Abstract
Common bean (Phaseolus vulgaris L.), besides being an agricultural product that can be consumed as fresh vegetable, is a significant legume widely being planted in both Turkey and world. Because of having different usage areas, it is being considered as a valuable plant for human nutrition, trade and in many respects. In this study, we aimed at genetically characterization of the local and registered common bean genotypes and population structure of genotype groups belong to these common bean genotypes in Turkey. For this purpose, total 102 common bean genotypes including 93 local genotypes from 8 provinces, 7 cultivars and 2 reference cultivars were analyzed by 13 fluorescent SSR markers. As the result of the study, it was determined that the total SSR allele number was 192 and the average allele number was 14.8. While it was found that there were no synonymous genotypes, the highest heterozygosity rate was determined in three loci. Factorial correspondence analysis partially demonstrated substructure among common bean genotype groups. Structure analysis showed the same results as the Nm values and the Fst values. In the study, it was observed that SSR markers could be easily used in the molecular studies of common bean germplasm. The obtained results will be able to be used at the conservation, utilization of local common bean genetic resources and at the marker assisted selection studyings.
Similar content being viewed by others
REFERENCES
Diaz-Camino, C., Annamalai, P., Sanchez, F., et al., An effective virus-based gene silencing method for functional genomics studies in common bean, Plant Methods, 2011, vol. 7, no. 1, pp. 1—11. https://doi.org/10.1186/1746-4811-7-16
Broughton, W.J., Hernandez, G., Blair, M., et al., Beans (Phaseolus spp.)—model food legumes, Plant and Soil, 2003, vol. 252, no. 1, pp. 55—128. https://doi.org/10.1023/A:1024146710611
Bozoglu, H. and Sozen, O., A sample for biodiversity in Turkey: common bean (Phaseolus vulgaris L.) landraces from Artvin, Afr. J. Biotechnol., 2011, vol. 10, no. 36, pp. 13789—13796. https://doi.org/10.5897/AJB11.942
Türkiye İstatistik Kurumu (Tuik), Bitkisel Üretim İstatistikleri, 2016. http://www.tuik.gov.tr/PreTabloArama.do.
Food and Agriculture Organization of the United Nations (FAO), FAOSTAT data, 2014. http://www.fao.org/faostat/en/#data.
Akdağ, C. and Düzdemir, O., Türkiye kuru fasulye (Phaseolus vulgaris L.) gen kaynaklarının karakterizasyonu: 1. Bazı morfolojik ve fenolojik özellikleri, Gaziosmanpaşa Üniv. Ziraat Fak. Dergisi, 2001, vol. 18, no. 1, pp. 95—100.
Ammar, M.H., Alghamdi, S.S., Migdadi, H.M., et al., Assessment of genetic diversity among faba bean genotypes using agro-morphological and molecular markers, Saudi J. Biol. Sci., 2015, vol. 22, no. 3, pp. 340—350. https://doi.org/10.1016/j.sjbs.2015.02.005
Jose, F.C., Mohammed, M.M.S., Thomas, G., et al., Genetic diversity and conservation of common bean (Phaseolus vulgaris L., Fabaceae) landraces in Nilgiris, Curr. Sci., 2009, vol. 97, no. 2, pp. 227—235.
Gill-Langarica, H.R., Muruaga-Martinez, J.S., Vargas-Vazquez, M.L.P., et al., Genetic diversity analysis of common beans based on molecular markers, Genet. Mol. Biol., 2011, vol. 34, no. 4, pp. 595—605. https://doi.org/10.1590/S1415-47572011005000056
Powell, W., Morgante, M., Andre, C., et al., The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis, Mol. Breed., 1996, vol. 2, no. 3, pp. 225—238. https://doi.org/10.1007/BF00564200
Sarıkamış, G., Yaşar, F., Bakır, M., et al., Genetic characterization of green bean (Phaseolus vulgaris L.) genotypes from eastern Turkey, Genet. Mol. Res., 2009, vol. 8, no. 3, pp. 880—887. https://doi.org/10.4238/vol8-3gmr605
Ince, A.G. and Karaca, M., Genetic variation in common bean landraces efficiently revealed by Td-DAMD-PCR markers, Plant Omics, 2011, vol. 4, no. 4, pp. 220—227.
Khaidizar, M.I., Haliloglu, K., Elkoca, E., et al., Genetic diversity of common bean (Phaseolus vulgaris L.) landraces grown in Northeast Anatolia of Turkey assessed with simple sequence repeat markers, Turk. J. Field Crops, 2012, vol. 17, no. 2, pp. 145—150.
