・藤田景子・福永健二・門田有希，DNA多型，28, 46-50 (2020)．
- Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato. Sasai, R., Tabuchi, H., Shirasawa, K., Kishimoto, K., Sato, S., Okada, Y., Kuramoto, A., Isobe, A.. Tahara, M. and Monden, Y. DNA Res., 26, 399-409 (2019).
- Genome-Wide Association Studies (GWAS) for Yield and Weevil Resistance in Sweet potato (Ipomoea batatas (L.) Lam). Okada, H., Monden, Y., Nokihara, K., Shirasawa, K., Isobe, S. and Tahara, M. Plant Cell Rep., 38, 1383-1392 (2019).
- 倍数性作物におけるNGS解析．田中剛・磯部祥子・門田有希・石川吾郎・瀬々潤．育種学研究 21, 55-60 (2019).
- Impairment of Lhca4, a subunit of LHCI, causes high accumulation of chlorophyll and the stay-green phenotype in rice. Yamatani, H., Kohzuma, K., Nakano, M., Takami, T., Kato, Y., Hayashi, Y., Monden, Y., Okumoto, Y., Abe, T., Kumamaru, T., Tanaka, A., Sakamoto, W. and Kusaba, M (2018) Journal of Experimental Botany 69: 1027-1035.
- Southern root-knot nematode race SP6 is divided into two races. Tabuchi, H., Kuranouchi, T., Kobayashi, A., Monden, Y., Kishimoto, K., Tahara, M., Okada, Y. and Iwahori, H (2018) Nematological Research accepted.