Japanese Biography Research Interests Software Extarnal Databases Refereed papers Review papers Books and book chapters
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IWATA, Hiroyoshi

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: +81-3-5841-5068
e-mail: hiroiwata@g.ecc.u-tokyo.ac.jp  

Biography


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.

External Database

  • Researchmap
  • ResearchGate
  • Google Scholar

    • Software

    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. Diot J, Iwata H (2023) Bayesian optimization for breeding schemes. Frontiers in Plant Science 13: 1050198
    2. Dang T, Kumaishi K, Usui E, Kobori S, Sato T, Toda Y, Yamasaki Y, TsujimotoH, Ichihashi Y, Iwata H (2022) Stochastic variational variable selection for high-dimensional microbiome data. Microbiome 10: 236
    3. Sakurai K, Toda Y, Kajiya-Kanegae H, Ohmori Y, Yamasaki Y, Takahashi H, Takanashi H, Tsuda M, Tsujimoto H, Kaga A, Nakazono M, Fujiwara T, Iwata H (in press) Time-series multispectral imaging in soybean for improving biomass and genomic prediction accuracy. The Plant Genome 15: e20244
    4. Takanashi H, Kajiya-Kanegae H, Nishimura A, Yamada J, Ishimori M, Kobayashi M, Yano K, Iwata H, Tsutsumi N, Sakamoto W (2022) DOMINANT AWN INHIBITOR encodes the ALOG protein originating from gene duplication and inhibits AWN elongation by suppressing cell proliferation and elongation in sorghum. Plant and Cell Physiology 63: 901-918
    5. Wahinya FW, Yamazaki K, Jing Z, Takami T, Kamiya T, Kajiya-Kanegae H, Takanashi H, Iwata H, Tsutsumi N, Fujiwara T, Sakamoto W (2022) Sorghum ionomics reveals the functional SbHMA3a allele that limits excess cadmium accumulation in grains. Plant and Cell Phisiology 63: 713-728
    6. Toda Y, Sasaki G, Ohmori Y, Yamasaki Y, Takahashi H, Takanashi H, Tsuda M, Kajiya-Kanegae H, Lopez-Lozano R, Tsujimoto H, Kaga A, Nakazono M, Fujiwara T, Baret F, Iwata H (2022) Genomic prediction of green fraction dynamics in soybean using unmanned aerial vehicles observations. Frontiers in Plant Science 13: 828864
    7. Minamikawa MF, Nonaka K, Hamada H, Shimizu T, Iwata H (2022) Dissecting breeder's sense via explainable machine learning approach: Application to fruit peelability and hardiness in citrus. Frontiers in Plant Science 13: 832749
    8. Kuroki K, Yan K, Iwata H, Shimizu KK, Tameshige T, Nasuda S, Guo W (2022) Development of a high-throughput field phenotyping rover optimized for size-limited breeding fields as open-source hardware. Breeding Science 72: 66-74
    9. Suzuki K, Abe MS, Kumakura D, Nakaoka S, Fujiwara F, Miyamoto H, Nakaguma T, Okada M, Sakurai K, Shimizu S, Iwata H, Masuya H, Nihei N, Ichihashi Y (2022) Chemical-mediated microbial interactions can reduce the effectiveness of time-series-based inference of ecological interaction networks. International Journal of Environmental Research and Public Health 19: 1228
    10. Hamazaki K, Iwata H (2021) Bayesian optimization of multivariate genomic prediction models based on secondary traits for improved accuracy gains and phenotyping costs. Theoretical and Applied Genetics 135: 35-50
    11. Kajiya-Kanegae H, Ohyanagi H, Ebata T, Tanizawa Y, Onogi A, Sawada Y, Hirai MY, Wang Z-X, Han B, Toyoda A, Fujiyama A, Iwata H, Tsuda K, Suzuki T, Nosaka-Takahashi M, Nonomura K, Nakamura Y, Kawamoto S, Kurata N, Sato Y (2021) OryzaGenome2.1: Database of diverse genotypes in wild Oryza species. Rice 14: 24
    12. Jing Z, Wacera FW, Takami T, Takanashi H, Fukuda F, Kawano Y, Kajiya-Kanegae H, Iwata H, Tsutsumi N, Sakamoto W (2021) NB-LRR-encoding genes conferring susceptibility to organophosphate pesticides in sorghum. Scientific Reports 11: 19828
    13. Tanaka R, Mandaharisoa ST, Rakotondramanana M, Ranoivo HN, Pariasca-Tanaka, J, Kajiya-Kanegae H, Iwata H, Wissuwa M (2021) From gene banks to farmer's fields: using genomic selection to identify donors for a breeding program in rice to close the yield gap on smallholder farms. Theoretical and Applied Genetics 134: 3397-3410
    14. Toda Y, Kaga A, Kajiya-Kanegae H, Hattori T, Yamaoka S, Okamoto M, Tsujimoto H, Iwata H (2021) Genomic prediction modeling of soybean biomass using UAV-based remote sensing and longitudinal model parameters. The Plant Genome 14: e20157
    15. Sekine D, Tsuda M, Yabe S, Shimizu T, Machita K, Saruta M, Yamada T, Ishimoto M, Iwata H, Kaga A (2021) Improving quantitative traits in self-pollinated crops using simulation-based selection with minimal crossing. Frontiers in Plant Science 12: 729645
