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Fenugreek ( Trigonella foenum-graecum ), an important spice crop belongs to the family Fabaceae. India is the largest producers as well as the largest exporter of fenugreek. Five common fenugreek varieties of India were included in this study for molecular analysis. For randomly amplified polymorphic DNA (RAPD) analysis, a total of 47 bands in the size range of 200 to 5000 bp were produced by examining across genotypes with 9 RAPD primers, with an average polymorphism of 62.4%. Total numbers of bands ranged from 3 (U407) to 7 (OPB-15). With 17 fluorescently labeled amplified fragment length polymorphism (AFLP) primer combinations (PCs), a total of 669 peaks in the size range of 50 to 538 bp were amplified. Total numbers of bands ranged from 21 (E-AAC/M-CT) to 60 (E-AAC/M-CAC). The mean genetic diversity (Nei's 1973) across all loci was found to be 23.83 and 2.1% with RAPD and AFLP markers, respectively. In all the fenugreek varieties, a total of 25 variety-specific AFLP markers were found. Phylogenetic trees among 5 plant varieties were constructed based on Nei's coefficient standard genetic distances using unweighted pair group method with arithmetic mean (UPGMA) method. For RAPD and AFLP analysis, Gujarat Methi-1 (GM-1) and Gujarat Methi-2 (GM-2) clustered together showed more similarities than other varieties. In fenugreek, RAPD markers were found more polymorphic than AFLP markers. RAPD markers also showed more diversity in comparison to AFLP markers, although the data generated for AFLP markers were more authenticated and reproducible than RAPD markers. Key words : AFLP, RAPD, genetic diversity, automated genetic analyzer, polymorphism.

Trigonella foenum-graecum L. (fenugreek) is a viable alternative for production of diosgenin because of its shorter growing cycle, lower production costs, and consistent yield and quality. We studied de novo transcriptome analysis along with the diosgenin pathway in Trigonella foenum-graecum and identified the genes responsible for diosgenin biosynthesis. The GMV-1 variety of Trigonella foenum-graecum has been used in the present study for transcriptome analysis by sequencing messenger ribonucleic acid (RNA) with a SOLiD 4 Genome Analyzer. Deep sequencing data of the transcriptome was assembled using various assembly tools along with functional annotation of genes, and pathway analysis for diosgenin biosynthesis was deciphered. A total of 42 million high quality reads were obtained. De novo assembly was performed using Velvet at different k-mer, Oases, and CLC Genomics Workbench, which generated 20,561 transcript contigs. CAP3 was used to reduce the redundancy of contigs obtained through these assemblers. A total of 18,333 transcript contigs were functionally annotated. Kyoto Encyclopedia of Genes and Genomes pathway mapping showed that 6775 transcripts were related to plant biochemical pathways including the diosgenin biosynthesis pathway. The large number of transcripts reported in the current study will serve as a valuable genetic resource for Trigonella foenum-graecum. Sequence information of the genes that were involved in diosgenin biosynthesis could be used for metabolic engineering of Trigonella foenum-graecum to increase diosgenin content.