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

Kusum Yadav, Sanjay Kumar Yadav, Anurag Yadav, Veda Prakash Pandey, Upendra Nath Dwivedi

Department of Biochemistry, University of Lucknow, Lucknow, India.
Department of Microbiology, Sardarkrushinagar Dantiwada Agricultural University, Palanpur, India.

DOI: 10.4236/ajps.2014.511181                

Abstract

Genetic relationships of 16 cultivars of pigeonpea (Cajanus cajan (L) Millsp.) and its two wild relatives (C. albicans and C. lineatus) from different parts of the India were analysed using 22 random amplified polymorphic DNAs (RAPDs) primers and 10 inter simple sequence repeats (ISSRs) primers. Twenty two RAPD primers yielded 151 polymorphic markers (71.2%) with an average of 6.8 polymorphic band/primer. Cluster analysis based on these 151 RAPD markers revealed relatively low level (0.434 - 0.714) of genetic diversity among cultivars and high level of diversity between cultivars and wild relatives. Ten ISSR primers produced 100 bands across 16 cultivars and its wild relatives out of which 93 (93%) were polymorphic with an average of 9.3 polymorphic band/primer. Cluster analysis based on these 93 ISSR markers also revealed relatively higher level (0.328 - 0.827) of genetic diversity among cultivars as compared to RAPD markers. The polymorphic markers obtained by both RAPD and ISSR primers were pooled and the genetic diversity analysis based on these 244 markers was analysed. Jaccard’s similarity coefficient obtained by pooled data revealed very narrow range (0.477 - 0.720) among cultivated and high range between cultivated and wild species C. albicans (0.240 - 0.331) and C. lineatus (0.163 - 0.193). In the UPGMA based dendrogram the 16 cultivars were grouped into three distinct clusters. Cluster I contained two genotypes, cluster II had six and cluster III had eight genotypes. Principal components analysis (PCA) also resulted in similar pattern as that of UPGMA based analysis. The first three PCs contributed 56.26%, 5.71% and 4.97% of variation, respectively, with cumulative variation of the first three PCs was 66.96%. Both the markers and the combined data revealed similar pattern with narrow diversity among cultivars and higher diversity between cultivars and wild one, but the genetic diversity range obtained by ISSR markers was relatively higher as compared to RAPD and pooled data. Furthermore, both the markers also correlated the clustering of stress resistant genotypes together. Cultivar Pusa-2002 possessed more diversity with other genotypes in ISSR dendrogram.