Ulukapı, K. and Onus, A.N., Molecular characterization of some selected landrace green bean (Phaseolus vulgaris L.) genotypes, J. Agric. Sci., 2012, vol. 18, no. 4, pp. 277—286.
Yu, K., Park, S.J., Poysa, V., and Gepts, P., Integration of simple sequence repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus vulgaris L.), J. Hered., 2001, vol. 91, no. 6, pp. 429—434.
Blair, M.W., Giraldo, M.C., Buendia, H.F., et al., Microsatellite marker diversity in common bean (Phaseolus vulgaris L.), Theor. Appl. Genet., 2006, vol. 113, no. 1, pp. 100—109. https://doi.org/10.1007/s00122-006-0276-4
Maras, M., Susnik, S., Meglic, V., and Sustar-Vozlic, J., Characterization and genetic diversity changes in the Slovenian common bean, Cesnjevec landrace, Acta Biol. Cracov Bot., 2006, vol. 48, no. 2, pp. 39—47.
Lefort, F., Lally, M., Thompson, D., and Douglas, G.C., Morphological traits, microsatellite fingerprinting and genetic relatedness of a stand of elite oaks (Q. robur L.) at Tullynally, Ireland, Silvae Genet., 1998, vol. 47, no. 5—6, pp. 257—262.
Gaitan-Solis, E., Duque, M.C., Edwards, K.J., and Tohme, J., Microsatellite repeats in common bean (Phaseolus vulgaris), Crop Sci., 2002, vol. 42, no. 6, pp. 2128—2136. https://doi.org/10.2135/cropsci2002.2128
Loridon, K., McPhee, K., Morin, J., et al., Microsatellite marker polymorphism and mapping in pea (Pisum sativum L.), Theor. Appl. Genet., 2005, vol. 111, no. 6, pp. 1022—1031. https://doi.org/10.1007/s00122-005-0014-3
Wagner, H.W. and Sefc, K.M., IDENTITY 1.0, Vienna: Centre for Applied Genetics, University of Agricultural Sciences, 1999.
Paetkau, D., Calvert, W., Stirling, I., and Strobeck, C., Microsatellite analysis of population structure in Canadian polar bears, Mol. Ecol., 1995, vol. 4, no. 3, pp. 347—354.
Minch, E., Ruiz-Linares, A., Goldstein, D., et al., Microsat (version 1.4d): A Computer Program for Calculating Various Statistics on Microsatellite Allele Data, Stanford, California: University of Stanford, 1995. http://hpgl.stanford.edu/projects/microsat/.
Bowcock., A.M., Ruiz-Linares, A., Tomfohrde, J., et al., High resolution of human evolutionary tress with polymorphic microsatellites, Nature, 1994, vol. 368, no. 6470, pp. 455—457. https://doi.org/10.1038/368455a0
Rohlf, F.J., NTSYS-pc: Numerical Taxonomy and Multivariate Analysis: Version 2.02, Setauket: Exeter Software, 1998.
Sneath, P.H.A. and Sokal, R.R., Numerical Taxonomy: The Principles and Practice of Numerical Classification, San Francisco, 1973.
Belkhir, K., Borsa, P., Goudet, J., et al., GENETIX, logiciel sous WindowsTM pour la genetique des populations, Laboratoire Genome Populations, 1996–1998, Montpellier: CNRS UPR 9060, Universite de Montpellier II. Free program distributed by the authors over the internet. http://ci.nii.ac.jp/naid/10027575711/.
Excoffier, L., Laval, G., and Schneider, S., Arlequin (version 3.0): an integrated software package for population genetics data analysis, Evol. Bioinf. Online, 2005, vol. 1, pp. 47—50.
Rohlf, F.J., NTSYS-pc: Numerical Taxonomy System, Version 2.1, Setauket: Exeter, 2002.
Pritchard, J.K., Stephens, M., and Donnelly, P., Inference of population structure using multilocus genotype data, Genetics, 2000, vol. 155, no. 2, pp. 945—959.
Falush, D., Stephens, M., and Pritchard, J.K., Inference of population structure: extensions to linked loci and correlated allele frequencies, Genetics, 2003, vol. 164, no. 4, pp. 1567—1587.
Corander, J., Marttinen, P., Sir’en, J., and Tang, J., Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations, BMC Bioinformatics, 2008, vol. 9, no. 539, pp. 1—14. https://doi.org/10.1186/1471-2105-9-539
Nei, M., Genetic distance between populations, Am. Nat., 1972, vol. 106, no. 949, pp. 283—292.
