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Yoshiyuki Yamagata Last modified date:2022.06.05

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

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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. Mitsukazu Sakata, Noriko Takano-Kai, Yuta Miyazaki, Hiroyuki Kanamori, Jianzhong Wu, Takashi Matsumoto, Kazuyuki Doi, Hideshi Yasui, Atsushi Yoshimura, Yoshiyuki Yamagata, Domain Unknown Function DUF1668-Containing Genes in Multiple Lineages Are Responsible for F1 Pollen Sterility in Rice, Frontiers in Plant Science, 10.3389/fpls.2020.632420, 11, 632420-632420, 2021.01, Postzygotic reproductive isolation maintains species integrity and uniformity and contributes to speciation by restricting the free gene flow between divergent species. In this study we identify causal genes of two Mendelian factors S22A and S22B on rice chromosome 2 inducing F1 pollen sterility in hybrids between Oryza sativa japonica-type cultivar Taichung 65 (T65) and a wild relative of rice species Oryza glumaepatula. The causal gene of S22B in T65 encodes a protein containing DUF1668 and gametophytically expressed in the anthers, designated S22B_j. The O. glumaepatula allele S22B-g, allelic to S22B_j, possesses three non-synonymous substitutions and a 2-bp deletion, leading to a frameshifted translation at the S22B C-terminal region. Transcription level of S22B-j and/or S22B_g did not solely determine the fertility of pollen grains by genotypes at S22B. Western blotting of S22B found that one major band with approximately 46 kDa appeared only at the mature stage and was reduced on semi-sterile heterozygotes at S22B, implying that the 46 kDa band may associated in hybrid sterility. In addition, causal genes of S22A in T65 were found to be S22A_j1 and S22A_j3 encoding DUF1668-containing protein. The allele of a wild rice species Oryza meridionalis Ng at S22B, designated S22B_m, is a loss-of-function allele probably due to large deletion of the gene lacking DUF1668 domain and evolved from the different lineage of O. glumaepatula. Phylogenetic analysis of DUF1668 suggested that many gene duplications occurred before the divergence of current crops in Poaceae, and loss-of-function mutations of DUF1668-containing genes represent the candidate causal genetic events contributing to hybrid incompatibilities. The duplicated DUF1668-domain gene may provide genetic potential to induce hybrid incompatibility by consequent mutations after divergence..
2. Takayuki Ogami, Hideshi Yasui, Atsushi Yoshimura, Yoshiyuki Yamagata, Identification of Anther Length QTL and Construction of Chromosome Segment Substitution Lines of Oryza longistaminata., Plants (Basel, Switzerland), 10.3390/plants8100388, 8, 10, 2019.09, Life histories and breeding systems strongly affect the genetic diversity of seed plants, but the genetic architectures that promote outcrossing in Oryza longistaminata, a perennial wild species in Africa, are not understood. We conducted a genetic analysis of the anther length of O. longistaminata accession W1508 using advanced backcross quantitative trait locus (QTL) analysis and chromosomal segment substitution lines (CSSLs) in the genetic background of O. sativa Taichung 65 (T65), with simple sequence repeat markers. QTL analysis of the BC3F1 population (n = 100) revealed that four main QTL regions on chromosomes 3, 5, and 6 were associated to anther length. We selected a minimum set of BC3F2 plants for the development of CSSLs to cover as much of the W1508 genome as possible. The additional minor QTLs were suggested in the regional QTL analysis, using 21 to 24 plants in each of the selected BC3F2 population. The main QTLs found on chromosomes 3, 5, and 6 were validated and designated qATL3, qATL5, qATL6.1, and qATL6.2, as novel QTLs identified in O. longistaminata in the mapping populations of 94, 88, 70, and 95 BC3F4 plants. qATL3, qATL5, and qATL6.1 likely contributed to anther length by cell elongation, whereas qATL6.2 likely contributed by cell multiplication. The QTLs were confirmed again in an evaluation of the W1508ILs. In several chromosome segment substitution lines without the four validated QTLs, the anthers were also longer than those of T65, suggesting that other QTLs also increase anther length in W1508. The cloning and diversity analyses of genes conferring anther length QTLs promotes utilization of the genetic resources of wild species, and the understanding of haplotype evolution on the differentiation of annuality and perenniality in the genus Oryza..
3. Yoshiyuki Yamagata, Khin Thanda Win, Yuta Miyazaki, Chika Ogata, Hideshi Yasui, Atsushi Yoshimura, Development of introgression lines of AA genome Oryza species, O. glaberrima, O. rufipogon, and O. nivara, in the genetic background of O. sativa L. cv. Taichung 65., Breeding science, 10.1270/jsbbs.19002, 69, 2, 359-363, 2019.06, To evaluate and utilize potentially valuable quantitative trait loci or genes of wild relatives in the genetic background of domesticated crop species, chromosome segment substitution lines (CSSLs) are a valuable tool. CSSLs can be constructed through the exchange of chromosome segments of AA genome species of the genus Oryza with cultivated rice, Oryza sativa L. Here we report the development of three sets of CSSLs carrying segments of AA genome species closely related to Oryza sativa-O. glaberrima (IRGC 103777 from Mali), O. rufipogon (W1962 from China), and O. nivara (IRGC 105715 from Cambodia)-in the genetic background of ssp. japonica cultivar Taichung 65 through the use of 101 to 121 simple-sequence-repeat markers in whole-genome genotyping and marker-assisted selection. The materials are available via the National Bioresource Project (Rice) Oryzabase Web page..
