We will accelerate breed improvement by using genome information of rice varieties!
Using rice productivity and environmental stress tolerance as a material, we clarified the characteristics of enormous rice genetic resources, which is the driving force for breeding improvement, from the viewpoint of genome composition, and found a method to find genes (group) that can cope with various breeding targets I will develop it. In addition, we will clarify the dynamics of genome and chromosome in crossbreeding, and develop techniques to connect useful genes and agronomic characters to breed cultivation in the shortest possible time.
Research
Exploring and utilization of useful traits from diverse rice genetic resources
Development of remote cross breeding in rice via polyploidization
Boosting up crop breeding by integrated bioinformatics and statistical genetics
Prof. YAMAMOTO, Toshio E-mail: yamamo101040@ (Please, add "okayama-u.ac.jp" after the at mark) Assoc. Prof. NAGAKI, Kiyotaka E-mail: nagaki@ (Please, add "okayama-u.ac.jp" after the at mark) Assist. Prof. Furuta, Tomoyuki E-mail: f.tomoyuki@ (Please, add "okayama-u.ac.jp" after the at mark) KASHIHARA, Kazunari
Furuta, T., Yamamoto, T., Ashikari, M. GBScleanR: Robust genotyping error correction using a hidden Markov model with error pattern recognition. Genetics.
https://doi.org/10.1093/genetics/iyad055
Kanako Bessho-Uehara, Kengo Masuda, Diane R Wang, Rosalyn B Angeles-Shim, Keisuke Obara, Keisuke Nagai, Riri Murase, Shin-Ichiro Aoki, Tomoyuki Furuta, Kotaro Miura, Jianzhong Wu, Yoshiyuki Yamagata, Hideshi Yasui, Michael B Kantar, Atsushi Yoshimura, Takumi Kamura, Susan R McCouch, Motoyuki Ashikari. Regulator of Awn Elongation 3, an E3 ubiquitin ligase, is responsible for loss of awns during African rice domestication.
Proceedings of the National Academy of Sciences of the United States of America. 120(4).
https://www.pnas.org/doi/10.1073/pnas.2207105120
Asami Michikawa, Moeko Okada, Tatsuya M. Ikeda, Kiyotaka Nagaki, Kentaro Yoshida , Shigeo Takumi. Phenotypic effects of Am genomes in nascent synthetic hexaploids derived from interspecific crosses between durum and wild einkorn wheat. PLoS ONE 18(4): e0284408.
https://doi.org/10.1371/journal.pone.0284408
Potlapalli, B. P., Ishii, T., Nagaki, K., Somasundaram, S., Houben, A. CRISPR-FISH: A CRISPR/Cas9-based labeling method. In Plant Cytogenetics and Cytogenomics. Ed. Heitkam, T., Garcia, S. Humana New York. https://doi.org/10.1007/978-1-0716-3226-0
Nagata, K., Nonoue, Y., Matsubara, K., Mizobuchi, R., Ono, N., Shibaya, T., Ebana, K., Ogiso-Tanaka, E., Tanabata, T., Sugimoto, K., Taguchi-Shiobara, F., Yonemaru, J., Uga, Y., Fukuda, A., Ueda, T., Yamamoto, S., Yamanouchi, U., Takai, T., Ikka, T., Kondo, K., Hoshino, T., Yamamoto, E., Adachi, S., Sun, J., Kuya, N., Kitomi, Y., Iijima, K., Nagasaki, H., Shomura, A., Mizubayashi, T., Kitazawa, N., Hori, K., Ando, T., Yamamoto, T., Fukuoka, S., Yano, M. Development of 12 sets of chromosome segment substitution lines that enhance allele mining in Asian cultivated rice. Breed. Sci. 73: 332-342.
