"AbstractGenetic diversity analysis was undertaken in 42 accessions of geographically distantgenotypes (14 from north-east India and 28 from north India) of bottle gourd (Lagenariasiceraria) from India using inter-simple sequence repeat (ISSR) markers. A total of 209amplified bands were obtained from 20 ISSR primers used in this study, of which 186 werepolymorphic with 89.00 % band polymorphism. Various parameters namely, observednumber of alleles, effective number of alleles, Nei’s gene diversity/heterozygosity, resolvingpower, Shanon’s information index and gene flow were estimated under experiment.Jaccard’s similarity coefficient matrix was generated for pairwise comparisons betweenindividual ISSR profiles and UPGMA cluster analysis based on this matrix showedclustering into six groups.Jaccard’s coefficient of similarity values (GS) ranged from 0.409to 0.847, with a mean of 0.628 revealing a moderate level of genetic diversity (GD). TheBayesian model-based approach to infer hidden genetic population structures using themultilocus ISSR markers revealed two populations among the 42 genotypes. This is thefirst report on the assessment of genetic variation by using ISSR markers in this medicinalplant and this study of diversity analysis will be helpful in analysing future hybrid breedingstrategy and devising effective germplasm exploration and conservation strategy. IntroductionTwenty primers that produced clear, distinct and reproducible patterns across all the 42accessions were used for band scoring and genetic analysis. They generated a total of total 209 loci (bands) ranging from 150bp to 1500bp. Over all, the level of Percent Band Polymorphism(PBP) detected by these 20 ISSR primers ranged from 75 to 100 (Table 2). Average percent bandpolymorphism (PBP) detected was 88.49 % polymorphism with 186 polymorphic loci in thebottle gourd germplasm. Maximum band polymorphism for north India is 85.17 %, and north- east India is 75.60%. Resolving power (Rp) measures the ability of primers to distinguishbetween genotypes (Prevost & Wilkinson. 1999 and is based on the distribution of detectedbands within the sampled population. Primer sequence CAC ACA CAC ACA CAC ARC G,showed the maximum RP value of 8.105 and (GA) T shows least Rp value 1.421, indicating8their resolving capacity in population. The primers with high Rp ((GA) AT and C(AC) ARC G)9 7 can be used for varietal discrimination and DNA fingerprinting studies. A further sequenceinvestigation and conversion of these ISSR markers into sequence characterized amplified region(SCAR) markers would be very useful for a fast and effective identification of it’s medicinallyimportance genes.Inter-population analysis between north Indian and north-east Indian population revealed thatobserved numbers of alleles and expected no. of alleles were 1.8900 and 1.5385 respectively,shown in Table 3. Nei’s Gene Diversity which is equivalent to the average heterozygosity in the abovestudy was 0.3144 ± 0.1658. Another genetic diversity parameter which was obtained wasShanon’s information index with value of 0.4696 ± 0.2227. These results indicate thatpopulations harbor moderate inter population diversity, thereby, enhancing their chances tosurvive under variable climatic conditions. High gene flow value was obtained (12.99) for theabove two populations. This gene flow value suggests a high degree of movement of thegermplasm in the two areas and may also be due to the cross-pollinated nature of the crop. TheNei’s genetic distance between the populations of north India and north east India was 0.0203which indicates that both north-east Indian population and north Indian population aregenetically similar to each other. There is a high rate of movement of germplasm within Indiathat may be responsible for the low genetic distance between the two populations. The binary scoring data of the 20 primers was subjected to NTSYS-pc 2.01 software forderiving the UPGMA dendrogram based on the Jaccards coefficient for similarity indexing andis presented in Figure 1. UPGMA based dendrogram does not show correlation with thegeographical locations. The obtained matrix showed that Jaccard’s coefficient of similarityvalues (GS) ranging from 0.409 to 0.847, with a mean of 0.628 revealing a moderate level ofgenetic diversity (GD) within these 42 germplasm. The smallest similarity value (0.409)suggested the high divergence between Pusa Sandesh and BG49 and the maximum similarityvalue (0.847) was scored between BG45 and BG46 indicating that both cultivars were the mostsimilar. The dendrogram for 42 bottle gourd germplasm revealed two main clusters; Cluster Iwas the largest, comprising 38 germplasms which can be divided into numbers of sub clusters,and cluster II is very small consist of3 germplasm only. In cluster I there are two cultivarswhich were present as out group, that are BG13 and BG30. BG49 is present as an out group outside of these clusters.Bottle gourd is a cross pollinated crop, allowing admixture between different genotypes tooccur. Based on STRUCTURE analysis, the value of ?K peaked at K=2 (Fig. 3), hence thenumber of populations detected in the accessions were 2. Overall proportion of membership ofthe samples in each of the 2 populations were 0.527 and0.413.To ration the grade of mingling,we executed population structure analysis and the results specify that all the samples have a highgenetic relationship in their specific cluster (>60%) with few accessions (BG 40, BG 56, BG 21,BG 17, BG 16, BG 23 and BG 26) showing the contribution of the other population in theirancestry. This result argues that there has been a lot of gene flow in these accessions as was alsorevealed by the high gene flow value above. Also there were no geographic trends visible in thepopulation structure.In our study, ISSR markers proved to be useful tool for identifying individuals and assessing thegenetic structure in L.scieraria germplasm. This is the first report on the assessment of geneticvariation by using ISSR markers in this medicinal plant.The present data provide enoughevidence of its high applicability in diversity analysis of L.scieraria crop."