SSRs, SNPs and DArTs comparison on estimation of relatedness and genetic parameters’ precision from a small half-sib sample population of Eucalyptus grandis

Molecular Breeding

Volumn 36, Issue 7, 2016, Pages

  Cappa, Eduardo P ^a,b   Klápště, Jaroslav ^c,d,f   Garcia, Martín N ^e   Villalba, Pamela V ^e   Marcucci Poltri, Susana N ^e  

^a INSTITUTO NACIONAL DE TECNOLOGÍA AGROPECUARIA INTA   (Argentina)

^b Consejo Nacional de Investigaciones Científicas y Técnicas ^*  (Argentina)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^d CZECH UNIVERSITY OF LIFE SCIENCES PRAGUE   (Czech Republic)

^e INSTITUTO NACIONAL DE TECNOLOGÍA AGROPECUARIA   (Argentina)

^f SCION   (New Zealand)

Author keywords

Eucalyptus grandis; Heritability; Marker based relationship matrix; Molecular markers; Relatedness

Indexed keywords

DNA SEQUENCES; FORESTRY; MATRIX ALGEBRA;

EUCALYPTUS GRANDIS; GENETIC PARAMETERS; HERITABILITY; MARKER-BASED RELATIONSHIP MATRIX; MOLECULAR MARKER; RELATEDNESS; RELATEDNESS COEFFICIENT; RELATIONSHIP MATRIX; ROOT MEAN SQUARED ERRORS; SAMPLE POPULATION;

MEAN SQUARE ERROR;

EID: 84978044407     PISSN: 13803743     EISSN: 15729788     Source Type: Journal    
DOI: 10.1007/s11032-016-0522-7     Document Type: Article

References (79)

