Tree Genetics & Genomes

, Volume 7, Issue 1, pp 63–77 | Cite as

Genotyping systems for Eucalyptus based on tetra-, penta-, and hexanucleotide repeat EST microsatellites and their use for individual fingerprinting and assignment tests

  • Danielle Assis Faria
  • Eva Maria Celia Mamani
  • Georgios Joannis PappasJr.
  • Dario Grattapaglia
Original Paper

Abstract

Eucalypts are keystone species in their natural ranges and are extensively planted worldwide for high-quality woody biomass. A novel set of 21 polymorphic and interspecifically transferable microsatellite markers based on tetra-, penta- and hexanucleotide repeats were developed and tested for high-precision genotyping of species of Eucalyptus. These microsatellites were characterized in population samples of four species, Eucalyptus grandis, Eucalyptus globulus, Eucalyptus urophylla, and Eucalyptus camaldulensis, representing three phylogenetic sections of subgenus Symphyomyrtus. These markers provide a clear advantage for accurate allele calling due to their larger allele size difference. Two multiplexed microsatellite combinations, a 14-locus/four-dye and an 18-locus/five-dye set, analyzable in single lanes were designed, providing resolution and throughput analogous to those routinely used in human DNA profiling. This set of microsatellites was shown to have high resolution for clone fingerprinting, inter-individual genetic distance estimation, species distinction, and assignment of hybrid individuals to their most likely ancestral species. These systems will be particularly useful for comparative population genetics and molecular breeding applications that require consistent allele calling across different points in time or laboratories.

Keywords

Microsatellites Multiplex Assignment tests Eucalyptus 

Notes

Acknowledgments

This work was supported by the Brazilian Ministry of Science and Technology through FINEP grant 1755-01 and CNPq grant 520489/02-0 both within the Genolyptus project and EMBRAPA Macroprogram 3 project grant 03.07.01.001. DAF and EMCM were supported respectively by a CNPq post-doctoral and CAPES doctoral fellowships; GJPJr and DG have been awarded individual research fellowships from CNPq.

Supplementary material

11295_2010_315_MOESM1_ESM.pdf (69 kb)
Supplementary Figure S1(PDF 69 kb)
11295_2010_315_MOESM2_ESM.pdf (103 kb)
Supplementary Table S1(PDF 103 kb)

