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

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Abstract

Simple sequence repeats (SSR) are the most widely used molecular markers for relatedness inference due to their multi-allelic nature and high informativeness. However, there is a growing trend toward using high-throughput and inter-specific transferable single-nucleotide polymorphisms (SNP) and Diversity Arrays Technology (DArT) in forest genetics owing to their wide genome coverage. We compared the efficiency of 15 SSRs, 181 SNPs and 2816 DArTs to estimate the relatedness coefficients, and their effects on genetic parameters’ precision, in a relatively small data set of an open-pollinated progeny trial of Eucalyptus grandis (Hill ex Maiden) with limited relationship from the pedigree. Both simulations and real data of Eucalyptus grandis were used to study the statistical performance of three relatedness estimators based on co-dominant markers. Relatedness estimates in pairs of individuals belonging to the same family (related) were higher for DArTs than for SNPs and SSRs. DArTs performed better compared to SSRs and SNPs in estimated relatedness coefficients in pairs of individuals belonging to different families (unrelated) and showed higher ability to discriminate unrelated from related individuals. The likelihood-based estimator exhibited the lowest root mean squared error (RMSE); however, the differences in RMSE among the three estimators studied were small. For the growth traits, heritability estimates based on SNPs yielded, on average, smaller standard errors compared to those based on SSRs and DArTs. Estimated relatedness in the realized relationship matrix and heritabilities can be accurately inferred from co-dominant or sufficiently dense dominant markers in a relatively small E. grandis data set with shallow pedigree.

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References

  • 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

    Article  CAS  Google Scholar 

  • Anderson EC, Garza JC (2006) The power of single nucleotide polymorphisms for large-scale parentage inference. Genetics 172:2567–2582

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Blouin MS (2003) DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends Ecol Evol 18:503–511

    Article  Google Scholar 

  • Blouin MS, Parsons M, Lacaille V, Lotz S (1996) Use of microsatellite loci to classify individuals by relatedness. Mol Ecol 5:393–401

    Article  CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • Bush D, Thumma B (2013) Characterising a Eucalyptus cladocalyx breeding population using SNP markers. Tree Genet Genomes 9:741–752

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Cappa EP, Pathauer PS, Lopez GA (2010) Provenance variation and genetic parameters of Eucalyptus viminalis in Argentina. Tree Genet Genomes 6:981–994

    Article  Google Scholar 

  • Chapuis MP, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631

    Article  CAS  PubMed  Google Scholar 

  • Cornelius JP (1994) Heritabilities and additive genetic coefficients of variation in forest trees. Can J For Res 24:372–379

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • Dakin EE, Avise JC (2004) Microsatellite null alleles in parentage analysis. Heredity 93:504–509

    Article  CAS  PubMed  Google Scholar 

  • Eldridge K, Davidson J, Hardwood C, van Wyk G (1993) Eucalyptus domestication and breeding. Oxford University Press, New York

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • Gilmour AR, Gogel BJ, Cullis BR, Thompson R (2006) ASReml user guide release 2.0. VSN International Ltd, Hemel Hempstead

    Google Scholar 

  • 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

    Google Scholar 

  • Glaubitz JC, Rhodes OE Jr, Dewoody JD (2003) Prospects for inferring pairwise relationships with single nucleotide polymorphisms. Mol Ecol 12:1039–1047

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    Article  Google Scholar 

  • Hayes BJ, Goddard ME (2008) Technical note: prediction of breeding values using marker derived relationship matrices. J Anim Sci 86:2089–2092

    Article  CAS  PubMed  Google Scholar 

  • Henderson CR (1984) Applications of linear models in animal breeding. University of Guelph, Guelph

    Google Scholar 

  • Higham NJ (2002) Computing the nearest correlation matrix—a problem from finance. IMA J Numer Anal 22:329–343

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Hoisington D, Khairallah M, Gonzalez-De-Leon D (1994) Laboratory protocols: CIMMYT. Applied molecular genetics laboratory, 3rd edn. CIMMYT, D.F., Mexico 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • Kumar S, Richardson TE (2005) Inferring relatedness and heritability using molecular markers in Radiata pine. Mol Breed 15(1):55–64

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Li CC, Weeks DE, Chakravarti A (1993) Similarity of DNA fingerprints due to chance and relatedness. Hum Hered 43:45–52

    Article  CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • Lynch M, Ritland K (1999) Estimation of pairwise relatedness with molecular markers. Genetics 152:1753–1766

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sinauer Associates, Sunderland

    Google Scholar 

  • Marcó M, White TL (2002) Genetic parameter estimates and genetic gains for Eucalyptus grandis and E. dunnii in Argentina. For Genet 9:205–215

