Japanese Biography Research Interests Software Refereed papers Presentations Misc.

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IWATA, Hiroyoshi

Associate professor

  Laboratory of Biometry and Bioinformatics
Department of Agricultural and Environmental Biology
Graduate School of Agriculture and Life Science
The University of Tokyo
1-1-1 Yayoi, Bunkyo, Tokyo, Japan
Tel: +81-3-5841-5069
Fax: +81-3-5841-5069
e-mail: aiwata@mail.ecc.u-tokyo.ac.jp


1993 The University of Tokyo (B.A.)
1995 The University of Tokyo (M.A.)
1998 The University of Tokyo (Ph.D (Agriculture))

Research Interests

I am strongly interested in the application of theories and methods in various disciplines (e.g., biometrics, statistical genetics, populaiton genetics, information science) to promoting crop genetic improvement.


  1. SHAPE - software for biological shape analysis with elliptic Fourier descriptors
  2. AntMap - software for high-throughput linkage mapping
  3. Larva(e)Area - ImageJ plug-in for measuring colony development in honey bees by simple digital image analysis
  4. PCO - software for principal component analysis (MS-DOS version)

Refereed research papers

  1. Kobayashi M, Ohyanagi H, Takanashi H, Asano S, Kudo T, Kajiya-Kanegae H, Nagano AJ, Tainaka H, Tokunaga T, Sazuka T, Iwata H, Tsutsumi N, Yano K (2017) Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data. DNA Research :
  2. Ohyama A, Shirasawa K, Matsunaga H, Negoro S, Miyatake K, Yamaguchi H, Nunome T, Iwata H, Fukuoka H, Hayashi T (2017) Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F1 hybrids of tomato. Theoretical and Applied Genetics :
  3. Moriya S, Kunihisa M, Okada K, Shimizu T, Honda C, Yamamoto T, Muranty H, Denancé C, Katayose Y, Iwata H, Abe K (2017) Allelic composition of MdMYB1 drives red skin color intensity in apple (Malus × domestica Borkh.) and its application to breeding. Euphytica 213: 78
  4. Onogi A, Sasaki S, Kobayashi M, Ogino A, Nozaki T, Kurogi K, Yasumori T, Togashi K, Iwata H (2017) A genetic analysis of meat compositions in Japanese Black cattle: Genetic parameters and sex influence. Journal of Animal Breeding and Genetics :
  5. Watanabe K, Guo W, Arai K, Takanashi H, Kajiya-Kanegae H, Kobayashi M, Yano K, Tokunaga T, Fujiwara T, Tsutsumi N, Iwata H (2017) High-throughput phenotyping of sorghum plant height using an unmanned aerial vehicle and its application to genomic prediction modeling. Frontiers in Plant Science 8: 421
  6. Yabe S, Iwata H, Jannink JL (2017) A simple package to script and simulate breeding schemes: The breeding scheme language. Crop Science 57: 1-8
  7. Manickavelu A, Hattori T, Yamaoka S, Yoshimura K, Kondou Y, Onogi A, Matsui M, Iwata H, Ban T (2017) Genetic nature of elemental contents in wheat grains and its genomic prediction: Toward the effective use of wheat landraces from Afghanistan. PLoS ONE 12: e0169416
  8. Moriya S, Kunihisa M, Okada K, Iwanami H, Iwata H, Minamikawa M, Katayose Y, Matsumoto T, Mori S, Sasaki H, Matsumoto T, Nishitani C, Terakami S, Yamamoto T, Abe K (2017) Identification of QTLs for flesh mealiness in apple (Malus × domestica Borkh.). The Horticulture Journal 86: 159-170
  9. Atagi Y., Onogi A., Kinukawa, M., Ogino A., Kurogi K., Uchiyama K., Yasumori, T., Adachi K., Togashi K., Iwata H (2017) Genetic analysis of semen production traits of Japanese Black and Holstein bulls: genome-wide markers-based estimation of genetic parameters and environmental effect trends. Journal of Animal Science doi:10.2527/jas2016.1186.:
  10. Yamamoto E, Matsunaga H, Onogi A, Ohyama A, Miyatake K, Yamaguchi H, Nunome T, Iwata H, Fukuoka H (2017) Efficiency of genomic selection for breeding population design and phenotype prediction in tomato. Heredity 118: 202-209
