• Amit Kumar Tamrakar
• Dr.Vikash Singh Thakur
• Kapil Kumar Chourasiya

India stands as the largest global producer of pulses, with pigeonpea (Cajanus cajan L. Millspaugh) being one of its most vital pulse crops due to its high protein content and broad cultivation. However, low productivity, primarily due to poor seed quality and limited private sector interest, presents a major challenge. The present study aimed to assess genetic diversity and determine varietal-specific molecular markers in pigeonpea genotypes using Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeat (SSR) techniques. Eleven pigeonpea genotypes were evaluated using 13 RAPD and 12 SSR primers. RAPD analysis yielded a polymorphism rate of 58.3%, detecting high variability among genotypes, with similarity indices ranging from 0.454 to 0.948. RAPD primer OPA-16 exhibited the highest polymorphism, while several rare and unique loci were identified across genotypes. SSR analysis showed limited polymorphism, detecting only 8.33% polymorphic loci. Cluster analysis using Jaccard's similarity coefficients grouped genotypes into distinct clusters, highlighting the genetic relatedness and divergence, with GT-288A being the most divergent genotype. The study concluded that RAPD markers proved more efficient than SSR in differentiating pigeonpea genotypes, offering potential for use in marker-assisted selection, varietal identification, and genetic improvement programs. The findings contribute significantly to pigeonpea breeding strategies, enabling the identification of genetically distant lines suitable for hybridization and enhancing genetic gain in future breeding endeavors.

Pigeonpea, Genetic diversity, RAPD markers, SSR markers, Molecular characterization

"Molecular Characterization and Identification of Varietal-Specific Markers in Pigeonpea (Cajanus cajan L.) Using RAPD and SSR Techniques", International Journal of Emerging Technologies and Innovative Research (www.jetir.org), ISSN:2349-5162, Vol.12, Issue 11, page no.a824-a831, November-2025, Available :http://www.jetir.org/papers/JETIR2511095.pdf

"Molecular Characterization and Identification of Varietal-Specific Markers in Pigeonpea (Cajanus cajan L.) Using RAPD and SSR Techniques", International Journal of Emerging Technologies and Innovative Research (www.jetir.org | UGC and issn Approved), ISSN:2349-5162, Vol.12, Issue 11, page no. ppa824-a831, November-2025, Available at : http://www.jetir.org/papers/JETIR2511095.pdf