https://doi.org/10.1270/jsbbs.23006
Kojima, M., Makita, N., Miyata, K., Yoshino, M., Iwase, A., Ohashi, M., Surjana, A., Kudo, T., Takeda-Kamiya, N., Toyooka, K., Miyao, A., Hirochika, H., Ando, T., Shomura, A., Yano, M., Yamamoto, T., Hobo, T., Sakakibara, H. A cell wall-localized cytokinin/purine riboside nucleosidase is involved in apoplastic cytokinin metabolism in Oryza sativa. Proc. Natl. Acad. Sci. U S A. 120: e2217708120.
https://doi.org/10.1073/pnas.2217708120
Kiyosumi Hori, Tomoya Okunishi, Kenji Nakamura, Ken Iijima, Masahiro Hagimoto, Katsuyuki Hayakawa, Koka Shu, Takashi Ikka, Hiroto Yamashita, Masanori Yamasaki, Yoshinobu Takeuchi, Shota Koyama, Yoshimasa Tsujii, Toshiaki Kayano, Takuro Ishii, Toshihiro Kumamaru, Yasushi Kawagoe, Toshio Yamamoto. Genetic Background Negates Improvements in Rice Flour Characteristics and Food Processing Properties Caused by a Mutant Allele of the PDIL1-1 Seed Storage Protein Gene. Rice 15 (1) 13-13 https://thericejournal.springeropen.com/articles/10.1186/s12284-022-00560-w
Masahiro Yamashita, Chikako Ootsuka, Hikaru Kubota, Shunsuke Adachi, Takuya Yamaguchi, Kazumasa Murata, Toshio Yamamoto, Tadamasa Ueda, Taiichiro Ookawa, Tadashi Hirasawa. Alleles of high-yielding indica rice that improve root hydraulic conductance also increase flag leaf photosynthesis, biomass, and grain production of japonica rice in the paddy field. Field Crops Research 289: 108725
https://www.sciencedirect.com/science/article/abs/pii/S0378429022002969
Kiyotaka Nagaki, Tomoyuki Furuta, Naoki Yamaji, Daichi Kuniyoshi, Megumi Ishihara, Yuji Kishima, Minoru Murata, Atsushi Hoshino and Hirotomo Takatsuka. Effectiveness of Create ML in microscopy image classifications: A simple and inexpensive deep learning pipeline for non-data scientists. Chromosome Research in press, 2021. DOI：
https://doi.org/10.1007/s10577-021-09676-z
Zhang Guangchen, Liu Zimeng, Liu Youhong, Kuya Noriyuki, Hua Yuchen, Shi Hongru, Zhao Weilin, Han Yuqing, Yamamoto Toshio, Chen Wenfu, Sun Jian. (2021) iTRAQ-Based Proteomics Investigation of Critical Response Proteins in Embryo and Coleoptile During Rice Anaerobic Germination. Rice Science 28(4) 391-401
Kuniyoshi, D., Masuda, I., Kanaoka, Y., Shimazaki-Kishi, Y., Okamoto, Y., Yasui, H., Yamamoto, T., Nagaki, K., Hoshino, Y., Koide, Y., Takamure, I., Kishima, Y. Diploid male gametes circumvent hybrid sterility between Asian and African rice. Frontiers in Plant Science 10.3389/fpls.2020.579305.
Inoue, K., Takahagi, K., Kouzai, Y., Koda, S., Shimizu, M., Uehara-Yamaguchi, Y., Nakayama, R., Kita, T., Onda, Y., Nomura, T., Matsui, H., Nagaki, K., Nishii, R. and Mochida, K. Parental legacy and regulatory novelty in Brachypodium diurnal transcriptomes accompanying their polyploidy. NAR Genomics and Bioinformatics 2: 1-14.
Nagai, K., Mori, Y., Ishikawa, S., Furuta, T., Gamuyao, R., Niimi, Y., Hobo, T., Fukuda, M., Kojima, M., Takebayashi, Y., Fukushima, A., Himuro, Y., Kobayashi, M., Ackley, W., Hisano, H., Sato, K., Yoshida, A., Wu, J., Sakakibara, H., Sato, Y., Tsuji, H., Akagi, T., Ashikari, M. Antagonistic regulation of the gibberellic acid response during stem growth in rice. Nature 584 :109-114. doi: 10.1038/s41586-020-2501-8.