  11. Tanaka J, Hayashi T, Iwata H (2016) A practical, rapid generation-advancement system for rice breeding using simplified biotron breeding system. Breeding Science 66: 542-551
  12. Hori T, Montocho D, Agbangla C, Ebana K, Futakuchi K, Iwata H (2016) Multi-task Gaussian process for imputing missing data in multi-trait and multi-environment trials. Theoretical and Applied Genetics 129: 2101-2115
  13. Kondou Y, Manickavelu A, Komatsu K, Arifi M, Kawashima M, Ishii T, Hattori T, Iwata H, Tsujimoto H, Ban T, Matsui M (2016) Analysis of grain elements and identification of best genotypes for Fe and P in Afghan wheat landraces. Breeding Science :
  14. Yabe S, Yamasaki M, Ebana K, Hayashi T, Iwata H (2016) Island-model genomic selection for long-term genetic improvement of autogamous crops. PLoS ONE 11: e0153945
  15. Onogi A, Iwata H (2016) VIGoR: Variational Bayesian inference for genome-wide regression. Journal of Open Research Software 4: e11
  16. Onogi A, Ideta O, Yoshioka T, Ebana K, Yamasaki M, Iwata H (2016) Uncovering a nuisance influence of a phenological trait of plants using a nonlinear structural equation: Application to days to heading and culm length in Asian cultivated rice (Oryza sativa L.). PLoS ONE 11: e0148609
  17. Yamamoto E, Matsunaga H, Onogi A, Kajiya-Kanegae H, Minamikawa M, Suzuki A, Shirasawa K, Hirakawa H, Nunome T, Yamaguchi H, Miyatake K, Ohyama A, Iwata H, Fukuoka H (2016) A simulation-based breeding design that uses whole-genome prediction in tomato. Scientific Reports 6: 19454
  18. Onogi A, Watanabe M, Mochizuki T, Hayashi T, Nakagawa H, Hasegawa T, Iwata H (2016) Toward integration of genomic selection with crop modelling: the development of an integrated approach to predicting rice heading dates. Theoretical and Applied Genetics 129: 805-817
  19. Blondel M, Onogi A, Iwata H, Ueda N (2015) A ranking approach to genomic selection. PLoS ONE 10: e0128570
  20. Onogi A, Ogino A, Komatsu T, Shoji N, Shimizu K, Kurogi K, Yasumori T, Togashi K, Iwata H (2015) Whole-genome prediction of fatty acid composition in meat of Japanese Black cattle. Animal Genetics 46:557-559
  21. Iwata H, Ebana K, Uga Y, Hayashi T (2015) Genomic prediction of biological shape: elliptic Fourier analysis and kernel partial least squares (PLS) regression applied to grain shape prediction in rice (Oryza sativa L.). PLoS ONE 10: e0120610
  22. Onogi A, Ideta O, Inoshita Y, Ebana K, Yoshioka T, Yamasaki M, Iwata H (2014) Exploring the areas of applicability of whole-genome prediction methods for Asian rice (Oryza sativa L.). Theoretical and Applied Genetics 128:41-53
  23. Yabe S, Hara T, Ueno M, Enoki H, Kimura T, Nishimura S, Yasui Y, Ohsawa R, Iwata H (2014) Rapid genotyping with DNA micro-arrays for high-density linakge mappng and QTL mapping in common buckwheat (Fagopyrum esculentum Moench). Breeding Science 64: 291-299
  24. Yamamoto E, Iwata H, Tanabata T, Mozobuchi R, Yonemaru J, Yamamoto T, 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
  25. Yabe S, Ohsawa R, Iwata H (2014) Genomic selection for the traits expressed after pollination in allogamous plants. Crop Science 54: 1448-1457
  26. Onogi A, Ogino A, Komatsu T, Shoji N, Simizu K, Kurogi K, Yasumori T, Togashi K, Iwata H (2014) Genomic prediction in Japanese Black cattle: application of a single-step approach to beef cattle. J Anim Sci 92: 1931-1938
  27. Babil P, Kondo S, Iwata H, Kushikawa S, Shiwachi H (2013) Intra-Specific Ploidy Variations in Cultivated Chinese Yam (Dioscorea polystachya Turcz.). Trop. Agr. Develop. 57: 101-107
