Hostname: page-component-797576ffbb-vjhkx Total loading time: 0 Render date: 2023-12-10T18:30:39.745Z Has data issue: false Feature Flags: { "corePageComponentGetUserInfoFromSharedSession": true, "coreDisableEcommerce": false, "useRatesEcommerce": true } hasContentIssue false

Assessment of genetic diversity and population structure of Indian common bean accessions using microsatellite markers

Published online by Cambridge University Press:  29 August 2023

Yogita Bisht
G. B. Pant National Institute of Himalayan Environment, Garhwal Regional Centre, Srinagar-246174, Uttarakhand, India
Himanshu Sharma
Agri-Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, Punjab-140306, India
Arun K. Jugran*
G. B. Pant National Institute of Himalayan Environment, Garhwal Regional Centre, Srinagar-246174, Uttarakhand, India
Ajay Veer Singh
G. B. Pant University of Agriculture & Technology, Pantnagar, Uttarakhand, India
Pankaj K. Mishra
ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, India
Navneet Pareek
G. B. Pant University of Agriculture & Technology, Pantnagar, Uttarakhand, India
Corresponding author: Arun K. Jugran; Email:;


Common bean (Phaseolus vulgaris L.) is an important crop of family Fabaceae used as a potential source of proteins, fibres and minerals. Thus, characterization of existing germplasm is useful for improvement and conservation. The Indian Himalayan Region harbours plentiful varieties of common bean, but it is nearly unexplored till date. In the present study, physical and genetic diversity of common bean was examined. Fifteen newly designed chloroplast microsatellite (cpSSR) markers were used to assess genetic diversity and population structure in 119 common bean individuals from 20 diverse accessions gathered from Uttarakhand, India. Significantly, positive (p< 0.05) relationship of seed weight was found with seed length (r = 0.813), seed width (r = 0.692) and seed length- width ratio (r = 0.694) using Pearson correlation analysis. A total of 20 alleles were identified using eight cpSSR markers. Mean number of alleles per locus (Na = 1.55), effective allele number (Ne = 1.370), expected heterozygosity (He = 0.213), average polymorphic loci (10.9) and Shannon information index (I = 0.313) were estimated based on cpSSR data. Maximum genetic diversity (He) was recorded in the AKJ/KK/DP/Jhalla/23 accession and minimum in the AKJ/YB/PS/Supi/43 accession. Bayesian-based STRUCTURE evaluation using cpSSR-based information partitioned 20 accessions into two distinct clusters which were also supported by neighbor-joining cluster analysis. These cpSSR markers also demonstrated transferability among other members like Vigna radiata, Macrotyloma uniflorum, Glycine max, Vigna mungo of Fabaceae family, therefore can be used to monitor their genetic heterogeneity. The findings from the study might be valuable to identify elite common bean accessions for production, conservation and future breeding programmes.

