Diversity of Ricebean (Vigna umbellata L.) Germplasm in the Northern Philippine Highlands Based on Agro-morphological Characteristics and Simple Sequence Repeat Markers

Main Article Content

Belinda A. Tad-awan Hilda V. Palaes


Rice bean (Vigna umbellata L.) is one of the underutilized food legumes in the Philippines but is integral in the cropping system of highland local farmers. To get more understanding on the germplasm diversity of this legume in the area for conservation and breeding purposes, morpho-agronomic and genetic characterization using simple sequence repeats (SSR) markers were carried out on 28 ricebean germplasm. Morpho-agronomic characters exhibited mid to high diversity (0.42 to 0.71). Characters such as climbing habit, primary leaflet width, seed width, terminal leaf width, and pod width had the highest diversity indices. Ward’s cluster analysis grouped the ricebean germplasm into five clusters. In SSR analysis using a set of 10 SSR primer pairs, the genetic similarities among selected ricebean germplasm ranged from 0.39 to 0.86 showing mid to high similarities. A total of 89 alleles were detected with an average of 8.9 alleles for each locus, and the polymorphism information content value for SSR loci varied from 0.45 for CEDG021 to 0.94 for primer CEDG003 with an average of 0.78. Cluster diagram based on the similarity matrix generated six clusters at 0.86 similarity index. Fruit setting ability, pod width, seed width, and 100-seed weight are important characters for seed yield improvement in ricebean germplasm. Further, the grouping of ricebean germplasm with high seed weight and yield, many pods per cluster, and many seeds per pod suggest a potential gene pool of ricebean in the northern Philippine highlands, which can be utilized for future breeding improvement programs.

Article Details



Ahmad, S., Singh, M., Lamb-Palmer, N.D., Lefsrud, M., & Singh, J. (2012). Assessment of genetic diversity in 35 Pisum sativum using microsatellite markers. Canadian Journal of Plant Science, 92(6): 1075-1081.

Ahamed, K.U., Akhter, B., Islam, M.R., Humaun, M.R., & Alam, M.J. (2014). Morphological characterization and genetic diversity in lentil (Lens culinaris medikus ssp. Culinaris) germplasm. International Journal of Agricultural Research, Innovation and Technology, 4(1): 70-76.

Al-Saady, N. A., Nadaf, S. K., Al-Lawati, A. H., & Al-Hinai, S. A. (2018). Germplasm collection and seed diversity of cowpea (Vigna unguiculata (L.) Walp.). Asian Journal of Agriculture and Food Sciences, 6(4).

Arif, A., Kendarini, N., & Kuswanto, K. (2016). Evaluation of Genetik Purity on 20 Genotypes of Bambara Groundnut (Vigna subterranea L. Verdcourt) Selected From Single Seed Descent Morphological Characters. Doctoral dissertation. Brawijaya University.

Babasaheb, W., Parihar, A., Chaurasia, P., Pachchigar, K., & Chauhan, R.M. (2013). Genetic analysis of wild and cultivated germplasm of pigeonpea using random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) markers. African Journal of Biotechnology, 12(40): 5823-5832.

Belshaw, H. (1947). Races, Lands and Foods. Pacific Affairs, 20(1), 71-80.

Bhalodiya, D., Dhaduk, H.K.L., Kumar, S., Gediya, L.N., & Patel, H.P. (2019). Line× tester analysis for seed yield, protein and oil content and SSR based diversity in sesame (Sesamum indicum L.). Ecological Genetics and Genomics, 13, 100048.

Carović-Stanko, K., Liber, Z., Vidak, M., Barešić, A., Grdiša, M., Lazarević, B., & Šatović, Z. (2017). Genetic diversity of Croatian common bean landraces. Frontiers in Plant Science, 8, 604.

Chen, H., Chen, X., Tian, J., Yang, Y., Liu, Z., Hao, X., & Cheng, X. (2016). Development of gene-based SSR markers in rice bean (Vigna umbellata L.) based on transcriptome data. PloS one, 11(3), e0151040.