  28. Hayashi T, Iwata H (2013) A Bayesian method and its variational approximation for prediction of genomic breeding values in multiple traits.BMC Bioinformatics 14: 31
  29. Iwata H, Hayashi T, Terakami S, Takada N, Sawamura Y, Yamamoto T (2013) Potential assessment of genome-wide association study and genomic selection in Japanese pear Pyrus pyrifolia. Breed Sci. 63: 125-140
  30. Iwata H, Hayashi T, Terakami S, Takada N, Saito T, Yamamoto T (2013) Genomic prediction of trait segregation in a progeny population: a case study of Japanese pear (Pyrus pyrifolia). BMC Genet. 14: 81
  31. Ishii K, Yamanari M, Iwata H, Yasuno Y, Oshika T (2013) Relationship between changes in crystalline lens shape and axial elongation in young children. Invest Ophthalmol Vis Sci. 54: 771-777
  32. Yabe S, Ohsawa R, Iwata H (2013) Potential of genomic selection for mass selection breeding in annual allogamous crops. Crop Sci. 53: 95-105
  33. Uchiyama K, Iwata H, Moriguchi Y, Ujino-Ihara T, Ueno S, Taguchi Y, Tsubomura M, Mishima K, Iki T, Watanabe A, Ftamura N, Shinohara K, Tsumura Y (2013) Genome wide association mapping for wood property and amounts of male strobili in Cryptomeria japonica. PLoS ONE :
  34. Kato S, Kato S, Kato J, Kato M, Nagamitsu T, Iwata H, Tsumura Y, Mukai Y (2012) Impact of negative frequency-dependent selection on mating pattern and genetic structure: a comparative analysis of the S-locus and nuclear SSR loci in Prunus lannesiana var. speciosa..Heredity 109: 188-198
  35. Hayashi T, Ohyama A, Iwata H (2012) Bayesian QTL mapping for recombinant inbred lines derived from a four-way cross. Euphytica 183: 277-287
  36. Ujino-Ihara T, Iwata H, Taguchi Y, Tsumura Y (2012) Identification of QTLs associated with male strobilus abundance in Cryptomeria japonica.Tree Genetics and Genomes 8: 1319-1329
  37. Iwata H, Jannink JL (2011) Accuracy of genomic selection prediction in barley breeding programs: a simulation study based on the real SNP data of barley breeding lines. Crop Science 51: 1915-1927
  38. Iwata H, Hayashi T, Tsumura Y (2011) Prospects for genomic selection in conifer breeding: a simulation study of Cryptomeria japonica. Tree Genetics and Genomes 7: 747-758
  39. Yoshiyama M, Kimura K, Saitoh K, Iwata H (2011) Measuring colony development in honey bees by simple digital image analysis. Journal of Apicultural Research 50: 170-172
  40. Ishii K, Iwata H, Oshika T (2011) Quantitative evaluation of changes in eyeball shape in emmetropization and myopic changes based on elliptic Fourier descriptors. IOVS 52: 8585-8591
  41. Heffner EL, Jannink JL, Iwata H, Souza E, Sorrells ME (2011) Genomic selection accuracy for grain quality traits in biparental wheat populations. Crop Science 51: 2597-2606
  42. Moriguchi Y, Yomogida H, Iwata H, Takahashi M, Taira H, Tsumura Y (2011) Paternity analysis in a progeny test of Cryptomeria japonica revealed adverse effects of pollen contamination from outside seed orchards on morphological traits. Tree Genetics and Genomes 7: 1089-1097
  43. Hara T, Iwata H, Okuno K, Matsui K, Ohsawa R (2011) QTL analysis of photoperiod sensitivity in common buckwheat by using markers for expressed sequence tags and photoperiod-sensitivity candidate genes. Breeding Science 61: 394-404
  44. Kai S, Tanaka H, Hashiguchi M, Iwata H, Akashi R (2010) Analysis of genetic diversity and morphological traits of Japanese Lotus japonicus for establishment of a core collection. Breeding Science 60: 436-446
  45. Ebana K, Yonemaru J, Fukuoka S, Iwata H, Kanamori H, Namiki N, Nagasaki H, Yano M (2010) Genetic structure revealed by a whole-genome single-nucleotide polymorphism survey of diverse accessions of cultivated Asian rice (Oryza sativa L.). Breeding Science 60: 390-397
