Genetic Diversity Analysis Research Articles

Whole-Genome Sequencing Analysis of Antimicrobial Resistance, Virulence Factors, and Genetic Diversity of Salmonella from Wenzhou, China

Salmonella species are important foodborne pathogens worldwide. Salmonella pathogenicity is associated with multiple virulence factors and enhanced antimicrobial resistance. To determine the molecular characteristics and genetic correlations of Salmonella, 24 strains of Salmonella isolated from different sources (raw poultry, human stool, and food) in the Wenzhou area were investigated to determine the distribution of antimicrobial resistance and virulence determinants using whole-genome sequencing (WGS). Aminoglycoside resistance genes were detected in all samples. Over half of the samples found antimicrobial resistance genes (ARGs) and point mutations for several clinically frequently used antibiotic, beta-lactams, tetracyclines, and quinolones. Of these strains, 62.5% were predicted to be multidrug-resistant (MDR). The quinolone-modifying enzyme gene aac(6’)-Ib-cr, detected in five samples (S1–S4 and S10), was located on integrons. The analysis of Salmonella pathogenicity island (SPI) profiles suggests that serotypes with close genetic relationships share the same distribution of virulence factors, revealing a link between genotype and SPI profiles. cgMLST analysis indicated that five isolates S14–S18 were closely related to strains originating from the United Kingdom, suggesting that they may share a common origin. Data from this study may enrich the molecular traceability database for Salmonella and provide a basis for effective public health policies.

Analysis of Genetic Variability, Heritability and Genetic Advance for Yield and Yield-related Traits of Linseed (Linum usitatissimum L.)

Linseed is recognized as an excellent source of essential minerals, nutrients, and is particularly rich in omega-3 fatty acids and alpha-linolenic acid (ALA), making it highly recommended for cardiovascular health. It is cultivated mainly for both linen and oil production, which is used for the production of paints, varnishes, and linoleum paste. The objective of the present investigation was to analyze genetic variability, heritability, and genetic advance for yield and yield traits among 75 linseed genotypes including ten checks using Randomized Block Design with three replications at Oilseeds Research Farm, Kalyanpur, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur, Uttar Pradesh, (India) during Rabi season 2019-20. Analysis of variance revealed significant variation across all studied traits. The genotypic coefficient of variation (GCV) and phenotypic coefficient of variation (PCV) ranged from low to high, with the lowest GCV and PCV observed for days to maturity, number of seeds per capsule, and days to 50% flowering. Conversely, the highest GCV and PCV values were recorded for seed yield per plant (g), number of capsules per plant, number of secondary branches per plant, and plant height. All traits recorded the highest heritability. High heritability and genetic advance were recorded for seed yield per plant, number of capsules per plant, number of secondary branches per plant, plant height, thousand seed weight, number of primary branches and oil content, indicating the presence of additive gene action for these characters. In conclusion, the genotypes studied show significant genetic variation for yield and its attributes, which should be leveraged in future breeding programs.

Telomere-to-telomere Genome Assembly of two representative Asian and European pear cultivars

As the third most important temperate fruit, Pear (Pyrus spp.) exhibits a remarkable genetic diversity and is classified into two mainly categories known as Asian pear and European pear. Although several pear genomes are available, most of the released versions are fragmented and not chromosome-level high-quality. In this study, we report two high-quality genomes for Pyrus bretschneideri Rhed. cv. ‘Danshansuli’ (DS) and Pyrus communis L. cv. ‘Conference’ (KFL), which represent the predominant Asian and European cultivars, respectively, with nearly telomere-to-telomere (T2T) gap-free level. The finally assembled genome sizes for DS and KFL were 510.98 Mb and 510.71 Mb, respectively, with Contig N50 of 29.47 Mb and 30.47 Mb, where each chromosome was represented by a single contig. The DS and KFL genomes yielded a total of 46,394 and 44,702 protein-coding genes, respectively. Among these genes, the functional annotation accounted for 96.47% and 96.46% in the DS and KFL genomes. The two novels nearly T2T genomic information offers an invaluable resource for comparative genomics, genetic diversity analysis, molecular breeding strategies, and functional exploration.

Genetic Diversity and Association Analysis of Traits Related to Water-Use Efficiency and Nitrogen-Use Efficiency of Populus deltoides Based on SSR Markers.

