1. Hasegawa, Y., S. Ueno, F.-J. Wei, A. Matsumoto, K. Uchiyama, T. Ujino-Ihara, T. Hakamata, T. Fujino, M. Kasahara, T. Bino, K. Yamaguchi, S. Shigenobu, Y. Tsumura, and Y. Moriguchi, Identification and genetic diversity analysis of a male-sterile gene (MS1) in Japanese cedar (Cryptomeria japonica D. Don). Scientific Reports, 2021. 11(1):1496
  2. Izuno, A., T.E. Maruyama, S. Ueno, T. Ujino-Ihara, and Y. Moriguchi, Genotype and transcriptome effects on somatic embryogenesis in Cryptomeria japonica. Plos One, 2020. 15(12):e0244634
  3. Maruyama TE, Ueno S, Hirayama S, Kaneeda T, Moriguchi Y. Somatic Embryogenesis and Plant Regeneration from Sugi (Japanese Cedar, Cryptomeria japonica D. Don, Cupressaceae) Seed Families by Marker Assisted Selection for the Male Sterility Allele ms1. Plants. 2020; 9(8):1029
  4. Hasegawa, Y., S. Ueno, F.J. Wei, A. Matsumoto, T. Ujino-Ihara, K. Uchiyama, Y. Moriguchi, M. Kasahara, T. Fujino, S. Shigenobu, K. Yamaguchi, T. Bino, and T. Hakamata, Development of diagnostic PCR and LAMP markers for MALE STERILITY 1 (MS1) in Cryptomeria japonica D. Don. BMC Res Notes, 2020. 13(1):457
  5. Moriguchi, Y., S. Ueno, Y. Hasegawa, T. Tadama, M. Watanabe, R. Saito, S. Hirayama, J. Iwai, and Y. Konno, Marker-assisted selection of trees with MALE STERILITY 1 in Cryptomeria japonica D. Don. Forests, 2020. 11(7):734
  6. Tsumura Y, Kimura M, Nakao K, Uchiyama K, Ujino-Ihara T, Wen Y, Tong Z, Han W: Effects of the last glacial period on genetic diversity and genetic differentiation in Cryptomeria japonica in East Asia. Tree Genetics & Genomes 2020, 16(1):19
  7. Mori H, Yamashita K, Saiki S-T, Matsumoto A, Ujino-Ihara T: Climate sensitivity of Cryptomeria japonica in two contrasting environments: Perspectives from QTL mapping. Plos One 2020, 15(1): e0228278-e0228278
  8. Ueno S, Uchiyama K, Moriguchi Y, Ujino-Ihara T, Matsumoto A, Wei FJ, Saito M, Higuchi Y, Futamura N, Kanamori H, Katayose Y, Tsumura Y: Scanning RNA-Seq and RAD-Seq approach to develop SNP markers closely linked to MALE STERILITY 1 (MS1) in Cryptomeria japonica D. Don. Breeding Science 2019, 69(1):19-29
  9. Tadama T, Totsuka S, Iwai J, Uchiyama K, Hasegawa Y, Moriguchi Y: Genetic evaluation of Cryptomeria japonica breeding materials for male-sterile trees. Silvae Genetica 2019, 68(1)
  10. Moriguchi N, Uchiyama K, Miyagi R, Moritsuka E, Takahashi A, Tamura K, Tsumura Y, Teshima KM, Tachida H, Kusumi J: Inferring the demographic history of Japanese cedar, Cryptomeria japonica, using amplicon sequencing. Heredity (Edinb) 2019, 123(3):371-383
  11. Mori H, Ueno S, Ujino-Ihara T, Fujiwara T, Yamashita K, Kanetani S, Endo R, Matsumoto A, Uchiyama K, Matsui Y, Yoshida T, Sakai Y, Moriguchi Y, Kusano R, Tsumura Y: Mapping quantitative trait loci for growth and wood property traits in Cryptomeria japonica across multiple environments. Tree Genetics & Genomes 2019, 15(3):43
  12. Uchiyama K, Matsumoto A: Development and utilization of a SNP panel for identification of the geographic origin of Cryptomeria japonica (in Japanese). Bulletin of FFPRI 2018, 17(2):141-148.