Keywords

Genetic Diversity, RAPD, ISSR, Pigeonpea

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Smartt, J. (1990) Evolution of Genetic Resources of Pigeonpea. In: Smartt, J., Ed., Grain Legumes, Cambridge University press, Cambridge, 278-293. http://dx.doi.org/10.1017/CBO9780511525483.009
[2]	Greilhuber, J. and Obermayer, R. (1998) Genome Size Variation in Cajanus cajan (Fabaceae): A Reconsideration. Plant Systematic and Evolution, 212, 135-141. http://dx.doi.org/10.1007/BF00985225
[3]	Nambiar, P.T.C., Ma, S.-W. and Iyer, V.N. (1990) Limiting an Insect Infestation of Nitrogen-Fixing Root Nodules of the Pigeon Pea (Cajanus cajan) by Engineering the Expression of an Entomocidal Gene in Its Root Nodules. Applied and Environmental Microbiology, 56, 2866-2869.
[4]	Santalla, M., Power, J.B. and Davey, M.R. (1998) Genetic Diversity in Mung Bean Germplasm Revealed by RAPD Markers. Plant Breeding, 117, 473-478. http://dx.doi.org/10.1111/j.1439-0523.1998.tb01976.x
[5]	Soller, M. and Beckmann, J.S. (1983) Genetic Polymorphism in Varietal Identification and Crop Improvement. Theoretical and Applied Genetics, 67, 25-33. http://dx.doi.org/10.1007/BF00303917
[6]	Ratnaparkhe, M.B., Gupta, V.S., Ven Murthy, M.R. and Ranjekar, P.K. (1995) Genetic Fingerprinting of Pigeonpea [Cajanus cajan (L.) Millsp.] and Its Wild Relatives using RAPD Markers. Theoretical and Applied Genetics, 91, 893-898.
[7]	Souframanien, J., Manjaya, J.G., Krishna, T.G. and Pawar, E.S. (2003) Randam Amplified Polymorphic DNA Analysis of Cytoplasmic Male Sterile and Male Fertile Pigeonpea (Cajanus cajan (L.) Millsp.). Euphytica, 129, 293-299. http://dx.doi.org/10.1023/A:1022212127025
[8]	Choudhury, P.R., Singh, I.P., George, B., Verman, A.K. and Singh, N.P. (2008) Assessment of Genetic Diversity of Pigeonpea Cultivars using RAPD Analysis. Biologia Plantarum, 52, 648-653. http://dx.doi.org/10.1007/s10535-008-0126-0
[9]	Wasike, S., Okori, P. and Rubaihayo, P.R. (2005) Genetic Variability and Relatedness of the Asian and African Pigeonpea as Revealed by AFLP. African Journal of Biotechnology, 4, 1228-1233.
[10]	Panguluri, S.K., Janaiah, K., Govil, J.N., Kumar, P.A. and Sharma, P.C. (2006) AFLP Fingerprinting in Pigeonpea (Cajanus cajan (L.) Millsp.) and Its Wild Relatives. Genetic Resources and Crop Evolution, 53, 523-531. http://dx.doi.org/10.1007/s10722-004-2031-5
[11]	Aruna, R., Manohar, R.D., Sivaramakrishnanan, S., Janardhan, R.L., Paula, B. and Upadhyaya, H. (2008) Efficiency of Three DNA Markers in Revealing Genetic Variation among Wild Cajanus Species. Plant Genetic Resources: Characterization and Utilization, 7, 113-121. http://dx.doi.org/10.1017/S1479262108061479
[12]	Nadimpalli, B.G., Jarret, R.L., Phatak, S.C. and Kochert, G. (1992) Phylogenetic Relationships of the Pigeonpea (Cajanus cajan) based on Nuclear Restriction Fragment Length Polymorphism. Genome, 36, 216-223. http://dx.doi.org/10.1139/g93-030
[13]	Odeny, D.A., Jayshree, B., Ferguson, M., Hoisington, D., Crouch, J. and Gebhardt, C. (2007) Development, Characterization and Utilization of Microsatellite Markers in Pigeonpea. Plant Breeding, 126, 130-136. http://dx.doi.org/10.1111/j.1439-0523.2007.01324.x
[14]	Lakshmi, M., Senthikumar, P., Parani, M., Narayana, J. and Parida, A.K. (2000) PCR-RFLP Analysis of Chloroplast Gene Regions in Cajanus (Leguminosae) and Allied Genera. Euphytica, 116, 243-250. http://dx.doi.org/10.1023/A:1004030207084