    16. Ishimori M, Takanashi H, Fujimoto M, Kajiya-Kanegae H, Yoneda J, Tokunaga T, Tsutsumi N, Iwata H (2021) Spatial kernel models capturing field heterogeneity for accurate estimation of genetic potential. Breeding Science 71: 444-455
    17. Ishimori M, Takanashi H, Fukami K, Cervantes K, Nagano AJ, Kajiya-Kanegae H, Grauke LJ, Tsutsumi N, Randall JJ, Iwata H (2021) Genome-wide RAD-Seq analysis revealed subpopulation structures of the pecan (Carya illinoinensis) germplasm collection and their relationship to geographical distribution patterns. Acta Horticulturae 1318 (10.17660/ActaHortic.2021.1318.26)
    18. Goto S, Mori H, Uchiyama K, Ishizuka W, Taneda H, Kono M, Kajiya-Kanegae H, Iwata H (2021) Genetic dissection of growth and eco-physiological traits associated with altitudinal adaptation in Sakhalin Fir (Abies sachalinensis) based on QTL mapping. Genes 12: 1110
    19. Miyamoto-Maeta M, Kamiya T, Fujiwara T, Hirotomi D, Iwata H (2021) Time-course changes in the ionomic profiles of rice leaves and their application in growth stage prediction. Crop Science 61: 4239-4254
    20. Mahjoob MMM, Chen T-S, Gorafi YSA, Yamasaki Y Kamal NM, Abdelrahman M, Iwata H, Matsuoka Y, Tahir ISA, Tsujimoto H (2021) Traits to differentiate lineages and subspecies of Aegilops tauschii, the D genome progenitor species of bread wheat. Diverstiy 13: 217
    21. Takanashi H, Shichijo M, Sakamoto L, Kajiya-Kanegae H, Iwata H, Sakamoto W, Tsutsumi N (2021) Genetic dissection of QTLs associated with spikelet-related traits and grain size in sorghum. Scientific Reports 11: 1-16
    22. Minamikawa MF, Kunihisa M, Noshita K, Moriya S, Abe K, Hayashi T, Katayose Y, Matsumoto T, Nishitani C, Terakami S, Yamamoto T, Iwata H (2021) Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study. Horticulture Research 8: 1-14
    23. Kajiya-Kanegae H, Nagasaki H, Kaga A, Hirano K, Ogiso-Tanaka E, Matsuoka M, Ishimori M, Ishimoto M, Hashiguchi M, Tanaka H, Akashi R, Isobe S, Iwata H (2021) Whole-genome sequence diversity and association analysis of 198 soybean accessions in mini-core collections. DNA Research 28: dsaa032
    24. Fujii H, Nonaka K, Minamikawa MF, Endo T, Sugiyama A, Hamazaki K, Iwata H, Omura M, Shimada T (2021) Allelic composition of carotenoid metabolic genes in 13 founders influences carotenoid composition in juice sac tissues of fruits among Japanese citrus breeding population. PLOS ONE 16: e0246468
    25. Chen T-S, Aoike T, Yamasaki M, Kajiya-Kanegae H, Iwata H (2020) Predicting rice heading date using an integrated approach combining a machine learning method and a crop growth model. Frontiers in Genetics 11: 1643.
    26. Guo T, Mu Q, Wang J, Vanous AE, Onogi A, Iwata H, Li X, Yu J (2020) Dynamic effects of interacting genes underlying rice flowering-time phenotypic plasticity and global adaptation. Genome Research 30: 673-683
    27. Toda Y, Wakatsuki H, Aoike T, Kajiya-Kanegae H, Yamasaki M, Yoshioka T, Ebana K, Hayashi T, Nakagawa H, Hasegawa T, Iwata H (2020) Predicting biomass of rice with intermediate traits: Modeling method combining crop growth models and genomic prediction models. PLOS ONE 15: e0233951
    28. Hamazaki K, Iwata H (2020) RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method. PLoS Computational Biology 16: e1007663
    29. Hamazaki K, Kajiya-Kanegae H, Yamasaki M, Ebana K, Yabe S, Nakagawa H, Iwata H (2020) Choosing the optimal population for a genome-wide association study: A simulation of whole-genome sequences from rice. The Plant Genome 13: e20005
    30. Ishimori M, Hattori T, Yamazaki K, Takanashi H, Fujimoto M, Kajiya-Kanegae H, Yoneda J, Tokunaga T, Fujiwara T, Tsutsumi N, Iwata H (2020) Impacts of dominance effects on genomic prediction of sorghum hybrid performance. Breeding Science 70: 605-616
    31. Ishimori M, Takanashi H, Hamazaki K, Atagi Y, Kajiya-Kanegae H, Fujimoto M, Yoneda J, Tokunaga T, Tsutsumi N, Iwata H (2020) Dissecting the Genetic Architecture of Biofuel-Related Traits in a Sorghum Breeding Population. G3: Genes, Genomes, Genetics 10: 4565-4577.
    32. Jarquin D, Kajiya-Kanegae H, Taishen C, Yabe S, Persa R, Yu J, Nakagawa H, Yamasaki M, Iwata H (2020) Coupling day length data and genomic prediction tools for predicting time-related traits under complex scenarios. Scientific Reports 10: 1-12
