Assessment Of Genetic Diversity Research Articles

Assessment of Genetic Diversity and Construction of Core Germplasm in Populations of Acorus tatarinowii Based on SNP Markers

Acorus tatarinowii is a natural medicinal plant integral to traditional aromatic therapies. It is commonly employed in the treatment of depression, epilepsy, and Alzheimer's disease due to its significant medicinal and aromatic properties. However, the genetic diversity of wild A. tatarinowii resources has declined due to over-exploitation and habitat destruction. This study aims to assess the genetic diversity of the natural populations of A. tatarinowii, establish a core germplasm bank, explore its genetic richness and uniqueness, prevent genetic erosion, and identify beneficial genes. In this study, for the first time, 429A. tatarinowii samples from 40 populations were analyzed for genetic diversity and population structure using Hyper-Seq technology. A total of 4,772,850 high-quality Single Nucleotide Polymorphisms (SNPs) and 1,563,000 Insertions and Deletions (InDels) variant loci were identified, with C/T as the predominant variant type and a Ts/Tv ratio of 1.079. Annotation of these loci indicated that the majority of variants occurring in intergenic regions, accounting for 50.59% of the total. Moreover, the heterozygosity, nucleotide diversity, and FST of A. tatarinowii suggested low genetic diversity within this species within the populations. The analysis of molecular variance (AMOVA) revealed that the population variation of A. tatarinowii is mainly caused by the variation between populations (72.06%), while the variation within populations only contributes a small part (27.94%) Through NJ tree, PCA, and ADMIXTURE analyses, the 429A. tatarinowii samples were classified into five subgroups, with some genetic exchange observed. A total of 7,163 high-quality polymorphic SNPs were identified, and a core germplasm consisting of 85 samples was established, achieving genotype retention rates similar to those of the original germplasm. This indicates that a smaller number of germplasm resources can effectively represent the majority of the genetic diversity. Additionally, PCA analysis further confirmed the representativeness and validity of the constructed core germplasm resources. Furthermore, the DNA fingerprints of the 429 accessions were established using the most effective combinations of 26 SNP markers, which served as specific markers to effectively distinguish all samples. In conclusion, these findings offer valuable insights into the genetic structure of A. tatarinowii, facilitating the identification of high-quality genes and providing a scientific foundation for the development of breeding programs and conservation strategies for A. tatarinowii.

Plastid genome comparison and phylogenetic analyses of the Chinese group of medicinal species and related taxa within Asparagus genus

BackgroundAsparagus L. is a large genus widely distributed across the continents of the Old World. Among its members, approximately 14 species found in China are recognized as popular herbal medicines. However, accurate authentication of these medicinal species and their phylogenetic relationships with related taxa remains unresolved.MethodsTo identify simple sequence repeats (SSRs) and divergence hotspot regions appropriate for future authentication studies, as well as to infer the phylogenetic relationships among Asparagus species, we employed a plastid genome (plastome) dataset consisting of 25 Asparagus species (21 newly sequenced and four retrieved from GenBank), encompassing 12 Chinese medicinal species, for comparative and phylogenetic analyses.ResultsAll Asparagus plastomes displayed a typical quadripartite structure with sizes ranging from 155,948 bp to 157,128 bp and harbored 114 unique genes (80 protein-coding genes, 30 tRNA genes, and four rRNA genes). IRscope and Mauve analyses indicated minimal structural variation among Asparagus plastomes. We detected between 79 to 95 SSRs across the plastomes; most were located in the large single-copy (LSC) region and primarily consisted of mono-nucleotide repeat sequences (especially A and T repeats). The genus displayed mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide repeats, but with variations in types and numbers among different species. Additionally, we identified 12 special SSR motifs and seven divergent hotspot regions that may serve as potential molecular markers for future identification efforts. Phylogenetic analyses yielded a robust phylogeny for Asparagus taxa, which were split into Clades I, II, and III. Notably, medicinal Asparagus species were mainly found in Clade III. Although the phylogenetic relationships of most Asparagus species aligned with previous study findings, the phylogenetic positions of A. munitus, A. subscandens, A. gobicus, and A. dauricus were newly determined.ConclusionsThe plastomes of Asparagus are largely conserved in terms of genome structure, size, gene content, and arrangement. Nevertheless, SSRs analyses revealed significant interspecific polymorphism within Asparagus. In addition, special SSR motifs and divergent hotspot regions identified from Asparagus plastomes provided reference for subsequent identification investigations. The plastome-based phylogeny provided preliminary insights into the relationships among the Chinese group of medicinal species and related taxa within Asparagus. Overall, this study offers a wealth of informative genetic resources pertinent to Asparagus, thereby enhancing our understanding of its evolution and laying a foundation for species identification, assessment of genetic population diversity, as well as the exploration and conservation of germplasm resources.