Chen, H., Chen, H., Hu, L., Wang, L., Wang, S., Wang, M.L., & Cheng, X. (2017). Genetic diversity and a population structure analysis ofaccessions in the Chinese cowpea [Vigna unguiculata (L.) Walp.] germplasm collection. The Crop Journal, 5(5): 363-372.

Choudhary, P., Khanna, S.M., & Jain, P.K. (2012). Genetic structure and diversity analysis of the primary gene pool of chickpea using SSR markers. Genetics of Molecular Research, 11(2): 891-905.

Choudhury, P., Singh, I.P., George, B., Verma, A.K., & Singh, N.P. (2008). Assessment of genetic diversity of pigeonpea cultivars using RAPD analysis. Biologia Plantarum, 52(4): 648-653.

Doumbia, I.Z., Akromah, R., & Asibuo, J.Y. (2013). Comparative study of cowpea germplasms diversity from Ghana and Mali using morphological characteristics. Journal of Plant Breeding and Genetics, 1(3): 139-147.

Gaad, D., Laouar, M., Abdelguerfi, A., & Gaboun, F. (2018). Collection and agro-morphological characterization of Algerian accessions of lentil (Lens culinaris). Biodiversitas Journal of Biological Diversity, 19(1): 183-193.

Gangadhar B.H.M., & Mishra, R.K. (2016). Comparative study of EST-SSR, SSR, RAPD, and ISSR and their transferability analysis in pea, chickpea and mungbean. European Academic Research, 4(2): 1346- 1352.

Gerrano, A. S., Adebola, P. O., Jansen van Rensburg, W.S., & Laurie, S. M. (2015). Genetic variability in cowpea (Vigna unguiculata (L.) Walp.) genotypes. South African Journal of Plant and Soil, 32(3): 165-174.

Gixhari, B., Vrapi, H., & Hobdari, V. (2014). Morphological characterization of pea (Pisum sativum L.) genotypes stored in Albanian genebank. Albanian Journal of Agricultural Sciences, 169.

Gonné, S., Félix-Alain, W., & Benoît, K.B. (2013).

Assessment of twenty bambara groundnut

(Vigna subterranea (L.) Verdcourt) landraces using quantitative morphological traits. International Journal of Plant Research, 3(3): 39-45.

Gul, R., Khan, H., Bibi, M., & Imran, B. (2013). Genetic attributing traits in chickpea (Cicer arietinum L.). Journal of Animal and Plant Sciences, 23(2), 521-526.

Gupta, S., Kozak, M., Sahay, G., Durrai, A. A., Mitra, J., Verma, M. R. & Das, A. (2009). Genetic parameters of selection and stability and identification of divergent parents for hybridization in rice bean (Vigna umbellata Thunb. (Ohwi and Ohashi)) in India. The Journal of Agricultural Science, 147(5), 581-588.

Hamawaki, O.T., Rezende, G.F., Jorge, G.L., Silveira, I.C., Medeiros, L.A., & Hamawaki, R.L. (2017). Phenotypic and genotypic correlations between soybean agronomic traits and path analysis. Genet. Mol. Res., 16 2–11.

Hamwieh, A., Udupa, S.M., Sarker, A., Jung, C., & Baum, M. (2009). Development of new microsatellite markers and their application in the analysis of genetic diversity in lentils. Breeding Science, 59(1), 77-86.

Iangrai, B., Pattanayak, A., Khongwir, D.E.A., Pale, G., Gatphoh, E.M., Das, A., & Chrungoo, N.K. (2017). Development and characterization of a new set of genomic microsatellite markers in rice bean (Vigna umbellata (Thunb.) Ohwi and Ohashi) and their utilization in genetic diversity analysis of collections from North East India. PloS one, 12(7), e0179801.

IBPGR. (1985). Descriptors for Vigna mungo and Vigna radiata (Revised). International Board Plant Genetic Resources, Rome.