    33. Kajiya-Kanegae H, Takanashi H, Fujimoto M, Ishimori M, Ohnishi N, Wacera WF, Omollo EA, Kobayashi M, Yano K, Nakano M, Kozuka T, Kusaba M, Iwata H, Tsutsumi N, Sakamoto W (2020) RAD-seq-Based High-Density Linkage Map Construction and QTL Mapping of Biomass-Related Traits in Sorghum using the Japanese Landrace Takakibi NOG. Plant and Cell Physiology 61: 1262-1272
    34. Kar S, Garin V, Kholovﾃ｡ J, Vadez V, Durbha SS, Tanaka R, Iwata H, Urban MO, Adinarayana J (2020) SpaTemHTP: a data analysis pipeline for efficient processing and utilization of temporal high-throughput phenotyping data. Frontiers in Plant Science 11: 552509
    35. Kar S, Tanaka R, Korbu LB, Kholovﾃ｡ J, Iwata H, Durbha SS, Adinarayana J, Vadez V (2020) Automated discretization of 'transpiration restriction to increasing VPD' features from outdoors high-throughput phenotyping data. Plant Methods 16: 1-20
    36. Kirie S, Iwasaki H, Noshita K, Iwata H (2020) A theoretical morphological model for quantitative description of the three-dimensional floral morphology in water lily (Nymphaea). PLOS ONE 15: e0239781
    37. Persa R, Iwata H, Jarquin D (2020) Use of family structure information in interaction with environments for leveraging genomic prediction models. The Crop Journal 8: 843-854
    38. Yamazaki K, Ishimori M, Kajiya-Kanegae H, Takanashi H, Fujimoto M, Yoneda J, Yano K, Koshiba K, Tanaka R, Iwata H, Tokunaga T, Tsutsumi N, Fujiwara T (2020) Effect of salt tolerance on biomass production in a large population of sorghum accessions. Breeding Science 70: 167-175
    39. Sakamoto L, Kajiya-Kanegae H, Noshita K, Takanashi H, Kobayashi M, Kudo T, Yano K, Tokunaga T, Tsutsumi N, Iwata H (2019) Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology. PLoS ONE 14: e0224695
    40. Kajiya-Kanegae H, YabeS, Yoshida H, Ebana K,Yamasaki M,Nakagawa H, Iwata H (2019) Whole genome sequencing data of Oryza sativa L. cv. Takanari. Data in Brief 27: 104546
    41. Takahashi Y, Iwata H, Takahata Y, Wakui K (2019) Comparison of individual- and bulked-samples-based approaches using RAPD and ISSR markers for identifying genetic relationships in Brassica cultivars. Cytologia 84: 119-126.
    42. Yamazaki K,Tokunaga T, Iwata H, Tsutsumi N, Fujiwara T (2019) Accumulation of radioactive cesium in sorghum (Sorghum bicolor (L.) Moench) accessions cultivated in Fukushima in 2011 and 2012. Soil Science and Plant Nutrition 65: 298-304.
    43. Yabe S,Yoshida H, Kajiya-Kanegae H,Yamasaki M, Iwata H, Ebana K, Hayashi T, Nakagawa H (2018) Description of grain weight distribution leading to genomic selection for grain-filling characteristics in rice. PLoS ONE 13: e0207627
    44. Fujimoto M, Sazuka T, Oda Y, Kawahigashi H, Wu J, Takanashi H, Ohnishi T, Yoneda JI, Ishimori M, Kajiya-Kanegae H, Hibara KI, Ishizuma F, Ebine K, Ueda T, Tokunaga T, Iwata H, Matsumoto T, Kasuga S, Yonemaru JI, Tsutsumi N (2018) Transcriptional switch for programmed cell death in pith parenchyma of sorghum stems. Proceedings of the National Academy of Sciences USA 115: E8783-E8792
    45. Takahashi KH, Ishimori M, Iwata H (2018) HSP90 as a global genetic modifier for male genital morphology in Drosophila melanogaster. Evolution 72: 2419-2434
    46. Mimanikawa MF, Takada N, Terakami S, Saito T, Onogi A, Kajiya-Kanegae H, Hayashi T, Yamamoto T, Iwata H (2018) Genome-wide association study and genomic prediction using parental and breeding populations of Japanese pear (Pyrus pyrifolia Nakai). Scientific Reports 8: 11994
    47. Nishio S, Hayashi T, Yamamoto T, Terakami S, Iwata H, Imai A, takada N, Kato H, Saito T (2018) Bayesian genome-wide association study of nut traits in Japanese chestnut. Molecular Breeding, 38, 99
    48. Yabe S, Hara T, Ueno M, Enoki H, Kimura T, Nishimura S, Yasui Y, Ohsawa R, Iwata H (2018) Potential of genomic selection in mass selection breeding of an allogamous crop: An empirical study to increase yield of common buckwheat. Frontiers in Plant Science 9: 276
    49. Yabe S, Iwata H and JL Jannink (2018) Impact of mislabeling on genomic selection in cassava breeding. Crop Science 58: 1470-1480
    50. Tanaka R, Iwata H (2018) Bayesian optimization for genomic selection: a method for discovering the best genotype among a large number of candidates. Theoretical and Applied Genetics 131: 93-105
    51. Minamikawa MF, Nonaka K, Kaminuma E, Kajiya-Kanegae H, Onogi A, Goto S, Yoshioka T, Imai A, Hamada H, Hayashi T, Matsumoto S, Katayose Y, Toyoda A, Fujiyama A, Nakamura Y, Shimizu T, Iwata H (2017) Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits. Scientific Reports 7: 4721