Assessment of Genetic Variability, Correlation and Path Analysis in Bread Wheat (Triticum aestivum L.) Genotypes for Yield and its Attributing Traits

This study investigated the genetic variability and agronomic traits influencing wheat yield across multiple genotypes. Conducted during the 2021-2022 rabi season at the Research Farm of BRD PG College, Deoria, the experiment included 31 treatments and a standard check variety, HD-2967, arranged in a randomized block design (RBD) with three replications. Analysis of variance (ANOVA) revealed significant genetic variation among the genotypes for traits such as Days to 50% Flowering (DF), Days to Maturity (DM), Plant Height (PH), and Grain Yield per Plant (GYP). Genotypic correlation analysis showed significant positive associations between DF and DM, and negative correlations between DF, DM, and GYP, highlighting the complex trade-offs among traits. Traits like Test Weight (TW) and Biological Yield (BY) were positively correlated with GYP, indicating their potential as key selection criteria for breeding. Path coefficient analysis identified DF and Test Weight as having strong direct effects on GYP, while traits such as Plant Height and Number of Grains per Spike had negative impacts. These results provide valuable insights into the genetic and phenotypic relationships that can guide the development of superior wheat genotypes with improved yield potential.

Assessment of genetic diversity by multivariate analysis in Turkish Hawthorn (Crataegus azarolus) genetic resources

Abstract Due to its diverse climatic conditions, Türkiye provides a suitable environment for the cultivation of many fruit species. This study focused on natural hawthorn (Crataegus azarolus), one of these fruit species, to select 94 different hawthorn genotypes collected from natural populations in Türkiye and determine their molecular and morphological characteristics. A significant variation was observed among the hawthorn genotypes in terms of the analyzed traits. According to the results of the molecular study using the inter simple sequence repeat (ISSR) marker system, 178 polymorphic bands were obtained from 12 different primers (Invitrogen Life Technologies, USA), and the polymorphism rate was determined to be 100%. The similarity index for the genotypes ranged from 0.40 to 0.93, and the genotypes were completely differentiated from one another. In terms of fruit characteristics, there was considerable variation among the genotypes: fruit width ranged from 8.96 mm (genotype 72) to 29.75 mm (genotype 101), fruit length ranged from 9.19 mm (genotype 72) to 24.86 mm (genotype 101), and fruit weight ranged from 0.45 to 12.42 g. This study provides a foundation for developing hawthorn genotypes that will offer high productivity while conserving water and soil resources in arid and semi-arid regions by revealing the degree of genetic variation and the morphological characteristics of hawthorn genetic resources adapted to different ecological conditions in Türkiye. Furthermore, the study demonstrates that genotypes with superior traits can be utilized as genetic material in hawthorn breeding programs, medical research, and the development of new cultivars.

Assessment of genetic diversity in Nelumbo nucifera genotypes

Aim: The present investigation assessed the level of genetic diversity in the lotus (Nelumbo nucifera Gaertn.) genotypes grown naturally in Bihar (India). Methodology: In situ observations on 21 quantitative traits were recorded with five replications from each sampling site and data was analysed in a Completely Randomized Block Design. Results: Among all the genotypes BRL-01, BRL-08, BRL-21, and BRL-22 showed significant variation in the number of petals per flower, weight of flower, and flower colour. High values of genetic parameters were calculated for number of petals per flower, rhizome weight, rhizome length and weight of the flower. Number of petals per flower, number of leaf venation and diameter of the flower bud showed a significant positive correlation with the weight of flower. Path analysis revealed a highest positive direct effect of leaf length on flower weight at genotypic level. Interpretation: High GCV for all traits indicates the existence of genetic variation. The traits coupled with high heritability and genetic advance indicate the positive response for selection, primarily driven by additive gene action. Therefore, selection for traits such as number of petals per flower, length of flower stalk and weight of flower may be useful for the development of improved variety for flower attributes. Key words: Correlation coefficient, Diversity, Genotypes, Lotus, Path analysis

