hiro@naro
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Japanese Research interests Publications Presentation Software CV
Announcement
  • Minor update (2009/9/19)
  • My home page has been fully renewed (2005/05/19)
  • Affiliation is renewed.
    (2006/04/03)

Hiroyoshi Iwata, Ph.D

Senior Researcher

Data-mining and Grid Research Team,
National Agricultural Research Center,

National Agriculture and Food Science Research Organization,
3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666, JAPAN
Tel: +81-29-838-7176, Fax: +81-29-838-8551
Email: iwatah@affrc.go.jp



Research Interests

My main research field is applied genetics. Currently, I am interested in the development of data-mining method for extracting significant rules from various type of biological information such as phenotypic, environmental and genetic (including molecular) data.

Bioinformatics

  • Development of a novel algorithm for the construction of genetic map
  • Super high-dimensional data analysis using a novel regression method
  • QTL Analysis methodology for multi-dimensional phenotype such as plant organ shape


Biometrics & Statistical Genetics

  • Genetic analysis of crop plant morphology (i.e., shape, size, color and color pattern) using image analysis
  • Association between phenotype and genotype of crop germplasm
  • Development of molecular markers and their application to linkage mapping

Population Genetics
  • Construction of the genetic guide line for revegetation of natural devastated area

Publications

Refereed papers

  1. Iwata, H., T. Kamijo and Y. Tsumura (in press) Assessment of genetic diversity of native species in Izu Islands for a discriminate choice of source populations: implications for revegetation of volcanically devastated sites. Conservation Genetics.
  2. Yoshioka, Y. H. Iwata, N. Hase, S. Matsuura, R. Ohsawa, S. Ninomiya (in press) Genetic combining ability of petal shape in garden pansy (Viola x wittrockiana Gams) based on image analysis. Euphytica.
  3. Yoshioka, Y., H. Iwata, N. Fukuta, R. Ohsawa, S. Ninomiya (in press) Quantitative evaluation of petal shape and picotee color pattern in lisianthus by image analysis. Journal of the American Society for Horticultural Science.
  4. Naito, Y., A. Konuma, H. Iwata, Y. Suyama, K. Seiwa, T. Okuda, S.L. Lee, N. Muhammad, Y. Tsumura (2005) Selfing and inbreeding depression in seeds and seedlings of Neobalanocarpus heimii (Dipterocarpaceae). Journal of Plant Research 118: 423-430
  5. Goto, S., H. Iwata, S. Shibano, K. Ohya, A. Suzuki and H. Ogawa (2005) Fruit shape variation in Fraxinus mandshurica var. japonica characterized using elliptic Fourier descriptors and the effect on flight duration. Ecological Research 20: 733-738.
  6. Zheng, Z., H. Iwata, S. Ninomiya and Y. Tamura (2005) Quantitative evaluation of partial shape characteristics of petal in sacred lotus based on P-type Fourier descriptors. Ikushugaku-kenkyu 7: 133-142 (in Japanese).