Isemura, T., Kaga, A., Tomooka, N., Shimizu, T., & Vaughan, D.A. (2010). The genetics of domestication of rice bean, Vigna umbellata. Annals of Botany, 106(6): 927-944.

Joshi, K.D., Bhanduri, B., Gautam, R., Bajracharya, J., & Hollington, P.B. (2008). Rice bean: a multipurpose underutilized legume. In: Smart, J. Haq, N. New crops and uses: their role in a rapidly changing world. CUC, UK, 234-248.

Kameswara, R.N. (2004). Plant genetic resources: Advancing conservation and use through biotechnology. African Journal of Biotechnology, 3(2): 136-145.

Kalia, R.K., Rai, M.K., Kalia, S., Singh, R., & Dhawan, A.K. (2011). Microsatellite markers: an overview of the recent progress in plants. Euphytica, 177(3): 309-334.

Katoch, R. (2011). Morpho-physiological and nutritional characterization of rice bean (Vigna umbellata). Acta Agron. Hungarica, 59, 109–20.

Keneni, G., Bekele, E., Imtiaz, M., Dagne, K., Getu, E., & Assefa, F. (2012). Genetic diversity and population structure of Ethiopian chickpea (Cicer arietinum L.) germplasm accessions from different geographical origins as revealed by microsatellite markers. Plant Molecular Biology Reporter, 30(3), 654-665.

Khazaei, H., Caron, C.T., Fedoruk, M., Diapari, M., Vandenberg, A., Coyne, C.J., McGee, R., & Bett, K.E. (2016). Genetic diversity of cultivated lentil (Lens culinaris Medik.) and its relation to the world's agro-ecological zones. Frontiers in Plant Science, 7, 1093.

Kumar, A., Pandey, A., Aochen, C., & Pattanayak, A. (2015). Evaluation of genetic diversity and interrelationships of agro-morphological characters in soybean (Glycine max) genotypes. Proceedings of the National Academy of Sciences, India Section B: Biological Sciences, 85(2), 397-405.

Kumar, S., Hash, C.T., Singh, G., Basava, R.K., & Srivastava, R.K. (2020). Identification of polymorphic SSR markers in elite genotypes of pearl millet and diversity analysis. Ecological Genetics and Genomics, 14, 100051.

Lim, S., Lee, J., Lee, H.J., Park, K.H., Kim, D.S., Min, S.R., Jang, W.S., Kim, T., & Kim, H. (2017). The genetic diversity among strawberry breeding resources based on SSRs. Scientia Agricola, 74(3): 226-234.

Leila, O., Alane, F., Rahal-Bouziane, H., & Abdelguerfi, A. (2016). Agro-morphological diversity within field pea (Pisum sativum L.) genotypes. African Journal of Agricultural Research, 11(40): 4039-4047.

Macherey-Nagel. (2014). Genomic DNA from plant:

User manual, NucleoSpin 96 Plant II, NucleoSpin 96 Plant II Core Kit.

Madakbaş, S.Y., Sarıkamış, G., Başak, H., Karadavut, U., Özmen, C.Y., Daşçı, M.G., & Çayan, S. (2016). Genetic characterization of greenbean (Phaseolus vulgaris L.) accessions from Turkey with SCAR and SSR markers. Biochemicalgenetics, 54(4): 495505.

Mafakheri, K., Bihamta, M.R., & Abbasi, A.R. (2017). Assessment of genetic diversity in cowpea (Vigna unguiculata L.) germplasm using morphological and molecular characterisation. Cogent Food & Agriculture, 3(1), 1327092.

Malik, S. R., Shabbir, G., Zubir, M., Iqbal, S.M., & Ali, A. (2014). Genetic diversity analysis of morpho-genetic traits in desi chickpea (Cicer arietinum). International Journal of Agriculture and Biology, 16(5).

Malik, S.R., Bakhsh, A., Asif, M.A., Iqbal, U., & Iqbal, S.M. (2010). Assessment of genetic variability and interrelationship among some agronomic traits in chickpea. Int. J. Agric. Biol., 12: 81–85.