    52. Goto S, Kajiya-Kanegae H, Ishizuka W, Kitamura K, Ueno S, Hisamoto Y, Kudoh H, Yasugi M, nagano AJ, Iwata H (2017) Genetic mapping of local adaptation along the altitudinal gradient in Abies sachalinensis. Tree Genetics and Genomes 13: 104
    53. Okada S, Suehiro M, Ebana K, Hori K, Onogi A, Iwata H, Yamasaki M (2017) Genetic dissection of grain traits in Yamadanishiki, an excellent sake窶臣rewing rice cultivar. Theoretical and Applied Genetics 130: 2567-2585
    54. Okada S, Onogi A, Iijima K, Hori K, Iwata H, Yokoyama W, Suehiro M, Yamasaki M (2017) Identification of QTLs for rice grain size using a novel set of chromosomal segment substitution lines derived from Yamadanishiki in the genetic background of Koshihikari. Breeding Science 68: 210-218
    55. 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 24: 397-405
    56. 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 130: 1601-1616
    57. Moriya S, Kunihisa M, Okada K, Shimizu T, Honda C, Yamamoto T, Muranty H, Denancﾃｩ C, Katayose Y, Iwata H, Abe K (2017) Allelic composition of MdMYB1 drives red skin color intensity in apple (Malus ﾃ domestica Borkh.) and its application to breeding. Euphytica 213: 78
    58. 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 134: 373-382
    59. 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
    60. 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
    61. 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
    62. 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 ﾃ domestica Borkh.). The Horticulture Journal 86: 159-170
    63. 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 95: 1900-1912
    64. 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
    65. 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
    66. 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
    67. 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 66: 676-682
    68. 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
    69. Onogi A, Iwata H (2016) VIGoR: Variational Bayesian inference for genome-wide regression. Journal of Open Research Software 4: e11
    70. 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
    71. 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
    72. 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
    73. Blondel M, Onogi A, Iwata H, Ueda N (2015) A ranking approach to genomic selection. PLoS ONE 10: e0128570
    74. 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
    75. 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
    76. 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
    77. 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
    78. 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
    79. Yabe S, Ohsawa R, Iwata H (2014) Genomic selection for the traits expressed after pollination in allogamous plants. Crop Science 54: 1448-1457
    80. 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. Journal of Animal Science 92: 1931-1938
    81. Babil P, Kondo S, Iwata H, Kushikawa S, Shiwachi H (2013) Intra-Specific Ploidy Variations in Cultivated Chinese Yam (Dioscorea polystachya Turcz.). Tropopical Agriculture and Development 57: 101-107
    82. 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
    83. 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. Breeding Science 63: 125-140
    84. 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
    85. Ishii K, Yamanari M, Iwata H, Yasuno Y, Oshika T (2013) Relationship between changes in crystalline lens shape and axial elongation in young children. Investigate Ophthalmology & Visual Science 54: 771-777
    86. Yabe S, Ohsawa R, Iwata H (2013) Potential of genomic selection for mass selection breeding in annual allogamous crops. Crop Science 53: 95-105
    87. 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 8: e79866
    88. 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
    89. Hayashi T, Ohyama A, Iwata H (2012) Bayesian QTL mapping for recombinant inbred lines derived from a four-way cross. Euphytica 183: 277-287
    90. 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
    91. 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
    92. 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
    93. 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
    94. 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
    95. 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
    96. 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
    97. 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