Enhancing Food Security via selecting Superior Camelina (Camelina sativa L.) parents: a positive approach incorporating pheno-morphological traits, fatty acids composition, and Tocopherols Content

BackgroundPreserving plant genetic resources is essential for tackling global food security challenges. Effectively meeting future agricultural demands requires comprehensive and efficient assessments of genetic diversity in breeding programs and germplasm from gene banks. This research investigated the diversity of pheno-morphological traits, along with the fatty acid and tocopherol content and composition, in 135 double haploid lines of camelina.ResultsThe number of sub-branches, siliques number of main-branch and sub-branch, and seeds number in siliques of the main-branch displayed notable coefficients of variation with values of 33.19%, 30.32%, 29.23%, and 23.81% respectively. Within the current investigation, the measurements of height, sub-branch number, and thousand seed weight varied from 53.50 to 86.50 cm, 3.50 to 14, and 0.73 to 1.52 g, respectively. The analysis unveiled that the average content of omega-3, omega-6, and omega-9 fatty acids in the examined lines was approximately 33%, 20%, and 17%, respectively. The total tocopherol content varied between 675 and 877 ppm, predominantly consisting of gamma-tocopherol, which accounted for over 95% of the total content. The fatty acid C18:2 displayed a markedly strong positive correlation with alpha-tocopherol (0.99**), while C18:3 exhibited positive correlations with gamma-tocopherol (0.98**) and total tocopherol (0.98**). Furthermore, a positive correlation was evident between C20:1 and delta-tocopherol (0.98**). The scrutinized lines, specifically lines 35, 72, 94, and 126 demonstrated notable attributes regarding yield and yield components. Conversely, in the realm of biochemical traits, lines 35, 66, 47, 30, 65, 135, 83, 27, 4, 77, 62, 81, and 93 stood out for their elevated potential. The gene expression analysis related to the tocopherol biosynthesis pathway revealed distinct expression patterns. Specifically, the VTE1 gene exhibited the highest level of expression. In contrast, the VTE3 gene displayed the lowest level of expression compared to other genes.ConclusionsThe study’s findings hold great potential for improving food security by enabling the selection of superior camelina parent plants based on specific traits. This approach can drive the development of high-yielding varieties with enhanced nutritional value and better-quality camelina oil.

Empowering Regional Conservation: Genetic Diversity Assessments as a Tool for Eelgrass Management.

To halt the loss of biodiversity, collaboration among scientists, managers and decision-makers is vital. Although biodiversity loss is a global problem, management actions influencing diversity are often on a local to regional scale. Our study is an example of a regional conservation genomic assessment developed in collaboration between scientists and managers. We used 2bRAD sequencing to assess 18 eelgrass (Zostera marina) meadows in northwestern Sweden, an area that has experienced large losses of eelgrass since the 1980s. Genetic diversity was comparable to other assessed meadows in the Atlantic, but an order of magnitude lower than eelgrass in the Pacific. All but one meadow showed high rates of sexual reproduction. Almost all meadows were divergent but grouped into five genetic clusters. Four of the clusters correspond to geographic regions that can be used to define management units. Meadows in areas with a high decline in eelgrass between the 1980s and 2020s are more inbred than meadows in areas with an increase in eelgrass. Overall, our results indicate that striving to protect a number of large eelgrass meadows within each genetic cluster is important for maintaining the genetic diversity and connectivity of eelgrass in northwestern Sweden and is likely beneficial for the wider ecosystem. We estimate current indicators and essential biodiversity variables and discuss their challenges in marine facultative clonal species. We showcase how regional-scale conservation genomic assessments can serve as a foundation for protection and restoration of a priority species.

Assessment of Genetic Variability and Performance of Field Pea (Pisum sativum) Advanced Genotypes Across Environments

Assessment of Genetic Variability and Performance of Field Pea (Pisum sativum) Advanced Genotypes Across Environments

Genome‐wide SNP Detection in the Horse Mackerel (Trachurus trachurus, T. mediterraneus, T. picturatus) of Turkish Waters Using Illumina and Nanopore Sequencing