References

  1. Alfenas AC, Jeng R, Hubbes M (1983) Virulence of Cryphonectria cubensis on Eucalyptus species differing in resistance. Eur J For Pathol 13:197–205CrossRefGoogle Scholar
  2. Bar W, Brinkmann B, Lincoln P, Mayr WR, Rossi U, Budowle B, Bell C, Carracedo A, Eisenberg A, Fourney R, Gill P, Kloosterman A, Monson K, Pascal O, Rand S, Robertson J, Vandaal A (1995) DNA recommendations—1994 Report Concerning Further Recommendations of the DNA Commission of the ISFH Regarding PCR-Based Polymorphisms in STR (Short Tandem Repeat) Systems. Vox Sang 69:70–71CrossRefGoogle Scholar
  3. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic-linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331PubMedGoogle Scholar
  4. Bowcock AM, Ruizlinares A, Tomfohrde J, Minch E, Kidd JR, Cavallisforza LL (1994) High-resolution of human evolutionary trees with polymorphic microsatellites. Nature 368:455–457CrossRefPubMedGoogle Scholar
  5. Brondani RP, Grattapaglia D (2001) Cost-effective method to synthesize a fluorescent internal DNA standard for automated fragment sizing. Biotechniques 31:793–795, 798, 800Google Scholar
  6. Brondani RPV, Brondani C, Tarchini R, Grattapaglia D (1998) Development, characterization and mapping of microsatellite markers in Eucalyptus grandis and E. urophylla. Theor Appl Genet 97:816–827CrossRefGoogle Scholar
  7. Brondani RP, Williams ER, Brondani C, Grattapaglia D (2006) A microsatellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus. BMC Plant Biol 6:20CrossRefPubMedGoogle Scholar
  8. Burczyk J, Adams WT, Moran GF, Griffin AR (2002) Complex patterns of mating revealed in a Eucalyptus regnans seed orchard using allozyme markers and the neighbourhood model. Mol Ecol 11:2379–2391CrossRefPubMedGoogle Scholar
  9. Butcher PA, Otero A, McDonald MW, Moran GF (2002) Nuclear RFLP variation in Eucalyptus camaldulensis Dehnh. from northern Australia. Heredity 88:402–412CrossRefPubMedGoogle Scholar
  10. Ceresini PC, Silva CLSP, Missio RF, Souza EC, Fischer CN, Guillherme IR, Gregorio I, da Silva EHT, Cicarelli RMB, da Silva MTA, Garcia JF, Avelar GA, Neto LRP, Marcon AR, Bacci M, Marini DC (2005) Satellyptus: analysis and database of microsatellites from ESTs of Eucalyptus. Genet Mol Biol 28:589–600CrossRefGoogle Scholar
  11. Chaix G, Gerber S, Razafimaharo V, Vigneron P, Verhaegen D, Hamon S (2003) Gene flow estimation with microsatellites in a Malagasy seed orchard of Eucalyptus grandis. Theor Appl Genet 107:705–712CrossRefPubMedGoogle Scholar
  12. Chakraborty R, Kimmel M, Stivers DN, Davison LJ, Deka R (1997) Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci. Proc Natl Acad Sci USA 94:1041–1046CrossRefPubMedGoogle Scholar
  13. Chybicki IJ, Burczyk J (2009) Simultaneous estimation of null alleles and inbreeding coefficients. J Hered 100:106–113CrossRefPubMedGoogle Scholar
  14. Doughty RW (2000) The Eucalyptus. A natural and commercial history of the gum tree. The Johns Hopkins University Press, Baltimore and LondonGoogle Scholar
  15. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620CrossRefPubMedGoogle Scholar
  16. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform 1:47–50Google Scholar
  17. Feng SP, Li WG, Huang HS, Wang JY, Wu YT (2009) Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis). Mol Breed 23:85–97CrossRefGoogle Scholar
  18. Fujimori S, Washio T, Higo K, Ohtomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Tomita M (2003) A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription. FEBS Lett 554:17–22CrossRefPubMedGoogle Scholar
  19. Gaiotto FA, Bramucci M, Grattapaglia D (1997) Estimation of outcrossing rate in a breeding population of Eucalyptus urophylla with dominant RAPD and AFLP markers. Theor Appl Genet 95:842–849CrossRefGoogle Scholar
  20. Gill P, Kimpton C, Daloja E, Andersen JF, Bar W, Brinkmann B, Holgersson S, Johnsson V, Kloosterman AD, Lareu MV, Nellemann L, Pfitzinger H, Phillips CP, Schmitter H, Schneider PM, Stenersen M (1994) Report of the European DNA Profiling Group (Ednap)—towards standardization of short tandem repeat (Str) loci. Forensic Sci Int 65:51–59CrossRefPubMedGoogle Scholar
  21. Glaubitz JC, Emebiri LC, Moran GF (2001) Dinucleotide microsatellites from Eucalyptus sieberi: inheritance, diversity, and improved scoring of single-base differences. Genome 44:1041–1045CrossRefPubMedGoogle Scholar