  46. Iwata H, Jannink JL (2010) Marker genotype imputation in a low-marker-density panel with a high-marker-density reference panel: accuracy evaluation in barley breeding lines.. Crop Science 50: 1269-1278
  47. Iwata H, Ebana K, Uga Y, Hayashi T, Jannink JL (2010) Genome-wide association study of grain shape variation among Oryza sativa L. germplasms based on elliptic Fourier analysis. Molecular Breeding 25: 203-215
  48. Hayashi T, Iwata H (2010) EM algorithm for Bayesian estimates of genomic breeding values. BMC Genetics 11: 3
  49. Kato S, Iwata H, Tsumura Y, Mukai Y (2010) Genetic structure of island populations of Prunus lannesiana (Carr.) Wilson var. speciosa (Koidz.) Makino revealed by the chloroplast DNA, AFLP and nuclear SSR loci. Jounal of Plant Research 124: 11-23
  50. Akasaka M, Ushiki J, Iwata H, Ishikawa R, Ishii T (2009) Genetic relationships and diversity of weedy rice (Oryza sativa L.) and cultivated rice varieties in Okayama Prefecture, Japan. Breeding Science 59: 401-409
  51. Wakui K, Iwata H, Takahashi Y, Takahata Y, Fujigaki J (2009) Assessment of the congruity of genetic relationships and variation revealed by individual- and bulked-samples-based approaches using RAPD and ISSR markers in Japanese turnip (Brassica rapa ssp. rapa) cultivars.Breeding Science 59: 447-452
  52. Iwata H, Ebana K, Fukuoka S, Jannink JL, Hayashi T (2009) Bayesian multilocus association mapping on ordinal and censored traits and its application to the analysis of genetic variation among Oryza sativa L. germplasms. Theoretical and Applied Genetics 118: 865-880
  53. Jannink JL, Iwata H, Bhat PR, Chao S, Wenzl P, Muehlbauer GJ (2009) Marker imputation in barley association studies. The Plant Genome 2: 11-22
  54. Hayashi T, Iwata H (2009) Bayesian QTL mapping for multiple families derived from crossing a set of inbred lines to a reference line.Heredity 102: 497-505
  55. Shehzad T, Iwata H, Okuno K (2009) Genome-wide association mapping of quantitative traits in sorghum (Sorghum bicolor (L.) Moench) by using multiple models. Breeding Science 59: 217-227
  56. Zheng Z, Iwata H, Hirata Y, Tamura Y (2008) Quantitative evaluation of the degree of sprout leaf bending of rice cultivars using P-type Fourier descriptors and principal component analysis. Euphytica 163: 259-266
  57. Itakura M, Saeki K, Oori H, Yokoyama T, Kaneko T, Tabata S, Ohwada T, Tajima S, Uchiumi T, Honnma K, Fujita K, Iwata H, Saeki Y, Hara Y, Ikeda S, Eda S, Mitsui H, Minamisawa K (2008) Genomic comparison of Bradyrhizobium japonicum straints with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members. The ISME Journal 3: 326-339
  58. Naito Y, Kanzaki M, Iwata H, Obayashi K, Lee SL, Okuda T, Tsumura Y (2008) Density-dependent selfing and its effects on seed performance in a tropical canopy tree species, Shorea acuminate (Dipterocarpaceae). Forest Ecology and Management 256: 375-383
  59. Iwata H, Uga Y, Yoshioka Y, Ebana K, Hayashi T (2007) Bayesian association mapping of multiple quantitative trait loci and its application to the analysis of genetic variation among Oryza sativa L. germplasms. Theoretical and Applied Genetics 114: 1437-1449
  60. Yoshioka Y, Iwata H, Tabata M, Minomiya S, Ohsawa R (2007) Chalkiness in rice: potential for evaluation with image analysis. Crop Science47: 2113-2120
  61. Yoshioka Y, Honjo M, Iwata H, Ninomiya S, Ohsawa R (2007) Pattern of geographical variation in petal shape in wild populations of Primula sieboldii E. Morren. Plant Species Biology 22: 87-93