Research Article
Copyright © The Author(s), 2023. Published by Cambridge University Press on behalf of National Institute of Agricultural Botany

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)


Anderson, JA (1993) Optimizing parental selection for genetic linkage map. Genome 36, 181186.10.1139/g93-024CrossRefGoogle Scholar
Angioi, SA, Rau, D, Attene, G, Nanni, L, Bellucci, E, Logozzo, G, Negri, V, Zeuli, SPL and Papa, R (2010) Beans in Europe: origin and structure of the European landraces of Phaseolus vulgaris L. Theoretical and Applied Genetics 121, 829843.10.1007/s00122-010-1353-2CrossRefGoogle ScholarPubMed
Asfaw, A, Blair, MW and Almekinders, C (2009) Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) landraces from the East African highlands. Theoretical and Applied Genetics 120, 112.10.1007/s00122-009-1154-7CrossRefGoogle ScholarPubMed
Avican, O and Bilgen, BB (2022) Investigation of the genetic structure of some common bean (Phaseolus vulgaris L.) commercial varieties and genotypes used as a genitor with SSR and SNP markers. Genetic Resources and Crop Evolution 69, 27552768.10.1007/s10722-022-01396-5CrossRefGoogle Scholar
Bashir, H, Bashir, Z, Mahajan, R, Nazir, M, Mir, RA, Nehvi, FA and Zargar, SM (2020) Molecular characterization and insights into the origin of common bean (Phaseolus vulgaris L.) landraces of north western Himalayas. Nucleus 63, 271279.10.1007/s13237-020-00323-2CrossRefGoogle Scholar
Bilir, Ö, Özmen, CY, Özcan, S and Kibar, U (2019) Genetic analysis of Turkey common bean (Phaseolus vulgaris L.) genotypes by simple sequence repeats markers. Russian Journal of Genetics 55, 6170.10.1134/S1022795419010034CrossRefGoogle Scholar
Bisen, A, Khare, D, Nair, P and Tripathi, N (2015) SSR analysis of 38 genotypes of soybean (Glycine max (L.) Merr.) genetic diversity in India. Physiology and Molecular Biology of Plants 21, 109115.10.1007/s12298-014-0269-8CrossRefGoogle ScholarPubMed
Broughton, WJ, Hernandez, G, Blair, MW, Beebe, SE, Gepts, P and Vanderleyden, J (2003) Beans (Phaseolus spp.) – model food legumes. Plant and Soil 252, 55128.10.1023/A:1024146710611CrossRefGoogle Scholar
Cabral, PDS, Soares, TCB, Lima, ABP, Miranda, FD, Souza, FB and Gonçalves, LSA (2011) Genetic diversity in local and commercial dry bean (Phaseolus vulgaris) accessions based on microsatellite markers. Genetics and Molecular Research 10, 140149.CrossRefGoogle ScholarPubMed
Catarcione, G, Paolacci, AR, Alicandri, E, Gramiccia, E, Taviani, P, Rea, R, Costanza, MT, De Lorenzis, G, Puccio, G, Mercati, F and Ciaffi, M (2023) Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) landraces in the Lazio Region of Italy. Plants 12, 744.10.3390/plants12040744CrossRefGoogle ScholarPubMed
Celmeli, T, Sari, H, Canci, H, Sari, D, Adak, A, Eker, T and Toker, C (2018) The nutritional content of common bean (Phaseolus vulgaris L.) landraces in comparison to modern varieties. Agronomy 8, 166.10.3390/agronomy8090166CrossRefGoogle Scholar
Chacón-Sánchez, MI, Martínez-Castillo, J, Duitama, J and Debouck, DG (2021) Gene flow in Phaseolus beans and its role as a plausible driver of ecological fitness and expansion of cultigens. Frontiers in Ecology and Evolution 9, 618709.10.3389/fevo.2021.618709CrossRefGoogle Scholar
Chahota, RK, Shikha, D, Rana, M, Sharma, V, Nag, A, Sharma, TR, Rana, JC, Hirakawa, H and Isobe, S (2017) Development and characterization of SSR markers to study genetic diversity and population structure of horsegram germplasm (Macrotyloma uniflorum). Plant Molecular Biology Reporter 35, 550561.10.1007/s11105-017-1045-zCrossRefGoogle Scholar