Populus deltoides is one of the primary tree species for bioenergy production in temperate regions. In arid/semi-arid northern China, the scarcity of water and nitrogen significantly limits the productivity of poplar plantations. The identification of relevant molecular markers can promote the breeding of resource-efficient varieties. In this study, 188 genotypes of P. deltoides from six provenances served as experimental material. Genetic differentiation analysis, analysis of molecular variance (AMOVA), principal coordinate analysis (PCoA), unweighted pair group method with arithmetic mean (UPGMA) clustering, and genetic structure analysis were performed using selected simple sequence repeat (SSR) markers. Based on these analyses, the association analysis of water-use efficiency (WUE) and nitrogen-use efficiency (NUE) were conducted using general linear model (GLM) and mixed linear model (MLM) approaches. The results showed that 15 pairs of SSR primers successfully amplified across all 188 individuals, with an average of 7.33 alleles (Na) observed per primer pair. The polymorphism information content (PIC) ranged from 0.060 to 0.897, with an average of 0.544, indicating high genetic diversity in the selected markers. The average inbreeding coefficient intra-population (Fis), inbreeding coefficient inter-population (Fit), and inter-population genetic fraction coefficient (Fst) values were 0.005, 0.135, and 0.132, respectively, indicating high heterozygosity, substantial inbreeding within populations, and moderate genetic differentiation, with an average gene flow (Nm) of 1.964, suggesting substantial gene flow between populations. Additionally, molecular variance was primarily within individuals (84.12%). Genetic structure analysis revealed four subgroups, with some degree of genetic admixture among the provenances. In the GLM model, 11 markers were significantly associated with five traits (p < 0.05), with an average contribution rate of 15.82%. Notably, SSR132 and SSR143 were significantly associated with multiple traits (p < 0.05). The MLM model identified two markers (SSR47 and SSR85) significantly associated with ground diameter (p < 0.05) and one marker (SSR80) significantly associated with NUE (p < 0.05). This study identifies loci associated with WUE and NUE, laying a foundation for future genetic improvement and marker-assisted breeding strategies in poplar.

Phylogenetic and Genetic Diversity of the Spiny Eel Mastacembelus unicolor (Mastacembelidae) from Kediri, East Java, Indonesia

The spiny eel from the family Mastacembelidae are potential fish for aquaculture because it’s high economic value as an ornamental and as a consumption fish. Unfortunately, this fish have not been cultivated yet and up to present local people depend on wild-caught. This situation leads to severe population decline of this species in nature. Efforts to cultivate or protect this species in nature are therefore crucial. Species identification is the first and essential step performing domestication or conservation of a species. In this study, we conducted morphological identification as well as phylogenetic and genetic diversity analyses using cytochrom c oxidase subunit I gene. The results revealed spiny eel from Kediri can be identified as Mastacembelus unicolor based on both morphological and molecular analyses. The phylogenetic analyses suggested that individuals from Kediri have the closest relationship to M. unicolor individuals from West Java. Individuals sequenced from Kediri exhibit identical haplotype which indicating no genetic polymorphism between individuals. The individuals of Mastacembelidae in the Kediri were morphologically and genetically identified as Mastacembelus unicolor. The genetic analysis result shows Kediri have 53.13% AT, 48.67% GC, and one haplotype with low hd and low π value.

Population genetic diversity analyses reveal the determinants of genetic variation of banana endogenous virus sequences in China

Population genetic diversity analyses reveal the determinants of genetic variation of banana endogenous virus sequences in China

Genetic diversity and fingerprinting of Elaeagnus angustifolia based on SSR molecular markers