The horse mackerel, distributed in the Pacific, Atlantic, Indian Ocean, and Mediterranean waters, is economically valuable due to its high nutritional content and fishing capacity. Global market demand for this species has been increasing over the years. This rising demand causes fishing pressure, endangering the species' sustainability. Especially the horse mackerel species (Trachurus trachurus, Trachurus mediterraneus and Trachurus picturatus), which are found as mixed stocks in Turkish waters and under fishing pressure, should be considered as different stocks and evaluated with distinct management strategies. However, due to the difficulty of distinguishing these three Trachurus species based on morphological characteristics, conflicting reports have emerged, particularly regarding their distribution areas, and species identification is not always precise. In our study, we sequenced the genomes of these species using next-generation sequencing (Illumina) and third-generation sequencing technologies (Oxford Nanopore), and identified SNP (single nucleotide polymorphism) differences to distinguish the species. We identified a total of 2311386 SNPs in the Trachurus trachurus genome, of which 1313612 were transitions and 997774 were transversions. 5099766 SNPs in the Trachurus picturatus genome, of which 2927066 transitions and 2172700 transversions. Similarly, 5007863 SNPs in the Trachurus mediterraneus genome, of which 2940560 transitions and 2067303 transversions. These SNP datasets provide a robust genetic marker toolkit for accurately distinguishing Trachurus species and evaluating genetic diversity within and between populations. The findings of this study contribute essential genetic resources for defining the stock structures of these species, informing sustainable fisheries management strategies, and guiding conservation initiatives. By addressing the challenges of species identification and genetic diversity assessment, this research lays the groundwork for mitigating the impact of overfishing and ensuring the sustainability of horse mackerel populations in Turkish and global waters.

Assessment of Genetic Variability, Heritability and Correlation in Crossandra (Crossandra infundibuliformis (L.) (Nees) Genotypes

Assessment of Genetic Variability, Heritability and Correlation in Crossandra (Crossandra infundibuliformis (L.) (Nees) Genotypes

Assessment of genetic diversity in Sehima nervosum for yield, nutritional traits and ensiling quality

Assessment of genetic diversity in Sehima nervosum for yield, nutritional traits and ensiling quality

Assessment of genetic variability, heritability and genetic advance in bread wheat (Triticum aestivum L.)

Assessment of genetic variability, heritability and genetic advance in bread wheat (Triticum aestivum L.)

Evaluation of three mitochondrial DNA markers for species identification, genetic diversity assessment, and phylogenetic positioning of five Hyalomma tick species from Tunisia

Evaluation of three mitochondrial DNA markers for species identification, genetic diversity assessment, and phylogenetic positioning of five Hyalomma tick species from Tunisia

Genetic diversity assessment of black pepper (Piper nigrum L.) cultivars of Western Ghats

The Western Ghats of Kerala, the centre of origin of black pepper (Piper nigrum L.), hold a rich repository of landraces and local cultivars, that farmers have maintained over centuries. A survey conducted in these regions identified 21 genotypes with superior yields and distinct characteristics, reflecting the diverse genetic makeup of black pepper across agroclimatic conditions in the state. Moderate variability was observed among these genotypes in qualitative morphological traits, but it was still significant enough to differentiate them. Using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), the genotypes were grouped into 15 clusters at 73 % genetic similarity, indicating shared characteristics and unique differences. Biochemical evaluation revealed variations in their piperine (3.0–5.6 %), essential oil (3.0–5.6 %) and oleoresin (6.3–13.2 %), which could have implications for flavour, aroma and medicinal properties. Principal Component Analysis (PCA) identified 9 main and independent components explaining 86.59 % of the total variance, with yield-related and physiological traits contributing significantly to the overall diversity. Genotypes G16, G15, G21, G1, G5 and G4 exhibited considerable genetic divergence and desirable qualities. This highlights the potential for leveraging these genotypes to develop improved black pepper varieties with enhanced traits such as yield, quality and resilience to various environmental conditions. The study provides insights into the genetic and biochemical diversity of black pepper germplasm in the Western Ghats of Kerala, offering a foundation for future breeding efforts to enhance the productivity and sustainability of black pepper cultivation.

