Genetic Diversity Clusters in Germplasm of Cluster Bean (Cyamopsis tetragonoloba L., Taub), an Important Food and an Industrial Legume Crop

Authors
A. Ansari
P. Sikarwar
S. Lade
H. Yadav
S. Ranade
Molecular Biology and Genetics Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001. U. P. State, India.
Abstract
Genetic diversity in cluster bean (Cyamopsis tetragonoloba L.; Fabaceae) genotypes was studied using Inter-Simple Sequence Repeat (ISSR) and Random Amplified Polymorphic DNA (RAPD) to derive conclusions about diversity analysis in groups of accessions of a germplasm. The two methods, individually as well as cumulatively revealed the range of diversity in profiles among 104 genotypes collected from different geographical regions of India. A simulated clustering of the collected plant genotypes was divided into defined affinity groups using Structure program and the cluster analysis of molecular markers data revealed six broad sub-clusters. These results were validated with a Principal Coordinate analysis. The combined data was more informative than either of the individual method data. The diversity range was found to be wide and the presence of six broad clusters suggests the existence of many genetic lineages that can constitute useful starting points for the use of germplasm diversity in the selection and improvement of the cluster bean crop.

Keywords

1. Ajit, P., Yengkokpam, P., More, V., Ghorpade, B. and Swamy, M. K. 2013. Molecular Characterization of Cluster Bean (Cyamopsis tetragonoloba) Cultivars Using PCR-based molecular markers. Int. J. Adv. Biotechnol. Res., 4: 158-166.
2. Ammar, M. H., Alghamdi, S. S., Migdadi, H. M., Khan, M. A., El-Harty, E. H. and Al-Faifi, S. A. 2015. Assessment of Genetic Diversity among Faba Bean Genotypes Using Agro-morphological and Molecular Markers. Saudi J. Biol. Sci., 22: 340–350.
3. Anatala, T. J., Gajera, H. P., Savaliya, D. D., Domadiya, R. K., Patel, S. V. and Golakiya, B. A. 2014. Molecular Diversity Analysis of Cowpea (Vigna unguiculata L.) Genotypes Determined by ISSR and RAPD Markers. IJAEB, 7: 269 - 276.
4. Ayyangar, G. N. P. and Krishnaswami, N. 1933. A note on the Chromosome Number in Cluster Bean (Cyamopsis psoralioides DC). Indian J. Agr. Sci., 3: 934 - 935.
5. Chen, D., Yi, X., Yang, H., Zhou, H., Yu, Y., Tian, Y. and Lu, X. 2015. Genetic Diversity Evaluation of Winged Bean (Psophocarpus tetragonolobus (L.) DC.) Using Inter-Simple Sequence Repeat (ISSR). Genet. Resour. Crop Ev., DOI: 10.1007/s10722-015-0261-3
6. Das, S., Das, S. S. and Ghosh, P. 2014. A Comparative Analysis of Genetic Diversity across Certain Mung Bean and Urd Bean Cultivars of West Bengal, Using ISSR Markers. Asian J. Plant Sci. Res., 4: 56 - 61.
7. Dwivedi, N. K., Bhandari, D. C., Bhatnagar, N. and Dabas, B. S. 1999. Characterization of Cluster Bean [Cyamopsis tetragonoloba (L) Taub.] Germplasm for Yield and Quality Traits. Ann. Arid Zone, 38: 151-156.
8. Earl, D. A. and von Holdt, B. M. 2012. Structure Harvester: A Website and Program for Visualizing Structure Output and Implementing the Evanno Method. Conserv. Genet. Resour., 4: 359–361.
9. Evanno, G., Regnaut, S. and Goudet, J. 2005. Detecting the Number of Clusters of Individuals Using the Software Structure: A Simulation Study. Mol. Ecol., 14: 2611–2620.
10. Gajera, H. P., Domadiya, R. K., Patel, S. V. and Golakiya, B. A. 2014. Appraisal of RAPD and ISSR Markers for Genetic Diversity Analysis among Cowpea (Vigna unguiculata L.) Genotypes. J. Crop Sci. Biotechnol., 17: 79 - 88.
11. Henry, A. and Mathur, B. K. 2005. Genetic Diversity and Performance of Cluster Bean Varieties for Stability and Quantitative Characters in Arid Region. J. Arid Legum., 2: 145 - 148.
