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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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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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Correspondence to 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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