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Spatially structured genetic diversity of the Amerindian yam (Dioscorea trifida L.) assessed by SSR and ISSR markers in Southern Brazil

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Abstract

Dioscorea trifida L. (Dioscoreaceae) is among the economically most important cultivated Amerindian yam species, whose origin and domestication are still unresolved issues. In order to estimate the genetic diversity maintained by traditional farmers in Brazil, 53 accessions of D. trifida from 11 municipalities in the states of São Paulo, Santa Catarina, Mato Grosso and Amazonas were characterized on the basis of eight Simple Sequence Repeats (SSR) and 16 Inter Simple Sequence Repeats (ISSR) markers. The level of polymorphism among the accessions was high, 95 % for SSR and 75.8 % for ISSR. The SSR marker showed higher discrimination power among accessions compared to ISSR, with D parameter values of 0.79 and 0.44, respectively. Although SSR and ISSR markers led to dendrograms with different topologies, both separated the accessions into three main groups: I—Ubatuba-SP; II—Iguape-SP and Santa Catarina; and III—Mato Grosso. The accessions from Amazonas State were classified in group II with SSR and in a separate group with ISSR. Bayesian and principal coordinate analyzes conducted with both molecular markers corroborated the classification into three main groups. Higher variation was found within groups in the AMOVA analysis for both markers (66.5 and 60.6 % for ISSR and SSR, respectively), and higher Shannon diversity index was found for group II with SSR. Significant but low correlations were found between genetic and geographic distances (r = 0.08; p = 0.0007 for SSR and r = 0.16; p = 0.0002 for ISSR). Therefore, results from both markers showed a slight spatially structured genetic diversity in D. trifida accessions maintained by small traditional farmers in Brazil.

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Acknowledgments

The authors would like to thank the researchers Nivaldo Peroni, Antônio Henrique dos Santos, Lin Chau Ming, Edson Ferreira da Silva, Marcos V.B.M. Siqueira and Almecina Balbino Ferreira for their assistance in this research and the agriculturists for their contributions in the field collecting and interviews. The authors would also wish to thank FAPESP (process no. 2007/04805-2) and CNPq for the financial support given to this study.

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  1. Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Av. Pádua Dias 11, CP 83, Piracicaba, São Paulo, 13400-970, Brazil

    Wellington F. Nascimento, Jucelene F. Rodrigues & Elizabeth A. Veasey

  2. Department of Biological Sciences, Federal University of São Paulo, Rua Professor Artur Riedel 275, Diadema, São Paulo, 09972-270, Brazil

    Samantha Koehler

  3. Department of Plant Sciences/MS1, Section of Crop and Ecosystem Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616-8780, USA

    Paul Gepts

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  1. Wellington F. Nascimento
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  5. Elizabeth A. Veasey
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Correspondence to Elizabeth A. Veasey.

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Nascimento, W.F., Rodrigues, J.F., Koehler, S. et al. Spatially structured genetic diversity of the Amerindian yam (Dioscorea trifida L.) assessed by SSR and ISSR markers in Southern Brazil. Genet Resour Crop Evol 60, 2405–2420 (2013). https://doi.org/10.1007/s10722-013-0008-y

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