  62. Yoshioka Y, Ohashi K, Konuma A, Iwata H, Ohsawa R, Ninomiya S (2007) Ability of bumblebees to discriminate differences in the shape of artificial flowers of Primula sieboldii (Primulaceae). Annals of Botany 99: 1175-1182
  63. Kato S, Iwata H, Tsumura Y, Mukai Y (2007) Distribution of S-alleles in island populations of flowering cherry Prunus lannesiana var. speciosa.Genes and Genetic Systems 82: 77-88
  64. Tsumura Y, Matsumoto A, Tani N, Ujino-Ihara T, Kado T, Iwata H, Uchida K (2007) Genetic diversity and the genetic structure of natural populations of Chamaecyparis obtuse: implications for management and conservation. Heredity 99: 161-172
  65. Tsumura Y, Kado T, Takahashi T, Tani T, Ujino-Ihara T, Iwata H (2007) Genome scan to detect genetic structure and adaptive genes of natural populations of Cryptomeria japonica. Genetics 176: 2393-2403
  66. Dubouzet JG, Ishihara A, Matsuda F, Miyagawa H, Iwata H, Wakasa K (2007) Integrated metabolomic and transcriptomic analyses of high-tryptophan rice expressing a mutant anthranilate synthase alpha subunit. Journal of Experimental Botany 58: 3309-3321
  67. Iwata H, Ninomiya S (2006) AntMap: constructing genetic linkage maps using an ant colony optimization algorithm. Breeding Science 56: 371-377
  68. Yoshioka Y, Iwata H, Hase N, Matsuura S, Ohsawa R, Ninomiya S (2006) Genetic combining ability of petal shape in garden pansy (Viola x wittrockiana Gams) based on image analysis. Euphytica 151: 311-319
  69. Iwata H, Kamijo T, Tsumura Y (2006) Assessment of genetic diversity of native species in Izu Islands for a discriminate choice of source populations: implications for revegetation of volcanically devastated sites. Conservationn Genetics 7: 399-413
  70. Konishi T, Iwata H, Yashiro K, Tsumura Y, Ohsawa R, Yasui Y, Ohnishi O (2006) Development and characterization of microsatellite markers for common buckwheat. Breeding Science 56: 277-285
  71. Yoshioka Y, Iwata H, Fukuta N, Ohsawa R, Ninomiya S (2006) Quantitative evaluation of petal shape and picotee color pattern in lisianthus by image analysis. Journal of the American Society for Horticultural Science 131: 261-266
  72. Moriguchi Y, Tsuchiya S, Iwata H, Itoo S, Tani N, Tsumura Y (2006) Factors influencing male reproductive success in a Cryptomeria japonica seed orchard revealed by microsatellite marker analysis. Silvae Genetica 56: 207-214
  73. Hua C, Ban T, Tonghe X, Iwata H, Kikuchi F, Fujimaki H (2006) Characterization of wheat landraces of Xinjiang-Uygur Autonomous District of China based on genetic diversity of microsatellite DNA polymorphism and several agronomic traits. Breeding Research 8: 161-169 (in Japanese with English title and summary)
  74. Naito Y, Konuma A, Iwata H, Suyama Y, Seiwa K, Okuda T, Lee SL, Muhammad N, Tsumura Y (2005) Selfing and inbreeding depression in seeds and seedlings of Neobalanocarpus heimii (Dipterocarpaceae). Journal of Plant Research 118: 423-430
  75. Goto S, Iwata H, Shibano S, Ohya K, Suzuki A, Ogawa H (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
  76. Zheng Z, Iwata H, Ninomiya S, Tamura Y (2005) Quantitative evaluation of partial shape characteristics of petal in sacred lotus based on P-type Fourier descriptors. Breeding Research 7: 133-142 (in Japanese with English title and summary)
  77. Yoshioka Y, Iwata H, Ohsawa R, Ninomiya S (2005) Quantitative evaluation of the petal shape variation in Primula sieboldii caused by breeding process in the last 300 years. Heredity 94: 657-663
  78. Iwata H, Imon K, Tsumura Y, Ohsawa R (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
  79. Yashiro K, Iwata H, Akashi Y, Tomita K, Kazuya M, Tsumura Y, Kato K (2005) Genetic relationship among East and South Asian melon (Cucumis melo L.) revealed by AFLP analysis. Breeding Science 55: 197-206