Malek, M.A., Rafii, M.Y., Afroz, S.S., Nath, U.K., & Mondal, M. (2014). Morphological characterization and assessment of genetic variability, character association, and divergence in soybean mutants. The Scientific World Journal. https://doi.org/10.1155/2014/968796

Marconato, M.B., Pereira, E.M., Silva, F.M., Bizari, E.H., Pinheiro, J.B., Mauro, A.O., & UnêdaTrevisoli, S.H. (2016). Genetic divergence in a soybean (Glycine max) diversity panel based on agro-morphological traits. Genetics and molecular research, 15, 1-10.

Martínez‐Castillo, J., Zizumbo‐Villarreal, D., Gepts, P., Delgado‐Valerio, P., & Colunga‐García Marín, P. (2006). Structure and genetic diversity of wild populations of Lima bean (Phaseolus lunatus L.) from the Yucatan Peninsula, Mexico. Crop Science, 46(3): 1071-1080.

Mathivathana, M.K., Jagadeeshselvam, N., Madhumitha, B., Karthikeyan, A., Pandiyan,M., Karthikeyan, G., Vanniarajan, C., Raveendran, M., Senthil, N., & Sudha M. (2018). Screening and Identification of SSR Markers for Genetic Diversity for Mungbean [Vigna radiata (L.) Wilczek]. Int. J. Curr. Microbiol. Appl. Sci., 7, 789–93.

Mohammed, N.A., Refay, Y.A., Migdadi, H.M., Alsamin, B., Muharram, A.A., Al-Selwey, W., Abdela, K.A., Alghamdi, S.S. & Farooq, M. (2019). Agro-Morphological Characterization of Lentil Genotypes in Dry Environments. International Journal of Agriculture and Biology, 22(6): 1320-1330.

Moiana, L.D., Filho, P.S.V., Gonçalves-Vidigal, M.C., & de Carvalho, L.P. (2015).Genetic diversity and population structure of upland cotton Brazilian cultivars (Gossypium hirsutum L. race'latifolium'H.)using SSR markers. Australian Journal of Crop Science, 9(2): 143-152.

Musango, R., Kudzai, K., Mhungu, S., & Tibugar, H. (2016). Phenotypic characterization of common bean (Phaseolus vulgaris L.) accessions conserved at the genetic resources and biotechnology institute. Journal of Biodiversity and Environmental Sciences, 8(6): 26-36.

Ortiz-Burgos, S. (2016). Shannon-Weaver diversity index. U: Kennish MJ (ur.) Encyclopedia of estuaries. Encyclopaedia of Earth sciences series.

Painkra, P., Shrivastava, R. & Nag, S.K. (2019). Agro-morphological characterization of soybean germplasm. Indian Soc. Oilseeds Res., 85. 85–8.

Pandey, G., Prasad, R., Prasad, B., & Chauhan, P. (2015). Co-efficient of variation, heritability, genetic advance and variability for ricebean (Vigna umbellata (Thunb.) genotypes under mid hill conditions of Uttarakhand. Journal of Applied and Natural Science, 7(2): 794-798.

Pratap, A., Prajapati, U., Singh, C.M., Gupta, S., Rathore, M., Malviya, N., & Singh, N.P. (2018). Potential, constraints and applications of in vitro methods in improving grain legumes. Plant Breeding, 137(3): 235-249.

Punia, S.S., Gautam, N.K., Ram, B., Verma, P., Dheer, M., Jain, N.K., Koli, N.R., Mahavar, R., & Jat, V.S. (2014). Genetic variability and correlation studies in urdbean (Vigna mungo L.). Legume Research-An International Journal, 37(6): 580-584.

Pyngrope, A.H., Noren, S.K., Wricha, T., Sen, D., Khanna, V.K., & Pattanayak, A. (2015). Genetic diversity analysis of blackgram [Vigna mungo (L.) Hepper] using morphological and molecular markers. Int. J. Appl. Pure Sci. Agric, 1(8): 104-113.