    98. 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
    99. 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
    100. 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
    101. 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
    102. Hayashi T, Iwata H (2010) EM algorithm for Bayesian estimates of genomic breeding values. BMC Genetics 11: 3
    103. 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. Journal of Plant Research 124: 11-23
    104. 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
    105. 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
    106. 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
    107. 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
    108. 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
    109. 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
    110. 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
    111. 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
    112. 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
    113. 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
    114. Yoshioka Y, Iwata H, Tabata M, Minomiya S, Ohsawa R (2007) Chalkiness in rice: potential for evaluation with image analysis. Crop Science 47: 2113-2120
    115. 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
    116. 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
    117. 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
    118. 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
    119. 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
    120. 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
    121. Iwata H, Ninomiya S (2006) AntMap: constructing genetic linkage maps using an ant colony optimization algorithm. Breeding Science 56: 371-377
    122. 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
    123. 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
    124. 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
    125. 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
    126. 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
    127. (In Japanese) 叢花, Ban H, 許東河, Iwata H, Kikuchi F,  Fujimaki H. (2006) Characterization of Xinjiang wheat varieties in China by analysis of microsatellite DNA polymorphisms and agronomic trait variants. Journal of Breeding Science 8: 161-169 
    128. 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
    129. 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
    130. (n Japanese) 鄭澤宇，Iwata H，Ninomiya S，Tamura Y (2005) Quantitative Evaluation of Partial Shape Features of Lotus japonicus Petals Based on P-shaped Fourier Descriptors. Journal of Breeding Science 7: 133-142
    131. 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
    132. 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
    133. 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
    134. 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
    135. 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
    136. Iwata H, Niikura S, Matsuura S, Takano Y, Ukai Y (2004) Interaction between 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
    137. 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
    138. 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
    139. 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
    140. 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. Genetics 165: 1551-1568
    141. 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
    142. 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
    143. 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
    144. 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
    145. 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
    146. 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
    147. 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
    148. 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
    149. Iwata H, Konuma A, Tsumura Y (2000) Development of microsatellite markers in the tropical tree Neobalanocarpus heimii (Dipterocarpaceae). Molecular Ecology 9: 1684-1685
    150. 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
    151. 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
    152. 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
    153. 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
    154. (In Japanese) Omori H, Iwata Y (1998) BioImage ver.1, an area measurement and image analysis software for Windows. Agricultural Information Research 7: 71-8080

