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Potential of SNP markers for the characterization of Brazilian cassava germplasm

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High-throughput markers, such as SNPs, along with different methodologies were used to evaluate the applicability of the Bayesian approach and the multivariate analysis in structuring the genetic diversity in cassavas.

Abstract

The objective of the present work was to evaluate the diversity and genetic structure of the largest cassava germplasm bank in Brazil. Complementary methodological approaches such as discriminant analysis of principal components (DAPC), Bayesian analysis and molecular analysis of variance (AMOVA) were used to understand the structure and diversity of 1,280 accessions genotyped using 402 single nucleotide polymorphism markers. The genetic diversity (0.327) and the average observed heterozygosity (0.322) were high considering the bi-allelic markers. In terms of population, the presence of a complex genetic structure was observed indicating the formation of 30 clusters by DAPC and 34 clusters by Bayesian analysis. Both methodologies presented difficulties and controversies in terms of the allocation of some accessions to specific clusters. However, the clusters suggested by the DAPC analysis seemed to be more consistent for presenting higher probability of allocation of the accessions within the clusters. Prior information related to breeding patterns and geographic origins of the accessions were not sufficient for providing clear differentiation between the clusters according to the AMOVA analysis. In contrast, the F ST was maximized when considering the clusters suggested by the Bayesian and DAPC analyses. The high frequency of germplasm exchange between producers and the subsequent alteration of the name of the same material may be one of the causes of the low association between genetic diversity and geographic origin. The results of this study may benefit cassava germplasm conservation programs, and contribute to the maximization of genetic gains in breeding programs.

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Acknowledgments

The authors would like to thank Empresa Brasileira de Pesquisa Agropecuária (Embrapa) for the financial support. The authors gratefully acknowledge the support through fellowships from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).

Conflict of interest

The authors declare that they have no conflicts of interest.

Ethical standards

We declare that the experiments comply with the current Brazilian laws in which they were performed. In addition, we declare that the authors do not have any competing financial interests, including funding support, employment and personal financial interests.

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Authors and Affiliations

  1. Embrapa Cassava and Fruits, Rua da Embrapa s/n, Cruz das Almas, BA, Brazil

    Eder Jorge de Oliveira, Cláudia Fortes Ferreira, Vanderlei da Silva Santos & Onildo Nunes de Jesus

  2. Federal University of Recôncavo da Bahia, Cruz das Almas Campus, Cruz das Almas, BA, Brazil

    Gilmara Alvarenga Fachardo Oliveira & Maiane Suzarte da Silva

Authors
  1. Eder Jorge de Oliveira
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  2. Cláudia Fortes Ferreira
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  3. Vanderlei da Silva Santos
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  4. Onildo Nunes de Jesus
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  5. Gilmara Alvarenga Fachardo Oliveira
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  6. Maiane Suzarte da Silva
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Correspondence to Eder Jorge de Oliveira.

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Communicated by A. J. Bervillé.

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de Oliveira, E.J., Ferreira, C.F., da Silva Santos, V. et al. Potential of SNP markers for the characterization of Brazilian cassava germplasm. Theor Appl Genet 127, 1423–1440 (2014). https://doi.org/10.1007/s00122-014-2309-8

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