DNA fingerprinting can reveal the genetic diversity of Elaeagnus angustifolia germplasm resources and clarify the source and genetic background of E. angustifolia germplasm, which are the preconditions for the breeding of new varieties, the identification and protection of germplasm resources, and the comprehensive development of the E. angustifolia industry considering both ecological and economic benefits. We employed 11 pairs of primers with high polymorphism, clear bands, and high reproducibility to analyze the genetic diversity of 150 E. angustifolia germplasm accessions from Gansu and Beijing by the simple sequence repeat (SSR) molecular markers. We then employed the unweighted pair-group method with arithmetic means (UPGMA) to perform the cluster analysis based on genetic distance and analyzed the genetic structure of the 150 germplasm accessions based on a Bayesian model in Structure v2.3.3. The genetic diversity analysis revealed the mean number of alleles (Na) of 7.636 4, the mean number of effective alleles (Ne) of 2.832 6, the mean Shannon genetic diversity index (I) of 1.178 1, the mean Nei's gene diversity index (H) of 0.582 1, the mean observed heterozygosity (Ho) of 0.489 9, the mean expected heterozygosity (He) of 0.584 0, the mean polymorphism information content (PIC) of 0.535 4, and the mean genetic similarity (GS) of 0.831 5. These results suggested that the E. angustifolia germplasm resources we studied exhibited significant genetic differences and rich genetic diversity. The cluster analysis revealed that the tested materials can be classified into 3 groups, with the main genetic distance (GD) of 0.422 9. The clustering results were not completely consistent with the geographic origin. The population structure analysis classified the germplasm accessions into 2 populations. We used 8 pairs of primers with high PIC to construct the fingerprints of 150 E. angustifolia germplasm accessions. The present study successfully constructs the DNA fingerprints and clarified the genetic relationship of the E. angustifolia germplasm resources in Gansu and Beijing, providing a theoretical basis for germplasm resource identification, breeding of elite varieties, application in gardening, and molecular-assisted breeding of E. angustifolia.

A retrospective study on biotinidase deficiency: analysis of the Eastern Anatolia region patient cohort

ABTRACT This study retrospectively reviews individuals diagnosed with biotinidase deficiency in Eastern Anatolia to analyze the genetic variants and their relationship with biotinidase activity levels. The research focuses on determining the percentage impact of different variants on enzyme activity. The study included 357 patients who presented to Erzurum City Hospital with symptoms of biotinidase deficiency between 2018 and 2023 and were referred to the medical genetics department. Biotinidase enzyme levels were determined using spectrophotometric and colorimetric techniques, while Sanger sequencing analyzed the four exons and intron boundaries of the BTD gene. In the analysis of 357 patients (181 boys, 176 girls), the most frequent variant was c.1270G > C | p.Asp424His. Biotinidase enzyme activity was above 30% in 97.3% of patients with a homozygous p.D424His mutation. The mutations that caused the most significant decrease in enzyme activity were c.410G > A p.Arg137His, c.38_delinsTCC p.Cys13phefs*36, and c.1535C > T p.Thr512Met. Hearing loss (4 patients) and optic atrophy (1 patient) were mainly observed in patients with the c.38_delinsTCC mutation (homozygous or heterozygous). Most patients were asymptomatic, and mild symptoms were effectively prevented with biotin treatment. This study provides a detailed analysis of genetic diversity and clinical presentation in biotinidase deficiency cases in Eastern Anatolia, demonstrating the efficacy of biotin treatment. It highlights the significant role of genetic variants in phenotypic diversity and the need for personalized treatment, calling for further genetic research to enhance understanding of variant diversity and its impact on enzyme activity.

Identification of Diverse Maize Inbred Lines using Molecular and Phenotypic Genetic Divergence Analysis

Identification of Diverse Maize Inbred Lines using Molecular and Phenotypic Genetic Divergence Analysis

Spatial analysis and sequential equation modeling (SEM) of genetic diversity in date palm (Phoenix dactylifera L.)

Spatial analysis and sequential equation modeling (SEM) of genetic diversity in date palm (Phoenix dactylifera L.)

Single Nucleotide Polymorphisms and Insertion/Deletion Variation Analysis of Octoploid and Decaploid Tropical Oil Tea Camellia Populations Based on Whole-Genome Resequencing.

Oil tea camellia (Camellia spp.) is an important woody oil crop with a high nutritional and economic value. Whole-genome resequencing (WGR) technology can provide an in-depth understanding of the genetic background of this plant as well as a reference for breeding research, germplasm resource conservation, and genetic modification. In this study, we analyzed SNP and InDel variations in 49 individual oil tea camellia germplasm samples collected from five populations located in three provinces of China: Hainan, Guangdong and Guangxi. The samples were analyzed through WGR after the ploidy of the samples was determined through flow cytometry. A total of 239,441,603 high-quality single nucleotide polymorphisms (SNPs) and 23,510,374 high-quality insertion/deletion variation sites (InDels) were obtained. The distribution of SNPs and InDels in different functional regions differed significantly, with a high density of variations in non-coding regions, such as intergenic regions and introns, and a relatively low density of variations in coding regions. Transition was the main type of SNP variation. A population genetic diversity analysis revealed that the sampled oil tea camellia populations exhibited a high genetic diversity and extensive genetic variation. The genetic diversity of the oil tea camellia populations in the Hainan region was higher than inland regions. This study also determined the genetic diversity of and variations between octoploid and decaploid oil tea camellia in the tropics and between Hainan-based and inland oil tea camellia. Such findings provide a reference for the conservation of germplasm resources and the genetic modification of oil tea camellia.