Okada, M., Michikawa, A., Yoshida, K., Nagaki, K., Ikeda, T.M. and Takumi, S. Phenotypic effects of the U-genome variation in nascent synthetic hexaploids derived from interspecific crosses between durum wheat and its diploid relative Aegilops umbellulata. PLOS One 15 (4): e0231129
Nagaki, K. and Yamaji, N. Decrosslinking enables visualization of RNA-guided endonuclease–in situ labeling signals for DNA sequences in plant tissues. Journal of Experimental Botany 71(6): 1792-1800
Adachi, S., Ohkubo, S., San, N. S., and Yamamoto, T. Genetic determination for source capacity to support breeding of high-yielding rice (Oryza sativa). Molecular Breeding, 40(2): 20
San, N. S., Suzuki, K., Soda, K., Adachi, S., Kasahara, H., Yamamoto, T., Ikka, T., Kondo, K., Yamanouchi, U., Sugimoto, K., Nagamura, Y., Hirasawa, T. and Ookawa, T. Semi-dwarf 1 (sd1) gene enhances light penetration into the canopy through regulating leaf inclination angle in rice. Field Crops Research 246: 107694
Kuya, N., Sun, J., Iijima, K., Venuprasad, R. and Yamamoto, T. Novel method for evaluation of anaerobic germination in rice and its application to diverse genetic collections. Breeding Science 69(4): 633-639
Ogawa, D., Sakamoto, T., Tsunematsu, H., Yamamoto, T., Kanno, N., Nonoue, Y. and Yonemaru, J. Surveillance of panicle positions by unmanned aerial vehicle to reveal morphological features of rice. PLoS ONE 14(10): e0224386
Nomura, T., Arakawa, N., Yamamoto, T., Ueda, T., Adachi, S., Yonemaru, J., Abe, A., Takagi, H. and Ookawa, T. Next generation long-culm rice with superior lodging resistance and high grain yield, Monster Rice 1. PLoS ONE 14(8): e0221424
Adachi, S., Yamamoto, T., Nakae, T., Yamashita, M., Uchida, M., Karimata, R., Ichihara, N., Soda, K., Ochiai, T., Ao, R., Otsuka, C., Nakano, R., Takai, T., Ikka, T., Kondo, K., Ueda, T., Ookawa, T. and Hirasawa, T. Genetic architecture of leaf photosynthesis in rice revealed by different types of reciprocal mapping populations. Journal of Experimental Botany 70(19): 5131-5144
Sun, J., Ma, D., Tang, L., Zhao, M., Zhang, G., Wang, W., Song, J., Li, X., Liu, Z., Zhang, W., Xu, Q., Zhou, Y., Wu, J., Yamamoto, T., Dai, F., Li, S., Zhou, G., Zheng, H., Xu, Z. and Chen, W. Population Genomic Analysis and De novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game. Mol. Plant 12(5): 632-647
Samadi, A. F., Suzuki, H., Ueda, T., Yamamoto, T., Adachi, S. and Ookawa, T. Identification of quantitative trait loci for breaking and bending types lodging resistance in rice, using recombinant inbred lines derived from Koshihikari and a strong culm variety, Leaf Star. Plant Growth Regulation 89(1): 83-98
Fukuda, A., Kondo, K., Ikka, T., Takai, T., Tanabata, T., and Yamamoto, T. 2018. A novel QTL associated with rice canopy temperature difference affects stomatal conductance and leaf photosynthesis. Breeding Science, doi.org/10.1270/jsbbs.17129