  22. Grattapaglia D, Kirst M (2008) Eucalyptus applied genomics: from gene sequences to breeding tools. New Phytol 179:911–929CrossRefPubMedGoogle Scholar
  23. Grattapaglia D, Alfenas AC, Coelho ASG, Bearzoti E, Pappas GJ, Pasquali G, Pereira G, Colodette J, Gomide JL, Bueno J, Cascardo JC, Brondani RPV, Brommonschenkel SH (2004a) Building resources for molecular breeding of Eucalyptus. In: Borralho NMG, Pereira JS, Marques C, Coutinho J, Madeira M, Tomé M (eds) International IUFRO Conference: Eucalyptus in a changing world. RAIZ, Instituto Investigação da Floresta e Papel, Portugal, Aveiro Portugal, pp 20–32Google Scholar
  24. Grattapaglia D, Ribeiro VJ, Rezende GD (2004b) Retrospective selection of elite parent trees using paternity testing with microsatellite markers: an alternative short term breeding tactic for Eucalyptus. Theor Appl Genet 109:192–199CrossRefPubMedGoogle Scholar
  25. Heerden SW, Wingfield MJ (2002) Effect of environment on the response of Eucalyptus clones to inoculation with Cryphonectria cubensis. For Pathol 32:395–402Google Scholar
  26. Holt CL, Buoncristiani M, Wallin JM, Nguyen T, Lazaruk KD, Walsh PS (2002) TWGDAM validation of AmpFlSTR (TM) PCR amplification kits for forensic DNA casework. J Forensic Sci 47:66–96PubMedGoogle Scholar
  27. Honjo M, Ueno S, Tsumura Y, Handa T, Washitani I, Ohsawa R (2008) Tracing the origins of stocks of the endangered species Primula sieboldii using nuclear microsatellites and chloroplast DNA. Conserv Genet 9:1139–1147CrossRefGoogle Scholar
  28. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106CrossRefPubMedGoogle Scholar
  29. Kirst M, Cordeiro CM, Rezende GD, Grattapaglia D (2005) Power of microsatellite markers for fingerprinting and parentage analysis in Eucalyptus grandis breeding populations. J Hered 96:161–166CrossRefPubMedGoogle Scholar
  30. Kolpakov R, Bana G, Kucherov G (2003) MREPS: efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Res 31:3672–3678CrossRefPubMedGoogle Scholar
  31. Koskinen MT (2003) Individual assignment using microsatellite DNA reveals unambiguous breed identification in the domestic dog. Anim Genet 34:297–301CrossRefPubMedGoogle Scholar
  32. Krenke BE, Tereba A, Anderson SJ, Buel E, Culhane S, Finis CJ, Tomsey CS, Zachetti JM, Masibay A, Rabbach DR, Amiott EA, Sprecher CJ (2002) Validation of a 16-locus fluorescent multiplex system. J Forensic Sci 47:773–785PubMedGoogle Scholar
  33. Kulheim C, Yeoh SH, Maintz J, Foley WJ, Moran GF (2009) Comparative SNP diversity among four Eucalyptus species for genes from secondary metabolite biosynthetic pathways. BMC Genomics 10:452CrossRefPubMedGoogle Scholar
  34. Kumar P, Freeman AR, Loftus RT, Gaillard C, Fuller DQ, Bradley DG (2003) Admixture analysis of South Asian cattle. Heredity 91:43–50CrossRefPubMedGoogle Scholar
  35. Ladiges PY, Udovicic F, Nelson G (2003) Australian biogeographical connections and the phylogeny of large genera in the plant family Myrtaceae. J Biogeogr 30:989–998CrossRefGoogle Scholar
  36. Lins TC, Vieira RG, Abreu BS, Grattapaglia D, Pereira RW (2010) Genetic composition of Brazilian population samples based on a set of twenty-eight ancestry informative SNPs. Am J Hum Biol 22:187–192PubMedGoogle Scholar
  37. Litt M, Hauge X, Sharma V (1993) Shadow bands seen when typing polymorphic dinucleotide repeats—some causes and cures. Biotechniques 15:280–284PubMedGoogle Scholar
  38. Liu KJ, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129CrossRefPubMedGoogle Scholar
  39. Millar MA, Byrne M, Nuberg I, Sedgley M (2008) A rapid PCR-based diagnostic test for the identification of subspecies of Acacia saligna. Tree Genet & Genomes 4:625–635CrossRefGoogle Scholar
  40. Minch E, Ruíz-Linares A, Goldstein DB, Feldman M, Cavalli-Sforza LL (1995) MICROSAT—the Microsatellite Distance Program. Stanford University Press, StanfordGoogle Scholar
  41. Missiaggia AA, Piacezzi AL, Grattapaglia D (2005) Genetic mapping of Eef1, a major effect QTL for early flowering in Eucalyptus grandis. Tree Genet & Genomes 1:79–84CrossRefGoogle Scholar
  42. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200CrossRefPubMedGoogle Scholar
  43. Muir G, Schlotterer C (2005) Evidence for shared ancestral polymorphism rather than recurrent gene flow at microsatellite loci differentiating two hybridizing oaks (Quercus spp.). Mol Ecol 14:549–561CrossRefPubMedGoogle Scholar
  44. Myburg AA, Potts BM, Marques CM, Kirst M, Gion JM, Grattapaglia D, Grima-Pettenati J (2007) Eucalyptus. In: Kole C (ed) Genome mapping and molecular breeding in plants. Springer, New York, pp 115–160Google Scholar