  13. Ujino-Ihara T, Ueno S, Uchiyama K, Futamura N: Comprehensive analysis of small RNAs expressed in developing male strobili of Cryptomeria japonica. Plos One 2018, 13(3):e0193665.
  14. Hasegawa, Y., S. Ueno, A. Matsumoto, T. Ujino-Ihara, K. Uchiyama, S. Totsuka, J. Iwai, T. Hakamata, and Y. Moriguchi, Fine mapping of the male-sterile genes (MS1, MS2, MS3, and MS4) and development of SNP markers for marker-assisted selection in Japanese cedar (Cryptomeria japonica D. Don). Plos One, 2018. 13(11):e0206695.
  15. Moriguchi Y, Totsuka S, Iwai J, Matsumoto A, Ueno S, Tsumura Y: Pyramiding of male-sterile genes in Cryptomeria japonica D. Don with the aid of closely linked markers. Tree Genet Genomes 2017, 13(3):61.
  16. Moriguchi Y, Uchiyama K, Ueno S, Ujino-Ihara T, Matsumoto A, Iwai J, Miyajima D, Saito M, Sato M, Tsumura Y: A high-density linkage map with 2560 markers and its application for the localization of the male-sterile genes ms3 and ms4 in Cryptomeria japonica D. Don. Tree Genet Genomes 2016, 12(3):1-12.
  17. Tamura M, Hisataka Y, Moritsuka E, Watanabe A, Uchiyama K, Futamura N, Shinohara K, Tsumura Y, Tachida H: Analyses of random BAC clone sequences of Japanese cedar, Cryptomeria japonica. Tree Genet Genomes 2015, 11(3).
  18. Kusumi J, Tsumura Y, Tachida H: Evolutionary rate variation in two conifer species, Taxodium distichum (L.) Rich. var. distichum (baldcypress) and Cryptomeria japonica (Thunb. ex L.f.) D. Don (Sugi, Japanese cedar). Genes & Genetic Systems 2015, 90(5):305-315.
  19. de Miguel M, Bartholome J, Ehrenmann F, Murat F, Moriguchi Y, Uchiyama K, Ueno S, Tsumura Y, Lagraulet H, de Maria N et al: Evidence of Intense Chromosomal Shuffling during Conifer Evolution. Genome Biol Evol 2015, 7(10):2799-2809.
  20. Uchiyama K, Miyamoto N, Takahashi M, Watanabe A, Tsumura Y: Population genetic structure and the effect of historical human activity on the genetic variability of Cryptomeria japonica core collection, in Japan. Tree Genet Genomes 2014, 10(5):1257-1270.
  21. Tsumura Y, Uchiyama K, Moriguchi Y, Kimura MK, Ueno S, Ujino-Ihara T: Genetic Differentiation and Evolutionary Adaptation in Cryptomeria japonica. G3-Genes Genom Genet 2014, 4(12):2389-2402.
  22. Moriguchi Y, Ueno S, Saito M, Higuchi Y, Miyajima D, Itoo S, Tsumura Y: A simple allele-specific PCR marker for identifying male-sterile trees: Towards DNA marker-assisted selection in the Cryptomeria japonica breeding program. Tree Genet Genomes 2014, 10(4):1069-1077.
  23. Moriguchi Y, Ueno S, Higuchi Y, Miyajima D, Itoo S, Futamura N, Shinohara K, Tsumura Y: Establishment of a microsatellite panel covering the sugi (Cryptomeria japonica) genome, and its application for localization of a male-sterile gene (ms-2). Mol Breeding 2014, 33(2):315-325.
  24. Kimura MK, Uchiyama K, Nakao K, Moriguchi Y, San Jose-Maldia L, Tsumura Y: Evidence for cryptic northern refugia in the last glacial period in Cryptomeria japonica. Ann Bot-London 2014, 114(8):1687-1700.
  25. Uchiyama K, Iwata H, Moriguchi Y, Ujino-Ihara T, Ueno S, Taguchi Y, Tsubomura M, Mishima K, Iki T, Watanabe A et al: Demonstration of Genome-Wide Association Studies for Identifying Markers for Wood Property and Male Strobili Traits in Cryptomeria japonica. Plos One 2013, 8(11).