  80. Iwata H, Kamijo T, Tsumura Y (2005) Genetic structure of Miscanthus sinensis ssp. condensatus (Poaceae) on Miyake Island: implications for revegetagion of volcanically devastated sites. Ecological Research 20: 233-238
  81. Yoshioka Y, Iwata H, Ohsawa R, Ninomiya S (2005) Quantitative evaluation of flower colour pattern by image analysis and principal component analysis of Primula sieboldii E. Morren. Euphytica 139: 179-186
  82. Iwata H, Niikura S, Matsuura S, Takano Y, Ukai Y (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
  83. Yoshioka Y, Iwata H, Ohsawa R, Ninomiya S (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
  84. Tani N, Takahashi T, Ujino-Ihara T, Iwata H, Yoshimura K, Tsumura Y (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
  85. Iwata H, Niikura S, Matsuura S, Takano Y, Ukai Y (2004) Genetic control of root shape at different growth stages in radish (Raphanus sativus L.). Breeding Science 54: 117-124
  86. Tani N, Takahashi T, Iwata H, Mukai Y, Ujino-Ihara T, Matsumoto A, Yoshimura K, Yoshimaru K, Murai M, Nagasaka K, Tsumura Y (2003) A consensus linkage map for sugi (Cryptomeria japonica) from two pedigrees, based on microsatellites and expressed sequence tags. Genetics165: 1551-1568
  87. Uga Y, Fukuta Y, Cai HW, Iwata H, Ohsawa R, Morishima H, Fujimura T (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
  88. Moriguchi Y, Iwata H, Ujino-Ihara T, Yoshimura K, Taira H, Tsumura Y (2003) Development and characterization of microsatellite markers for Cryptomeria japonica D.Don. Theoretical and Applied Genetics 106: 751-758
  89. Iwata H, Ukai Y (2002) SHAPE: A computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors. Journal of Heredity 93: 384-385
  90. Iwata H, Nesumi H, Ninomiya S, Takano Y, Ukai Y (2002) The evaluation of genotype x environment interactions of citrus leaf morphology using image analysis and elliptic Fourier descriptors. Breeding Science 52: 243-251
  91. Ujino-Ihara T, Matsumoto A, Iwata H, Yoshimura K, Tsumura Y (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
  92. Iwata H, Nesumi H, Ninomiya S, Takano Y, Ukai Y (2002) Diallel analysis of leaf shape variations of citrus varieties based on elliptic Fourier descriptors. Breeding Science 52: 89-94
  93. Nakao Y, Iwata H, Matsumoto A, Tsumura Y, Tomaru N (2001) Highly polymorphic microsatellite markers in Chamaecyparis obtusa. Canadian Journal of Forest Research 31: 2248-2551
  94. Iwata H, Ujino-Ihara T, Yoshimura K, Nagasaka K, Mukai Y, Tsumura Y (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
  95. Iwata H, Konuma A, Tsumura Y (2000) Development of microsatellite markers in the tropical tree Neobalanocarpus heimii (Dipterocarpaceae). Molecular Ecology 9: 1684-1685
  96. Iwata H, Niikura S, Matsuura S, Takano Y, Ukai Y (2000) Diallel analysis of root shape of Japanese radish (Raphanus sativus L.) based on elliptic Fourier descriptors. Breeding Science 50: 73-80
  97. Nikaido AM, Ujino T, Iwata H, Yoshimura K, Yoshimaru H, Suyama Y, Murai M, Nagasaka K, Tsumura Y (2000) AFLP and CAPS linkage maps of Cryptomeria japonica. Theoretical and Applied Genetics 100: 825-831
  98. Toyohara H, Irie K, Ding W, Iwata H, Fujimaki H, Kikuchi F, Ukai Y (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
  99. Iwata H, Niikura S, Matsuura S, Takano Y, Ukai Y (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
  100. Omori H, Iwata H (1998) Development of image analysis software, BioImage ver.1, for Windows to measure leaf area. Agricultural Information Research 7: 71-80 (in Japanese with English title and summary)