12. Idrissi, O., Udupa, S. M., Houasli, C., De Keyser E., Van Damme, P. and De Riek, J. 2015. Genetic Diversity Analysis of Moroccan Lentil (Lens culinaris Medik.) Landraces Using Simple Sequence Repeat and Amplified Fragment Length Polymorphisms Reveals Functional Adaptation towards Agro-environmental Origins. Plant Breed., 134: 322 – 332.
13. Jayabalan, S., Tamilarasan, S., Shunmugiah, K. P. and Manikandan, R. 2013. Assessment of Genetic Diversity in Solanum trilobatum L., an Important Medicinal Plant from South India Using RAPD and ISSR Markers. Genet. Resour. Crop Ev., 60: 807 - 818.
14. Kallamadi, P. R., Nadigatla, V. G. R. and Mulpuri, S. 2015. Molecular Diversity in Castor (Ricinus communis L.). Ind. Crop. Prod., 66: 271 - 281.
15. Khaled, K. A., El-Demardash, I. S. and Amer, E. A. M. 2015. Genetic Polymorphism among Some Sugarcane Germplasm Collections as Revealed by RAPD and ISSR Analysis Life Sci. J., 12: 159 -167.
16. Khan, Md. T., Reza, Md. O. H., Khan, Md. A., Haque, Md. S., Islam, Md. S. and Khan, Md. B. 2015. Genetic Diversity Analysis of Cowpea by RAPD Markers. IJIAS, 10: 459 - 465.
17. Kumar, A., Mishra, P., Singh, S. C. and Sundaresan, V. 2014. Efficiency of ISSR and RAPD Markers in Genetic Divergence Analysis and Conservation Management of Justicia adhatoda L., a Medicinal Plant. Plant Syst. Evol., 300: 1409 -1420.
18. Lavanya, G. R. and Ranade, S. A. 2013. Comparative Analysis of Morphological and Molecular Diversity in Mung bean (Vigna radiata L. Wilczek). Trend. Biosci,. 6: 146 - 151.
19. Lavanya, G. R., Srivastava, J. and Ranade, S. A. 2008. Molecular Assessment of Genetic Diversity in Mung Bean Germplasm. J. Genet., 87: 65 - 74.
20. Li, H. and Geng, S. 2015. Assessment of Population Genetic Diversity of Derris elliptica (Fabaceae) in China Using Micro Satellite Markers. Ind. Crop. Prod., 73: 9 - 15.
21. Linos, A., Nikoloudakis, N., Katsiotis, A. and Hagidimitriou, M. 2014. Genetic structure of the Greek Olive Germplasm Revealed by RAPD, ISSR and SSR Markers. Sci. Hortic. (Amsterdam), 175: 33 - 43.
22. Muzila, M. M., Werlemark, G., Ortiz, R., Sehic, J., Fatih, M., Setshogo, M., Mpoloka, W. and Nybom, H. 2014. Assessment of Diversity in Harpagophytum with RAPD and ISSR Markers Provides Evidence of Introgression. Hereditas, 151: 91 - 101.
23. Page, R. D. M. 2001. Tree View (Win 32) Ver. 1.6.5. Distributed by Author, http://taxonomy.zoology.gla.ac.uk/rod/rod.html
24. Pathak, R., Singh, S. K., Manjit, S. and Henry, A. 2010. Genetic Divergence in Cluster Bean (Cyamopsis tetragonoloba) for Seed Yield and Gum Content under Rain-fed Conditions. Indian J. Agr. Sci. 79, 559 - 561.
25. Patil, D.V. 2014a. Genetic Components of Variance of Guar and Its Response to Sowing Dates in Semi Arid Region of Maharashtra, India. Plant Archiv., 14(1): 125 – 131.
26. Patil, D. V. 2014b. Genetic Variability and Sowing Dates Effect of Cluster Bean (Cyamopsis tetragonoloba L., Taub) Genotypes in Semi Arid Region of Maharashtra, India. Plant Archiv., 14(1): 1 – 6.
27. Pavlicek, A., Hrda, S. and Flegr, J. 1999. Free Tree: Freeware Program for Construction of Phylogenetic Trees on the Basis of Distance Data and Bootstrapping/Jackknife Analysis of the Tree Robustness. Application in the RAPD Analysis of the Genus Frenkelia. Folia Biol. (Praha.), 45: 97- 99.
28. Peakall, R. and Smouse, P. E. 2012. GenAlEx 6.5: Genetic Analysis in Excel. Population Genetic Software for Teaching and Research: An Update. Bioinforma., 28: 2537 - 2539.
