Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Single nucleotide polymorphisms in Cryptomeria japonica: their discovery and validation for genome mapping and diversity studies

  • 452 Accesses

  • 15 Citations

Abstract

In order to develop a large set of single-nucleotide polymorphisms (SNPs) in Cryptomeria japonica, for a wide range of applications, we adopted a systematic EST (expressed sequence tags) re-sequencing approach. We examined a group of four genotypes comprising parents of a mapping population as well as representatives of two main lines from natural populations. We sequenced 5,170 gene fragments, representing analysis of over 1.3 Mb of DNA sequences in C. japonica. This analysis leads to the discovery of 13,413 SNPs in 3,744 amplicons, with an average of one SNP for every 101.0 bp (one SNP for every 78.3 bp in introns and for every 106.7 bp in exon regions). Nucleotide diversity in C. japonica (π = 0.0045) was found to be similar to values recorded in highly polymorphic forest tree species such as pine. We also validated the use of the SNPs as molecular markers for genetic diversity studies using the high throughput SNP genotyping platform GoldenGate. From 1,536 candidate SNP sites tested, 1,164 (75.8 %) were confirmed to be polymorphic. We anticipate that the genome-wide SNP markers reported here will be useful for evaluating the species’ range-wide genetic structure and in marker-assisted selection used as part of the C. japonica tree improvement program.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2

References

  1. Altshuler D, Brooks L, Chakravarti A, Collins F, Daly M, Donnelly P (2005) A haplotype map of the human genome. Nature 437:1299–1320

  2. Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. PBioS 263(1377):1619–1626

  3. Bhattramakki D, Dolan M, Hanafey M, Wineland R, Vaske D, Register JC, Tingey SV, Rafalski A (2002) Insertion–deletion polymorphisms in 3′ regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Mol Biol 48(5):539–547

  4. Bogunic F, Muratovic E, Brown SC, Siljak-Yakovlev S (2003) Genome size and base composition of five Pinus species from the Balkan region. Plant Cell Rep 22(1):59–63

  5. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Amer J Hum Genet 32(3):314

  6. Bouillé M, Bousquet J (2005) Trans-species shared polymorphisms at orthologous nuclear gene loci among distant species in the conifer Picea (Pinaceae): implications for the long-term maintenance of genetic diversity in trees. Am J Bot 92(1):63–73

  7. Brookes AJ (1999) The essence of SNPs. Gene 234(2):177–186

  8. Brown GR, Gill GP, Kuntz RJ, Langley CH, Neale DB (2004) Nucleotide diversity and linkage disequilibrium in loblolly pine. Proc Nat Acad Sci USA 101(42):15255–15260

  9. Brumfield RT, Beerli P, Nickerson DA, Edwards SV (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends Ecol Evol 18(5):249–256

  10. Chen X, Sullivan PF (2003) Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput. Pharmacogenomics J 3(2):77–96

  11. Ching ADA, Caldwell KS, Jung M, Dolan M, Smith OSH, Tingey S, Morgante M, Rafalski AJ (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 3(1):19

  12. Collins FS, Brooks LD, Chakravarti A (1998) A DNA polymorphism discovery resource for research on human genetic variation. Genome Res 8(12):1229

  13. Dantec LL, Chagne D, Pot D, Cantin O, Garnier-Gere P, Bedon F, Frigerio JM, Chaumeil P, Leger P, Garcia V (2004) Automated SNP detection in expressed sequence tags: statistical considerations and application to maritime pine sequences. Plant Mol Biol 54(3):461–470

  14. Eckert AJ, Pande B, Ersoz ES, Wright MH, Rashbrook VK, Nicolet CM, Neale DB (2009) High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.). Tree Genet Genom 5(1):225–234

  15. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14(8):2611–2620

  16. Ewing B, Hillier LD, Wendl MC, Green P (1998) Base-calling of automated sequencer traces usingPhred. I. Accuracy assessment. Genome Res 8(3):175

  17. Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH (2004) An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res 14(9):1812

  18. Finnegan EJ, Genger RK, Peacock WJ, Dennis ES (1998) DNA methylation in plants. Annu Rev Plant Biol 49(1):223–247

  19. Fujimoto A, Kado T, Yoshimaru H, Tsumura Y, Tachida H (2008) Adaptive and slightly deleterious evolution in a conifer, Cryptomeria japonica. JMolE 67(2):201–210

