Skip to main content
SpringerLink
Log in

High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.)

  • Original Paper
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

The development and application of genomic tools to loblolly pine (Pinus taeda L.) offer promising insights into the organization and structure of conifer genomes. The application of a high-throughput genotyping assay across diverse forest tree species, however, is currently limited taxonomically. This is despite the ongoing development of genome-scale projects aiming at the construction of expressed sequence tag (EST) libraries and the resequencing of EST-derived unigenes for a diverse array of forest tree species. In this paper, we report on the application of Illumina’s high-throughput GoldenGate™ SNP genotyping assay to a loblolly pine mapping population. Single nucleotide polymorphisms (SNPs) were identified through resequencing of previously identified wood quality, drought tolerance, and disease resistance candidate genes prior to genotyping. From that effort, a 384 multiplexed SNP assay was developed for high-throughput genotyping. Approximately 67% of the 384 SNPs queried converted into high-quality genotypes for the 48 progeny samples. Of those 257 successfully genotyped SNPs, 70 were segregating within the mapping population. A total of 27 candidate genes were subsequently mapped onto the existing loblolly pine consensus map, which consists of 12 linkage groups spanning a total map distance of 1,227.6 cM. The ability of SNPs to be mapped to the same position as fragment-based markers previously developed within the same candidate genes, as well as the pivotal role that SNPs currently play in the dissection of complex phenotypic traits, illustrate the usefulness of high-throughput SNP genotyping technologies to the continued development of pine genomics.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Acheré V, Faivre-Rampant P, Jeandroz S, Besnard G, Markussen T, Aragones A, Fladung M, Ritter E, Favre J-M (2004) A full saturated linkage map of Picea abies including AFLP, SSR, ESTP, 5S rDNA and morphological markers. Theor Appl Genet 108:1602–1613

    Article  PubMed  CAS  Google Scholar 

  • Adams WT, Joly RJ (1980) Linkage relationships among twelve allozyme loci in loblolly pine. J Heredity 71:199–202

    CAS  Google Scholar 

  • Ahuja MR, Neale DB (2005) Evolution of genome size in conifers. Silvae Genet 54:126–137

    Google Scholar 

  • Brown GR, Kadel EE III, Bassoni DA, Kiehne KL, Temesgen B, van Buijtenen JP, Sewell MM, Marshall KA, Neale DB (2001) Anchored reference loci in loblolly pine (Pinus taeda L.) for integrating pine genomics. Genetics 159:799–809

    PubMed  CAS  Google Scholar 

  • Brown GR, Bassoni DL, Gill GP, Fontana JR, Wheeler NC, Megraw RA, Davis MF, Sewell MM, Tuskan GA, Neale DB (2003) Identification of quantitative trait loci influencing wood property traits in loblolly pine III. QTL verification and candidate gene mapping. Genetics 164:1537–1546

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Cardon LR, Bell JI (2001) Association study designs for complex diseases. Nat Rev Genet 2:91–99

    Article  PubMed  CAS  Google Scholar 

  • Clayton DG, Walker NM, Smyth DJ, Pask R, Cooper JD, Maier LM, Smink LJ, Lam AC, Ovington NR, Stevens HE, Nutland S, Howson JMM, Faham M, Moorhead M, Jones HB, Falkowski M, Hardenbol P, Willis TD, Todd JA (2005) Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat Genet 37:1243–1246

    Article  PubMed  CAS  Google Scholar 

  • Conkle MT (1981) Isozyme variation and linkage in six conifer species. In: Conkle MT (ed) Proceedings of the Symposium on Isozymes of North American Forest Trees and Forest Insects. General Technical Report GTR-PSW-048, USDA Forest Service, Berkeley

  • Devey ME, Fiddler TA, Liu BH, Knapp SJ, Neale DB (1994) An RFLP linkage map for loblolly pine based on a three-generation outbred pedigree. Theor Appl Genet 88:273–278

    Article  CAS  Google Scholar 

  • Fan JB, Oliphant A, Shen R, Kermani BG, Garcia F, Gunderson KL, Hansen M, Steemers F, Butler SL, Deloukas P, Galver L, Hunt S, McBride C, Bibikova M, Rubano T, Chen J, Wickham E, Doucet D, Chang W, Campbell D, Zhang B, Kruglyak S, Bentley D, Haas J, Rigault P, Zhou L, Stuelpnagel J, Chee MS (2003) Highly parallel SNP genotyping. Cold Spring Harbor Symp Quant Biol 68:69–78

    Article  PubMed  CAS  Google Scholar 

  • Gill GP, Brown GR, Neale DB (2003) A sequence mutation in the cinnamyl alcohol dehydronase gene associated with altered lignification in loblolly pine. Plant Biotech J 1:253–258

    Article  CAS  Google Scholar 

  • González-Martínez SC, Ersoz E, Brown GR, Wheeler NC, Neale DB (2006) DNA sequence variation and selection of tag SNPs at candidate genes for drought-stress response in Pinus taeda L. Genetics 172:1915–1926