Genetic variability, character association and path analyses effects on fiber yield and yield attributing morpho-agronomic traits of tossa jute (Corchorus olitorius L.)

Jute (Corchorus spp.) is a natural fiber crop having a lower extent of genetic variability due to its self-pollinating nature. The success of any breeding program for variety development primarily depends on the presence of genetic variation in the parental genotypes. A field experiment was conducted in a randomized complete block design at ManikganjStation of Bangladesh Jute Research Institute (BJRI) during 2019-2020. The genetic divergence of 58 tossa jute (C. olitorius) genotypes including two pre-released standard varieties (O-9897, BJRI Tossa pat 4) and 56 accessions were studied to select genotypes having the most divergence in natural rainy condition. The jute genotypes were categorized into five clusters based on Mahalanobis D2 analysis. Cluster I and IV showed maximum inter-cluster distance (181.44) while the maximum intra-cluster distance (16.15) was recorded in cluster I. Cluster V revealed the highest values for number of nodes, stem mid-diameter, core diameter, green weight with leaves, dry stick weight and dry fiber weight per plant while cluster IV showed higher means for plant height, green bark thickness and leaf area. The highest contribution (47.14%) was wielded by plant height of total deviations. The results recommended that hybridization between genotypes of cluster V, IV and III could provide a wide range of discrepancies in the segregating generation which could offer chance for isolation of good genotypes with high fibre yielding lines.

A Comprehensive Assessment of Nutritional Value, Antioxidant Potential, and Genetic Diversity in Metapenaeus ensis from Three Different Populations.

Due to its high tolerance to salinity and temperature, as well as its strong adaptability, Metapenaeus ensis holds an important position in the Chinese aquaculture industry. However, studies on the evaluation of its germplasm resources remain insufficient. This research conducted an in-depth comparative evaluation of M. ensis from three representative farming regions in China: Sanya, Zhuhai, and Raoping. The nutritional analysis of muscle tissue showed no statistically significant differences in crude ash, moisture, and crude protein content among the populations (p > 0.05). However, significant differences were observed in crude fat and total sugar content (p < 0.05). The MeSY and MeRP populations had higher crude fat content than the MeZH population (p < 0.05), while the MeZH population exhibited the highest total sugar content. In terms of amino acid composition, the MeSY population had relatively higher total essential amino acid content and proportion, as well as higher total amino acid content, both of which were statistically significant (p < 0.05). A fatty acid composition analysis further highlighted the advantages of the MeRP population in several key fatty acids (p < 0.05). Physiological and biochemical analyses showed no significant differences among the three populations in total antioxidant capacity, superoxide dismutase activity, or catalase activity (p > 0.05). A genetic diversity analysis indicated that M. ensis has relatively low diversity, with the MeSY population showing higher SNP density and nucleotide diversity. A genetic differentiation analysis revealed significant genetic differentiation between the MeSY and MeZH populations, while differentiation between the MeZH and MeRP populations was relatively smaller. This comprehensive assessment of nutritional components, amino acids, fatty acids, antioxidant capacity, and genetic diversity highlights the advantages of germplasm resources from different regions. These findings provide valuable insights for future research on the genetic characteristics and breeding potential of M. ensis.

Genetic diversity and structure of Persicaria amphibia (Polygonaceae) in South Korea using genotyping by sequencing.

