Institute of Crop Science, NARO

Rice Applied Genomics Research Unit

Rice is inhabited around the world, and shows numerous morphological and physiological differences as phenotypic variations. Some of such variations have been used as genetic resources to improve rice plants to satisfy human's need. Phenotypic variations considered to be genetically controlled by collective function of large number of genes on rice genome. However, genetic bases and biological functions of most of them are still unknown, which prevented us from wider practical using of any of rice germplasm. Rice Applied Genomics Research Unit exploits useful phenotypic variations from wide rice germplasms, and clarifies the genes involving them with biological functions by aid of recent advance of genome information and technology. Also, the unit tries to develop new breeding materials and to propose more effective breeding methodology. Through these research activities, the unit aims to establish a consecutive road map from genome information of rice germplasm to actual breeding.

Unit Leader

Research Topics :Marker assisted breeding, Yield components

Unit Members

Research Topics
Shuichi FUKUOKA Principal Researcher Germplasm enhancement, Blast resistance
Ritsuko MIZOBUCHI Principal Researcher Resistance to bacterial seedling/grain rot
Utako YAMANOUCHI Senior Researcher QTL mapping, Seed dormancy
Kiyosumi HORI Senior Researcher QTL mapping, Grain quality, Flowering time
Tadamasa UEDA Senior Researcher QTL cloning, Photosynthesis

Research Publications

  • Shibaya T, Hori K, Ogiso-Tanaka E, Yamanouchi U, Shu K, Kitazawa N, Shomura A, Ando T, Ebana K, Wu J, Yamazaki T, Yano M (2016) Hd18, encoding histone acetylase related to Arabidopsis FLOWERING LOCUS D, is involved in the control of flowering time in rice Plant and Cell Physiology 57(9):1828-1838
  • Hori K, Matsubara K, Yano M (2016) A novel Tos17 insertion upstream of Hd1 alters flowering time in rice Plant Breeding 135(5): 588-592
  • Hori K, Matsubara K, Uga Y, Yano M (2016) Genetic control of flowering time in rice: integration of Mendelian genetics and genomics Theoretical and Applied Genetics (Online First Articles; DOI: 10.1007/s00122-016-2773-4)
  • Hori K (2016) Detection of genetic factors responsible for grain quality and cooking characteristics of Japanese rice cultivars Nippon Shokuhin Kagaku Kogaku Kaishi 63(10): 484-487
  • Mizobuchi R, Fukuoka S, Tsushima S, Yano M Sato H (2016) QTLs for resistance to major rice diseases exacerbated by global warming: brown spot, bacterial seedling rot, and bacterial grain rot. Rice 9:23
  • Ookawa T, Aoba R, Yamamoto T, Ueda T, Takai T, Fukuoka S, Ando T, Adachi S, Matsuoka M, Ebitani T, Kato Y, Mulsanti IW, Kishii M, Reynolds M, Piñera F, Kotake T, Kawasaki S, Motobayashi T, 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 doi:10.1038/srep30572
  • Yamamoto T, Suzuki T, Suzuki K, Adachi S, Sun J, Yano M, Ookawa T, 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
  • Matsubara K, Yamamoto E, Kobayashi N, Ishii T, Tanaka J, Tsunematsu H, Yoshinaga S, Matsumura O, Yonemaru J, Mizobuchi R, Yamamoto T, Kato H, Yano M (2016) Improvement of rice biomass yield through QTL-based selection PLoS ONE 11(3):e01518303
  • Endo T, Chiba B, Wagatsuma K, Saeki K, Ando T, Shomura A, Mizubayashi T, Ueda T, Yamamoto T, 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
  • Mizobuchi R, Sato H, Fukuoka S, Tsushima S, Yano M (2015) Fine mapping of RBG2, a quantitative trait locus for resistance to Burkholderia glumae, on rice chromosome 1 Molecular Breeding 35(1):15
  • 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, Yano M (2015) Genetic architecture of variation in heading date among Asian rice accessions BMC Plant Biology 15:115
  • Nagata K, Ando T, Nonoue Y, Mizubayashi T, Kitazawa N, Shomura A, Matsubara K, Ono N, Mizobuchi R, Shibaya T, Ogiso-Tanaka E, Hori K, Yano M, Fukuoka S (2015) Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica × indica cross Breeding Science 65(4):308-318
  • Uga Y, Kitomi Y, Yamamoto E, Kanno N, Kawai S, Mizubayashi T, Fukuoka S (2015) A QTL for root growth angle on rice chromosome 7 is involved in the genetic pathway of DEEPER ROOTING 1 Rice 8:8
  • Kitomi Y, Kanno N, Kawai S, Mizubayashi T, Fukuoka S, Uga Y (2015) QTLs underlying natural variation of root growth angle among rice cultivars with the same functional allele of DEEPER ROOTING 1 Rice 8:16
  • Shinada H, Yamamoto T, Sato H, Yamamoto E, Hori K, Yonemaru J, Sato T, 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
  • Shinada H, Yamamoto T, Yamamoto E, Hori K, Hirayama Y, Maekawa T, Kiuchi H, Sato H, Sato T (2015) Quantitative trait loci for whiteness of cooked rice detected in improved rice cultivars in Hokkaido Breeding Science 65(3):201-207
  • 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, 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
  • Hori K, Suzuki K, Iijima K, Ebana K. (2015) Variation in cooking and eating quality traits in Japanese rice germplasm accessions. Breeding Science
  • Wada T, Miyahara K, Sonoda J, Tsukaguchi T, Miyazaki M, Tsubone M, Ando T, Ebana K, Yamamoto T, Iwasawa N, Umemoto T, Kondo M, 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
  • Yonemaru J, Choi S.H, Sakai H, Ando T, Shomura A, Yano M, Wu J, Fukuoka S (2015) Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar 'Koshihikari' Breeding Science 65(3):249-256
  • Fukuoka S, Saka N, Mizukami Y, Koga H, Yamanouchi U, Yoshioka Y, Hayashi N, Ebana K, Mizobuchi R, Yano M (2015) Gene pyramiding enhances durable blast disease resistance in rice Scientific Reports 5:7773
  • Matsubara K, Yamamoto E, Mizobuchi R, Yonemaru J, Yamamoto T, Kato H, 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, 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

Review Papers

  • Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke L.J, Dempewolf H, De Pace C, Edwards D, Gepts P, Greenland A, Hall A.E, Henry R, Hori K, Howe G.T, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen H.T, Ogbonnaya F.C, Ortiz R, Paterson A.H, Tuberosa R, Valliyodan B, Varshney R.K, Yano M (2016) Global agricultural intensification during climate change: a role for genomics Plant Biotechnology Journal 14(4):1095-1098
  • Kole C, Muthamilarasan M, Henry R, Edwards D, Sharma R, Abberton M, Batley J, Bentley A, Blakeney M, Bryant J, Cai H, Cakir M, Cseke L.J, Cockram J, Oliveira A.C, Pace C.D, Dempewolf H, Ellison S, Gepts P, Greenland A, Hall A, Hori K, Howe G.T, Hughes S, Humphreys M.W, Iorizzo M, Ismail A.M, Marshall A, Mayes S, Nguyen H.T, Ogbonnaya F.C, Ortiz R, Paterson A.H, Simon P.W, Tohme J, Tuberosa R, Valliyodan B, Varshney R.K, Wullschleger S.D, Yano M, Prasad M (2015) Application of genomics-assisted breeding for generation of climate resilient crops: Progress and prospects Frontiers in Plant Science 6:563