  7. Yoshioka, Y., H. Iwata, R. Ohsawa and S. Ninomiya (2005) Quantitative evaluation of the petal shape variation in Primula sieboldii caused by breeding process in the last 300 years. Heredity 94: 657-663.
  8. Iwata, H., K. Imon, Y. Tsumura and R. Ohsawa (2005) Genetic diversity among Japanese indigenous common buckwheat (Fagopyrum esculentum) cultivars as determined from AFLP and SSR markers and quantitative agronomic traits. Genome 48: 367-377. <Abstract>
  9. Yashiro, K., H. Iwata, Y. Akashi, K. Tomita, M. Kuzuya, Y. Tsumura and K. Kato (2005) Genetic relationship among East and South Asian melon (Cucumis melo L.) revealed by AFLP analysis. Breeding Science 55: 197-206.
  10. Iwata, H., T. Kamijo and Y. Tsumura (2005) Genetic structure of Miscanthus sinensis ssp. condensatus (Poaceae) on Miyake Island: implications for revegetagion of volcanically devastated sites. Ecological Research 20: 233-238. <Abstract>
  11. Yoshioka, Y., H. Iwata, R. Ohsawa and S. Ninomiya (2005) Quantitative evaluation of flower colour pattern by image analysis and principal component analysis of Primula sieboldii E. Morren. Euphytica.139: 179-186. <Abstract>
  12. Iwata, H., S. Niikura, S. Matuura, Y. Takano and Y. Ukai (2004) Genetic effects by soil type interaction in diallel analysis of root shape and size of Japanese radish (Raphanus sativus L.). Breeding Science 54: 313-318. <Abstract>
  13. Yoshioka, Y., H. Iwata, R. Ohsawa and S. Ninomiya (2004) Analysis of petal shape variation of Primula sieboldii E. Morren by elliptic Fourier descriptors and principal component analysis. Annals of Botany 94: 657-664. <Abstract>
  14. Yashiro, K., K. Tomita and H. Iwata (2004) AMMI analysis of monthly fluctuation in yield, firmness and sweetness on Japanese strawberry cultivars. Seikohken-kenkyu-houkoku 7: 17-21 (in Japanese with English summary).
  15. Tani, N., T. Takahashi, T. Ujino-Ihara, H. Iwata, K. Yoshimura, Y. Tsumura (2004) Development and characteristics of microsatellite markers for sugi (Cryptomeria japonica D. Don) derived from microsatellite-enriched library. Annals of Forest Science 61: 569-575. <Abstract>
  16. Iwata, H., S. Niikura, S. Matsuura, Y. Takano and Y. Ukai (2004) Genetic control of root shape at different growth stages in radish (Raphanus sativus L.). Breeding Science 54: 117-124. <Abstract>
  17. Tani, N., T. Takahashi, H. Iwata, Y. Mukai, T. Ujino-Ihara, A. Matsumoto, K. Yoshimura, K. Yoshimaru, M. Murai, K. Nagasaka and Y. Tsumura (2003) A consensus linkage map for sugi (Cryptomeria japonica) from two pedigrees, based on microsatellites and expressed sequence tags. Genetics 165: 1551-1568. <Abstract>
  18. Uga, Y., Y. Fukuta, H. W. Cai, H. Iwata, R. Ohsawa, H. Morishima and T. Fujimura (2003) Mapping QTLs influencing rice floral morphology using recombinant inbred lines derived from a cross between Oryza sativa L. and O. rufipogon Griff. Theoretical and Applied Genetics 107: 218-226. <Abstract>