[15]	Skroch, P.W., Santos, J.B. and Nienhuis, J. (1992) Genetic Relationships among Phaseolus vulgaris Genotypes Based on RAPD Marker Data. Annual Report of Bean Improvement Cooperation, 35, 23-24.
[16]	Mignouna, H.D., Ng, N.Q., Ikea, J. and Thottapilly, G. (1998) Genetic Diversity in Cowpea as Revealed by Random Amplified Polymorphic DNA. Journal of Genetics and Breeding, 53, 151-159.
[17]	Hoey, B.K., Crowe, K.R., Jones, V.M. and Polans, N.O. (1996) A Phylogenetic Analysis of Pisum Based on Morphological Characters, Allozyme and RAPD Markers. Theoretical and Applied Genetics, 92, 92-100. http://dx.doi.org/10.1007/BF00222957
[18]	Lakhanpaul, S., Chadha, S. and Bhat, K.V. (2000) Random Amplified Polymorphic DNA (RAPD) Analysis in Indian Mung Bean [Vigna radiata (L.) Wilczek] Cultivars. Genetica, 109, 227-234. http://dx.doi.org/10.1023/A:1017511918528
[19]	Yee, E., Kidwell, K.K., Sillis, G.R. and Lumpkin, T.A. (1999) Diversity among Selected Vigna Angularis (Azuki) Accessions on the Basis of RAPD and AFLP Markers. Crop Science, 39, 268-275. http://dx.doi.org/10.2135/cropsci1999.0011183X003900010041x
[20]	Zietkiewic, E., Rafalski, A. and Labuda, D. (1994) Genome Fingerprinting by Simple Sequence Repeat (SSR)-Anchored Polymerase Chain Reaction Amplification. Genomics, 20, 176-183. http://dx.doi.org/10.1006/geno.1994.1151
[21]	Joshi, S.P., Gupta, V.S., Agarwal, R.K., Ranjekar, P.K. and Brar, D.S. (2000) Genetic Diversity and Phylogenetic Relationship as Revealed by Inter Simple Sequence Repeat (ISSR) Polymorphism in the Genus Oryza. Theoretical and Applied Genetics, 100, 1311-1320. http://dx.doi.org/10.1007/s001220051440
[22]	Nagaoka, T. and Ogihara, Y. (1997) Applicability of Inter-Simple Sequence Repeat Polymorphisms in Wheat for Use as DNA Markers in Comparison to RFLP and RAPD Markers. Theoretical and Applied Genetics, 94, 597-602. http://dx.doi.org/10.1007/s001220050456
[23]	Ajibade, S.R., Weeden, N.F. and Michite, S.M. (2000) Inter Simple Sequence Repeat Analysis of Genetic Relationships in the Genus Vigna. Euphytica, 111, 47-55. http://dx.doi.org/10.1023/A:1003763328768
[24]	Souframanien, J. and Gopalakrishna, T. (2004) A Comparative Analysis of Genetic Diversity in Blackgram Genotypes Using RAPD and ISSR Markers. Theoretical and Applied Genetics, 109, 1687-1693. http://dx.doi.org/10.1007/s00122-004-1797-3
[25]	Fernandez, M., Figueiras, A. and Benito, C. (2002) The Use of ISSR and RAPD Marker for Detecting DNA Polymorphism, Genotype Identification and Genetic Diversity among Barley Cultivars with Known Origin. Theoretical and Applied Genetics, 104, 845-851. http://dx.doi.org/10.1007/s00122-001-0848-2
[26]	Yadav, K., Yadav, S.K., Yadav, A., Pandey, V.P. and Dwivedi, U.N. (2012) Genetic Diversity of Pigeonpea (Cajanus cajan (L) Millsp.) Cultivars and Its Wild Relatives Using RAPD Markers. American Journal of Plant Sciences, 3, 322-330. http://dx.doi.org/10.4236/ajps.2012.33038
[27]	Jaccard, P. (1908) Nouvelles Researches Sur Ladistribution Florale. Bulletin de la Societe Vaudoise des Sciences Naturelles, 44, 223-270.
[28]	Pavlicek, A., Hrda, S. and Flegr, J. (1999) Free Tree: Freeware Program for Construction of Phylogenetic Trees on the Basis of Distance Data and Bootstrap/Jackknife Analysis of the Tree Robustness. Application in the RAPD Analysis of Genus Frenkelia. Folia Biologica (Praha), 45, 97-99.