4. 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, 2018.09, 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..
5. Giao Ngoc Nguyen, Yoshiyuki Yamagata, Yuko Shigematsu, Miyako Watanabe, Yuta Miyazaki, Kazuyuki Doi, Kosuke Tashiro, Satoru Kuhara, Hiroyuki Kanamori, Jianzhong Wu, Takashi Matsumoto, Hideshi Yasui, Atsushi Yoshimura, Duplication and Loss of Function of Genes Encoding RNA Polymerase III Subunit C4 Causes Hybrid Incompatibility in Rice., G3 (Bethesda, Md.), 10.1534/g3.117.043943, 7, 8, 2565-2575, 2017.08, [URL], Reproductive barriers are commonly observed in both animals and plants, in which they maintain species integrity and contribute to speciation. This report shows that a combination of loss-of-function alleles at two duplicated loci, DUPLICATED GAMETOPHYTIC STERILITY 1 (DGS1) on chromosome 4 and DGS2 on chromosome 7, causes pollen sterility in hybrid progeny derived from an interspecific cross between cultivated rice, Oryza sativa, and an Asian annual wild rice, O. nivara Male gametes carrying the DGS1 allele from O. nivara (DGS1-nivaras ) and the DGS2 allele from O. sativa (DGS2-T65s ) were sterile, but female gametes carrying the same genotype were fertile. We isolated the causal gene, which encodes a protein homologous to DNA-dependent RNA polymerase (RNAP) III subunit C4 (RPC4). RPC4 facilitates the transcription of 5S rRNAs and tRNAs. The loss-of-function alleles at DGS1-nivaras and DGS2-T65s were caused by weak or nonexpression of RPC4 and an absence of RPC4, respectively. Phylogenetic analysis demonstrated that gene duplication of RPC4 at DGS1 and DGS2 was a recent event that occurred after divergence of the ancestral population of Oryza from other Poaceae or during diversification of AA-genome species..
6. Khin Thanda Win, Yoshiyuki Yamagata, Kazuyuki Doi, Kazuhiro Uyama, Yasuko Nagai, Yosuke Toda, Takahiro Kani, Motoyuki Ashikari, Hideshi Yasui, Atsushi Yoshimura, A single base change explains the independent origin of and selection for the nonshattering gene in African rice domestication., The New phytologist, 10.1111/nph.14290, 213, 4, 1925-1935, 2017.03, [URL], Reduced seed shattering was a critical evolutionary step in crop domestication. Two cultivated rice species, Oryza sativa and Oryza glaberrima, were independently domesticated from the wild species Oryza rufipogon in Asia and Oryza barthii in Africa, respectively. A single nucleotide polymorphism (SNP) in the c gene, which encodes a trihelix transcription factor, causes nonshattering in O. sativa. However, the genetic mechanism of nonshattering in O. glaberrima is poorly understood. We conducted an association analysis for the coding sequences of SH3/SH4 in AA- genome rice species and the mutation suggested to cause nonshattering was demonstrated to do so using a positional-cloning approach in the O. sativa genetic background. We found that the loss of seed shattering in O. glaberrima was caused by an SNP resulting in a truncated SH3/SH4 protein. This mutation appears to be endemic and to have spread in the African gene pool by hybridization with some O. barthii accessions. We showed that interaction between the O. sativa and O. glaberrima domestication alleles of SH3 in heterozygotes induces a 'throwback' seed-shattering phenotype similar to that in the wild species. Identification of the causative SNP provides new insights into the molecular basis of seed shattering in crops and may facilitate investigation of the history of African rice domestication..
7. Yoshiyuki Yamagata, Eiji Yamamoto, Kohichiro Aya, Khin Thanda Win, Kazuyuki Doi, Sobrizal, Tomoko Ito, Hiroyuki Kanamori, Jianzhong Wu, Takashi Matsumoto, Makoto Matsuoka, Motoyuki Ashikari, Atsushi 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, 1494-9, 2010.01, [URL], Hybrid incompatibility in F(1) hybrids or later generations is often observed as sterility or inviability. This incompatibility acts as postzygotic reproductive isolation, which results in the irreversible divergence of species. Here, we show that the reciprocal loss of duplicated genes encoding mitochondrial ribosomal protein L27 causes hybrid pollen sterility in F(1) hybrids of the cultivated rice Oryza sativa and its wild relative O. glumaepatula. Functional analysis revealed that this gene is essential for the later stage of pollen development, and distribution analysis suggests that the gene duplication occurred before the divergence of the AA genome species. On the basis of these results, we discuss the possible contribution of the "founder effect" in establishing this reproductive barrier..
8. Y. Yamagata, K. Doi, H. Yasui, A. Yoshimura, Linkage analysis of SPS6, SPS9 and SPS12, the sporophytic rice genes acting in pollen development, Rice Genetics Newsletter, 24, 14-15, 24: 14-15, 2008.01.
Membership in Academic Society
  • Interspecific hybrid sterility mechanism by duplicate gametic lethals theory and the speciation in genus Oryza