Persicaria amphibia, a member of the Polygonaceae family, exists both aquatic and terrestrial forms. It is native to North America, Asia, Europe, and some parts of Africa. This study aimed to determine the genetic diversity within and among populations of P. amphibia and the distribution characteristics of each population to investigate insights into the genetic structure and conservation of P. amphibia. In this study, the genetic diversity and structure of 84 P. amphibia individuals from 7 populations in South Korea were analyzed using genotyping-by-sequencing (GBS). We used 2,469 single nucleotide polymorphisms (SNPs) to analyze genetic diversity, principal components, structure, and phylogeny. Our results showed a mean observed heterozygosity and mean expected heterozygosity of 0.34409 and 0.34082, respectively. Genetic diversity analysis indicated that the variation among populations (60.08%) was greater than that within populations (39.92%). Fixation index values, principal components analysis, structure, and phylogeny analyses showed that the population in Gyodongdo, Ganghwa Island was highly different. These results provide important insights for better understand the population history and genetic structure of P. amphibia.

Monitoring the genetic diversity in holothurian populations from the Italian coasts with mitochondrial DNA sequences

Sea cucumbers are deposit feeding members of marine benthic communities. The over-exploitation of sea cucumber natural stocks, especially in the Mediterranean basin, is having negative impacts on the marine ecosystem. This concerns had led the Italian government to take legal actions to preserve these important marine resources. The aim of this study was to evaluate the level of genetic diversity and population structures within two sympatric Holothuria sea cucumber species, H. polii and H. tubulosa, across ten Mediterranean areas along Italy. A 323 bp portion of the COI mitochondrial gene was sequenced in a total of 441 holothurians (251 H. polii, 177 H. tubulosa and 13 from other species). Genetic diversity analyses and analysis of molecular variance (AMOVA) suggest that H. polii and H. tubulosa species are distinct, but within and among populations are homogeneous, indicating active gene flows across the Mediterranean areas investigated. H. polii showed a lower genetic diversity than H. tubulosa, probably related to differences in life history traits. Phylogenetic analyses showed a clear differentiation between the two species, even if six specimens morphologically assigned to a species clustered within the other species, indicating a possible occurrence of hybridization events. These data will be useful in implementing conservation actions for these holothurian genetic resources.

Population Genetic Investigation of Hypophthalmichthys nobilis in the Yangtze River Basin Based on RAD Sequencing Data.

The Bighead carp (Hypophthalmichthys nobilis), a primary freshwater aquaculture species in China, faces challenges due to over-exploitation and environmental changes. We leveraged RAD-seq to perform a comprehensive population genetic analysis on 14 H. nobilis populations sampled from the Yangtze River (13 populations) and the Marseilles Reach of the Illinois River (one population). Analysis of genetic diversity showed that different parameters demonstrated varied inferences, and notably, Zhongxian (ZX2), Wanhzou (WZ2), Yangzhou hatchery (YZYZ), Yangzhou (YZ), and Taihu (TH) populations showed apparent heterozygote deficiency. Linkage disequilibrium (LD) analysis exhibited a trend of higher linkage disequilibrium in populations from the upper reaches of the Yangtze River, followed by those from the middle reaches and then those from the lower reaches. Additionally, the reconstructed polygenetic tree and PCA plot clustered all populations into 2 major subgroups, while the results of structure analysis indicated 4 ancestors. The pairwise FST values ranged from 0 to 0.5530. Among these, high FST values (0.1931-0.5530) were only observed between populations WZ2, YZ, YZYZ, and the remaining 11 populations. Furthermore, genetic bottlenecks were observed in all populations 20-30 thousand years ago. Overall, the research offers insights essential for genetic management practices for sustainable aquaculture and biodiversity conservation of bighead carp.

Genome-wide association studies in a diverse strawberry collection unveil loci controlling agronomic and fruit quality traits.

Strawberries (Fragaria sp.) are cherished for their organoleptic properties and nutritional value. However, breeding new cultivars involves the simultaneous selection of many agronomic and fruit quality traits, including fruit firmness and extended postharvest life. The strawberry germplasm collection here studied exhibited extensive phenotypic variation in 26 agronomic and fruit quality traits across three consecutive seasons. Phenotypic correlations and principal component analysis revealed relationships among traits and accessions, emphasizing the impact of plant breeding on fruit weight and firmness to the detriment of sugar or vitamin C content. Genetic diversity analysis on 124 accessions using 44,408 markers denoted a population structure divided into six subpopulations still retaining considerable diversity. Genome-wide association studies for the 26 traits unveiled 121 significant marker-trait associations distributed across 95 quantitative trait loci (QTLs). Multiple associations were detected for fruit firmness, a key breeding target, including a prominent locus on chromosome 6A. The candidate gene FaPG1, controlling fruit softening and postharvest shelf life, was identified within this QTL region. Differential expression of FaPG1 confirmed its role as the primary contributor to natural variation in fruit firmness. A kompetitive allele-specific PCR assay based on the single nucleotide polymorphism (SNP) AX-184242253, associated with the 6A QTL, predicts a substantial increase in fruit firmness, validating its utility for marker-assisted selection. In essence, this comprehensive study provides insights into the phenotypic and genetic landscape of the strawberry collection and lays a robust foundation for propelling the development of superior strawberry cultivars through precision breeding.