  20. Futamura N, Ujino-Ihara T, Nishiguchi M, Kanamori H, Yoshimura K, Sakaguchi M, Shinohara K (2006) Analysis of expressed sequence tags from Cryptomeria japonica pollen reveals novel pollen-specific transcripts. Tree Physiol 26(12):1517–1528

  21. Futamura N, Totoki Y, Toyoda A, Igasaki T, Nanjo T, Seki M, Sakaki Y, Mari A, Shinozaki K, Shinohara K (2008) Characterization of expressed sequence tags from a full-length enriched cDNA library of Cryptomeria japonica male strobili. BMC Genomics 9(1):383

  22. Ganal MW, Altmann T, R der MS (2009) SNP identification in crop plants. Curr Opin Plant Biol 12(2):211–217

  23. Garcia-Gil MR, Mikkonen M, Savolainen O (2003) Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris. Mol Ecol 12(5):1195–1206

  24. Grantham R (1974) Amino acid difference formula to help explain protein evolution. Science 185(4154):862

  25. Gupta PK, Roy JK, Prasad M (2001) Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Current Science Bangalore 80(4):524–535

  26. Gut IG (2001) Automation in genotyping of single nucleotide polymorphisms. Hum Mutat 17(6):475–492

  27. Halushka MK, Fan JB, Bentley K, Hsie L, Shen N, Weder A, Cooper R, Lipshutz R, Chakravarti A (1999) Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet 22(3):239–247

  28. Hizume M, Kondo T, Shibata F, Ishizuka R (2001) Flow cytometric determination of genome size in die Taxodiaceae, Cupressaceae sensu stricto and Sciadopityaceae. Cytologia 66(3):307–312

  29. Holliday R, Grigg GW (1993) DNA methylation and mutation. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 285(1):61–67

  30. Hoskins RA, Phan AC, Naeemuddin M, Mapa FA, Ruddy DA, Ryan JJ, Young LM, Wells T, Kopczynski C, Ellis MC (2001) Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster. Genome Res 11(6):1100–1113

  31. Huang XQ, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9(9):868–877

  32. Ingvarsson PK (2005) Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae). Genetics 169(2):945

  33. 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. Theor Appl Genet 103(6):881–895

  34. Iwata H, Hayashi T, Tsumura Y (2011) Prospects for genomic selection in conifer breeding: a simulation study of Cryptomeria japonica. Tree Genet Genom 1–12

  35. Jander G, Norris SR, Rounsley SD, Bush DF, Levin IM, Last RL (2002) Arabidopsis map-based cloning in the post-genome era. Plant Physiol 129(2):440

  36. Kado T, Yoshimaru H, Tsumura Y, Tachida H (2003) DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato). Genetics 164(4):1547

  37. Kado T, Ushio Y, Yoshimaru H, Tsumura Y, Tachida H (2006) Contrasting patterns of DNA variation in natural populations of two related conifers, Cryptomeria japonica and Taxodium distichum (Cupressaceae sensu lato). Genes Genet Syst 81(2):103–113

  38. Kado T, Matsumoto A, Ujino-Ihara T, Tsumura Y (2008) Amounts and patterns of nucleotide variation within and between two Japanese conifers, sugi (Cryptomeria japonica) and hinoki (Chamaecyparis obtusa)(Cupressaceae sensu lato). Tree Genet Genom 4(1):133–141

  39. Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33(2):511

  40. Landegren U, Kaiser R, Sanders J, Hood L (1988) A ligase-mediated gene detection technique. Science 241(4869):1077

  41. Ma XF, Szmidt AE, Wang XR (2006) Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from the nucleotide variation at seven gene loci. Mol Biol Evol 23(4):807

  42. Marth GT, Korf I, Yandell MD, Yeh RT, Gu Z, Zakeri H, Stitziel NO, Hillier L, Kwok PY, Gish WR (1999) A general approach to single-nucleotide polymorphism discovery. Nat Genet 23(4):452–456

  43. Meyers BC, Tingey SV, Morgante M (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res 11(10):1660

  44. Morin PA, Luikart G, Wayne RK (2004) SNPs in ecology, evolution and conservation. Trends Ecol Evol 19(4):208–216

  45. Mott R (1997) EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA. Computer applications in the biosciences: CABIOS 13(4):477