  26. Kimura MK, Kabeya D, Saito T, Moriguchi Y, Uchiyama K, Migita C, Chiba Y, Tsumura Y: Effects of genetic and environmental factors on clonal reproduction in old-growth natural populations of Cryptomeria japonica. Forest Ecol Manag 2013, 304:10-19.
  27. Ujino-Ihara T, Iwata H, Taguchi Y, Tsumura Y: Identification of QTLs associated with male strobilus abundance in Cryptomeria japonica. Tree Genet Genomes 2012, 8(6):1319-1329.
  28. Ueno S, Moriguchi Y, Uchiyama K, Ujino-Ihara T, Futamura N, Sakurai T, Shinohara K, Tsumura Y: A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica. Bmc Genomics 2012, 13.
  29. Uchiyama K, Ujino-Ihara T, Ueno S, Taguchi Y, Futamura N, Shinohara K, Tsumura Y: Single nucleotide polymorphisms in Cryptomeria japonica: their discovery and validation for genome mapping and diversity studies. Tree Genet Genomes 2012, 8(6):1213-1222.
  30. Tsumura Y, Uchiyama K, Moriguchi Y, Ueno S, Ihara-Ujino T: Genome scanning for detecting adaptive genes along environmental gradients in the Japanese conifer, Cryptomeria japonica. Heredity 2012, 109(6):349-360.
  31. Tanaka A, Ohtani M, Suyama Y, Inomata N, Tsumura Y, Middleton BA, Tachida H, Kusumi J: Population genetic structure of a widespread coniferous tree, Taxodium distichum [L.] Rich. (Cupressaceae), in the Mississippi River Alluvial Valley and Florida. Tree Genet Genomes 2012, 8(5):1135-1147.
  32. Moritsuka E, Hisataka Y, Tamura M, Uchiyama K, Watanabe A, Tsumura Y, Tachida H: Extended Linkage Disequilibrium in Noncoding Regions in a Conifer, Cryptomeria japonica. Genetics 2012, 190(3):1145-1148.
  33. Moriguchi Y, Ujino-Ihara T, Uchiyama K, Futamura N, Saito M, Ueno S, Matsumoto A, Tani N, Taira H, Shinohara K et al: The construction of a high-density linkage map for identifying SNP markers that are tightly linked to a nuclear-recessive major gene for male sterility in Cryptomeria japonica D. Don. Bmc Genomics 2012, 13.
  34. Tsumura Y: Cryptomeria. In: Wild Crop Relatives: Genomics and Breeding Resources, Forest Trees. Edited by Kole C: Springer; 2011: 49-64.
  35. Sakaguchi S, Uchiyama K, Ueno S, Ujino-Ihara T, Tsumura Y, Prior LD, Bowman DMJS, Crisp MD, Isagi Y: Isolation and Characterization of 52 Polymorphic Est-Ssr Markers for Callitris Columellaris (Cupressaceae). American journal of botany 2011, 98(12):E363-E368.
  36. Ritland K, Krutovsky KV, Tsumura Y, Pelgas B, Isabel N, Bousquet J: Genetic mapping in conifers. In: Genetics, Genomics and Breeding of Conifers. Edited by Plomion C, Bousquet J, Kole C: CRC Press; 2011: 196-238.
  37. Moriguchi Y, Yomogida H, Iwata H, Takahashi M, Taira H, Tsumura Y: Paternity analysis in a progeny test of Cryptomeria japonica revealed adverse effects of pollen contamination from outside seed orchards on morphological traits. Tree Genet Genomes 2011, 7(5):1089-1097.
  38. Iwata H, Hayashi T, Tsumura Y: Prospects for genomic selection in conifer breeding: a simulation study of Cryptomeria japonica. Tree Genet Genomes 2011, 7(4):747-758.