  19. Moriguchi, Y., H. Iwata, T. Ujino-Ihara, K. Yoshimura, H. Taira and Y. Tsumura (2003) Development and characterization of microsatellite markers for Cryptomeria japonica D.Don. Theoretical and Applied Genetics 106: 751-758. <Abstract>
  20. Iwata, H. and Y. Ukai (2002) SHAPE: A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors. Journal of Heredity 93: 384-385.<Abstract>
  21. Iwata, H., H. Nesumi, S. Ninomiya, Y. Takano and Y. Ukai (2002) The evaluation of genotype x environment interactions of citrus leaf morphology using image analysis and elliptic Fourier descriptors. Breeding Science 52: 243-251. <Abstract>
  22. Ujino-Ihara, T., A. Matsumoto, H. Iwata, K. Yoshimura and Y. Tsumura (2002) Single-strand conformation polymorphism of sequence-tagged site markers based on partial sequences of cDNA clones in Cryptomeria japonica. Genes and Genetic Systems 77: 251-257. <Abstract>
  23. Iwata, H., H. Nesumi, S. Ninomiya, Y. Takano and Y. Ukai (2002) Diallel analysis of leaf shape variations of citrus varieties based on elliptic Fourier descriptors. Breeding Science 52: 98-94. <Abstract>
  24. Nakao, Y., H. Iwata, A. Matsumoto, Y. Tsumura and N. Tomaru (2001) Highly polymorphic microsatellite markers in Chamaecyparis obtusa. Canadian Journal of Forest Research 31: 2248-2251. <Abstract>
  25. Iwata, H., T. Ujino-Ihara, K. Yoshimura, K. Nagasaka, Y. Mukai and Y. Tsumura (2001) Cleaved amplified polymorphic sequence markers in sugi, Cryptomeria japonica D. Don, and their locations on a linkage map. Theoretical and Applied Genetics 103: 881-895.<Abstract>
  26. Iwata, H., A. Konuma and Y. Tsumura (2000) Development of microsatellite markers in the tropical tree Neobalanocarpus heimii (Dipterocarpaceae). Molecular Ecology 9: 1684-1685. <Abstract>
  27. Iwata, H., S. Niikura, S. Matsuura, Y. Takano and Y. Ukai (2000) Diallel analysis of root shape of Japanese radish (Raphanus sativus L.) based on elliptic Fourier descriptors. Breeding Science 50: 73-80.
  28. Nikaido, A.M., T. Ujino, H. Iwata, K. Yoshimura, H. Yoshimaru, Y. Suyama, M. Murai, K. Nagasaka and Y. Tsumura (2000) AFLP and CAPS linkage maps of Cryptomeria japonica. Theoretical and Applied Genetics 100: 825-831. <Abstract>
  29. Toyohara, H., K. Irie, W. Ding, H. Iwata, H. Fujimaki, F. Kikuchi and Y. Ukai (2000) Evaluation of tuber shape of yam (Dioscorea alta L.) cultivars by image analysis and elliptic Fourier descriptors. SABRAO Journal of Breeding and Genetics 32: 31-37.
  30. Iwata, H., S. Niikura, S. Matsuura, Y. Takano and Y. Ukai (1998) Evaluation of variation of root shape of Japanese radish (Raphanus sativus L.) based on image analysis using elliptic Fourier descriptors. Euphytica 102: 143-149. <Abstract>
  31. Omori, H. and H. Iwata (1998) Development of image analysis software, BioImage ver.1, for Windows to measure leaf area. Agricultural Information Research 7: 71-80. (in Japanese)