  46. Mukai Y, Suyama Y, Tsumura Y, Kawahara T, Yoshimaru H, Kondo T, Tomaru N, Kuramoto N, Murai M (1995) A linkage map for sugi (Cryptomeria japonica) based on RFLP, RAPD, and isozyme loci. Theor Appl Genet 90(6):835–840

  47. Murai S (1947) Major forestry tree species in the Tohoku region and their varietal problems. Kokudo Saiken Zourin Gijutsu Kouenshu, Aomori-rinyukai, (eds):131-151 (in Japanese)

  48. Namroud MC, Beaulieu J, Juge N, Laroche J, Bousquet J (2008) Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce. Mol Ecol 17(16):3599–3613

  49. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences 76(10):5269–5273

  50. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

  51. Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E, Calabrese P, Gladstone J, Goyal R (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 3(7):e196

  52. Oliphant A, Barker DL, Stuelpnagel JR, Chee MS (2002) BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques 32:S56–S61

  53. Pavy N, Parsons LS, Paule C, MacKay J, Bousquet J (2006) Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs. BMC Genomics 7(1):174

  54. Pavy N, Pelgas B, Beauseigle S, Blais S, Gagnon F, Gosselin I, Lamothe M, Isabel N, Bousquet J (2008) Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce. BMC Genomics 9(1):21

  55. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Note 6(1):288–295

  56. Pot D, McMillan L, Echt C, Cato S, Plomion C (2005) Nucleotide variation in genes involved in wood formation in two pine species. New Phytol 167(1):101–111

  57. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959

  58. Pritchard JK, Wen W, Falush D (2003) Documentation for STRUCTURE software: version 2. Department of Human Genetics, University of Chicago

  59. Ravel C, Praud S, Murigneux A, Canaguier A, Sapet F, Samson D, Balfourier F, Dufour P, Chalhoub B, Brunel D (2006) Single-nucleotide polymorphism frequency in a set of selected lines of bread wheat (Triticum aestivum L.). Genome 49:1131–1139

  60. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16(6):276–277

  61. Rostoks N, Borevitz J, Hedley P, Russell J, Mudie S, Morris J, Cardle L, Marshall D, Waugh R (2005a) Single-feature polymorphism discovery in the barley transcriptome. Genome Biol 6(6):R54

  62. Rostoks N, Mudie S, Cardle L, Russell J, Ramsay L, Booth A, Svensson J, Wanamaker S, Walia H, Rodriguez E, Hedley P, Liu H, Morris J, Close T, Marshall D, Waugh R (2005b) Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol Genet Genomics 274(5):515–527

  63. Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19(18):2496–2497

  64. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132(3):365–386

  65. Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409(6822):928–933

  66. Savolainen O, Pyhajarvi T (2007) Genomic diversity in forest trees. Curr Opin Plant Biol 10(2):162–167

  67. Schlötterer C (2002) A microsatellite-based multilocus screen for the identification of local selective sweeps. Genetics 160(2):753

  68. Schmid KJ, Sorensen TR, Stracke R, Torjek O, Altmann T, Mitchell-Olds T, Weisshaar B (2003) Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Res 13(6a):1250

  69. Shen YJ, Jiang H, Jin JP, Zhang ZB, Xi B, He YY, Wang G, Wang C, Qian L, Li X (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol 135(3):1198

  70. Somers DJ, Kirkpatrick R, Moniwa M, Walsh A (2003) Mining single-nucleotide polymorphisms from hexaploid wheat ESTs. Genome 46(3):431–437

  71. Takahashi T, Tani N, Taira H, Tsumura Y (2005) Microsatellite markers reveal high allelic variation in natural populations of Cryptomeria japonica near refugial areas of the last glacial period. J Plant Res 118(2):83–90

  72. Tani N, Takahashi T, Iwata H, Mukai Y, Ujino-Ihara T, Matsumoto A, Yoshimura K, Yoshimaru H, Murai M, Nagasaka K (2003) A consensus linkage map for sugi (Cryptomeria japonica) from two pedigrees, based on microsatellites and expressed sequence tags. Genetics 165(3):1551

