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Polymorphism of Microsatellite Markers in Papaya (Carica papaya L.)

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Abstract

A set of 81 new microsatellite markers for Carica papaya L. previously identified by data mining using freely available sequence information from Genbank were tested for polymorphism using 30 germplasm accessions from the Papaya Germplasm Bank (PGM) at Embrapa Mandioca e Fruticultura Tropical (CNPMF) and 18 landraces. The data were used to estimate pairwise genetic distances between the genotypes. A neighbor-joining based dendrogram was used to define clusters and infer possible genetic structuring of the collection. Most microsatellites were polymorphic (73%), with an observed number of alleles per locus ranging from one to eleven. The levels of observed and expected heterozygosity for 51 polymorphic loci varied from 0.00 to 0.85 and from 0.08 to 0.82, averaging 0.19 and 0.59, respectively. Forty-four percent of microsatellites showed polymorphism information content (PIC) higher than 0.50. The compound microsatellites seem to be more informative than dinucleotide and trinucleotide repeats in average alleles per locus and PIC. Among dinucleotides, AG/TC or GA/CT repeat motifs exhibited more informativeness than TA/AT, GT/CA and TG/AC repeat motifs. The neighbor-joining analysis based on shared allele distance could differentiate all the papaya accessions and landraces as well as differences in their genetic structure. This set of markers will be useful for examining parentage, inbreeding and population structure in papaya.

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Acknowledgements

This work was supported by Embrapa Macroprograma 2, CNPq-Conselho Nacional de Desenvolvimento Científico e Tecnológico (National Counsel of Technological and Scientific Development) and FAPESB–Fundação de Amparo à Pesquisa do Estado da Bahia (Bahia State Research Funding Institution).

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Authors and Affiliations

  1. Embrapa Mandioca e Fruticultura Tropical (CNPMF), Cruz das Almas, BA, Brazil

    Eder Jorge de Oliveira, Vanusia Batista Oliveira Amorim & Jorge Luiz Loyola Dantas

  2. Universidade Federal do Recôncavo da Bahia (UFRB), Cruz das Almas, BA, Brazil

    Edneide Luciana Santiago Matos & Juliana Leles Costa

  3. Embrapa Sede, Brasília, DF, Brazil

    Milene da Silva Castellen

  4. Embrapa Recursos Genéticos e Biotecnologia (CENARGEN), Brasília, DF, Brazil

    Juliano Gomes Pádua

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  1. Eder Jorge de Oliveira
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  2. Vanusia Batista Oliveira Amorim
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  3. Edneide Luciana Santiago Matos
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  4. Juliana Leles Costa
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  6. Juliano Gomes Pádua
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  7. Jorge Luiz Loyola Dantas
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Correspondence to Eder Jorge de Oliveira.

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de Oliveira, E.J., Amorim, V.B.O., Matos, E.L.S. et al. Polymorphism of Microsatellite Markers in Papaya (Carica papaya L.). Plant Mol Biol Rep 28, 519–530 (2010). https://doi.org/10.1007/s11105-010-0180-6

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