Choudhary, N, Hamid, A, Singh, B, Khandy, I, Sofi, PA, Bhat, MA and Mir, RR (2017) Insight into the origin of common bean (Phaseolus vulgaris L.) grown in the state of Jammu and Kashmir of north-western Himalayas. Genetic Resources and Crop Evolution 65, 963977.10.1007/s10722-017-0588-zCrossRefGoogle Scholar
Dar, FA, Verma, S and Rehman, RU (2016) Genetic diversity assessment of Phaseolus vulgaris L. in two Himalayan districts of India. Proceedings of the National Academy of Sciences, India, Section B Biological Sciences 88, 165173.10.1007/s40011-016-0742-yCrossRefGoogle Scholar
Delfini, J, Moda-Cirino, V, Neto, JS, Ruas, PM, Sant'Ana, GC, Gepts, P and Gonçalves, LSA (2021) Population structure, genetic diversity and genomic selection signatures among a Brazilian P. vulgaris germplasm. Scientific Reports 11, 2964.10.1038/s41598-021-82437-4CrossRefGoogle Scholar
Desiderio, F, Bitocchi, E, Bellucci, E, Rau, D, Rodriguez, M, Attene, G, Papa, R and Nanni, L (2013) Chloroplast microsatellite diversity in Phaseolus vulgaris. Frontiers of Plant Science 3, 312.10.3389/fpls.2012.00312CrossRefGoogle ScholarPubMed
Dutta, SK, Singh, SB, Chatterjee, D, Boopathi, T, Singh, AR and Saha, S (2016) Morphological and genetic diversity of pole type common bean (Phaseolus vulgaris L.) landraces of Mizoram (India). Indian Journal of Biotechnology 15, 550559.Google Scholar
Earl, DA and VonHoldt, BM (2012) Structure Harvester: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4, 359361.10.1007/s12686-011-9548-7CrossRefGoogle Scholar
Eliades, NG and Eliades, DG (2009) HAPLOTYPE ANALYSIS: Software for Analysis of Haplotype Data. Goettingen: Forest Goettingen (Germany): Genetics and Forest Tree Breeding, Georg-August University.Google Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14, 26112620.10.1111/j.1365-294X.2005.02553.xCrossRefGoogle ScholarPubMed
FAO (2020) FAOSTAT: FAO Statistical Databases. Available at Scholar
Felsenstein, J (1995) PHYLIP – Phylogeny Inference Package (Version 3.68). Seattle, USA: University of Washington.Google Scholar
Flores-Sosa, AR, Aquino-Bolaños, EN, Cardador-Martínez, A, Chávez-Servia, JL, Vera-Guzmán, AM, Carrillo-Rodríguez, JC and Jiménez, JEA (2020) Variation in protein and amino acids content among landraces of common bean (Phaseolus vulgaris L.). Emirates Journal of Food and Agriculture 32, 750760.10.9755/ejfa.2020.v32.i10.2175CrossRefGoogle Scholar
Gill-Langarica, HR, Muruaga-Martínez, JS, Vargas-Vázquez, MLP, Rosales-Serna, R and Mayek-Pérez, N (2011) Genetic diversity analysis of common beans based on molecular markers. Genetics and Molecular Biology 34, 595605.10.1590/S1415-47572011005000056CrossRefGoogle ScholarPubMed
Gioia, T, Logozzo, G, Marzario, S, Spagnoletti Zeuli, P and Gepts, P (2019) Evolution of SSR diversity from wild types to US advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris). PLoS ONE 14, e0211342.CrossRefGoogle ScholarPubMed
Głowacka, A, Gruszecki, T, Szostak, B and Michałek, S (2019) The response of common bean to sulphur and molybdenum fertilization. International Journal of Agronomy 2, 18.10.1155/2019/3830712CrossRefGoogle Scholar