Ogawa, D., Yamamoto, E., Ootani, T., Kanno, N., Tsunematsu, H., Nonoue, Y., Yano, M., Yamamoto. T. (co-corresponding), and Yonemaru, J. 2018. Haplotype-based allele mining with JAPAN MAGIC population in rice. Scientific reports, 8: 4379
San, N.S., Ootsuki, Y., Adachi, S., Yamamoto, T., Ueda, T., Tanabata, T., Motobayashi, T., Ookawa, T., and Hirasawa, T. 2018. A near-isogenic rice line carrying a QTL for larger leaf inclination angle yields heavier biomass and grain. Field Crops Research, 219:131-138
Kobayashi, A., Hori, K., Yamamoto, T. (corresponding), and Yano, M. 2018. Koshihikari: a premium short-grain rice cultivar – its expansion and breeding in Japan. Rice 11: 15
Reuscher, S., Furuta, T., Bessho-Uehara, K., Cosi, M., Jena, K.K., Toyoda, A., Fujiyama, A., Kurata, N., Ashikari, M. 2018. Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species. Communications biology, 1:162
Kuroha, T., Nagai, K., Gamuyao, R., Wang, D.R., Furuta, T., Nakamori, M., Kitaoka, T., Adachi, K., Minami, A., Mori, Y., Mashiguchi, K., Seto, Y., Yamaguchi, S., Kojima, M., Sakakibara, H., Wu, J., Ebana, K., Mitsuda, N., Ohme-Takagi, M., Yanagisawa, S., Yamasaki, M., Yokoyama, R., Nishitani, K., Mochizuki, T., Tamiya, G., McCouch, S.R., Ashikari, M. 2018. Ethylene-gibberellin signaling underlies adaptation of rice to periodic flooding. Science, 361(6398):181-186, 2018
Nagaki, K., Yamaji, N., and Murata, M. 2017. ePro-ClearSee: a simple immunohistochemical method that does not require sectioning of plant samples. Scientific reports, 7: 42203
Nakano, H., Yoshinaga, S., Takai, T., Arai-Sanoh, Y., Kondo, K., Yamamoto, T., Sakai, H., Tokida, T., Usui, Y., Nakamura, H., Hasegawa, T., and Kondo, M. 2017. Quantitative trait loci for large sink capacity enhance rice grain yield under free-air CO2 enrichment conditions. Scientific reports 7: 1827
Yamamoto, T., Suzuki, T., Suzuki, K., Adachi, S., Sun, J., Yano, M., Ookawa, T., and Hirasawa, T. 2017. Characterization of a genomic region that maintains chlorophyll and nitrogen contents during ripening in a high-yielding stay-green rice cultivar. Field Crops Research 206: 54-64
Adachi, S., Yoshikawa, K., Yamanouchi, U., Tanabata, T., Sun, J., Ookawa, T., Yamamoto, T., Sage, R.F., Hirasawa, T., and Yonemaru, J. 2017. Fine mapping of Carbon Assimilation Rate 8, a quantitative trait locus for flag leaf nitrogen content, stomatal conductance and photosynthesis in rice. Frontiers in plant science 8: 60
Hori, K., Yamamoto, T., and Yano, M. 2017. Genetic dissection of agronomically important traits in closely related temperate japonica rice cultivars. Breeding Science 67(5): 427-434
Bessho-Uehara, K., Furuta, T., Masuda, K., Yamada, S., Angeles-Shim, R.B., Ashikari, M., Takashi, T. 2017. Construction of rice chromosome segment substitution lines harboring
Oryza barthii genome and evaluation of yield-related traits.