    Article  PubMed  CAS  Google Scholar 

  • González-Martínez SC, Wheeler NC, Ersoz E, Nelson CD, Neale DB (2007) Association genetics in Pinus taeda L. I. Wood property traits. Genetics 175:399–409

    Article  PubMed  Google Scholar 

  • González-Martínez SC, Huber D, Ersoz E, Davis JM, Neale DB (2008) Association genetics in Pinus taeda L. II. Carbon isotope discrimination. Heredity 101:19–26

    Article  PubMed  CAS  Google Scholar 

  • Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-test cross: mapping strategy and RAPD markers. Genetics 137:1121–1137

    PubMed  CAS  Google Scholar 

  • Groover AT, Devey ME, Fiddler TA, Lee JM, Megraw RA, Mitchell-Olds T, Sherman BK, Vujcic SL, Williams CG, Neale DB (1994) Identification of quantitative trait loci influencing wood specific gravity in an outbred pedigree of loblolly pine. Genetics 138:1293–1300

    PubMed  CAS  Google Scholar 

  • Harry DE, Temesgen B, Neale DB (1998) Codominant PCR-based markers for Pinus taeda developed from mapped cDNA clones. Theor Appl Genet 97:327–336

    Article  CAS  Google Scholar 

  • Heuertz M, De Paoli E, Källman T, Larsson H, Jurman I, Morgante M, Lascoux M, Gyllenstrand N (2006) Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]. Genetics 174:2095–2105

    Article  PubMed  CAS  Google Scholar 

  • Hu X-S, Goodwillie C, Ritland KM (2004) Joining genetic linkage maps using a joint likelihood function. Theor Appl Genet 109:996–1004

    Article  PubMed  Google Scholar 

  • Hyten DL, Song Q, Choi I-Y, Yoon M-S, Specht JE, Matulumalli LK, Nelso RL, Shoemaker RC, Young ND, Cregan PB (2008) High-throughput genotyping with the GoldenGate assay in the complex genome of soybean. Theor Appl Genet 116:945–952

    Article  PubMed  CAS  Google Scholar 

  • Ihaka R, Gentleman R (1996) R: a language for data analysis and graphics. J Comput Graph Stat 5:299–314

    Article  Google Scholar 

  • Jermstad KD, Bassoni DL, Jech KS, Wheeler NC, Neale DB (2001) Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir I. Timing of vegetative bud flush. Theor Appl Genet 102:1142–1151

    Article  CAS  Google Scholar 

  • Kinlaw CS, Neale DB (1997) Complex gene families in pine genomes. Trends Plant Sci 2:356–359

    Article  Google Scholar 

  • Komulainen P, Brown GR, Mikkonen M, Karku A, Garcia-Gil MR, O’Malley D, Lee B, Neale DB, Savolainen O (2003) Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda. Theor Appl Genet 107:667–678

    Article  PubMed  CAS  Google Scholar 

  • Kosambi DD (1944) The estimation of map values from recombination values. Ann Eugen 12:172–175

    Google Scholar 

  • Krutovsky KV, Troggio M, Brown GR, Jermstad KD, Neale DB (2004) Comparative mapping in the Pinaceae. Genetics 168:447–461

    Article  PubMed  CAS  Google Scholar 

  • Kwok P-Y (2001) SNP genotyping with fluorescence polarization detection. Human Mutat 19:315–323

    Article  CAS  Google Scholar 

  • Landegren U, Kaiser R, Sanders J, Hood L (1988) A ligase-mediated gene detection technique. Science 241:1077–1080

    Article  PubMed  CAS  Google Scholar 

  • Ledig FT (1998) Genetic variation in pines. In: Richardson DM (ed) Ecology and biogeography of Pinus. Cambridge University Press, Cambridge, pp 251–280

    Google Scholar 

  • Long AD, Langley CH (1999) The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits. Genome Res 9:720–731

    PubMed  CAS  Google Scholar 

  • McKay SD, Schnabel RD, Murdoch BM, Aerts J, Gill CA, Gao C, Li C, Matukumalli LK, Stothard P, Wang Z, Van Tassell CP, Williams JL, Taylor JF, Moore SS (2007) Construction of bovine whole-genome radiation hybrid and linkage maps using high-throughput genotyping. Anim Genet 38:120–125

    Article  PubMed  CAS  Google Scholar 

  • Murray BG (1998) Nuclear DNA amount in gymnosperms. Ann Bot 82(Suppl A):3–15

    Article  CAS  Google Scholar 

  • Myers S, Bottolo L, Freeman C, McVean G, Donnelly P (2005) A fine-scale map of recombination rates and hotspots across the human genome. Science 310:321–324

    Article  PubMed  CAS  Google Scholar 

  • Neale DB (2007) Genomics to tree breeding and forest health. Curr Opin Genet Dev 17:539–544

