A selected set of EST-derived microsatellites, polymorphic and transferable across 6 species of eucalyptus

Journal of Heredity

Volumn 101, Issue 4, 2010, Pages 512-520

  Faria, Danielle A ^a,b   Mamani, Eva Maria Celia ^a,c   Pappas, Marilia R ^a   Pappas Jr , Georgios Joannis ^a,b   Grattapaglia, Dario ^a,b,c  

^a EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA   (Brazil)

^b UNIVERSIDADE CATÓLICA DE BRASÍLIA   (Brazil)

^c UNIVERSITY OF BRASILIA   (Brazil)

Author keywords

EST SSR; Eucalyptus; tropical trees

Indexed keywords

DINUCLEOTIDE; TRINUCLEOTIDE; MICROSATELLITE DNA; PLANT DNA;

ARTICLE; BREEDING; DINUCLEOTIDE REPEAT; DNA FINGERPRINTING; EUCALYPTUS; EXPRESSED SEQUENCE TAG; GENETIC POLYMORPHISM; INTRASPECIFIC VARIATION; MICROSATELLITE MARKER; MYRTLE; NONHUMAN; NUCLEOTIDE SEQUENCE; PARENTAGE ANALYSIS; PHYLOGENY; POLYMORPHIC LOCUS; POPULATION GENETICS; PRIORITY JOURNAL; SPECIES CONSERVATION; TRINUCLEOTIDE REPEAT; DNA SEQUENCE; GENETICS; METABOLISM; PLANT GENOME; SPECIES DIFFERENCE;

EUCALYPTUS; SYMPHYOMYRTUS;

DNA, PLANT; EUCALYPTUS; EXPRESSED SEQUENCE TAGS; GENETICS, POPULATION; GENOME, PLANT; MICROSATELLITE REPEATS; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 77953860276     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/esq024     Document Type: Article

References (43)