Breeding science, 67(4): 408–415
Furuta, T., Ashikari, M., Jena, K.K., Doi, K., Reuscher, S. 2017. Adapting genotyping-by-sequencing for rice F2 populations. G3, 7(3): 881-893
Ookawa, T., Aoba, R., Yamamoto, T., Ueda, T., Takai, T., Fukuoka, S., Ando, T., Adachi, S., Matsuoka, M., Ebitani, T., Kato, Y., Mulsanti, I.W., Kishii, M., Reynolds, M., Piñera, F., Kotake, T., Kawasaki, S., Motobayashi, T., and Hirasawa, T. 2016. Precise estimation of genome regions controlling lodging resistance using a set of reciprocal chromosome segment substitution lines in rice. Scientific Reports 6: 30572
Matsubara, K., Yamamoto, E., Kobayashi, N., Ishii, T., Tanaka, J., Tsunematsu, H., Yoshinaga, S., Matsumura, O., Yonemaru, J., Mizobuchi, R., Yamamoto, T., Kato, H., and Yano, M. 2016. Improvement of rice biomass yield through QTL-based selection. PLoS ONE 11(3): e0151830
Endo, T., Chiba, B., Wagatsuma, K., Saeki, K., Ando, T., Shomura, A., Mizubayashi, T., Ueda, T., Yamamoto, T., and Nishio, T. 2016. Detection of QTLs for cold tolerance of rice cultivar ‘Kuchum’ and effect of QTL pyramiding. Theoretical and Applied Genetics 129(3): 631-640
Yamamoto, T., Suzuki, T., Suzuki, K., Adachi, S., Sun, J., Yano, M., Ookawa, T., and Hirasawa, T. 2016. Detection of QTL for exudation rate at ripening stage in rice and its contribution to hydraulic conductance. Plant Science 242: 270-277
Furuta, T., Uehara, K., Angeles-Shim, R.B., Shim, J., Nagai, K., Ashikari, M., Takashi, T. 2016. Development of chromosome segment substitution lines harboring
Oryza nivara genomic segments in Koshihikari and evaluation of yield-related traits.
Breeding science, 66(5): 845-850
Bessho-Uehara, K., Wang, D.R., Furuta, T., Minami, A., Nagai, K., Gamuyao, R., Asano, K., Angeles-Shim, R.B., Shimizu, Y., Ayano, M., Komeda, N., Doi, K., Miura, K., Toda, Y., Kinoshita, T., Okuda, S., Higashiyama, T., Nomoto, M., Tada, Y., Shinohara, H., Matsubayashi, Y., Greenberg, A., Wu, J., Yasui, H.,Yoshimura, A., Mori, H., McCouch, S.R., Ashikari, M. 2016. Loss of function at RAE2, a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice. PNAS, 113(32): 8969-8974
Ramos, J.M., Furuta, T., Uehara, K., Chihiro, N., Angeles-Shim, R.B., Shim, J., Brar, D.S., Ashikari, M., Jena, K.K. 2016. Development of chromosome segment substitution lines (CSSLs) of
Oryza longistaminata A. Chev. & Röhr in the background of the elite japonica rice cultivar, Taichung 65 and their evaluation for yield traits. Euphytica, 210(2): 151-163
Kurokawa, Y., Noda, T., Yamagata, Y., Angeles-Shim, R., Sunohara, H., Uehara, K., Furuta, T., Nagai, K., Jena, K.K., Yasui, H., Yoshimura, A., Ashikari, M., Doi, K. 2016. Construction of a versatile SNP array for pyramiding useful genes of rice. Plant science, 242: 131-139
Shinada, H., Yamamoto, T., Sato, H., Yamamoto, E., Hori, K., Yonemaru, J., Sato, T., and Fujino, K. 2015. Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping. Breeding Science 65(5): 388-395
Taguchi-Shiobara, F., Ota, T., Ebana, K., Ookawa, T., Yamasaki, M., Tanabata, T., Yamanouchi, U., Wu, J., Ono, N., Nonoue, Y., Nagata, K., Fukuoka, S., Hirabayashi, H., Yamamoto, T., and Yano, M. 2015. Natural variation in the flag leaf morphology of rice due to a mutation of the NARROW LEAF 1 gene in Oryza sativa L. Genetics 201(2): 795-808
