"1. Partial Sequences Description In the present study, we have reported 49 sequences (Table 5), maximum amidst them are partialsequences.InordertofindthefunctionofthesesequencesweperformedBLAST,whichidentified the sequences. From these sequences, we found various microsatellites fragments,some partial coding sequences of gene like clp protease proteolytic subunit protein (clpP) gene,cytochrome b6 (petB) gene, tRNA-Arg (trnR) gene, NADH dehydrogenase subunit I (nad1)gene,ribosomal protein L5 gene, cytochrome c oxidase subunit 1 gene, psbD protein (psbD)gene, C-repeat/DRE binding factor 1 (CBFI) gene and complete sequence of ycf15-like gene,two resistance protein fragments—NBS-LRR-like protein gene and sk20 resistance-like proteingene, some partial ribosomal RNA genes—18S, 25S, 26S, 5.8S and complete gene of 5Sribosomal RNA, three AFLP and two RAPD fragments and one uncharacterized region. Thesesequences can be used in future analysis of these genes by utilizing the primers and performingother downstream analysis for gene characterization. 2. SSR polymorphism In order to evaluate the potential of the developed SSR markers to measure the variability inbottle gourd accession, the 40 accession were profiled with the 30 primer pairs.The allelesidentified by the seven novel polymorphic marker pairs varied from 2 to 5 with an average of2.85 alleles per locus. The PIC values for these polymorphic markers varied from 0.45 (B 113) to0.6 (B 30) with a mean of 0.27. The polymorphic marker B-9 harboring the tri-nucleotide SSRsrepeat TTG had 4 alleles with PIC value 0.13 while B-30 harboring tetra repeat ACAT had 24 3 alleles with a PIC value of 0.06. Various parameters like number of alleles, gene diversity,Shannon’s information index, gene flow etc of each of these seven polymorhic markers and of both populations are shown in Table 4a and Table 4b respectively. 3 Genetic Diversity Analysis Polymorphic markers were utilized for diversity analysis, based on the distinctive DNA markerprofiles of all the accession of bottle gourd used in the study. Data were subjected to NTSYS- PC 2.01softwareforderivingtheUPGMAdendrogrambasedontheJaccard’ssimilaritycoefficient. Dendrogram classified the 40 accession in two groups —group I with 32 accessionsand group II with eight accessions (Fig. 3). Each of these groups had further sub clusters, butnone had significant geographical concordance. This may be due to the cross pollinated nature ofbottle gourd and also corroborates the genetic structure found in these accessions by Bayesiananalyses in 3.2.The obtained similarity matrix of Jaccard’s coefficient (GS) ranged from 0.12 to 0.92, with amean of 0.56 revealing a moderate level of genetic diversity (GD) within these 40 accession. Theminimum similarity value, 0.12, suggested high divergence between BG22 and BG16 and themaximum similarity value 0.92 was scored between Arka Bahar and BG46 indicating that bothcultivars were most similar. The diverse accession can be used as prospective parents to generatehybrids with vigor as well as for generating the mapping population(s) for linkage studies.The UPGMAbaseddendrogramdoesnotshowcorrelationwiththegeographical locations,possibly due to cross pollinated nature of bottle gourd. Selection and exact utilization of diverseaccession in breeding programs is required to improve the breeding populations in the future(Krishna et al., 2004). Inter-population analysis between North Indian and Northeast Indian population revealed that observed number of alleles and expected number of alleles were 1.9 and 1.52 respectively. Nei’sGene Diversity which is equivalent to the average heterozygosity was 0.43 ± 0.08 andShannon’s Information Index was 0.62 ± 0.09. These results indicate that populations harbor amoderate inter population diversity, thereby, enhancing their chances to survive under variableclimatic conditions.Highgeneflowvaluewasobtained,i.e.,3.46fortheabovetwopopulations. This gene flow value is probably due to the cross-pollinated nature of the crop andno impediment on genetic exchange within India. Nei’s genetic distance between the populationsof North India and Northeast India was 0.1, which indicatesthatbothNortheastIndian populationandNorthIndianpopulationaregenetically similar to each other and there is ahigh rate of movement of accession within India that may be responsible for the low geneticdistance between the two populations. 4 Population Structure analyses When performing STRUCTURE on the dataset, a maximum value of the rate of change in thelog probability of data using the Evanno method (Evanno et al., 2005) was observed at K 9,although the value of delta K (3.84) was quite low, meaning that this structuring of populationswas not strong. The value of Fst obtained was 0.067, which also explains that there is only amoderate genetic differentiation between the populations. The second higher value of delta K(3.35) was observed at K 5, which provided a better picture of the groupings. The same situationwas also remarked when populations were identified by means of their geographical origin, usingthe LOCPRIOR option in STRUCTURE (Fig. 4).In mostcases,individuals from a populationwere admixed with the other entire populations, which was as expected due to the cross- pollinated nature of the crop and also corroborateswiththediversity parametersoutlinedinthisanalysis.Similar clustering was observed in the UPGMA method as well, reiterating thefact that in bottle gourd geographically the gene flow is not restricted. Although the morphologyof the Northeast Indian population is different and the accession show adaptation to localenvironmental conditions there are nobarrierstomovementthatpreventtheexchangeof geneswithNorthIndian population. In the Bayesian assignment tests five genetic clusters withsubstantial admixture were identified and could not clearly differentiate previously identifiedgeographical boundaries, corroborating admixture because of movement of accession withinIndia. Specifically, there is little geographic structure and high levels of admixture. Thesefindings have important implications for the management of Lagenaria siceraria populations inIndia, especially for genetic resources conservation, and more broadly, for studies that aim tounderstand the evolutionary dynamics of the historical domesticated crop."