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A case study of Eucalyptus globulus fingerprinting for breeding

  • Original Paper
  • Published:
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Abstract

• Introduction

Tree genetic improvement programs usually lack, in general, pedigree information. Since molecular markers can be used to estimate the level of genetic similarity between individuals, we genotyped a sample of a Portuguese Eucalyptus globulus breeding population—a reference population of 125 individuals—with 16 microsatellites (SSR).

• Materials and methods

Using genotypes from the reference population, we developed a simulation approach to recurrently generate (105 replicates) virtual offspring with different relatedness: selfed, half-sib, full-sib and unrelated individuals. Four commonly used pairwise similarity coefficients were tested on these groups of simulated offspring. Significant deficits in heterozygosity were found for some markers in the reference population, likely due to the presence of null alleles. Therefore, the impact of null alleles in the relatedness estimates was also studied. We conservatively assumed that all homozygotes in the reference population were carriers of null alleles.

• Results

All estimators were unbiased, but one of them was better adjusted to our data set, even when null alleles were considered. The estimator’s accuracy and precision were validated with individuals of known pedigree obtained from controlled crosses made with the same reference population’s parents. Additionally, a clustering algorithm based on the estimator of choice was constructed, in order to infer the relatedness among 24 E. globulus elite individuals. We detected four putatively related elite individuals’ pairs (six pairs considering the presence of null alleles).

• Conclusions

This work demonstrates that in the absence of pedigree information, our approach could be useful to identify relatives and minimize consanguinity in breeding populations.

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Notes

  1. Appendix is available online only at www.asf-journal.org.

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Authors and Affiliations

  1. Departamento de Recursos Naturais e Desenvolvimento Sustentável, Escola Superior Agrária do Instituto Politécnico de Castelo Branco, 6001-909, Castelo Branco, Portugal

    Maria Margarida Ribeiro

  2. INRA Centre d’Orléans, Unité Amélioration, Génétique et Physiologie Forestière, 45166, Olivet, France

    Leopoldo Sanchez

  3. Centro de Biologia Ambiental, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa Edifício C2, 1749-016, Lisboa, Portugal

    Carla Ribeiro

  4. RAIZ-Direcção de Investigação Florestal, Herdade de Espirra, 2985-270, Pegões, Portugal

    Fátima Cunha, José Araújo & Cristina Marques

  5. BorralhoIDea, Urbanização S. Francisco, 18, 2070-220, Cartaxo, Portugal

    Nuno M. G. Borralho

  6. Centro de Estudos Florestais, Universidade Técnica de Lisboa, Instituto Superior de Agronomia, 1349-017, Tapada da Ajuda, Lisboa

    Nuno M. G. Borralho

Authors
  1. Maria Margarida Ribeiro
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  2. Leopoldo Sanchez
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  3. Carla Ribeiro
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  4. Fátima Cunha
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  5. José Araújo
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  6. Nuno M. G. Borralho
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  7. Cristina Marques
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Corresponding author

Correspondence to Maria Margarida Ribeiro.

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Handling Editor: Christophe Plomion

Electronic supplementary material

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Appendix 1

Description of the 16 SSR loci used in this study. SSR grou** (1 to 3 according to different polymerase chain reaction (PCR) conditions, as detailed in Section 2), locus name, range size in base pairs (bp), type of repeat and linkage group (LG) location. The linkage groups to which markers were assigned are based on genetic linkage map data of an E. globulus pedigree (unpublished results) and the E. grandis × E. urophylla consensus map of Brondani et al. (2006). (DOC 62 kb)

Appendix 2

Allele frequency distributions of loci EMBRA23 and EMCRC5. The 21 alleles were ranked from the more to the less frequent ones. Frequency ranking is different in the two loci, i.e. the most frequent allele in one locus is not the most frequent allele in the other. (DOC 46 kb)

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Ribeiro, M.M., Sanchez, L., Ribeiro, C. et al. A case study of Eucalyptus globulus fingerprinting for breeding. Annals of Forest Science 68, 701–714 (2011). https://doi.org/10.1007/s13595-011-0087-x

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  • DOI: https://doi.org/10.1007/s13595-011-0087-x

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