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Genetic analysis across life stages of Metrodorea nigra (Rutaceae) in a population located in an urban landscape of Southeastern Brazil using a new set of microsatellite markers

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Abstract

Metrodorea nigra A. St.-Hil. (Rutaceae) is a submontane tropical tree species that develops preferably in the shade and innermost preserved regions of the semi-deciduous forests of Brazil; as a result, its presence can indicate good levels of conservation. Therefore, it is important to have a set of molecular markers to facilitate genetic studies on this species of tree. The goal of this study was to perform genetic analyses of three generations of one population of M. nigra located in an urban landscape (Ribeirão Preto, São Paulo state) using a new set of microsatellite molecular markers (i.e., SSR—simple sequence repeat). A genomic library was developed from M. nigra, and 11 putative molecular markers were isolated and characterized using samples from different life stages. Seven SSR markers amplified and showed polymorphism across 61 M. nigra samples. A total of 83 alleles were detected, with an average of 11.85 alleles per locus. The genetic diversity index (He) across M. nigra generations was high and ranged from a mean of 0.804 (saplings) to 0.827 (adults). These results show the resilience of M. nigra population located in Bosque Municipal de Ribeirão Preto-SP, Brazil, to adverse effects of fragmentation, and can serve as a base for conservation programs. Furthermore, more than 50 % of the primers were also amplified for the congeneric tree species Metrodorea stipularis. Overall, the new marker set developed here will be useful for studies of population genetics of M. nigra and other key tree species from the Atlantic Rainforest of Brazil.

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Acknowledgments

This work was funded by a grant from São Paulo Research Foundation to A.L.A.M: FAPESP (2013/01265-8). We also acknowledge the support of Pró-Reitoria de Pesquisa of São Paulo University and CAPES-PROEX grants. R.M.M.F. and F.B.A. were supported by a doctoral CAPES and FAPESP fellowships (TTIII-2013/18633-0), respectively. A.L.A.M was supported by research assistantships from CNPq (PD Senior 150277/2009-1, PV 300140/2011-8, PD Senior 150737/2014-9). We thank Dr. Marcela Corbo Guidugli, Dr. Juliana Massimino Feres, Dr. Ronai Ferreira Ramos, Dr. Cláudia Emília Vieira Wiezel, and Dr. Geussa Simone de Freitas for their invaluable technical and scientific support in the first and second effort for the development of the genomic libraries in the Laboratory of Plant Genetics, FMRP/USP/RP; Dr. Alexandre Carvalho Gouvêa (Head of Bosque Zoológico Municipal Ribeirão Preto/SP) for providing authorization to collect sample; Dr. Olga Kotchetkoff-Henriques (Prefeitura Municipal Ribeirão Preto/SP) for sharing part of her extensive knowledge with our research group and for collaborating on the sample collections, Dr. Milton Groppo Júnior (FFCLRP/USP) for providing DNA samples of Rutaceae species used for transferability analysis, and Dr. Maria Helena de Souza Goldman and Dr. Andrea Carla Quiapim (FFCLRP/USP) for their help with DNA sequencing.

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Authors and Affiliations

  1. Laboratório de Genética Vegetal, Departamento de Genética - Bloco B, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP, 14049-900, Brazil

    Ana Lilia Alzate-Marin, Fernando Bonifacio-Anacleto, Rômulo M. de Moraes Filho & Gabriel Pinheiro Machado

  2. Programa de Pós-graduação do Departamento de Genética da Faculdade de Medicina de Ribeirão Preto (FMRP-USP/RP), Ribeirão Preto, Brazil

    Ana Lilia Alzate-Marin & Rômulo M. de Moraes Filho

  3. Depto. Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, Cidade Universitária, São Paulo, SP, CEP 05508-090, Brazil

    Alison Gonçalves Nazareno

Authors
  1. Ana Lilia Alzate-Marin
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  2. Fernando Bonifacio-Anacleto
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  3. Rômulo M. de Moraes Filho
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  4. Gabriel Pinheiro Machado
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  5. Alison Gonçalves Nazareno
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Correspondence to Ana Lilia Alzate-Marin.

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Alzate-Marin, A.L., Bonifacio-Anacleto, F., de Moraes Filho, R.M. et al. Genetic analysis across life stages of Metrodorea nigra (Rutaceae) in a population located in an urban landscape of Southeastern Brazil using a new set of microsatellite markers. Braz. J. Bot 39, 795–799 (2016). https://doi.org/10.1007/s40415-016-0255-1

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  • DOI: https://doi.org/10.1007/s40415-016-0255-1

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