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Estimation of natural outcrossing rate and genetic diversity in Lima bean (Phaseolus lunatus L. var. lunatus) from Brazil using SSR markers: implications for conservation and breeding

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Abstract

Lima bean (Phaseolus lunatus L.) is an important food source in Brazil, especially in the northeast region, where its production and consumption are high. The goals of the present study were to estimate natural outcrossing rates and genetic diversity levels of Lima bean from Brazil, using ten microsatellite loci to obtain information for their conservation and breeding. Fourteen accessions were selected from an experiment in field with open-pollinated and with the presence of pollinating insects. Twelve seeds of each of the 14 selected accessions were grown in screenhouse for tissue harvest and DNA extraction. The multilocus model was used to determine the reproductive system. The outcrossing rate was 38.1 % (tm = 0.381; ts = 0.078), and the results indicated a mixed mating system with a predominance of selfing (1 − tm = 61.9 %). The biparental inbreeding rate was high (t m  − t s  = 0.303) and the multilocus correlated paternity was quite high (r p(m) = 0.889), indicating that the progeny was mostly composed of full sibs. The average effective number of pollen donors per maternal plant (N ep ) was low (1.12), and the fixation index for maternal genotypes (F m ) was 0.945, indicating that most genitors resulted from inbreeding. The studied families presented considerable genetic variability: A = 6.10;  %P = 30; H e  = 0.60 and H o  = 0.077. Total diversity was high (H T = 0.596), and a portion was distributed within families (H S = 0.058). In addition, diversity was higher between families (D ST = 0.538), and genetic differentiation was high (G ST = 0.902). The results presented here can be used in the implementation of Lima bean conservation and breeding programs in Brazil.

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Acknowledgments

The authors thank the Laboratory of Genetic Diversity and Breeding of the Luiz de Queiroz College of Agriculture (ESALQ), where the present study was performed. Thanks are also due to Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq for the financing and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior- CAPES for the scholarship granted to the first author.

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Authors and Affiliations

  1. Genetics Department, Luiz de Queiroz College of Agriculture, University of São Paulo, Avenue Pádua Dias, N. 11, Piracicaba, São Paulo, C.E.P 13418-900, Brazil

    J. S. Penha, J. B. Pinheiro & J. R. Assunção Filho

  2. Plant Technology Department, Campus Ministro Petrônio Portella, Federal University of Piauí, Avenue Universitária, Teresina, Piauí, C.E.P 64.049-550, Brazil

    A. C. A. Lopes & R. L. F. Gomes

  3. Biology Institute, University of Campinas, Avenue Bertrand Russel, University City Zeferino Vaz, Campinas, São Paulo, C.E.P 13083-970, Brazil

    E. A. Silvestre & J. P. G. Viana

  4. Centro de Investigación Científica de Yucatán (CICY), Calle 43 N. 130, Colonia Chuburná de Hidalgo, C. P. 97200, Mérida, Yucatán, Mexico

    J. Martínez-Castillo

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  1. J. S. Penha
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Correspondence to J. S. Penha.

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Penha, J.S., Lopes, A.C.A., Gomes, R.L.F. et al. Estimation of natural outcrossing rate and genetic diversity in Lima bean (Phaseolus lunatus L. var. lunatus) from Brazil using SSR markers: implications for conservation and breeding. Genet Resour Crop Evol 64, 1355–1364 (2017). https://doi.org/10.1007/s10722-016-0441-9

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