    Google Scholar 

  • Marshall TC, Slate J, Kruuk LEB, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 7:639–655

    Article  CAS  PubMed  Google Scholar 

  • Milligan BG (2003) Maximum-likelihood estimation of relatedness. Genetics 163:1153–1167

    PubMed  PubMed Central  Google Scholar 

  • Mousseau TA, Ritland K, Heath DD (1998) A novel method for estimating heritability using molecular markers. Heredity 80:218–224

    Article  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • Patterson HD, Thompson R (1971) Recovery of inter-block information when block sizes are unequal. Biometrika 58:545–554

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:845–959

    Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • Queller DC, Goodnight KF (1989) Estimating relatedness using molecular markers. Evolution 43:258–275

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Ritland K (1996) A marker-based method for inferences about quantitative inheritance in natural populations. Evolution 50:1062–1073

    Article  Google Scholar 

  • Rodríguez-Ramilo ST, Toro MA, Caballero A, Fernández J (2007) The accuracy of a heritability estimator using molecular information. Conserv Genet 8:1189–1198

    Article  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • SAS Institute (2002) SAS user’s guide: statistics Version 9.1. SAS Institute, Cary

    Google Scholar 

  • Sillanpää MJ (2011) On statistical methods for estimating heritability in wild populations. Mol Ecol 20:1324–1332

    Article  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Thomas SC, Hill WG (2000) Estimating quantitative genetic parameters using sibships reconstructed from marker data. Genetics 155:1961–1972

    CAS  PubMed  PubMed Central  Google Scholar 

  • van de Casteele T, Galbusera P, Matthysen E (2001) A comparison of microsatellite-based pairwise relatedness estimators. Mol Ecol 10:1539–1549

    Article  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Wang J (2002) An estimator for pairwise relatedness using molecular markers. Genetics 160:1203–1215

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang J (2006) Informativeness of genetic markers for pairwise relationship and relatedness inference. Theor Popul Biol 70:300–332

    Article  PubMed  Google Scholar 

  • Wang J (2007) Triadic IBD coefficients and applications to estimating pairwise relatedness. Genet Res 89:135–153

    Article  CAS  PubMed  Google Scholar 

  • Wang J (2011) COANCESTRY: a program for simulating, estimating and analysing relatedness and inbreeding coefficients. Mol Ecol Resour 11:141–145

    Article  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Wright S (1922) Coefficients of inbreeding and relationship. Am Nat 56:330–338

    Article  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The authors are grateful to the company Forestal Las Marias for providing the land for the test and logistical support. The authors also thank Leonel Harrand, Javier Oberschelp, Mauro Surenciski and Juan López who assisted with field work and data collection. The contribution of José Rodrigues and colleagues at the IICT lab in Portugal, in the development of specific NIR models and subsequent processing and spectral evaluation of wood samples for the wood quality traits used in this study is also greatly acknowledged. We also thank to Cintia Acuña, Andrea Puebla and María Carolina Martínez for their help with the DNA extraction and SNPs analysis, and Dario Grattapaglia, Carolina Sansaloni, Cesar Petroli and Danielle Paiva for their work for generation of DArTs and SNPs data. Finally, we would like to thank the helpful suggestions and support given by Yousry El-Kassaby and Esteban Hopp during this work, and Leopoldo Sanchez and two anonymous referees for their insightful comments on early version of this manuscript.

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  1. Jaroslav Klápště

    Present address: Scion (New Zealand Forest Research Institute Ltd.), Private bag 3020, 49 Sala Street, Rotorua, 3046, New Zealand

Authors and Affiliations

  1. Bosques Cultivados, Instituto de Recursos Biológicos, Centro de Investigación en Recursos Naturales, Instituto Nacional de Tecnología Agropecuaria (INTA), De Los Reseros y Dr. Nicolás Repetto s/n, 1686, Hurlingham, Buenos Aires, Argentina

    Eduardo P. Cappa

  2. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina

    Eduardo P. Cappa

  3. Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada

    Jaroslav Klápště

  4. Department of Genetics and Physiology of Forest Trees, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Praha 6, Czech Republic

    Jaroslav Klápště

  5. Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria (INTA), De Los Reseros y Dr. Nicolás Repetto s/n, 1686, Hurlingham, Buenos Aires, Argentina

    Martín N. Garcia, Pamela V. Villalba & Susana N. Marcucci Poltri

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  1. Eduardo P. Cappa
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Cappa, E.P., Klápště, J., Garcia, M.N. et al. SSRs, SNPs and DArTs comparison on estimation of relatedness and genetic parameters’ precision from a small half-sib sample population of Eucalyptus grandis . Mol Breeding 36, 97 (2016). https://doi.org/10.1007/s11032-016-0522-7

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