1. 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. 32:314-331.
2. Brondani RP, Grattapaglia D. 2001. Cost-effective method to synthesize a fluorescent internal DNA standard for automated fragment sizing. Biotechniques. 31:793-795, 798, 800.
3. 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. 6:20.
4. 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. 97:816-827.
5. Brooker MIH. 2000. A new classification of the genus Eucalyptus L'Her. (Myrtaceae). Aust Syst Bot. 13:79-148.
6. 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. 11:2379-2391.
7. Butcher PA, Otero A, McDonald MW, Moran GF. 2002. Nuclear RFLP variation in Eucalyptus camaldulensis Dehnh. from northern Australia. Heredity. 88:402-412.
8. Byrne M, Marquezgarcia MI, Uren T, Smith DS, Moran GF. 1996. Conservation and genetic diversity of microsatellite loci in the genus Eucalyptus. Aust J Bot. 44:331-341.
9. 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. 107:705-712.
10. Chakraborty R, Jin L. 1993. Determination of relatedness between individuals using DNA-fingerprinting. Human Biol. 65:875-895.
11. 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 U S A. 94:1041-1046.
12. Chybicki IJ, Burczyk J. 2009. Simultaneous estimation of null alleles and inbreeding coefficients. J Hered. 100:106-113.
13. Dakin EE, Avise JC. 2004. Microsatellite null alleles in parentage analysis. Heredity. 93:504-509.
14. Doughty RW. 2000. The eucalyptus. A natural and commercial history of the gum tree. Baltimore (MD) and London: The Johns Hopkins University Press.
15. Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 14:2611-2620.
16. 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. 95:842-849.
17. Glaubitz JC, Emebiri LC, Moran GF. 2001. Dinucleotide microsatellites from Eucalyptus sieberi: inheritance, diversity, and improved scoring of singlebase differences. Genome. 44:1041-1045.
18. Grattapaglia D. 2004. Integrating genomics into Eucalyptus breeding. Genet Mol Res. 3:369-379.
19. Grattapaglia D, Alfenas AC, Coelho ASG, Bearzoti E, Pappas GJ, Pasquali G, Pereira G, Colodette J, Gomide JL, Bueno J, et al. 2004. Building resources for molecular breeding of Eucalyptus. In: Borralho NMG, Pereira JS, Marques C, Coutinho J, Madeira M, Tomé M, editors. International IUFRO Conference: Eucalyptus in a changing world. Oct 11-15 Aveiro (Portugal): RAIZ, Instituto Investigacxão da Floresta e Papel. p. 20-32.
20. Grattapaglia D, Kirst M. 2008. Eucalyptus applied genomics: from gene sequences to breeding tools. New Phytol. 179:911-929.
21. Grattapaglia D, Ribeiro VJ, Rezende GD. 2004. Retrospective selection of elite parent trees using paternity testing with microsatellite markers: an alternative short term breeding tactic for Eucalyptus. Theor Appl Genet. 109:192-199.
22. Jones ME, Shepherd M, Henry R, Delves A. 2008. Pollen flow in Eucalyptus grandis determined by paternity analysis using microsatellite markers. Tree Genet Genomes. 4:37-47.
23. Kalinowski ST, Taper ML, Marshall TC. 2007. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol. 16:1099-1106.
24. Kirst M, Brondani RPV, Brondani C, Grattapaglia D. 1997. Screening of designed primer pairs for recovery of microsatellite markers and their transferability among species of Eucalyptus. In: EMBRAPA, editor.
25. Proceedings of the IUFRO Conference on Eucalyptus Genetics and Silviculture. 1997 August 24-29; Salvador, BA (Brazil). EMBRAPA CNPF. p. 167-171.
26. 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. 96:161-166.
27. Kolpakov R, Bana G, Kucherov G. 2003. MREPS: efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Res. 31:3672-3678.
28. 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. 10:452.
29. Liu KJ, Muse SV. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics. 21:2128-2129.
30. Missiaggia AA, Piacezzi AL, Grattapaglia D. 2005. Genetic mapping of Eef1, a major effect QTL for early flowering in Eucalyptus grandis. Tree Genet Genomes. 1:79-84.
31. Myburg AA, Potts BM, Marques CM, Kirst M, Gion JM, Grattapaglia D, Grima-Pettenati J. 2007. Eucalyptus. In: Kole C, editor. Genome mapping and molecular breeding in plants. New York: Springer. p. 115-160.
32. Nevill PG, Reed A, Bossinger G, Vaillancourt RE, Larcombe M, Ades PK. 2008. Cross-species amplification of Eucalyptus microsatellite loci. Mol Ecol Resour. 8:1277-1280.
33. Novaes E, Drost DR, Farmerie WG, Pappas GJ Jr., Grattapaglia D, Sederoff RR, Kirst M. 2008. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics. 9: 312.
34. 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. 96:445-451.
35. 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. 4:519-530.
36. Poke FS, Vaillancourt RE, Elliott RC, Reid JB. 2003. Sequence variation in two lignin biosynthesis genes, cinnamoyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase 2 (CAD2). Mol Breeding. 12:107-118.
37. Potts BM. 2004. Genetic improvement of eucalypts. In: Burley J, Evans J, Youngquist JA, editors. Encyclopedia of forest science. Oxford: Elsevier Science. p. 1480-1490.
38. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics. 155:945-959.
39. Rosenberg NA. 2004. DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes. 4:137-138.
40. Steane DA, Conod N, Jones RC, Vaillancourt RE, Potts BM. 2006. A comparative analysis of population structure of a forest tree, Eucalyptus globutus (Myrtaceae), using microsatellite markers and quantitative traits. Tree Genet Genomes. 2:30-38.
41. 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. 50:89-91.
42. Varshney RK, Graner A, Sorrells ME. 2005. Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 23: 48-55.
43. 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. 19:1251-1260.