Shinada, H., Yamamoto, T., Yamamoto, E., Hori, K., Hirayama, Y., Maekawa, T., Kiuchi, H., Sato, H., and Sato, T. 2015. Quantitative trait loci for whiteness of cooked rice detected in improved rice cultivars in Hokkaido. Breeding Science 65(3): 201-207
Wada, T., Miyahara, K., Sonoda, J., Tsukaguchi, T., Miyazaki, M., Tsubone, M., Ando, T., Ebana, K., Yamamoto, T., Iwasawa, N., Umemoto, T., Kondo, M., and Yano, M. 2015. Detection of QTLs for white-back and basal-white grains caused by high temperature during ripening period in japonica rice. Breeding Science 65(3): 216-225
Ujiie, K., Yamamoto, T., Yano, M., and Ishimaru, K. 2015. Genetic factors determining varietal differences in characters affecting yield between two rice (
Oryza sativa L.) varieties, Koshihikari and IR64. Genetic Resources and Crop Evolution 63(1): 97-123
Hori, K., Nonoue, Y., Ono, N., Shibaya, T., Ebana, K., Matsubara, K., Ogiso-Tanaka, E., Tanabata, T., Sugimoto, K., Taguchi-Shiobara, F., Yonemaru, J., Mizobuchi, R., Uga, Y., Fukuda, A., Ueda, T., Yamamoto, S., Yamanouchi, U., Takai, T., Ikka, T., Kondo, K., Hoshino, T., Yamamoto, E., Adachi, S., Nagasaki, H., Shomura, A., Shimizu, T., Kono, I., Ito, S., Mizubayashi, T., Kitazawa, N., Nagata, K., Ando, T., Fukuoka, S., Yamamoto, T., and Yano, M. 2015. Genetic architecture of variation in heading date among Asian rice accessions. BMC Plant Biology 15: 115
Matsubara, K., Yamamoto, E., Mizobuchi, R., Yonemaru, J., Yamamoto, T., Kato, H., and Yano, M. 2015. Hybrid breakdown caused by epistasis-based recessive incompatibility in a cross of rice (
Oryza sativa L.). Journal of Heredity 106(1): 113-122
Fukuda, A., Sugimoto, K., Ando, T., Yamamoto, T., and Yano, M. 2015. Chromosomal locations of a gene underlying heat-accelerated brown spot formation and its suppressor genes in rice. Molecular Genetics and Genomics 290(3): 1085-1094
Yano, K., Ookawa, T., Aya, K., Ochiai, Y., Hirasawa, T., Ebitani, T., Takarada, T., Yano, M., Yamamoto, T., Fukuoka, S., Wu, J., Ando, T., Ordonio, R.L., Hirano, K., and Matsuoka, M. 2015. Isolation of a novel lodging resistance QTL gene involved in strigolactone signaling and its pyramiding with a QTL gene involved in another mechanism. Molecular Plant 8(2): 303-314
Nagaki, K., Tanaka, K., Yamaji, N., Kobayashi, H., and Murata, M. 2015. Sunflower centromeres consist of a centromere-specific LINE and a chromosome-specific tandem repeat. Frontiers in Plant Science, 6: 912
Habu, Y., Ando, T., Ito, S., Nagaki, K., Kishimoto, N., Taguchi-Shiobara, F., Numa, H., Yamaguchi, K., Shigenobu, S., Murata, M., Meshi, T., and Yano, M. 2015. Epigenomic modification in rice controls meiotic recombination and segregation distortion. Molecular Breeding 35: 644-653
Tek, A. L., Stupar, R. M., Nagaki, K. 2015. Modification of centromere structure: a promising approach for haploid line production in plant breeding. Turkish Journal of Agriculture and Forestry, 38: 1-6
Furuta, T., Komeda, N., Asano, K., Uehara, K., Gamuyao, R., Angeles-Shim, R.B., Nagai, K., Doi, K., Wang, D.R., Yasui, H., Yoshimura, A., Wu, J., McCouch, S.R., Ashikari, M. 2015. Convergent loss of awn in two cultivated rice species
Oryza sativa and
Oryza glaberrima is caused by mutations in different loci. G3, 5(11): 2267-2274
Song, X.J., Kuroha, T., Ayano, M., Furuta, T., Nagai, K., Komeda, N., Segami, S., Miura, K., Ogawa, D., Kamura, T., Suzuki, T., Higashiyama, T., Yamasaki, M., Mori, H., Inukai, Y., Wu, J., Kitano, H., Sakakibara, H., Jacobsen, S.E., Ashikari, M. 2015.
Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice. PNAS, 112(1): 76-81
Takai, T., Ikka, T., Kondo, K., Nonoue, Y., Ono, N., Arai-Sanoh, Y., Yoshinaga, S., Nakano, H., Yano, M., Kondo, M., and Yamamoto, T. 2014. Genetic mechanisms underlying yield potential in the rice high-yielding cultivar Takanari, based on reciprocal chromosome segment substitution lines. BMC plant biology 14: 295
Ookawa, T., Inoue, K., Matsuoka, M., Ebitani, T., Takarada, T., Yamamoto, T., Ueda, T., Yokoyama, T., Sugiyama, C., Nakaba, S., Funada, R., Kato, H., Kanekatsu, M., Toyota, K., Motobayashi, T., Vazirzanjani, M., Tojo, S., and Hirasawa, T. 2014. Increased lodging resistance in long-culm, low-lignin gh2 rice for improved feed and bioenergy production. Scientific Reports 4: 6567
Yamamoto, E., Iwata, H., Tanabata, T., Mizobuchi, R., Yonemaru, J., Yamamoto, T. (corresponding), and Yano, M. 2014. Effect of advanced intercrossing on genome structure and on the power to detect linked quantitative trait loci in a multi-parent population: a simulation study in rice. BMC Genetics 15: 50
Yonemaru, J., Mizobuchi, R., Kato, H., Yamamoto, T., Yamamoto, E., Matsubara, K., Hirabayashi, H., Takeuchi, Y., Tsunematsu, H., Ishii, T., Ohta, H., Maeda, H., Ebana, K., and Yano, M. 2014. Genomic regions involved in yield potential detected by genome-wide association analysis in Japanese high-yielding rice cultivars. BMC Genomics 15: 346
Shinada, H., Yamamoto, T., Yamamoto, E., Hori, K., Yonemaru, J., Matsuba, S., and Fujino, K. 2014. Historical changes in population structure during rice breeding programs in the northern limits of rice cultivation. Theoretical and Applied Genetics 127(4): 995-1004
Adachi, S., Baptista, L.Z., Sueyoshi, T., Murata, K., Yamamoto, T., Ebitani, T., Ookawa, T., Hirasawa, T. 2014. Introgression of two chromosome regions for leaf photosynthesis from an indica rice into the genetic background of a japonica rice. Journal of Experimental Botany 65(8): 2049-2056
Tek, A. L., Kashihara, K., Murata, M., Nagaki, K. 2014. Identification of the centromere-specific histone H3 variant in Lotus japonicus. Gene 538: 8-11.