Genetic analysis of yield and yield components and powdery mildew resistance in F4 and F5 populations of blackgram

The present investigation aimed to evaluate 96 F4 and F5 genotypes, including two parental lines (VBN11 and LBG17) of blackgram, across two locations for yield, yield components, and resistance to powdery mildew. Pooled analysis, genetic variability assessment, correlation studies, parent-regression coefficient analysis, and the Multi-trait Genotype Ideotype Distance Index (MGIDI) were performed. Combined ANOVA revealed significant differences for all the traits studied. In the combined analysis, genotypes G3 and G1 exhibited desirable yields along with powdery mildew resistance. High heritability and genetic advance as a percentage of the mean (GAM) were observed for the traits such as single plant yield, the number of pods per plant, and percent disease index (PDI). Seed yield per plant recorded significant and positive correlations with the number of clusters per plant, number of pods per plant, number of seeds per pod, and 100-seed weight in both generations. Among the traits, PDI showed the highest regression coefficient. Principal component analysis exhibited four principal components (PCs) explaining the total variance in the F4 and F5 generations. The MGIDI index analysis revealed a total genetic gain for specific traits, including the number of pods per plant, single plant yield, and the number of capsules per plant in the F5 generation. Genotypes G18, G19, G4, and G38 were identified as valuable genetic resource through MGIDI, contributing significantly to blackgram improvement for high yield and powdery mildew resistance.

Intraspecific Chloroplast Genome Genetic Polymorphism of Pinellia ternata (Xi Junecry) and Its Revelation of a Single Origin in Phylogeny.

Background: Xi Junecry (Pinellia ternata), a perennial herb of the Araceae family, is indigenous to Xinxian County, Henan Province, China, and is regarded as a premium variety among similar medicinal materials. However, the lack of comprehensive genetic information on Xi Junecry germplasm resources has constrained the cultivation and identification of high-quality varieties. Methods: In this study, six chloroplast genomes of Xi Junecry were assembled and annotated using high-throughput sequencing. Subsequently, comparative analyses were conducted, and a phylogenetic tree was constructed. Results: The six Xi Junecry chloroplast genome lengths ranged from 157,456 to 158,406 bp, and the GC content was between 36.0% and 36.2%. A total of 265 single nucleotide polymorphism sites were identified across the six genomes, with a whole-genome nucleotide diversity (Pi) value of 0.00084. Among the four genomic regions, the small single-copy region exhibited the highest Pi, followed by the large single-copy region, while the inverted repeat region showed the lowest. Nucleotide polymorphism in coding regions was significantly lower than in non-coding regions. Nine hypervariable regions were identified, as follows: ndhE-ndhG, trnN-GUU-ndhF, trnS-GCU-trnG-UCC, atpB-rbcL, psaI, accD-ycf4, psbE-petL, psaC-ndhE, and psbI-trnG-UCC. Positive selection sites were detected in the accD and rbcL genes. Phylogenetic analysis clustered the six Xi Junecry samples into a distinct clade, separating them from other regional Pinellia samples. Conclusions: These findings elucidate the genetic variation levels in Xi Junecry and provide high-variability loci for population history inference, genetic diversity assessment, species domestication studies, and new cultivar development.

High-Resolution Genome Assembly and Population Genetic Study of the Endangered Maple Acer pentaphyllum (Sapindaceae): Implications for Conservation Strategies

Abstract Acer pentaphyllum Diels (Sapindaceae), a highly threatened maple endemic to the dry-hot valleys of the Yalong River in western Sichuan, China, represents a valuable resource for horticulture and conservation. This study presents the first chromosomal-scale genome assembly of A. pentaphyllum (~626 Mb, 2n = 26), constructed using PacBio HiFi and Hi-C sequencing technologies. Comparative genomic analyses revealed significant recent genomic changes through rapid amplification of transposable elements, particularly long terminal repeat retrotransposons, coinciding with the dramatic climate change during recent uplift of the Hengduan Mountains. Genes involved in photosynthesis, plant hormone signal transduction, and plant-pathogen interaction showed expansion and/or positive selection, potentially reflecting adaptation to the species’ unique dry-hot valley habitat. Population genomic analysis of 227 individuals from 28 populations revealed low genetic diversity (1.04 ± 0.97 × 10-3) compared to other woody species. Phylogeographic patterns suggest an unexpected upstream colonization along the Yalong River, while Quaternary climate fluctuations drove its continuous lineage diversification and population contraction. Assessment of genetic diversity, inbreeding, and genetic load across populations revealed concerning levels of inbreeding and accumulation of deleterious mutations in small, isolated populations, particularly those at range edges (TKX, CDG, TES). Based on these results, we propose conservation strategies, including the identification of management units and recommendations for genetic rescue. These findings not only facilitate the conservation of A. pentaphyllum but also serve as a valuable resource for future horticultural development and as a model for similar studies on other endangered plant species adapted to extreme environments.