1. Alves A, Santos A, Rozenberg P, Paques LE, Charpentier JP, Schwanninger M, Rodrigues J (2012) A common near infrared-based partial least squares regression model for the prediction of wood density of Pinus pinaster and Larix × eurolepis. Wood Sci Technol 46:157–175
2. Anderson EC, Garza JC (2006) The power of single nucleotide polymorphisms for large-scale parentage inference. Genetics 172:2567–2582
3. Bessega C, Saidman BO, Darquier MR, Ewens M, Felker P, Vilardi JC (2011) Accuracy of dominant markers for estimation of relatedness and heritability in an experimental stand of Prosopis alba (leguminosae). Tree Genet Genomes 7:103–115
4. Bloomfield JA, Nevill P, Potts BM, Vaillancourt RE, Steane DA (2011) Molecular genetic variation in a widespread forest tree species Eucalyptus obliqua (Myrtaceae) on the island of Tasmania. Aust J Bot 59:226–237
5. Blouin MS (2003) DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends Ecol Evol 18:503–511
6. Blouin MS, Parsons M, Lacaille V, Lotz S (1996) Use of microsatellite loci to classify individuals by relatedness. Mol Ecol 5:393–401
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 22:6–20
8. Bush D, Thumma B (2013) Characterising a Eucalyptus cladocalyx breeding population using SNP markers. Tree Genet Genomes 9:741–752
9. Butcher PA, McDonald MW, Bell JC (2009) Congruence between environmental parameters, morphology and genetic structure in Australia’s most widely distributed eucalypt, Eucalyptus camaldulensis. Tree Genet Genomes 5:189–210
10. Cappa EP, Pathauer PS, Lopez GA (2010) Provenance variation and genetic parameters of Eucalyptus viminalis in Argentina. Tree Genet Genomes 6:981–994
11. Chapuis MP, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631
12. Cornelius JP (1994) Heritabilities and additive genetic coefficients of variation in forest trees. Can J For Res 24:372–379
13. Crossa J, Burgueno J, Dreisigacker S, Vargas M, Herrera-Foessel S, Lillemo M, Singh R, Trethowan R, Warburton M, Franco J, Reynolds M, Crouch J, Ortiz R (2007) Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics 177:1889–1913
14. Csilléry K, Johnson T, Beraldi D, Clutton-Brock T, Coltman D, Hansson B, Spong G, Pemberton JM (2006) Performance of marker-based relatedness estimators in natural populations of outbred vertebrates. Genetics 173:2091–2101
15. Dakin EE, Avise JC (2004) Microsatellite null alleles in parentage analysis. Heredity 93:504–509
16. Eldridge K, Davidson J, Hardwood C, van Wyk G (1993) Eucalyptus domestication and breeding. Oxford University Press, New York
17. El-Kassaby YA, Cappa EP, Liewlaksaneeyanawin C, Klápšte J, Lstiburek M (2011) Breeding without breeding: is a complete pedigree necessarily for efficient breeding? PLoS One 6(10):e25737
18. El-Kassaby YA, Klápšte J, Guy RD (2012) Breeding without Breeding: selection using the genomic best linear unbiased predictor method (GBLUP). New For 43:631–637
19. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K et al (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6(5):e19379. doi:10.1371/journal.pone.0019379
20. 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
21. Frentiu FD, Clegg SM, Chittock J, Burke T, Blows MW, Owens IPF (2008) Pedigree-free animal models: the relatedness matrix reloaded. Proc R Soc B 275:639–647
22. Gilmour AR, Gogel BJ, Cullis BR, Thompson R (2006) ASReml user guide release 2.0. VSN International Ltd, Hemel Hempstead
23. Gion JM, Carouché A, Deweer S, Bedon F, Pichavant F, Charpentier JP, Baillères H, Rozenberg P, Carocha V, Ognouabi N, Verhaegen D, Grima-Pettenati J, Vigneron P, Plomion C (2011) Comprehensive genetic dissection of wood properties in a widely-grown tropical tree: Eucalyptus. BMC Genom 8:12–301
24. Glaubitz JC, Rhodes OE Jr, Dewoody JD (2003) Prospects for inferring pairwise relationships with single nucleotide polymorphisms. Mol Ecol 12:1039–1047
25. Grattapaglia D, Silva-Junior OB, Kirst M, Marco de Lima B, Faria DA, Pappas GJ Jr (2011) High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across. BMC Plant Biol 11:65
26. Griffin AR, Cotterill PP (1988) Genetic variation in growth of outcrossed, selfed and open-pollinated progenies of Eucalyptus regnans and some implications for breeding strategy. Silvae Genet 37:124–131
27. Hardy OJ (2003) Estimation of pairwise relatedness between individuals and characterization of isolation-by-distance processes using dominant genetic markers. Mol Ecol 12:1577–1588
28. Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620
29. Hayes BJ, Goddard ME (2008) Technical note: prediction of breeding values using marker derived relationship matrices. J Anim Sci 86:2089–2092
30. Henderson CR (1984) Applications of linear models in animal breeding. University of Guelph, Guelph
31. Higham NJ (2002) Computing the nearest correlation matrix—a problem from finance. IMA J Numer Anal 22:329–343
32. Hodge GR, Volker PW, Potts BM, Owen JV (1996) A comparison of genetic information from open-pollinated and control-pollinated progeny tests in two eucalypt species. Theor Appl Genet 92:53–63
33. Hoisington D, Khairallah M, Gonzalez-De-Leon D (1994) Laboratory protocols: CIMMYT. Applied molecular genetics laboratory, 3rd edn. CIMMYT, D.F., Mexico
34. Hudson CJ, Freeman JS, Kullan ARK, Petroli CD, Sansaloni CP et al (2012) A reference linkage map for Eucalyptus. BMC Genom 13:240. doi:10.1186/1471-2164-13-240
35. Kilian A, Wenzl P, Huttner E, Carling J, Xia L, Blois H, Caig V, Heller-Uszynska K, Jaccoud D, Hopper C, Aschenbrenner-Kilian M, Evers M, Peng K, Cayla C, Hok P, Uszynski G (2012) Diversity arrays technology: a generic genome profiling technology on open platforms. Methods Mol Biol 888:67–89. doi:10.1007/978-1-61779-870-2_5
36. Kumar S, Richardson TE (2005) Inferring relatedness and heritability using molecular markers in Radiata pine. Mol Breed 15(1):55–64
37. Laidó G, Mangini G, Taranto F, Gadaleta A, Blanco A et al (2013) Genetic diversity and population structure of tetraploid wheats (Triticum turgidum L.) estimated by SSR, DArT and pedigree data. PLoS One 8(6):e67280. doi:10.1371/journal.pone.0067280
38. Lamara M, Zhang LY, Marchand S, Tinker NA, Belzilea F (2013) Comparative analysis of genetic diversity in Canadian barley assessed by SSR, DArT, and pedigree data. Genome 56:351–358