Furuta, T., Uehara, K., Angeles-Shim, R.B., Shim, J., Ashikari, M., Takashi, T. 2014. Development and evaluation of chromosome segment substitution lines (CSSLs) carrying chromosome segments derived from
Oryza rufipogon in the genetic background of
Oryza sativa L. Breeding science, 63(5): 468-475
Abe, T., Nonoue, Y., Ono, N., Omoteno, M., Kuramata, M., Fukuoka, S., Yamamoto, T., Yano, M., and Ishikawa, S. 2013. Detection of QTLs to reduce cadmium content in rice grains using LAC23/Koshihikari chromosome segment substitution lines. Breeding Science 63(3): 284-291
Takai, T., Adachi, S., Taguchi-Shiobara, F., Sanoh-Arai, Y., Iwasawa, N., Yoshinaga, S., Hirose, S., Taniguchi, Y., Yamanouchi, U., Wu, J., Matsumoto, T., Sugimoto, K., Kondo, K., Ikka, T., Ando, T., Kono, I., Ito, S., Shomura, A., Ookawa, T., Hirasawa, T., Yano, M., Kondo, M., and Yamamoto, T. 2013. A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate. Scientific Reports 3: 2149
Adachi, S., Nakae, T., Uchida, M., Soda, K., Takai, T., Oi, T., Yamamoto, T., Ookawa, T., Miyake, H., Yano, M., and Hirasawa, T. 2013. The mesophyll anatomy enhancing CO2 diffusion is a key trait for improving rice photosynthesis. Journal of Experimental Botany 64 (4): 1061-1072
Iwata, A., Tek, A. L., Richard, M. M, Abernathy, B., Fonsêca, A., Schmutz, J., Chen, N. W., Thareau, V., Magdelenat, G., Li, Y., Murata, M., Pedrosa-Harand, A., Geffroy, V., Nagaki, K., Jackson, S. A. 2013. Identification and characterization of functional centromeres of common bean. Plant Journal 76: 47-60.
Shibata, F., Nagaki, K., Yokota, E., Murata, M. 2013. Tobacco karyotyping by accurate centromere identification and novel repetitive DNA localization. Chromosome Res. 21: 375-381.
Murata, M., Shibata, F., Hironaka, A., Kashihara, K., Fujimoto, F., Yokota, E., Nagaki, K. 2013. Generation of an artificial ring chromosome in Arabidopsis by the Cre/LoxP-mediated recombination. Plant Journal 74: 363-371.
Takai, T., Ohsumi, A., Arai, Y., Iwasawa, N., Yano, M., Yamamoto, T., Yoshinaga, S., and Kondo, M. 2013. QTL analysis of leaf photosynthesis in rice. Japan Agricultural Research Quarterly 47(3): 227-235
Yamamoto, E., Yonemaru, J., Yamamoto, T., and Yano, M. 2012. OGRO: The overview of functionally characterized genes in rice online database. Rice 5: 26
Yonemaru, J., Yamamoto, T. (co-first), Ebana, K., Yamamoto, E., Nagasaki, H., Shibaya, T., and Yano, M. 2012. Genome-wide haplotype changes produced by artificial selection during modern rice breeding in Japan. PLoS ONE 7(3): e32982
Nagaki, K., Yamamoto, M., Yamaji, N., Mukai, Y., Murata, M. 2012. Chromosome dynamics visualized with an anti-centromeric histone H3 antibody in Allium. PLOS ONE 7(12): e51315.
Banaei-Moghaddam, A. M., Schubert, V., Kumke, K., Klemme, S., Weiß, O., Nagaki, K., Macas, J., González-Sánchez, M., Heredia, V., Gómez-Revilla, D., González-García, M., Vega, J., Puertas, M. and Houben, A. 2012. Nondisjuction in favour of a chromosome - the mechanism of rye B chromosome accumulation at pollen mitosis. The Plant Cell 24: 4124-4134.
Nagaki, K., Shibata, F., Kanatani, A., Kashihara, K. and Murata, M. 2012. Isolation of centromeric-tandem repetitive DNA sequences by chromatin affinity purification using a HaloTag7-fused centromere-specific histone H3 in tobacco. Plant Cell Reports 31: 771-779.
Links to lists of publications of the members Link to a publication list of Prof. YAMAMOTO, Toshio （Research map） Link to a publication list of Assoc. Prof. NAGAKI, Kiyotaka（Elsevier Pure） Link to a publication list of Assist. Prof. Furuta, Tomoyuki（Research map）
