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The effects of encoding data in diversity studies and the applicability of the weighting index approach for data analysis from different molecular markers

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Abstract

The use of molecular markers to study genetic diversity represents a breakthrough in this area, because of the increase in polymorphism levels and phenotypic neutrality. Codominant markers, such as microsatellites (SSR), are sensitive enough to distinguish the heterozygotes in genetic studies. Despite this advantage, there are some studies that ignore this feature and work with encoded data because of the simplicity of the evaluation, existence of polyploids and need for the combined analysis of different types of molecular markers. Thus, our study aims to investigate the consequences of these encodings on simulated and real data. In addition, we suggest an alternative analysis for genetic evaluations using different molecular markers. For the simulated data, we proposed the following two scenarios: the first uses SNP markers, and the second SSR markers. For real data, we used the SSR genotyping data from Coffea canephora accessions maintained in the Embrapa Germplasm Collection. The genetic diversity was studied using cluster analysis, the dissimilarity index, and the Bayesian approach implemented in the STRUCTURE software. For the simulated data, we observed a loss of genetic information to the encoded data in both scenarios. The same result was observed in the coffee studies. This loss of information was discussed in the context of a plant-breeding program, and the consequences were weighted to germplasm evaluations and the selection of parents for hybridization. In the studies that involved different types of markers, an alternative to the combined analysis is discussed, where the informativeness, coverage and quality of markers are weighted in the genetic diversity studies.

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Acknowledgments

The authors thank Dr. Romário G. Ferrão, Dr. Abrãao C. Verdin-Filho and Paulo Volpi for giving us additional coffee samples from the Capixaba Research Institute—Technical Assistance and Rural Extension (Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural -Incaper). We also thank Milton M. Santos, João Maria Diocleciano and Gilvan O. Ferro for the technical support at Embrapa Experimental Station, in Rondônia, and, Rejane L. Freitas, Telma Fallieri and Tesfahun A. Sotetaw for the technical support at UFV laboratory, in Viçosa. This work was financially supported by Consórcio Brasileiro de Pesquisa e Desenvolvimento do Café, Agrofuturo—Embrapa and National Council of Scientific and Technological Development (CNPq).

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Authors and Affiliations

  1. BIOAGRO, BIOCAFÉ, Universidade Federal de Viçosa, Viçosa, MG, 3650-000, Brazil

    Luís Felipe V. Ferrão & Eunize Maciel-Zambolim

  2. Embrapa Café, BIOAGRO, BIOCAFÉ, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil

    Eveline T. Caixeta

  3. Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil

    Cosme D. Cruz

  4. Embrapa Rondônia, BR 364, Km 5,5, Zona Rural. Caixa Postal 127, Porto Velho, RO, 76815-000, Brazil

    Flávio F. de Souza

  5. Embrapa Café/Incaper, Rua Afonso Sarlo, 160 Bento Ferreira, Vitória, ES, 29052-010, Brazil

    Maria Amélia G. Ferrão

  6. Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil

    Laércio Zambolim

  7. Departamento de Fitotecnia, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil

    Ney S. Sakiyama

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  1. Luís Felipe V. Ferrão
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Correspondence to Eveline T. Caixeta.

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Ferrão, L.F.V., Caixeta, E.T., Cruz, C.D. et al. The effects of encoding data in diversity studies and the applicability of the weighting index approach for data analysis from different molecular markers. Plant Syst Evol 300, 1649–1661 (2014). https://doi.org/10.1007/s00606-014-0990-3

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  • DOI: https://doi.org/10.1007/s00606-014-0990-3

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