  39. Gonzalez-Martinez S, Dillon S, Garnier-Gere P, Krutovsky K, Alia R, Burgarella C, Eckert A, Garcia-Gil M, Grivet D, Heuertz M et al: Patterns of nucleotide diversity and association mapping. In: Genetics, Genomics and Breeding of Conifers. Edited by Plomion C, Bousquet J, Kole C: CRC Press; 2011: 239-275.
  40. Ujino-Ihara T, Taguchi Y, Moriguchi Y, Tsumura Y: An efficient method for developing SNP markers based on EST data combined with high resolution melting (HRM) analysis. BMC Research Notes 2010, 3(1):1-5.
  41. Moriguchi Y, Yamazaki Y, Taira H, Tsumura Y: Mating patterns in an indoor miniature Cryptomeria japonica seed orchard as revealed by microsatellite markers. New Forest 2010, 39(3):261-273.
  42. Matsumoto A, Uchida K, Taguchi Y, Tani N, Tsumura Y: Genetic diversity and structure of natural fragmented Chamaecyparis obtusa populations as revealed by microsatellite markers. J Plant Res 2010, 123(5):689-699.
  43. Moriguchi Y, Ueno S, Ujino-Ihara T, Futamura N, Matsumoto A, Shinohara K, Tsumura Y: Characterization of EST-SSRs from Cryptomeria japonica. Conserv Genet Resour 2009, 1(1):373-376.
  44. Moriguchi Y, Ishiduka D, Kaneko T, Itoo S, Taira H, Tsumura Y: The Contribution of Pollen Germination Rates to Uneven Paternity Among Polycrosses of Cryptomeria japonica. Silvae Genet 2009, 58(3):139-144.
  45. Ujino-Ihara T, Tsumura Y: Screening for genes specific to coniferous species. Tree Physiol 2008, 28(9):1325-1330.
  46. Takahashi T, Tani N, Niiyama K, Yoshida S, Taira H, Tsumura Y: Genetic succession and spatial genetic structure in a natural old growth Cryptomeria japonica forest revealed by nuclear and chloroplast microsatellite markers. Forest Ecol Manag 2008, 255(7):2820-2828.
  47. Kado T, Matsumoto A, Ujino-Ihara T, Tsumura Y: Amounts and patterns of nucleotide variation within and between two Japanese conifers, sugi (Cryptomeria japonica) and hinoki (Chamaecyparis obtusa) (Cupressaceae sensu lato). Tree Genet Genomes 2008, 4(1):133-141.
  48. Goto S, Takahashi M, Matsumoto A, Ieiri R, Tsumura Y: Genetic relationships and origin of commercial clones of Nangouhi, a vegetatively propagated cultivar of hinoki cypress (Chamaecyparis obtusa). Breeding Sci 2008, 58(4):411-418.
  49. Fujimoto A, Kado T, Yoshimaru H, Tsumura Y, Tachida H: Adaptive and slightly deleterious evolution in a conifer, Cryptomeria japonica. J Mol Evol 2008, 67(2):201-210.
  50. Tsumura Y, Matsumoto A, Tani N, Ujino-Ihara T, Kado T, Iwata H, Uchida K: Genetic diversity and the genetic structure of natural populations of Chamaecyparis obtusa: implications for management and conservation. Heredity 2007, 99(2):161-172.
  51. Tsumura Y, Kado T, Takahashi T, Tani N, Ujino-Ihara T, Iwata H: Genome scan to detect genetic structure and adaptive genes of natural populations of Cryptomeria japonica. Genetics 2007, 176(4):2393-2403.
  52. Tsumura Y: The phylogeographic structure of Japanese coniferous species as revealed by genetic markers. Taxon 2006, 55(1):53-66.
  53. Matsumoto A, Tani N, Li XG, Nakao Y, Tomaru N, Tsumura Y: Development and polymorphisms of microsatellite markers for hinoki (Chamaecyparis obtusa). Mol Ecol Notes 2006, 6(2):310-312.
  54. Kado T, Ushio Y, Yoshimaru H, Tsumura Y, Tachida H: Contrasting patterns of DNA variation in natural populations of two related conifers, Cryptomeria japonica and Taxodium distichum (Cupressaceae sensu lato). Genes & Genetic Systems 2006, 81(2):103-113.
