Molecular characterization of cultivated and wild Cajanus species using Simple Sequence Repeat markers

DOI: 10.18805/lr.v38i6.6717    | Article Id: LR-3154 | Page : 742-747
Citation :- Molecular characterization of cultivated and wild Cajanus speciesusing Simple Sequence Repeat markers .Legume Research.2015.(38):742-747

K. Indira Petchiammal, A.R. Muthiah and P. Jayamani

Address :

Department of Pulses, Tamil Nadu Agricultural University, Coimbatore-641 003, India.


Twenty pigeonpea specific SSR markers were used to test the molecular diversity  among 21 cultivated genotypes and three wild species. Twelve markers were monomorphic and twenty two alleles were produced by eight polymorphic markers. Ten markers were transferrable among the cultivated and wild species. The PIC value of the markers ranged from 0.081(PGM 3 and PGM 82) to 0.603 (PGM 106). The average PIC value of the markers was 0.30. Based on the dendrogram constructed using the dissimilarity values, 24 accessions were grouped into two main clusters. Main cluster I comprises all the cultivated genotypes, and wild species viz., Cajanus scarabaeoides and Cajanus cajaniolius. Cajanus sericeus formed the separate cluster (Main cluster II). Within the main cluster I, seven sub-clusters were observed. Cajanus scarabaeoides and Cajanus cajaniolius formed a separate sub-cluster within the main cluster I. Most of the diversity was observed in between the wild species and cultivated genotypes. There is no significant molecular diversity among the cultivated genotypes. Such a narrow genetic base is likely to represent a serious impediment to breeding programs in pigeonpea. This study suggested the need for broadening the genetic base of cultivated genotypes to improve the productivity of the crop.


Cajanus cajan Cajanus cajaniolius Cajanus scarabaeoides Cajanus sericeus Molecular diversity SSR markers Wild species.


  1. Botstein, D, White, RL, Skolnick, M. and Davis, RW. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am.J.Hum.Genet. 32, 314-331.
  2. Buhariwalla, HK, Crouch, JH. (2004). Optimization of marker screening protocol to assess the degree and distribution of genetic diversity in landraces of Pigeonpea. In: Bramel PJ(ed). Assessing the risk of losses of biodiversity in traditional cropping systems:A case study of Pigeonpea in Andhra Pradesh. International Crops Research Institute for the Semi-Arid Tropics, Pattancheru, AP, India. P 168.
  3. Burns, M.J., Edwards, K.J., New bury, H.J., Ford-Lloyd B.V. and Baggott. (2001). CD: Development of simple sequence repeat (SSR) markers for the assessment of gene flow and genetic diversity in pigeonpea (Cajanus cajan). Mol. Ecol. Notes. 1:283-285.
  4. Datta, S, Kaashyap, M and Kumar, S. (2009). Amplification of chickpea specific SSR markers in cajanus species and their validity in diversity analysis. Plant Breeding. 129: 334-340. Datta, J, Lal, N, Kaashyap, M. and Gupta, P.P. (2009). Efficiency of Three PCR based marker Systems for detecting DNA Polymorphism in Cicer arietinum (L.) and Cajanus cajan (L.)Millspaugh. Genet. Eng. And Biotech.J. 5: 1-15.
  5. Gupta, PK, and Varshney, RK. (2000). The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113: 163-185.
  6. Liu, S, Cantrell, RG, McCary, JC and Sterwart, J. (2000). Simple sequence based assessment of genetic diversity in cotton race stock accessions. Crop Sci. 40: 1459-1469.
  7. Mace, E.S, Buhariwalla, H.K and Crouch, JH. (2003). A High Throughput DNA Extraction Protocol for Tropical Molecular Breeding Programs. Plant Mol. Biol. Reporter. 21, 459a-459h
  8. Mallikarjuna, N, Saxena, K.B and Jadhav, D.R. (2011). Cajanus. In: Wild Crop Relatives: Genomic and Breeding Resources, Legume Crops and Forages. [Kole C (ed)]. P 21-33.
  9. Odeny, D.A, Jayashree, B, Ferguson, M, Hoisington, D.A, Crouch and Gebhardt, C. (2007). Development, characterization and utilization of microsatellite markers in pigeonpea [Cajanus cajan(L.) Millsp.]. Plant Breeding. 126: 130-137.
  10. Odeny, D.A, Jayashree, B, Gebhardt, C and Crouch, J. (2009). New Microsatellite Markers for Pigeonpea (Cajanus cajan(L.) Millsp.). BMC Research Notes. 2:35.
  11. Perrier, X. and Jaqeuemond-Collet, J.P. (2005). DARwin- 5.0: Dissimilarity analysis and representation for windows. Equipe Mathematique et Informatique, France.
  12. Saxena, K.B. (2008). Genetic improvement of pigeonpea – a review. Trop. Plant Biol. 1: 159-178.
  13. Saxena, R.K, Prathima, C, Saxena, K.B, Hoisinngton, D.A, Singh, N.K and Varshney, R.K. (2010). Novel SSR markers for    polymorphism detection in Pigeonpea (Cajanus spp.). Plant Breeding. 129: 142-148.
  14. Singh, S, Singh, K.N, Kant, R, Mehfooz, S and Dutta, S. (2008). Assessment of genetic diversity among Pigeonpea genotypes using SSR markers. Indian J. Genet., 68: 255-260.
  15. Smith, J.S.C, Chin, E.C.L, Shu, H, Smith, O.S, Wall, S.J, Senior, M.L, Mitchell, S.E, Kresovich,S and Zeigle, J. (1997). An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisions with data from RFLPs and pedigree. Theor. Appl. Genetics, 95: 163-173.
  16. Songok, S, Ferguson, M, Muigai, A.W and Silim, S. (2010). Genetic diversity in Pigeonpea (Cajanus cajan (L.) Millsp.) land races as revealed by simple sequence repeat markers. African J. of Biotech. 9: 3231-3241.
  17. Upadhyaya, H.D, Bhattacharjee, R, Hoisington, D.A, Chandra, S, Varshney, R.K, Reddy, K.N and Saxena, K.B. (2006). Molecular characterization of Pigeonpea (Cajanus cajan (L.) Millspaugh) composite collection. Poster presented in the Generation Challenge program Annual Research Meeting, 12-16 September 2006, Sao Paulo, Brazil. 1p.
  18. Yang, S, Pang, W, Ash, G, Harper, J, Carling, J, Wenzl, P, Huttner, E, Zong, X and Kilian, A. (2006). Low level of genetic diversity in cultivated Pigeonpea compared to its wild relatives is revealed by diversity arrays technology. Theor. Appl. Genet. 113: 585-595. 

Global Footprints