Guo, X, Castillo-Ramirez, S, Gonzalez, V, Bustos, P, Fernandez-Vazquez, JL, Santamaria, RI, Arellano, J, Cevallos, MA and Davila, G (2007) Rapid evolutionary change of common bean (Phaseolus vulgaris L.) plastome, and the genomic diversification of legume chloroplasts. BMC Genomics 8, 228.CrossRefGoogle ScholarPubMed
Gupta, N, Zargar, SM, Salgotra, RK, Sharma, MK, Gupta, SK and Rai, GK (2019) Variability estimates for yield determining characters in common bean (Phaseolus vulgaris L.). International Journal of Current Microbiology and Applied Science 8, 4757.10.20546/ijcmas.2019.808.006CrossRefGoogle Scholar
Gupta, N, Zargar, SM, Singh, R, Nazir, M, Mahajan, R and Salgotra, RK (2020) Marker association study of yield attributing traits in common bean (Phaseolus vulgaris L.). Molecular Biology Reports 47, 67696783.10.1007/s11033-020-05735-6CrossRefGoogle ScholarPubMed
Hao, J, Song, F, Cui, X, Hua, Z, Zhu, T, Wu, Z, Wang, J, Chen, M and Zhang, X (2023) Genetic diversity and population structure of snap bean (Phaseolus vulgaris L.) from China revealed by microsatellite markers. Crop Science 63, 13641380.CrossRefGoogle Scholar
Hegay, S, Geleta, M, Bryngelsson, T, Gustavsson, L, Hovmalm, HP and Ortiz, R (2012) Comparing genetic diversity and population structure of common beans grown in Kyrgyzstan using microsatellites. Scientific Journal of Crop Science 1, 6375.Google Scholar
Jugran, AK, Bhatt, ID, Rawal, RS, Nandi, SK and Pande, V (2013a) Patterns of morphological and genetic diversity of Valeriana jatamansi Jones in different habitats and altitudinal range of West Himalaya, India. Flora-Morphology, Distribution, Functional Ecology of Plants 208, 1321.10.1016/j.flora.2012.12.003CrossRefGoogle Scholar
Jugran, AK, Rawat, S, Dauthal, P, Mondal, S, Bhatt, ID and Rawal, RS (2013b) Association of ISSR markers with some biochemical traits of Valeriana jatamansi Jones. Industrial Crops and Products 44, 671676.CrossRefGoogle Scholar
Kumar, J, Vijeshwar, V, Shahi, AK, Qazi, GN and Balyan, HS (2006) Development of simple sequence repeat markers in Cymbopogon species. Planta Medica 73, 262266.CrossRefGoogle Scholar
Kumar, A, Singh, PK, Rai, N, Bhaskar, GP and Datta, D (2013) Genetic diversity of French bean (Phaseolus vulgaris L.) genotypes on the basis of morphological traits and molecular markers. Indian Journal of Biotechnology 13, 207213.Google Scholar
Lima, ER, Santiago, AS, Araújo, AP and Teixeira, MG (2005) Effects of the size of sown seed on growth and yield of common bean cultivars of different seed sizes. Brazilian Journal of Plant Physiology 17, 273281.CrossRefGoogle Scholar
Mahajan, R, Zargar, SM, Singh, R, Salgotra, RK, Farhat, S and Sonah, H (2017) Population structure analysis and selection of core set among common bean genotypes from Jammu and Kashmir, India. Applied Biochemistry and Biotechnology 182, 1628.10.1007/s12010-016-2307-1CrossRefGoogle ScholarPubMed
Matondo, NK, Yao, KN, Kyalo, M, Skilton, R, Nkongolo, KK, Mumba, D, Tshilenge, DK and Lubobo, AK (2017) Assessment of the genetic diversity and the relationship among common bean (Phaseolus vulgaris L.) accessions from DR-Congo germplasm using SSR molecular markers. International Journal of Current Research 9, 4781447821.Google Scholar
Mazhar, KA, Sayinci, B, Elkoca, E, Öztürk, İ and Özmen, T (2013) Seed size and shape analysis of registered common bean (Phaseolus vulgaris L.) cultivars in Turkey using digital photography. Journal of Agricultural Sciences 19, 219234.Google Scholar