Review papers and others

  1. Iwata H, Minamikawa MF, Kajiya-Kanegae H, Ishimori M, Hayashi T (2016.3) Genomics-assisted breeding in fruit trees. Breeding Science 66: 100-115
  2. (In Japanese) Iwata H (2015) Machine learning and simulation for accelerating crop genetic improvement. Simulation 34: 260-267
  3. Isik F, Kumar S, Martinez-Gonrcia PJ, Iwata H, Yamamoto T (2015) Acceleration of forest and fruit tree domestication by genomic selection. Advances in Botanical Research (Land Plants – Trees) 74: 93-124
  4. (In Japanese) Sazuka T, Iwata H (2014) From genome to breeding: Challenge of genome-assisted breeding of sorghum (Special article in Biotechnology in Biorefinary I).Journal of the Japan Institute of Energy 93: 429-435
  5. (In Japanese) Iwata H (2012) Whole genome breeding: Will next-generation sequencing open the door to a new paradigm of breeding? (Proceedings of the 40th symposium) Sakumotsu Kenkyu 57: 77-82
  6. Lorenz AJ, Chao S, Asoro FG, Heffner EL, Hayashi T, Iwata H, Smith KP, Sorrells ME, Jannink J (2011) Genomic selection in plant breeding: knowledge and prospects. Advances in Agronomy 110: 77-123
  7. Jannink JL, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: From theory to practice. Brief. Funct. Genomic. Proteomic. 9: 166-177
  8. (In Japanese) Iwata H (2009) Development of data-mining methods and programs for plant breeding. Breeding Researh 11: 177-184
  9. (In Japanese)Tsumura Y, Iwata H (2003) Considering genetic diversity and differentiation in revegetation(SPECIAL ISSUE: Potentialities of locality-certified seedlings). Landscape and Ecological Engineering 28: 470-475

Book and book chapter (ones in English only)

  1. Iwata H (2011) Quantitative genetic analysis of crop organ shape based on principal components of elliptic Fourier descriptors. In: Lestrel PE editor. Biological shape analysis: Proceedings of the 1st international symposium, Tsukuba, Japan, 3-6 June 2009. Singapore: World Scientific Publishing, pp. 50–66.