Books and unrefereed papers

See Japanese page


Presentation

International congress

  1. Iwata, H. Y. Uga, Y. Yoshioka, S. Ninomiya, K. Ebana (2006) QTL mapping and identification of marker-trait associations for shape variaiton of brown rice. Plant and Animal Genome XIV Conference, San Diego, USA.
  2. Iwata, H. (2005) Quantitative shape analysis of plant organ and its application in plant breeding. 10th International Congress of SABRAO, Tsukuba, Japan.
  3. Iwata, H., T. Miwa and S. Ninomiya (2004) HyDRAS: Hyper-Dimensional Regression Analysis Service on the Internet. AFITA/WCCA2004. Bangkok, Thailand.
  4. Iwata, H. and S. Ninomiya (2004) Ant colony optimization for linkage grouping and locus ordering in genome mapping. Plant and Animal Genome XII. San Diego. USA.
  5. Uga, Y., Y. Fukuta, H. Cai, H. Iwata, R. Ohsawa, H. Morishima, T. Fujimura (2003) Mapping the quantitative trait loci responsible for differences in floral morphology between Oryza sativa L. and O. rufipogon Griff. International Genetic Resources Workshops on the genus Oryza.
  6. Iwata, H., K. Imon, K. Yoshimura, Y. Tsumura and R. Ohsawa (2002) Genetic differentiation process from late-summer to summer agroecotypes of common buckwheat (Fagopyrum esculentum) varieties in Japan revealed by AFLP and SSR markers. Plant and Animal Genome X. San Diego. USA.
  7. Tsumura, Y., H. Iwata, N. Tani, T. Ujino-Ihara, A. Matsumoto (2002) Population genetic study of Cryptomeria japonica based on linkage map. Plant and Animal Genome X. San Diego. USA.
  8. N. Tani, H. Iwata, A. Matsumoto, T. Takahashi, T. Ujino-Ihara, K. Yoshimura, M. Murai, H. Yoshimaru, Y. Mukai and Y. Tsumura (2002) Construction of a consensus map for sugi (Cryptomeria japonica) from three outbred Pedigrees. Plant and Animal Genome X. San Diego. USA.
  9. Iwata, H., K. Imon, K. Yoshimura, Y. Tsumura and R. Ohsawa (2001) Genetic diversity of common buckwheat varieties in Japan based on microsatellite markers. VIII International Symposium on Buckwheat. Chunchon. Korea.
  10. Iwata, H., T. Ujino-Ihara, K. Yoshimura, K. Nagasaka, Y. Mukai and Y. Tsumura (2001) Cleaved amplified polymorphic sequence markers in sugi, Cryptomeria japonica D. Don, and their locations on a linkage map. Plant and Animal Genome IX. San Diego. USA.
  11. Tani, N., T. Takahashi, H. Iwata, T. Ujino-Ihara, K. Yoshimura and Y. Tsumura (2001) Development of microsatellite markers in Cryptomeria japonica for genetic mapping and other applications. Tree Biotechnology in the New Millennium. IUFRO/Molecular Biology of Forest Trees.
  12. Tani, N., H. Iwata, A. Matsumoto, K. Yoshimura, M. Murai, H. Yoshimaru, Y. Mukai and Y. Tsumura (2001) Construction of EST map in sugi (Cryptomeria japonica) using RFLP and CAPS markers. Plant and Animal Genome IX. San Diego. USA.
  13. Matsumoto, A., T. Ujino-Ihara, H. Iwata, K. Yoshimura, N. Tani and Y. Tsumura (2001) Development of CAPS markers in Chamaecyparis obtusa based on ESTs from Cryptomeria japonica. Plant and Animal Genome IX. San Diego. USA.
  14. Ninomiya, S., and H. Iwata (1997) Evaluation of crop shape based on elliptic Fourier method. 8th International Congress of SABRAO.
  15. Yamamoto, C., K. E. Hadipoentyanti, H. Iwata, M. Niwa, S. Ninomiya and Y. Ukai (1994) Diversity in Indonesian clove [Syzygium aromaticum (L) Merr. & Perr.] populations as surveyed by elliptic Fourier descriptors of leaf shape. 7th International Congress of SABRAO & WSAA.

Domestic congress

See Japanese page.


Software

I have developed a number of programs to promote the efficiency of our study. Some of them can be freely downloaded from the following links.

Name Descriptions Current version
SHAPE A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors Ver. 1.2
AntMap A computer program for high performance linkage mapping using Ant Colony Optimization (ACO) algorithm Ver. 1.2
GDIVERSE A computer program for calculating the index of genetic marker polymorphism such as observed and expected heterozytosity, the number of alleles observed, PIC (polymorphic Information Content) and PEP (Paternity Exclusion Probability) -
PCO A small C++ program for principal coordinate analysis Ver. 1.0
Makijaku A Windows program for measuring length, area and angle on digital images Ver. 1.1


CV

Education

  • 1993 - B. S. University of Tokyo, Faculty of Agriculture, Lab. Biometrics
  • 1995 - M. S. University of Tokyo, Graduate School of Agriculture and Life Sciences
  • 1998 - Ph.D. University of Tokyo, Graduate School of Agriculture and Life Sciences
    Title of doctoral thesis
    "Evaluation and statistical genetic analysis of plant morphology based on elliptic Fourier descriptors"
    Supervisor in the doctoral course
    Prof. Yasuo Ukai


Employment history

  • 1998 - 2002, Post-doc Fellow, Forestry and Forest Products Research Institute, Department of Forest Genetics
  • 2002 - 2004, Research Scientist, National Agricultural Research Center, Department of Information Science and Technology
  • 2005 - present, Senior Researcher, National Agricultural Research Center



Copyright (c) 2005 Hiroyoshi Iwata