  55. Futamura N, Tani N, Tsumura Y, Nakajima N, Sakaguchi M, Shinohara K: Characterization of genes for novel thaumatin-like proteins in Cryptomeria japonica. Tree Physiol 2006, 26(1):51-62.
  56. Futamura N, Tani N, Tsumura Y, Nakajima N, Sakaguchi M, Shinohara K: Characterization of genes for novel thaumatin-like proteins in Cryptomeria japonica. Tree Physiol 2006, 26(1):51-62.
  57. Ujino-Ihara T, Kanamori H, Yamane H, Taguchi Y, Namiki N, Mukai Y, Yoshimura K, Tsumura Y: Comparative analysis of expressed sequence tags of conifers and angiosperms reveals sequences specifically conserved in conifers. Plant Molecular Biology 2005, 59(6):895-907.
  58. Saito M, Hideaki T, Tsumura Y: Study of sugi (Cryptomeria japonica D. Don) with male-sterility gene using CAPS markers. J for Res-Jpn 2005, 10(1):61-66.
  59. Moriguchi Y, Tani N, Itoo S, Kanehira F, Tanaka K, Yomogida H, Taira H, Tsumura Y: Gene flow and mating system in five Cryptomeria japonica D. Don seed orchards as revealed by analysis of microsatellite markers. Tree Genet Genomes 2005, 1(4):174-183.
  60. Tsumura Y: Utilization of microsatellite marker for genetic and breeding studies in forest tree species (In Japanese). Journal of the Japanese Forest Society 2004, 86(2):184-190.
  61. Tani N, Takahashi T, Ujino-Ihara T, Iwata H, Yishimura K, Tsumura Y: Development and characteristics of microsatellite markers for sugi (Cryptomeria japonica D. Don) derived from microsatellite-enriched libraries. Ann Forest Sci 2004, 61(6):569-575.
  62. Moriguchi Y, Taira H, Tani N, Tsumura Y: Variation of paternal contribution in a seed orchard of Cryptomeria japonica determined using microsatellite markers. Can J Forest Res 2004, 34(8):1683-1690.
  63. Matsumoto A, Tsumura Y: Evaluation of cleaved amplified polymorphic sequence markers for Chamaecyparis obtusa based on expressed sequence tag information from Cryptomeria japonica. Theoretical and Applied Genetics 2004, 110(1):80-91.
  64. Ujino-Ihara T, Taguchi Y, Yoshimura K, Tsumura Y: Analysis of expressed sequence tags derived from developing seed and pollen cones of Cryptomeria japonica. Plant Biology 2003, 5(6):600-607.
  65. Tani N, Tsumura Y, Sato H: Nuclear gene sequences and DNA variation of Cryptomeria japonica samples from the postglacial period. Molecular ecology 2003, 12(4):859-868.
  66. Tani N, Takahashi T, Iwata H, Mukai Y, Ujino-Ihara T, Matsumoto A, Yoshimura K, Yoshimaru H, Murai M, Nagasaka K et al: A consensus linkage map for sugi (Cryptomeria japonica) from two pedigrees, based on microsatellites and expressed sequence tags. Genetics 2003, 165(3):1551-1568.
  67. Moriguchi Y, Iwata H, Ujino-Ihara T, Yoshimura K, Taira H, Tsumura Y: Development and characterization of microsatellite markers for Cryptomeria japonica D.Don. Theor Appl Genet 2003, 106(4):751-758.
  68. Kado T, Yoshimaru H, Tsumura Y, Tachida H: DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato). Genetics 2003, 164(4):1547-1559.
  69. Ujino-Ihara T, Matsumuto A, Iwata H, Yoshimura K, Tsumura Y: Single-strand conformation polymorphism of sequence-tagged site markers based on partial sequences of cDNA clones in Cryptomeria japonica. Genes Genet Syst 2002, 77(4):251-257.
  70. Kusumi J, Tsumura Y, Yoshimaru H, Tachida H: Molecular evolution of nuclear genes in Cupressacea, a group of conifer trees. Molecular biology and evolution 2002, 19(5):736-747.