  73. 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 libraries. Ann Forest Sci 61(6):569–575

  74. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Nat Acad Sci USA 98(16):9161

  75. Thornton K (2003) Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19(17):2325

  76. Tsumura Y, Yoshimura K, Tomaru N, Ohba K (1995) Molecular phylogeny of conifers using RFLP analysis of PCR-amplified specific chloroplast genes. Theor Appl Genet 91(8):1222–1236

  77. Tsumura Y, Suyama Y, Yoshimura K, Shirato N, Mukai Y (1997) Sequence-tagged-sites (STSs) of cDNA clones in Cryptomeria japonica and their evaluation as molecular markers in conifers. TAG Theoretical and Applied Genetics 94(6):764–772

  78. Tsumura Y, Kado T, Takahashi T, Tani N, Ujino-Ihara T, Iwata H (2007) Genome scan to detect genetic structure and adaptive genes of natural populations of Cryptomeria japonica. Genetics 176(4):2393–2403. doi:10.1534/genetics.107.072652

  79. Ujino-Ihara T, Yoshimura K, Ugawa Y, Yoshimaru H, Nagasaka K, Tsumura Y (2000) Expression analysis of ESTs derived from the inner bark of Cryptomeria japonica. Plant Mol Biol 43(4):451–457

  80. Ujino-Ihara T, Taguchi Y, Yoshimura K, Tsumura Y (2003) Analysis of expressed sequence tags derived from developing seed and pollen cones of Cryptomeria japonica. Plant Biol 5(6):600–607

  81. Ujino-Ihara T, Kanamori H, Yamane H, Taguchi Y, Namiki N, Mukai Y, Yoshimura K, Tsumura Y (2005) Comparative analysis of expressed sequence tags of conifers and angiosperms reveals sequences specifically conserved in conifers. Plant Mol Biol 59(6):895–907

  82. Vitalis R, Dawson K, Boursot P (2001) Interpretation of variation across marker loci as evidence of selection. Genetics 158(4):1811

  83. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562

  84. Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7(2):256–276

  85. Wheelan SJ, Church DM, Ostell JM (2001) Spidey: a tool for mRNA-to-genomic alignments. Genome Res 11(11):1952

  86. Yang Z, Yoder AD (1999) Estimation of the transition/transversion rate bias and species sampling. JMolE 48(3):274–283

  87. Yasue M, Ogiyama K, Suto S, Tsukahara H, Miyahara F, Ohba K (1987) Geographical differentiation of natural Cryptomeria stands analyzed by diterpene hydrocarbon constituents of individual trees. J Jpn For Soc 69:152–156

  88. Yoshida K, Nishiguchi M, Futamura N, Nanjo T (2007) Expressed sequence tags from Cryptomeria japonica sapwood during the drying process. Tree Physiol 27(1):1

  89. Yuan Q, Ouyang S, Wang A, Zhu W, Maiti R, Lin H, Hamilton J, Haas B, Sultana R, Cheung F (2005) The institute for genomic research Osa1 rice genome annotation database. Plant Physiol 138(1):18

  90. Zhang J (2000) Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes. JMolE 50(1):56–68

  91. Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163(3):1123

Download references

Acknowledgments

Authors would like to thank M. Yano, K. Ebana, and T. Shibaya at the QTL Genomics Research Center of the National Institute of Agrobiological Sciences for their technical advice on GoldenGate SNP genotyping and allowing us to use the bead array reader for GoldenGate SNP genotyping. We would also like to thank two anonymous reviewers for helpful comments. This research was supported by the Program for Promotion of Basic and Applied Researches for Innovations in Bio-oriented Industry.

Author information

Correspondence to Yoshihiko Tsumura.

Additional information

Communicated by P. Ingvarsson

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Uchiyama, K., Ujino-Ihara, T., Ueno, S. et al. Single nucleotide polymorphisms in Cryptomeria japonica: their discovery and validation for genome mapping and diversity studies. Tree Genetics & Genomes 8, 1213–1222 (2012). https://doi.org/10.1007/s11295-012-0508-5

Download citation

Keywords

  • Cryptomeria japonica
  • Nucleotide diversity
  • Genome-wide SNPs (Single nucleotide polymorphisms)
  • GoldenGate™
  • Genotyping