Simple Sequence Repeat Marker-Based Genetic Diversity and Chemical Composition Analysis of Ancient Camellia sinensis in Jiulong County, Sichuan Province, China.

The ancient tea plant germplasm resources are rich in genetic diversity and provide an important basis for the genetic diversity in tea germplasm resources. To explore the genetic diversity of ancient tea plant germplasm resources in Jiulong County, Sichuan Province. 59 ancient tea tree germplasm resources were analyzed using simple sequence repeat (SSR) molecular markers and chemical composition analysis. The results showed that a total of 83 alleles were amplified by 23 pairs of SSR primers, with an average observed allele number (Na) of 3.6 and an effective allele number (Ne) of 2.335. The average Shannon information index (I) and the polymorphic information content (PIC) of the primers were 0.896 and 0.446, respectively. The results of the UPGMA cluster analysis showed that 59 ancient tea tree samples could be classified into five different subgroups. Based on the results of chemical composition analysis, two specific tea germplasm resources with high amino acid content, 10 excellent germplasm resources with tea polyphenol content over 20% and some other tea germplasm resources were identified. This study reveals that Jiulong's ancient tea tree germplasm exhibits significant genetic diversity and includes valuable tea tree planting resources. These findings provide a foundational framework for the conservation, detailed exploration and sustainable utilization of these resources.

Unveiling the genetic variability, character association and principal component analysis for yield and yield contributing traits in brinjal (Solanum melongena) genotypes

The experiment was conducted during rainy (kharif) and winter (rabi) seasons of 2023 and 2024 at Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu to assess 45 brinjal (Solanum melongena L.) genotypes for growth and yield related parameters. The experiment was laid out in randomized block design (RBD) with three replications. The result showed high genotypic coefficient of variance (GCV) and phenotypic coefficient of variance (PCV) values for plant height, number of primary branches/plant, length of fruit and weight of fruit and yield/plant. Whereas, the traits such as days to first flowering, days to 50% flowering, fruit girth, fruit borer infestation and number of fruits/ plant exhibited medium GCV and PCV values. The registered high heritability values ranged from 94.29–99.49% and genetic advance as a percentage of the mean ranged from 19.25–70.25%. Correlation analysis on number of fruits/ plant showed positive and significant association with fruit yield/plant. Principal component analysis showed four principal components with eigen values of unity and accounted for 75.81% of total variance.

Multivariate genetic analysis and diversity assessment in lotus (Nelumbo nucifera) accessions

The present study was carried out during 2019 to 2022 at the Floriculture Research Station (Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu), Thovalai, Kanyakumari, Tamil Nadu to access the genetic variability in lotus accessions (Nelumbo nucifera) collected from 6 diverse locations. The research presents significant insights into the growth and flowering characteristics of these extraordinary aquatic plants and their adaptability to various environmental conditions. The analysis of mean performance showcases noteworthy variations in plant height, leaf dimensions, flowering time and the number of leaves, and flowers/plant across different collection sites, highlighting the profound influence of local environmental conditions on lotus growth. Lotus traits with significant genetic diversity and heritability, presenting opportunities for targeted selective breeding were identified. Principal component analysis uncovers key trait influencers, while cluster analysis categorizes accessions based on similarities, streamlining research and cultivation. Correlation and path analysis unveil relationships among lotus traits, enhancing our understanding of growth factors. D2 cluster composition reveals distinct groupings; Cluster I includes KNn1 and KNn5, Cluster II features KNn2, Cluster III comprises KNn6, Cluster IV contains KNn3, and Cluster V houses KNn4. Genetic divergence analysis identifies the number of flowers/plant as the primary driver of genetic diversity, emphasizing its importance for breeding. It underscores the need to consider both genetic and environmental factors in lotus cultivation and highlights the importance of targeted breeding efforts to unlock the full potential of lotus.