Rajković, D., Taški-Ajduković, K., Nagl, N., Isakov, M., Milić, D., Karagić, Đ., & Mikić, A. (2015). Potential use of SSR and ISSR markers in estimation of DNA polymorphism within genus Vicia. Ratarstvo i povrtarstvo, 52(2): 85-89.

Ramya, B., Nallathambi, G., & Ram, S.G. (2014). Genetic variability, heritability and genetic advance in induced mutagenesis blackgram (Vigna mungo (L.)Hepper). Plant Archives, 14(1): 139-141.

Rana, J.C., Chahota, R.K., Sharma, V., Rana, M., Verma, N., Verma, B., & Sharma, T.R. (2015). Genetic diversity and structure of Pyrus accessions of Indian Himalayan region based on morphological and SSR markers. Tree genetics & genomes, 11(1): 1-14.

Razvi, S.M., Khan, M.N., Bhat, M.A., Ahmad, M., Ganaie, S.A., Sheikh, F.A., & Parry, F.A. (2018). Morphological variability and phylogenetic analysis in Common bean (Phaseolus vulgaris L.). Legume Research-An International Journal, 41(2): 208-2012.

Rohlf, J.F. (1993). Numerical Taxonomy and Multivariate Analysis System, version 2.1. Exeter Software, New York.

Roy, S., Islam, M.A., Sarker, A., Malek, M.A., Rafii, M.Y., & Ismail, M.R. (2013). Determination of genetic diversity in lentil germplasm based on quantitative traits. Australian Journal of Crop Science, 7(1): 14-21.

Sachan, M.S., (2017). Genetics of yield and its components in rice bean under mid altitude areas of Mon district Nagaland India. Journal of Hill Agriculture, 8(4), 366-371.

Sarikamis, G., Yanmaz, R., Ermis, S., Bakir, M.E.L.İ.K.E., & Yuksel, C. (2010). Genetic characterization of pea (Pisum sativum) germplasm from Turkey using morphological and SSR markers.Genetics and Molecular Research, 9(1).

Sathees, N., Shoba, D., Saravanan, S., Kumari, S.M.P., & Pillai, M.A. (2021). Assessment of the genetic diversity of black gram [Vigna mungo (L.) hepper] collections for yellow mosaic virus resistance using simple sequence repeat markers. Legume Research: An International Journal, 44(7).

Sefera, T., Abebie, B., Gaur, P.M., Assefa, K., & Varshney, R.K. (2011). Characterisation and genetic diversity analysis of selected chickpea cultivars of nine countries using simple sequence repeat (SSR)markers. Crop and Pasture Science, 62(2): 177-187.

Shafiqul I., Dutta M., Shachi S., Kumar P., & Bhatt, K.V. (2017). Assessment of Genetic Diversity of Ricebean [(Vigna umbellata) (Thunb.) Ohwi & Ohashi)] Varieties and their Narrow Leaf Cross Derivatives using RAPD Markers. Int. J. Agric. Environ. Biotechnol., 10, 415.

Sharma, L.A., Singh, M.R.K., & Singh, N. (2015). Heterosis and combining ability for grain yield and its components in rice bean (Vigna umbellata (thunb) Ohwi and Ohashi). Indian Journal of Hill Farming, 11, 27-33.

Silva, R.N.O., Lopes, A.C.A., Gomes, R.L.F., Pádua, J.G., & Burle, M.L. (2019). High diversity of cultivated lima beans (Phaseolus lunatus) in Brazil consisting of one Andean and two Mesoamerican groups with strong introgression between the gene pools. Genet. Mol. Res., 18(4): GMR18441. https://doi.org/10.4238/gmr18441

Singh, A., Dikshit, H.K., Jain, N., Singh, D., & Yadav, R.N. (2014). Efficiency of SSR, ISSR and RAPD markers in molecular characterization of mungbean and other Vigna species. Indian Journal of Biotechnology, 13, 81-88.