  45. Ottewell KM, Donnellan SC, Moran GF, Paton DC (2005) Multiplexed microsatellite markers for the genetic analysis of Eucalyptus leucoxylon (Myrtaceae) and their utility for ecological and breeding studies in other Eucalyptus species. J Hered 96:445–451CrossRefPubMedGoogle Scholar
  46. Parida SK, Dalal V, Singh AK, Singh NK, Mohapatra T (2009) Genic non-coding microsatellites in the rice genome: characterization, marker design and use in assessing genetic and evolutionary relationships among domesticated groups. BMC Genomics 10:140CrossRefPubMedGoogle Scholar
  47. Payn KG, Dvorak WS, Janse BJH, Myburg AA (2008) Microsatellite diversity and genetic structure of the commercially important tropical tree species Eucalyptus urophylla, endemic to seven islands in eastern Indonesia. Tree Genet & Genomes 4:519–530CrossRefGoogle Scholar
  48. Potts BM (2004) Genetic improvement of eucalypts. In: Burley J, Evans J, Youngquist JA (eds) Encyclopedia of forest science. Elsevier Science, Oxford, pp 1480–1490CrossRefGoogle Scholar
  49. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  50. Rabello E, de Souza AN, Saito D, Tsai SM (2005) In silico characterization of microsatellites in Eucalyptus spp.: abundance, length variation and transposon associations. Genet Mol Biol 28:582–588CrossRefGoogle Scholar
  51. Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138CrossRefGoogle Scholar
  52. Sharma PC, Grover A, Kahl G (2007) Mining microsatellites in eukaryotic genomes. Trends Biotechnol 25:490–498CrossRefPubMedGoogle Scholar
  53. Sampson JF, Byrne M (2008) Outcrossing between an agroforestry plantation and remnant native populations of Eucalyptus loxophleba. Mol Ecol 17:2769–2781CrossRefPubMedGoogle Scholar
  54. Sarri V, Baldoni L, Porceddu A, Cultrera NGM, Contento A, Frediani M, Belaj A, Trujillo I, Cionini PG (2006) Microsatellite markers are powerful tools for discriminating among olive cultivars and assigning them to geographically defined populations. Genome 49:1606–1615CrossRefPubMedGoogle Scholar
  55. Steane DA, Vaillancourt RE, Russell J, Powell W, Marshall D, Potts BM (2001) Development and characterisation of microsatellite loci in Eucalyptus globulus (Myrtaceae). Silvae Genet 50:89–91Google Scholar
  56. Steane DA, Conod N, Jones RC, Vaillancourt RE, Potts BM (2006) A comparative analysis of population structure of a forest tree, Eucalyptus globulus (Myrtaceae), using microsatellite markers and quantitative traits. Tree Genet & Genomes 2:30–38CrossRefGoogle Scholar
  57. Stephens MR, Clipperton NW, May B (2009) Subspecies-informative SNP assays for evaluating introgression between native golden trout and introduced rainbow trout. Molecular Ecology Resources 9(1):339–343Google Scholar
  58. Tadano R, Nishibori M, Tsudzuki M (2008) High accuracy of genetic discrimination among chicken lines obtained through an individual assignment test. Anim Genet 39:567–571CrossRefPubMedGoogle Scholar
  59. Vallone PM, Butler JM (2004) AutoDimer: a screening tool for primer-dimer and hairpin structures. Biotechniques 37:226–231PubMedGoogle Scholar
  60. Vigouroux Y, Jaqueth JS, Matsuoka Y, Smith OS, Beavis WF, Smith JSC, Doebley J (2002) Rate and pattern of mutation at microsatellite loci in maize. Mol Biol Evol 19:1251–1260PubMedGoogle Scholar
  61. Yasodha R, Sumathi R, Chezhian P, Kavitha S, Ghosh M (2008) Eucalyptus microsatellites mined in silico: survey and evaluation. J Genet 87:21–25CrossRefPubMedGoogle Scholar
  62. Yi GB, Lee JM, Lee S, Choi D, Kim BD (2006) Exploitation of pepper EST-SSRs and an SSR-based linkage map. Theor Appl Genet 114:113–130CrossRefPubMedGoogle Scholar
  63. Zhang LD, Yuan DJ, Yu SW, Li ZG, Cao YF, Miao ZQ, Qian HM, Tang KX (2004) Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana. Bioinformatics 20:1081–1086CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Danielle Assis Faria
    • 1
    • 3
  • Eva Maria Celia Mamani
    • 1
    • 2
  • Georgios Joannis PappasJr.
    • 1
    • 3
  • Dario Grattapaglia
    • 1
    • 2
    • 3
  1. 1.Plant Genetics LaboratoryEmbrapa–Recursos Genéticos e BiotecnologiaBrasíliaBrazil
  2. 2.Department of Cell BiologyUniversidade de Brasília–UnBBrasíliaBrazil
  3. 3.Graduate Program in Genomic Sciences and BiotechnologyUniversidade Católica de Brasília–SGAN 916 modulo BBrasíliaBrazil

Personalised recommendations