Mercati, F, Leone, M, Lupini, A, Sorgonà, A, Bacchi, M, Abenavoli, MR and Sunseri, F (2013) Genetic diversity and population structure of a common bean (Phaseolus vulgaris L.) collection from Calabria (Italy). Genetic Resources and Crop Evolution 60, 839852.CrossRefGoogle Scholar
Mina-Vargas, AM, McKeown, PC, Flanagan, NS, Debouck, DG, Kilian, A, Hodkinson, TR and Spillane, C (2016) Origin of year-long bean (Phaseolus dumosus Macfady, Fabaceae) from reticulated hybridization events between multiple Phaseolus species. Annals of Botany 118, 957969.10.1093/aob/mcw138CrossRefGoogle ScholarPubMed
Mir, RR, Choudhary, N, Bawa, V, Jan, S, Singh, B, Bhat, MA, Paliwal, R, Kumar, A, Chitikineni, A, Thudi, M and Varhney, RK (2021) Allelic diversity, structural analysis, and genome-wide association study (GWAS) for yield and related traits using unexplored common bean (Phaseolus vulgaris L.) germplasm from Western Himalayas. Frontiers in Genetics 11, 609603.CrossRefGoogle ScholarPubMed
Moraes, RM and Angelucci, E (1971) Chemical composition and amino acid contents of Brazilian beans (Phaseolus vulgaris). Journal of Food Science 36, 493494.CrossRefGoogle Scholar
Nadeem, MA, Habyarimana, E, Ciftci, V, Nawaz, MA, Karaköy, T, Shahid, MQ, Hatipoğlu, R, Yeken, MZ, Ali, F, Ercişli, S, Chung, G and Baloch, FS (2018) Characterization of genetic diversity in Turkish P. vulgaris gene pool using phenotypic and whole-genome DArTseq-generated silicoDArT marker information. PLoS ONE 13, e0205363.10.1371/journal.pone.0205363CrossRefGoogle Scholar
Nei, M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89, 583590.10.1093/genetics/89.3.583CrossRefGoogle ScholarPubMed
Oliveira, EJ, Pádua, JG, Zucchi, MI, Vencovsky, R and Vieira, MLC (2006) Origin, evolution and genome distribution of microsatellites. Genetics and Molecular Biology 29, 294307.10.1590/S1415-47572006000200018CrossRefGoogle Scholar
Ozkan, G, Haliloğlu, K, Türkoğlu, A, Özturk, HI, Elkoca, E and Poczai, P (2022) Determining genetic diversity and population structure of common bean (Phaseolus vulgaris L.) landraces from Türkiye using SSR markers. Genes 13, 1410.CrossRefGoogle ScholarPubMed
Pan, L, Li, Y, Guo, R, Wu, H, Hu, Z and Chen, C (2014) Development of 12 chloroplast microsatellite markers in Vigna unguiculata (Fabaceae) and amplification in Phaseolus vulgaris. Applications in Plant Sciences 2, 1300075.10.3732/apps.1300075CrossRefGoogle ScholarPubMed
Peakall, R and Smouse, PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics 28, 25372539.CrossRefGoogle ScholarPubMed
Petit, RJ, El Mousadik, A and Pons, O (1998) Identifying populations for conservation on the basis of genetic markers. Biological Conservation 12, 844855.CrossRefGoogle Scholar
Petry, N, Boy, E, Wirth, J and Hurrell, R (2015) Review: the potential of the common bean (Phaseolus vulgaris) as a vehicle for iron biofortification. Nutrients 7, 11441173.10.3390/nu7021144CrossRefGoogle ScholarPubMed
Pratap, A, Gupta, S, Tomar, R, Malviya, N, Maurya, R, Pandey, VR, Mehndi, S and Singh, NP (2016) Cross-genera amplification of informative microsatellite markers from common bean and scarlet runner bean for assessment of genetic diversity in mungbean (Vigna radiata). Plant breeding 134, 499505.10.1111/pbr.12376CrossRefGoogle Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945959.10.1093/genetics/155.2.945CrossRefGoogle ScholarPubMed