Smýkal, P., Hýbl, M., Corander, J., Jarkovský, J., Flavell, A.J., & Griga, M. (2008). Genetic diversity and population structure of pea (Pisum sativum L.) varieties derived from combined retrotransposon, microsatellite and morphological marker analysis. Theoretical and Applied Genetics, 117(3): 413-424.

Stoilova, T., & Pereira, G. (2013). Assessment of the genetic diversity in a germplasm collection of cowpea (Vigna unguiculata (L.) Walp.) using morphological traits. African J. Agric. Res., 8, 208–15.

Tad-awan B.A. & Sagalla E.J.D. (2015). Cultivation and Conservation of Traditional Food Crops and Perceptions of Farmers on Biodiversity Loss in the Cordillera Administrative Region. Mt. J. Sci. Interdiscip. Res. (formerly Benguet State Univ. Res. Journal), 74: 62–81.

Tajoddin, M., Manohar, S., & Lalitha, J. (2012). Agronomic Characteristics and Seed Yield of Mung Bean Cultivars Differing in Seed Color using Organic and Conventional Farming in Indian Subtropical Region. The Asian and Australasian Journal of Plant Science and Biotechnology, 6, 38-40.

Tantasawat, P., Trongchuen, J., Prajongjai, T., Jenweerawat, S., & Chaowiset, W. (2011). SSR Analysis of Soybean ('Glycine max' (L.) Merr.) Genetic Relationship and Variety Identification in Thailand.Australian Journal of Crop Science, 5(3): 283-290.

Teixeira, F.G., Hamawaki, O.T., Nogueira, A.P.O., Hamawaki, R.L., Jorge, G.L., Hamawaki, C.L. & Santana, A.J.O. (2017). Genetic parameters and selection of soybean lines based on selection indexes. Genetics and Molecular Research, 16(3).

Thakur, S., Bhardwaj, N., & Chahota, R.K. (2017). Evaluation of genetic diversity in ricebean [Vigna umbellata (Thunb.) Ohwi and Ohashi] germplasm using SSR markers. Electronic Journal of Plant Breeding, 8(2): 674-679.

Tian, J., Isemura, T., Kaga, A., Vaughan, D.A., & Tomooka, N. (2013). Genetic diversity of the rice bean (Vigna umbellata) genepool as assessed by SSR markers. Genome, 56(12), 717-727.

Upadhyaya, H.D., Reddy, K.N., Vetriventhan, M., Ahmed, M.I., Krishna, G.M., Reddy, M.T., & Singh, S.K. (2017). Sorghum germplasm from West and Central Africa maintained in the ICRISAT genebank: Status, gaps, and diversity. The Crop Journal, 5(6), 518-532.

Valladares, F., Gianoli, E., & Gómez, J.M. (2007). Ecological limits to plant phenotypic plasticity. New phytologist, 176(4): 749-763.

Wamalwa, E.N., Muoma, J., & Wekesa, C. (2016). Genetic diversity of cowpea (Vigna unguiculata (L.) Walp.) accession in Kenya gene bank based on simple sequence repeat markers. International journal of genomics. https://doi.org/10.1155/2016/8956412

Wang, L., Bai, P., Yuan, X., Chen, H., Wang, S., Chen, X., & Cheng, X. (2018). Genetic diversity assessment of a set of introduced mung bean accessions (Vigna radiata L.). The Crop Journal, 6(2), 207-213.

Wang, L.X., Elbaidouri, M., Abernathy, B., Chen, H.L., Wang, S.H., Lee, S.H. & Cheng, X.Z. (2015). Distribution and analysis of SSR in mung bean (Vigna radiata L.) genome based on an SSRenriched library. Molecular breeding, 35(1), 1-10.

Zaccardelli, M., Lupo, F., Piergiovanni, A.R., Laghetti, G., Sonnante, G., Daminati, M.G., Sparvoli, F., & Lioi, L. (2012). Characterization of Italian lentil (Lens culinaris Medik.) germplasm by agronomic traits, biochemical and molecular markers. Genetic Resources and Crop Evolution, 59, 727–738. https://doi.org/10.1007/s10722-011-9714-5