Kyushu University Academic Staff Educational and Research Activities Database
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Yoshiyuki Yamagata Last modified date:2020.06.15

Associate Professor / Agricultural Bioresource Sciences
Department of Bioresource Sciences
Faculty of Agriculture

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Undergraduate School
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Academic Degree
Ph. D.
Country of degree conferring institution (Overseas)
Field of Specialization
Plant breeding
ORCID(Open Researcher and Contributor ID)
Total Priod of education and research career in the foreign country
Research Interests
  • Study of F1 pollen sterility observed in interspecific hybrids of genus Oryza
    Functional analysis of genes controlling pollen formation using abnormal pollen development in rice
    keyword : rice, pollen, reproductive isolation, interspecific hybridization
Academic Activities
1. Yoshiyuki Yamagata, Atsushi Yoshimura, Toyoaki Anai, Satoshi Watanabe, Selection criteria for SNP loci to maximize robustness of high-resolution melting analysis for plant breeding, Breeding Science, 10.1270/jsbbs.18048, 68, 4, 488-498, 2018.01, DNA markers are useful for identifying genes and developing new genetic materials for breeding and genetic research. High-resolution melting (HRM) analysis can detect a single nucleotide polymorphism (SNP) in two polymerase chain reaction (PCR) fragments as a melting temperature (Tm) difference without additional experimental steps, such as gel electrophoresis. To design a method for developing reliable HRM markers that discriminate between homozygous alleles containing SNPs, we tested new evaluation indexes related to the thermodynamics of double-stranded DNA to find one that maximizes the difference in Tm values between PCR fragments. We found that differences in the change in Gibbs free energy (ΔG°) correlated with actual differences in Tm values. Optimization of the nearest neighboring nucleotide (NNN) of a SNP by nucleotide substitution in the primer and reducing the size of the PCR fragment both enlarged the actual differences in Tm. The genetic DNA markers we developed by NNN substitution, termed NNNs-HRM markers, could be precisely mapped within soybean chromosomes by linkage analysis. We developed a Perl script pipeline to enable the automatic design of a massive number of NNNs-HRM markers; these scripts are freely available and would be useful for practical breeding programs for other plant species..
2. Nguyen, G. N.*, Y. Yamagata*, Y. Shigematsu, M. Watanabe, Y. Miyazaki, K. Doi, K. Tashiro, S. Kuhara, H. Kanamori, J. Wu, T. Matsumoto, H. Yasui, A. Yoshimura (2017) Duplication and loss of function of genes encoding RNA polymerase III subunit C4 causes hybrid incompatibility in rice. *Co-first authors , Duplication and Loss of Function of Genes Encoding RNA Polymerase III Subunit C4 Causes Hybrid Incompatibility in Rice, G3-GENES GENOMES GENETICS, 10.1534/g3.117.043943, 7, 8, 2565-2575, 2017.08, [URL].
3. Khin Thanda Win*, Yoshiyuki Yamagata*, Kazuyuki Doi, Kazuhiro Uyama, Yasuko Nagai, Yosuke Toda, Takahiro Kani, Motoyuki Ashikari, Hideshi Yasui, Atsushi Yoshimura *Co-first authors, A single base change explains the independent origin of and selection for the nonshattering gene in African rice domestication, New Phytologist, 10.1111/nph.14290, 213, 4, 1925-1935, 2017.03, [URL].
4. Yamagata, Y., E. Yamamoto, K. Aya, K. Thanda Win, K. Doi, Sobrizal, T. Ito, H. Kanamori, J. Wu, T. Matsumoto, M. Matsuoka, M. Ashikari and A. Yoshimura, Mitochondrial gene in the nuclear genome induces reproductive barrier in rice, Proceedings of the National Academy of Sciences of the United States of America, 10.1073/pnas.0908283107, 107, 4, 1494-1499, 2010.01, [URL].
5. Yamagata, Y., K. Doi, H. Yasui and A. Yoshimura, Linkage analysis of SPS6, SPS9 and SPS12, the sporophytic rice genes acting in pollen development, Rice Genetics Newsletter, 24: 14-15, 2008.01.
6. Yamagata, Y., K. Doi, H. Yasui and A. Yoshimura, Identification of mutants for abnormal pollen development in rice, Breeding Science, 57: 331-337, 2007.12.
Membership in Academic Society
  • Japanese society of breeding