29. Pritchard, J. K., Stephens, M. and Donnelly, P. 2000. Inference of Population Structure Using Multi Locus Genotype Data. Genet., 155: 945 - 959.
30. Punia, A., Arora, P., Yadav, R. and Chaudhury, A. 2009a. Optimization and Inference of PCR Conditions for Genetic Variability Studies of Commercially Important Cluster Bean Varieties by RAPD Analysis. Asia Pacific J. Mol. Biol. Biotechnol., 17: 33 - 38.
31. Punia, A., Yadav, R., Arora, P. and Chaudhury, A. 2009b. Molecular and Morpho-physiological Characterization of Superior Cluster Bean (Cymopsis tetragonoloba) Varieties. J. Crop Sci. Biotechnol., 12: 143-148.
32. Saini, R. K., Saad, K. R., Ravishankar, G. A., Giridhar, P. and Shetty, N. P. 2013. Genetic Diversity of Commercially Grown Moringa oleifera Lam. Cultivars from India by RAPD, ISSR and Cytochrome P450-based Markers. Plant Syst. Evol., 299: 1205-1213.
33. Sharma, P., Sharma, V. and Kumar, V. 2014. Genetic Diversity Analysis of Cluster Bean [Cyamopsis tetragonoloba (L.) Taub] Genotypes Using RAPD and ISSR Markers. J. Agri. Sci. Tech., 16: 433 - 443.
34. Sharma, V., Sharma, T. R., Rana, J. C. and Chahota, R. C. 2015. Analysis of Genetic Diversity and Population Structure in Horse Gram (Macrotyloma uniflorum) Using RAPD and ISSR Markers. Agr. Res., DOI: 10.1007/s40003-015-0165-7.
35. Singh, A., Dikshit, H. K., Jain, N., Singh, D. and Yadav, R. N. 2014. Efficiency of SSR, ISSR and RAPD Markers in Molecular Characterization of Mung Bean and Other Vigna Species. Indian J. Biotechnol., 13: 81-88.
36. Singh, P. K., Sharma, H., Srivastava, N. and Bhagyawant, S. S. 2014. Analysis of Genetic Diversity among Wild and Cultivated Chickpea Genotypes Employing ISSR and RAPD Markers. Am. J. Plant Sci., 5: 7.
37. Thompson, M. G. and Murray, W. F. 1980. Rapid Isolation of High Molecular Weight Plant DNA. Nucleic Acid. Res., 8: 4321-4325.
38. Vaishali, Khan S., Singh, N. P. and Sharma, V. 2014. Genetic Diversity Analysis of Butea monosperma from Different Agro-ecological Regions of India Using ISSR Marker System and Its Comparison with RAPD. Euro. J. Biotechnol. Biosci., 2: 32 - 36.
39. Welsh, J. and McClelland, M. 1990. Fingerprinting Genomes Using PCR with Arbitrary Primers. Nucleic Acids Res. 18, 7213 - 7218.
40. Williams, J. G. K., Kubelik, A. R., Livak, K. J., Rafalski, J. A. and Tingey, S. V. 1990. DNA Polymorphism Amplified by Arbitrary Primers Are Useful as Genetic Markers. Nucleic Acid. Res., 18: 6531- 6535.
41. Yadav, K., Yadav, S. K., Yadav, A., Pandey, V. P. and Dwivedi, U. N. 2014. Comparative Analysis of Genetic Diversity among Cultivated Pigeonpea (Cajanus cajan (L) Millsp.) and Its Wild Relatives (C. albicans and C. lineatus) Using Randomly Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR) Fingerprinting. Am. J. Plant Sci., 5: 1665 - 1678.
42. Yahia, Y., Hannachi, H. and Ferchichi, A. 2014. Genetic Diversity of Vicia faba L. Based on Random Amplified Polymorphic DNA and Simple Sequence Repeat Markers. Acta Botanica Gallica Bot. Lett., 161: 151-158.
43. Zhao, F., Nie, J., Chen, M. and Wu, G. 2015. Assessment of Genetic Characteristics of Aconitum Germplasm in Xinjiang Province (China) by RAPD and ISSR Markers. Biotech. Biotechnol. Equip., 29: 309 - 314.
44. Zietkiewicz, E., Rafalski, A. J. and Labuda. D. 1994. Genome Fingerprinting by Simple Sequence Repeat (SSR): Anchored Polymerase Chain Reaction Amplification. Genom., 20: 176 - 183.
Journal of Agricultural Science and Technology
Volume 18, Issue 5
September and October 2016
Pages 1407-1418