[29]	Page, R.D.M. (1999) Tree View: An Application to Display Phylogenetic Trees on Personal Computers. Computer Applications in the Biosciences, 12, 357-358.
[30]	Rohlf, F.J. (1997) NTSYS-pc Version. 2.02i Numerical Taxonomy and Multivariate Analysis System. Applied Biostatistics Inc., Exeter Software, Setauket, New York.
[31]	Datta, J., Lal, N., Kaashyap, M. and Gupta, P.P. (2010) Efficiency of Three PCR Based Marker Systems for Detecting DNA Polymorphismin Cicer arietinum L and Cajanus cajan L Millspaugh. Genetic Engineering and Biotechnology Journal. (on Line)
[32]	Hemalatha, T. and Shanmugasundaram, P. (2010) Efficiency of DNA Marker Systems in Discriminating Cajanus cajan (L.) Millsp. and It’s Wild Relatives. Indian Journal of Plant Genetics Recourse, 23, 93-99.
[33]	Raina, S.N., Rani, V., Kojima, T., Ogihara, Y. and Singh, K.P. (2001) RAPD and ISSR Fingerprints as Useful Genetic Markers for Analysis of Genetic Diversity, Varietal Identification, and Phylogenetic Relationships in Peanut (Arachis hypogaea L.) Cultivars and Wild Species. Genome, 44, 763-772. http://dx.doi.org/10.1139/gen-44-5-763
[34]	Salimath, S.S., de Oliveira, A.C., Godwin, I.D. and Bennetzen, J.L. (1995) Assessment of Genome Origins and Genetic Diversity in the Genus Eleusine with DNA Markers. Genome, 38, 757-763. http://dx.doi.org/10.1139/g95-096
[35]	Goulao, L., Valdiviesso, T., Santana, C. and Oliveira, C.M. (2001) Comparison between Phenetic Characterisation Using RAPD and ISSR Markers and Phenotypic Data of Cultivated Chestnut (Castanea sativa Mill.). Genetic Resources and Crop Evolution, 48, 329-338. http://dx.doi.org/10.1023/A:1012053731052
[36]	Yang, W., de Oliveira, A.C., Godwin, I., Schertz, K. and Bennetzen, J.L. (1996) Comparison of DNA Marker Technologies in Characterizing Plant Genome Diversity: Variability in Chinese Sorghums. Crop Science, 36, 1669-1676. http://dx.doi.org/10.2135/cropsci1996.0011183X003600060042x
[37]	Rao, L.S., Rani, P.U., Deshmukh, P.S., Kumar, P.A. and Panguluri, S.K. (2007) RAPD and ISSR Fingerprinting in Cultivated Chickpea (Cicer arietinum L.) and Its Wild Progenitor Cicer reticulatum Ladizinsky. Genetic Resources and Crop Evolution, 54, 1235-1244. http://dx.doi.org/10.1007/s10722-006-9104-6
[38]	Gupta, S., Srivastava, M., Mishra, G.P., Naik, P.K., Chauhan, R.S., Tiwari, S.K., Kumar, M. and Singh, R. (2008) Analogy of ISSR and RAPD Markers for Comparative Analysis of Genetic Diversity among Different Jatropha curcas Genotypes. African Journal of Biotechnology, 7, 4230-4243.
[39]	Yang, S.Y., Pang, W., Ash, G., Harper, J., Carling, J., Wenzl, P., Huttner, E., Zong, X.X. and Kilian, A. (2006) Low Level of Genetic Diversity in Cultivated Pigeonpea Compared to Its Wild Relatives Is Revealed by Diversity Arrays Technology. Theoretical and Applied Genetics, 113, 585-595. http://dx.doi.org/10.1007/s00122-006-0317-z
[40]	Kumar, S., Gupta, S., Chandra, S. and Singh, B.B. (2004) How Wide Is the Genetic Base of Pulse Crops. In: Ali, M., Singh, B.B., Kumar, S. and Vishwa, D., Eds., Pulses in New Perspective, IIPR, Kanpur, 211-221.
[41]	Kumar, J., Choudhary, A.K., Solanki, R.K. and Pratap, A. (2011) Towards Marker-Assisted Selection in Pulses: A Review. Plant Breeding, 130, 297-313. http://dx.doi.org/10.1111/j.1439-0523.2011.01851.x