  71. Nakao Y, Iwata H, Matsumoto A, Tsumura Y, Tomaru N: Highly polymorphic microsatellite markers in Chamaecyparis obtusa. Canadian Journal of Forest Research 2001, 31(12):2248-2251.
  72. Moriguchi Y, Matsumoto A, Saito M, Tsumura Y, Taira H: DNA analysis of clonal structure of an old growth, isolated forest of Cryptomeria japonica in a snowy region. Canadian Journal of Forest Research 2001, 31(3):377-383.
  73. Iwata H, Ujino-Ihara T, Yoshimura K, Nagasaka K, Mukai Y, Tsumura Y: Cleaved amplified polymorphic sequence markers in sugi, Cryptomeria japonica D. Don, and their locations on a linkage map. Theoretical and Applied Genetics 2001, 103(6):881-895.
  74. Ujino-Ihara T, Yoshimura K, Ugawa Y, Yoshimaru H, Nagasaka K, Tsumura Y: Expression analysis of ESTs derived from the inner bark of Cryptomeria japonica. Plant Molecular Biology 2000, 43(4):451-457.
  75. Nikaido MA, Ujino T, Iwata H, Yoshimura K, Yoshimura H, Suyama Y, Murai M, Nagasaka K, Tsumura Y: AFLP and CAPS linkage maps of Cryptomeria japonica. Theoretical and Applied Genetics 2000, 100(6):825-831.
  76. Kusumi J, Tsumura Y, Yoshimaru H, Tachida H: Phylogenetic relationships in Taxodiaceae and Cupressaceae sensu stricto based on matK gene, chlL gene, trnL-trnF IGS region, and trnL intron sequences. American journal of botany 2000, 87(10):1480-1488.
  77. Tsumura Y, Tomaru N, Suyama Y, Bacchus S: Genetic diversity and differentiation of Taxodium in the south-eastern United States using cleaved amplified polymorphic sequences. Heredity 1999, 83(3):229-238.
  78. Tsumura Y, Tomaru N: Genetic diversity of Cryptomeria japonica using co-dominant DNA markers based on sequenced-tagged sites. Theoretical and Applied Genetics 1999, 98(3):396-404.
  79. Nikaido A, Yoshimaru H, Tsumura Y, Suyama Y, Murai M, Nagasaka K: Segregation distortion for AFLP markers in Cryptomeria japonica. Genes & Genetic Systems 1999, 74(2):55-59.
  80. Yoshimaru H, Ohba K, Tsurumi K, Tomaru N, Murai M, Mukai Y, Suyama Y, Tsumura Y, Kawahara T, Sakamaki Y: Detection of quantitative trait loci for juvenile growth, flower bearing and rooting ability based on a linkage map of sugi (Cryptomeria japonica D. Don). Theoretical and Applied Genetics 1998, 97(1):45-50.
  81. Kondo T, Tsumura Y, Kawahara T, Okamura M: Paternal Inheritance of Chloroplast and Mitochondrial DNA in Interspecific Hybrids of Chamaecyparis spp. Japanese Journal of Breeding 1998, 48(2):177-179.
  82. Tsumura Y, Suyama Y, Yoshimura K, Shirato N, Mukai Y: Sequence-tagged-sites (STSs) of cDNA clones in Cryptomeria japonica and their evaluation as molecular markers in conifers. Theoretical and Applied Genetics 1997, 94(6):764-772.
  83. Taira H, Tsumura Y, Tomaru Y, Ohba K: Regeneration system and genetic diversity of Cryptomeria japonica growing at different altitudes. Canadian Journal of Forest Research 1997, 27(4):447-452.
  84. Suyama Y, Mukai Y, Kondo T: Assignment of RFLP linkage groups to their respective chromosomes in aneuploids of sugi (Cryptomeria japonica). Theoretical and Applied Genetics 1996, 92(3):292-296.
  85. Mukai Y, Suyama Y, Tsumura Y, Kawahara T, Yoshimaru H, Kondo T, Tomaru N, Kuramoto N, Murai M: A linkage map for sugi (Cryptomeria japonica) based on RFLP, RAPD, and isozyme loci. Theoretical and Applied Genetics 1995, 90(6):835-840.

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