Martinez, L.F.G., Evaluación de la diversidad genética en una colección de germoplasma de frijol común (Phaseolus vulgaris L.) de Ruanda (Africa), Ciencias Sci. (Biol.) Dissertation, Bogota: Pontificia Universidad Javeriana, 2008. https://repository.javeriana.edu.co/handle/10554/8743.
Blair, M.W., Gonzalez, L.F., Kimani, P.M., and Butare, L., Genetic diversity, inter-gene pool introgression and nutritional quality of common beans (Phaseolus vulgaris L.) from Central Africa, Theor. Appl. Genet., 2010, vol. 121, no. 2, pp. 237—248. https://doi.org/10.1007/s00122-010-1305-x
Blair, M.W., Diaz, J.M., Hidalgo, R., and Diaz, L.M., Microsatellite characterization of Andean races of common bean (Phaseolus vulgaris L.), Theor. Appl. Genet., 2007, vol. 116, no. 1, pp. 29—43. https://doi.org/10.1007/s00122-007-0644-8
Blair, M.W., Soler, A., and Cortes, A.J., Diversification and population structure in common beans (Phaseolus vulgaris L.), PLoS One, 2012, vol. 7, no. 11. https://doi.org/10.1371/journal.pone.0049488
Diaz, L.M. and Blair, M.W., Race structure within the Mesoamerican gene pool of common bean (Phaseolus vulgaris L.) as determined by microsatellite markers, Theor. Appl. Genet., 2006, vol. 114, no. 4, pp. 143—154. https://doi.org/10.1007/s00122-006-0417-9
Burle, M.L., Fonseca, J.R., Kami, J.A., and Gepts, P., Microsatellite diversity and genetic structure among common bean (Phaseolus vulgaris L.) landraces in Brazil, a secondary center of diversity, Theor. Appl. Genet., 2010, vol. 121, no. 5, pp. 801—813. https://doi.org/10.1007/s00122-010-1350-5
Shabib, J.M., Shehata, A.I., Al-Hazzani, A.A., and Al-Rumaih, M., Assessment the genetic diversity of common bean Phaseolus vulgaris collection by microsatellite SSR markers, Afr. J. Agric. Res., 2013, vol. 8, no. 40, pp. 5032—5046. https://doi.org/10.5897/AJAR12.1013
Cabral, P.D.S., Soares, T.C.B., Lima, A.B.P., et al., Genetic diversity in local and commercial dry bean (Phaseolus vulgaris L.) genotypes based on microsatellite markers, Genet. Mol. Res., 2011, vol. 10, no. 1, pp. 140—149. https://doi.org/10.4238/vol10-1gmr993
Ceylan, A., Öcal, N., and Akbulut, M., Genetic diversity among the Turkish common bean cultivars (Phaseolus vulgaris L.) as assessed by SRAP, POGP and cpSSR markers, Biochem. Syst. Ecol., 2014, vol. 54, pp. 219—229. https://doi.org/10.1016/j.bse.2014.01.014
Okii, D., Tukamuhabwa, P., Kami, J., et al., The genetic diversity and population structure of common bean (Phaseolus vulgaris L.) germplasm in Uganda, Afr. J. Biotechnol., 2014, vol. 13, no. 29, pp. 2935—2949. https://doi.org/10.5897/AJB2014.13916
Asfaw, A., Blair, M.W., and Almekinders, C., Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) landraces from the East African Highlands, Theor. Appl. Genet., 2009, vol. 120, no. 1, pp. 1—12. https://doi.org/10.1007/s00122-009-1154-7
Madakbaş, S.Y., Sarıkamış, G., Başak, H., et al., Genetic characterization of green bean (Phaseolus vulgaris L.) accessions from Turkey with SCAR and SSR markers, Biochem. Genet., 2016, vol. 54, no. 4, pp. 495—505. https://doi.org/10.1007/s10528-016-9737-x
Author information
Authors and Affiliations
Corresponding author
Additional information
The article is published in the original.
Rights and permissions
About this article
Cite this article
Bilir, Ö., Özmen, C.Y., Özcan, S. et al. Genetic Analysis of Turkey Common Bean (Phaseolus vulgaris L.) Genotypes by Simple Sequence Repeats Markers. Russ J Genet 55, 61–70 (2019). https://doi.org/10.1134/S1022795419010034
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S1022795419010034