    Article  PubMed  CAS  Google Scholar 

  • Neale DB, Savolainen O (2004) Association genetics of complex traits in conifers. Trends Plant Sci 9:325–330

    Article  PubMed  CAS  Google Scholar 

  • Neale DB, Sewell MM, Brown GR (2002) Molecular dissection of the quantitative inheritance of wood property traits in loblolly pine. Ann For Sci 59:595–605

    Article  Google Scholar 

  • Oliphant A, Barker DL, Stuelpnagel JR, Chee MS (2002) BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques (Suppl):56–58 (60–61)

  • 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 9:21

    Article  PubMed  CAS  Google Scholar 

  • Remington DL, Wheten RW, Liu B-H, O’Malley DM (1999) Construction of an AFLP genetic map with nearly complete genome coverage in Pinus taeda. Theor Appl Genet 98:1279–1292

    Article  PubMed  CAS  Google Scholar 

  • Ritter E, Aragonés A, Markussen T, Acheré V, Espinel S, Fladung M, Wrobel S, Faivre-Rampant, Jeandroz S, Favre JM (2002) Towards construction of an ultra high density linkage map for Pinus pinaster. Ann For Sci 59:637–643

    Article  Google Scholar 

  • Rostoks N, Ramsay L, MacKenzie K, Cardle L, Bhat PR, Roose ML, Svensson JT, Stein N, Varshney RK, Marshall DF, Graner A, Close TJ, Waugh R (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc Natl Acad Sci USA 103:18656–18661

    Article  PubMed  CAS  Google Scholar 

  • Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES, The International HapMap Consortium (2007) Genome-wide detection and characterization of positive selection in human populations. Nature 449:913–918

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Sewell MM, Sherman BK, Neale DB (1999) A consensus map for loblolly pine (Pinus taeda L.) I. Construction and integration of individual linkage maps from two outbred three-generation pedigrees. Genetics 151:321–330

    PubMed  CAS  Google Scholar 

  • Sewell MM, Bassoni DL, Megraw RA, Wheeler NC, Neale DB (2000) Identification of QTLs influencing wood property traits in loblolly pine (Pinus taeda L.) I. Physical wood properties. Theor Appl Genet 101:1273–1281

    Article  CAS  Google Scholar 

  • Sewell MM, Davis MF, Tuskan GA, Wheeler NC, Elam CC, Bassoni DL, Neale DB (2002) Identification of QTLs influencing wood property traits in loblolly pine (Pinus taeda L.) II. Chemical wood properties. Theor Appl Genet 104:214–222

    Article  PubMed  CAS  Google Scholar 

  • Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 3:739–744

    Article  CAS  Google Scholar 

  • Steemers FJ, Gunderson KL (2007) Whole genome genotyping technologies on the BeadArray platform. Bitechnol J 2:41–49

    Article  CAS  Google Scholar 

  • Tani N, Takahashi T, Iwata H, Mukai Y, Ujino-Ihara T, Matsumoto A, Yoshimura K, Yoshimuru H, 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

    PubMed  CAS  Google Scholar 

  • Temesgen B, Brown GR, Harry DE, Kinlaw CS, Sewell MM, Neale DB (2001) Genetic mapping of expressed sequence tag polymorphism (ESTP) markers in loblolly pine (Pinus taeda L.). Theor Appl Genet 102:664–675

    Article  CAS  Google Scholar 

  • Thorisson GA, Smith AV, Krishman L, Stein LD (2005) The International HapMap project website. Genome Res 15:1592–1593

    Article  PubMed  CAS  Google Scholar 

  • Zhou Y, Bui T, Auckland LD, Williams CG (2002) Undermethylated DNA as a source of microsatellites from a conifer genome. Genome 45:91–99

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

We would like to thank Jill Wegrzyn and Jennifer Lee for the bioinformatic support, as well as Kathleen Jermsted for the help in the production and interpretation of linkage maps. We would also like to thank C. Dana Nelson and Craig Echt for providing the SSR data. This research was supported by NSF grant DBI-0501763.

Author information

Authors and Affiliations

  1. Section of Evolution and Ecology, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA

    Andrew J. Eckert

  2. Department of Plant Sciences, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA

    Barnaly Pande & David B. Neale

  3. Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14850, USA

    Elhan S. Ersoz

  4. Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA

    Mark H. Wright

  5. DNA Technologies Core Facility, Genome Center, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA

    Vanessa K. Rashbrook & Charles M. Nicolet

Authors
  1. Andrew J. Eckert
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Barnaly Pande
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Elhan S. Ersoz
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mark H. Wright
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Vanessa K. Rashbrook
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Charles M. Nicolet
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. David B. Neale
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to David B. Neale.

Additional information

Communicated by D. Grattapaglia

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(DOC 127 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Eckert, A.J., Pande, B., Ersoz, E.S. et al. High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.). Tree Genetics & Genomes 5, 225–234 (2009). https://doi.org/10.1007/s11295-008-0183-8

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11295-008-0183-8

Keywords

Search

Navigation