39. Li CC, Weeks DE, Chakravarti A (1993) Similarity of DNA fingerprints due to chance and relatedness. Hum Hered 43:45–52
40. Lopez GA, Potts BM, Dutkowski GW, Apiolaza LA, Gelid P (2002) Genetic variation and inter-trait correlations in Eucalyptus globulus base population trials in Argentina. For Gen 9:223–237
41. Lynch M, Ritland K (1999) Estimation of pairwise relatedness with molecular markers. Genetics 152:1753–1766
42. Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sinauer Associates, Sunderland
43. Marcó M, White TL (2002) Genetic parameter estimates and genetic gains for Eucalyptus grandis and E. dunnii in Argentina. For Genet 9:205–215
44. Marshall TC, Slate J, Kruuk LEB, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 7:639–655
45. Milligan BG (2003) Maximum-likelihood estimation of relatedness. Genetics 163:1153–1167
46. Mousseau TA, Ritland K, Heath DD (1998) A novel method for estimating heritability using molecular markers. Heredity 80:218–224
47. Ødegård J, Meuwissen THE (2012) Estimation of heritability from limited family data using genome-wide identity-by-descent sharing. Genet Sel Evol 44:16–25
48. Patterson HD, Thompson R (1971) Recovery of inter-block information when block sizes are unequal. Biometrika 58:545–554
49. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537–2539
50. Petroli CD, Sansaloni CP, Carling J, Steane DA, Vaillancourt RE et al (2012) Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome. PLoS One 7:e44684. doi:10.1371/journal.pone.0044684
51. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:845–959
52. Przyborowski JA, Sulima P, Kuszewska A, Załuski D, Kilian A (2013) Phylogenetic relationships between four Salix L. species based on DArT markers. Int J Mol Sci 14:24113–24125
53. Queller DC, Goodnight KF (1989) Estimating relatedness using molecular markers. Evolution 43:258–275
54. Ribeiro MM, Sanchez L, Ribeiro C, Cunha F, Araújo J, Borralho NMG, Marques C (2011) A case study of Eucalyptus globulus fingerprinting for breeding. Ann For Sci 68:701–714
55. Ritland K (1996) A marker-based method for inferences about quantitative inheritance in natural populations. Evolution 50:1062–1073
56. Rodríguez-Ramilo ST, Toro MA, Caballero A, Fernández J (2007) The accuracy of a heritability estimator using molecular information. Conserv Genet 8:1189–1198
57. Sansaloni CP, Petroli CD, Carling J, Hudson CJ, Steane DA, Myburg AA, Grattapaglia D, Vaillancourt RE, Kilian A (2010) A high high-density Diversity Arrays Technology (DArT) microarray for genome genome-wide genotyping in Eucalyptus. Plant Methods 6:16–26
58. Santure A, Stapley J, Ball AD, Birkhead TR, Burke T, Slate J (2010) On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs. Mol Ecol 19:1439–1451
59. SAS Institute (2002) SAS user’s guide: statistics Version 9.1. SAS Institute, Cary
60. Sillanpää MJ (2011) On statistical methods for estimating heritability in wild populations. Mol Ecol 20:1324–1332
61. Simko I, Eujayl I, van Hintum TJL (2012) Empirical evaluation of DArT, SNP, and SSR marker-systems for genotyping, clustering, and assigning sugar beet hybrid varieties into populations. Plant Sci 184:54–62
62. Stackpole DJ, Vaillancourt RE, Alves A, Rodrigues J, Potts BM (2011) Genetic variation in the chemical components of Eucalyptus globulus wood. G3 Genes Genomes Genet 1:151–159
63. Steane DA, Nicolle D, Sansaloni CP, Petroli CD, Carling J et al (2011) Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping. Mol Phylogenet Evol 59:206–224
64. Telfer EJ, Stovold GT, Li Y, Silva-Junior OB, Grattapaglia DG, Dungey HS (2015) Parentage reconstruction in Eucalyptus nitens using SNPs and microsatellite markers: a comparative analysis of marker data power and robustness. PLoS One 10(7):e0130601. doi:10.1371/journal.pone.0130601
65. Thamarus KA, Groom K, Murrell J, Byrne M, Moran GF (2002) A genetic linkage map for Eucalyptus globulus with candidate loci for wood, fibre, and floral traits. Theor Appl Genet 104:379–387
66. Thomas SC (2005) The estimation of genetic relationships using molecular markers and their efficiency in estimating heritability in natural populations. Philos Trans R Soc B 360:1457–1467
67. Thomas SC, Hill WG (2000) Estimating quantitative genetic parameters using sibships reconstructed from marker data. Genetics 155:1961–1972
68. van de Casteele T, Galbusera P, Matthysen E (2001) A comparison of microsatellite-based pairwise relatedness estimators. Mol Ecol 10:1539–1549
69. Vignal A, Milan D, SanCristobal M, Eggen A (2002) A review on SNP and other types of molecular markers and their use in animal genetics. Genet Sel Evol 34:275–305
70. Villanueva B, Pong-Wong R, Fernández J, Toro MA (2005) Benefits from marker-assisted selection under an additive polygenic genetic model. J Anim Sci 83:1747–1752
71. Wang J (2002) An estimator for pairwise relatedness using molecular markers. Genetics 160:1203–1215
72. Wang J (2006) Informativeness of genetic markers for pairwise relationship and relatedness inference. Theor Popul Biol 70:300–332
73. Wang J (2007) Triadic IBD coefficients and applications to estimating pairwise relatedness. Genet Res 89:135–153
74. Wang J (2011) COANCESTRY: a program for simulating, estimating and analysing relatedness and inbreeding coefficients. Mol Ecol Resour 11:141–145
75. Wenzl P, Carling J, Kudrna D, Jaccoud D, Huttner E, Kleinhofs A, Kilian A (2004) Diversity Arrays Technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci 101:9915–9920
76. Williams PC, Sobering DC (1993) Comparison of commercial near-infrared transmittance and reflectance instruments for analysis of whole grains and seeds. J Near Infrared Spectrosc 1:25–32
77. Wright S (1922) Coefficients of inbreeding and relationship. Am Nat 56:330–338
78. Yu J, Zhang Z, Zhu C, Tabanao DA, Pressoir G, Tuinstra MR, Kresovich S, Todhunter RJ, Buckler ES (2009) Simulation appraisal of the adequacy of number of background markers for relationship estimation in association mapping. Plant Genome 2:63–77
79. Zelener N, Marcucci Poltri SN, Bartoloni N, López C, Hopp HE (2005) Selection strategy for a seedling seed orchard design based on trait selection index and genomic analysis by molecular markers: a case for Eucalyptus dunnii Maiden. Tree Physiol 25:1457–1467