Rana, JC, Sharma, TR, Tyagi, RK, Chahota, RK, Gautam, NK, Singh, M, Sharma, PN and Ojha, SN (2015) Characterisation of 4274 accessions of common bean (Phaseolus vulgaris L.) germplasm conserved in the Indian gene bank for phenological, morphological and agricultural traits. Euphytica 205, 441457.CrossRefGoogle Scholar
Sharma, JK and Singh, A (2014) Microsatellite marker-based characterization of P. vulgaris varieties of north-western Himalayan region. Indian Journal of Agricultural Biochemistry 27, 123128.Google Scholar
Sharma, H, Hyvönen, J and Poczai, P (2020) Development of chloroplast microsatellite markers for giant ragweed (Ambrosia trifida). Applications in Plant Sciences 8, e11313.10.1002/aps3.11313CrossRefGoogle ScholarPubMed
Suvan, P, Patel, KV and Kumar, S (2019) Evaluation of SSR-based genetic diversity, protein and mineral content in black gram genotypes. Journal of King Saud University-Science 32, 10291033.CrossRefGoogle Scholar
Thiel, T, Michalek, W, Varshney, RK and Graner, A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics 106, 411422.10.1007/s00122-002-1031-0CrossRefGoogle ScholarPubMed
Ulloa Ulloa, C, Acevedo-Rodríguez, P, Beck, S, Belgrano, MJ, Bernal, R, Berry, PE, Brako L, Celis M, Davidse G, Forzza RC and Gradstein SR (2018) Vascular plants of the Americas VPA website. Available at Scholar
Valentini, G, Gonçalves-Vidigal, MC, Elias, JCF, Moiana, LD and Mindo, NNA (2018) Population structure and genetic diversity of common bean accessions from Brazil. Plant Molecular Biology Reporter 36, 897906.CrossRefGoogle Scholar
Venkidasamy, B, Selvaraj, D, Nile, AS, Ramalingam, S, Kaia, G and Nile, SH (2019) Indian pulses: a review on nutritional, functional and biochemical properties with future perspectives. Trends in Food Science and Technology 88, 228242.10.1016/j.tifs.2019.03.012CrossRefGoogle Scholar
Vidak, M, Šatović, Z, Liber, Z, Grdiša, M, Gunjača, J, Kilian, A and Carović-Stanko, K (2021) Assessment of the origin and diversity of Croatian common bean germplasm using phaseolin type, SSR and SNP markers and morphological Traits. Plants 10, 665.10.3390/plants10040665CrossRefGoogle ScholarPubMed
Wang, A, Ding, Y, Hu, Z, Lin, C, Wang, S, Wang, B, Zhang, H and Zhou, G (2012) Isolation and characterization of 13 new polymorphic microsatellite markers in the Phaseolus vulgaris L. (common bean) genome. International Journal of Molecular Sciences 13, 1118811193.CrossRefGoogle ScholarPubMed
Wani, IA, Sogi, DS, Wani, AA and Gill, BS (2017) Physical and cooking characteristics of some Indian kidney bean (Phaseolus vulgaris L.) cultivars. Journal of the Saudi Society of Agricultural Sciences 16, 715.CrossRefGoogle Scholar
Westphal, E (1974) Pulses in Ethiopia, their taxonomy and agricultural significance. Centre for Agricultural Publishing and Documentation 815, 129176.Google Scholar
Yeh, FC, Yang, RC and Boyle, T (1999) POPGENE Version 1.32: Microsoft Window-Based Freeware for Population Genetics Analysis. Edmonton: University of Alberta.Google Scholar
You, FM, Huo, N, Gu, YQ, Luo, MC, Ma, Y, Hane, D, Lazo, GR, Dvorak J and Anderson OD (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9, 1–13.10.1186/1471-2105-9-253CrossRefGoogle ScholarPubMed
Zhang, X, Blair, MW and Wang, S (2008) Genetic diversity of Chinese common bean (Phaseolus vulgaris L.) landraces assessed with simple sequence repeat markers. Theoretical and Applied Genetics 117, 629640.CrossRefGoogle ScholarPubMed
Supplementary material: File

Bisht et al. supplementary material
Download undefined(File)
File 1 MB