Genetic Structural Changes While Maintaining Effective Population Size of Bighead Catfish in Nong Han Lake: Implications of Metapopulation Dynamics or Release Activities

ABSTRACTThe Bighead Catfish (Clarias macrocephalus) plays crucial roles in the ecosystem and as a protein source for humans in Nong Han Lake, Thailand, but their ecological and population dynamics, along with their genetic diversity and structure, are poorly understood. Therefore, the dynamics of genetic diversity and differentiation of bighead catfish populations in Nong Han Lake were investigated during 2018–2023 to provide essential insights into preserving biodiversity and maintaining ecological balance. Microsatellite genotyping was used to assess the genetic diversity of one bighead catfish population in 2018, two populations in 2023, and one hatchery population. Potentially stable, effective population sizes and distinct genetic clusters of these populations were identified, which represented the resilience of populations and the complexity of their genetic dynamics. Genetic differentiation between sample dates and among populations suggested that limited recent and historical genetic exchanges could potentially influence genetic structure. The impact of ecological factors, including flooding, metapopulation dynamics, and human interventions, was indicated by unique and shared gene pools among populations and subpopulations in different years. Ongoing assessment of genetic diversity and structure of bighead populations is essential for developing conservation strategies and ensuring sustainable management.

Assessment of Genetic Variability and Trait Associations in Chickpea (Cicer arietinum L.) Germplasms for Targeted Breeding Strategies

Chickpea (Cicer arietinum L.) is a pivotal legume crop with substantial contributions to global food security and agricultural sustainability due to its high protein content, adaptability and nitrogen-fixing ability. The efficiency of breeding programs in enhancing chickpea productivity and resilience relies heavily on understanding and utilizing genetic variability within the germplasm. This study investigates the extent of genetic variability among forty-three chickpea genotypes, focusing on key traits such as number of pods (NPP), biological yield (BY), harvest index (HI), days to flowering (DTF), days to maturity (DTM), that influence yield and other agronomic characteristics. Analysis of variance showed significant variability among genotypes for various traits. Higher phenotypic coefficients of variation (PCV) compared to genotypic coefficients (GCV) indicated the presence of environmental influence, particularly for traits like number of pods per plant (NPP) and biological yield (BY). High heritability was observed for days to flowering (DTF) and maturity (DTM), while genetic advance as percent of mean (GAM) varied, indicating additive gene action for some traits. Correlation and path analysis revealed positive relationships between plot yield and traits such as Days to Flowering (DTF), plant height (PH), and harvest index (HI). Principal component analysis (PCA) and cluster analysis indicated significant genetic diversity, grouping genotypes into clusters and identifying top performers like GJG1801 and NBEG 924. This study emphasizes the importance of genetic variability in breeding programs, aiding in the selection of elite genotypes for targeted traits improvement.

Assessment of genetic diversity and population structure analysis in Himalayan garlic genotypes from Sikkim using SSR markers.

Garlic (Allium sativum L.) is an important crop with significant medicinal and culinary uses. Understanding the genetic diversity and population structure of Himalayan garlic genotypes from Sikkim is crucial for effective breeding and conservation efforts. This study aims to analyze the genetic diversity among 60 Himalayan garlic genotypes collected from various altitudinal locations of Sikkim, India, using 27 Simple Sequence Repeats (SSR) markers. The genetic diversity was assessed using SSR markers, which revealed substantial variation among the genotypes. The number of alleles (Na) ranged from 1.13 to 2.00, while the major allele frequency (MAF) varied from 0.672 to 0.963. The observed heterozygosity (Ho) ranged from 0.0667 to 0.475, indicating moderate genetic diversity. Population structure analysis using STRUCTURE software grouped the genotypes into three distinct sub-populations, suggesting genetic differentiation not solely based on leaf morphology. Analysis of Molecular Variance (AMOVA) showed that genetic variation was more significant among individuals within populations (41%) than among populations (16%). UPGMA dendrogram and Principal Coordinates Analysis (PCoA) further confirmed the genetic relationships among the genotypes. This study reveals significant genetic diversity among Himalayan garlic genotypes from Sikkim, with clear genetic differentiation observed within and between populations. The results highlight the importance of both leaf morphology types and genetic structure in understanding the genetic basis of phenotypic variation in garlic. The finding provides valuable insights for future breeding programs and conservation strategies, emphasizing the need to consider morphological and genetic data for effective germplasm management and improvement of garlic cultivars.