    Review papers (only ones in English)

    1. Yabe S, Iwata H (2020) Genomics-assisted breeding in minor and pseudo-cereals. Breeding Science 70: 19-31.
    2. van Eeuwijk FA, Bustos-Korts D, Millet EJ, Boer MP, Kruijer W, Thompson A, Malosetti M, Iwata H, Quiroz R, Kuppe C, Muller O, Blazakis KN, Yu K, Tardieu F, Chapman SC (2019) Modelling strategies for assessing and increasing the effectiveness of new phenotyping techniques in plant breeding. Plant Science 282: 23-39
    3. Iwata H, Minamikawa MF, Kajiya-Kanegae H, Ishimori M, Hayashi T (2016) Genomics-assisted breeding in fruit trees. Breeding Science 66: 100-115
    4. 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
    5. 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
    6. Jannink JL, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: From theory to practice. Brief. Funct. Genomic. Proteomic. 9: 166-177

    Book and book chapter (only ones in English)

    1. Morota G, Jarquin D, Campbell MT, Iwata H (2022) Statistical methods for the quantitative genetic analysis of high-throughput phenotyping data. In: Lorence, A., Medina Jimenez, K. (eds) High-Throughput Plant Phenotyping. Methods in Molecular Biology, vol 2539. Humana, New York, NY, pp. 269-296
    2. Spindel J, Iwata H (2018) Genomic selection in rice breeding. In: Sasaki T, Ashikari M editors. Rice Genomics, Genetics and Breeding. Springer Nature Singapore Pte Ltd., pp. 473-496
    3. 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