Gene Diversity Index Research Articles

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.

Evaluation of germplasm resources of Sarcomyxa edulis in the Changbai Mountains of Northeast China

ABSTRACT In this study, we evaluated 16 strains of Sarcomyxa edulis from the Changbai Mountains, China through antagonism tests and ISSR molecular marker technique for cytological and molecular biological evaluation. Q-type and R-type cluster analyses were utilised to evaluate and classify agronomic traits according to the test guidelines for distinctness, uniformity, and stability. The tested strains showed antagonistic reactions. The differences in antagonistic reactions among different germplasm resources are helpful for evaluating genetic diversity and provide a basis for better development and utilisation of fungal germplasm resources. A total of 330 bands were amplified by 21 ISSR primers, including 321 polymorphic bands. The percentage of polymorphic bands observed was 97.07%. Using PopGen32 software, the effective number of alleles (Ne), Nei's gene diversity index (H), and Shannon's diversity index (I) were calculated, yielding average values of 1.6638, 0.3796, and 0.5480, respectively. In addition, the genetic similarity coefficient of 16 strains ranged from 0.4306–0.7778. According to the Q-type clustering, the tested strains were classified into two categories based on the Euclidean distance of 8.52. While R-type cluster analysis revealed a significant correlation between the traits. At the Euclidean distance of 6.298, the traits could be classified into three distinct categories. According to the findings, all 16 strains demonstrated high genetic diversity. The ISSR clustering results revealed that strains with shorter genetic distances were more similar in specific traits. However, there were notable differences between the results of comprehensive trait clustering (Q-type clustering) and ISSR clustering.

Genetic diversity of SP1 population of space mutagenized Pueraria montana

To explore the mutagenic effect of the space environment on Pueraria montana and select the elite germplasm with good growth conditions and high isoflavone content, this study observed the agronomic traits, determined the flower isoflavone content, and labeled amplified fragment length polymorphism(AFLP) fluorescent molecular markers of 79 P. montana plants exposed to space mutagenesis(SP1 group) and 10 control plants of P. montana(CK group). Excel 2019, SPSS 25.0, NTSYSpc-2.11F, and Popgen 32 were employed to analyze the genetic diversity and perform the cluster analysis. The results showed that the SP1 group presented changed leaf hairy attitude and flower structure and higher CV and H' of quantitative traits than the CK group. The cluster analysis screened out five plants in the SP1 group. Ten P. montana plants in the SP1 group had higher content of 6″-O-xylosyl-tectoridin and tectoridin in the flowers than the control group, with the total content of both exceeding 11%. After clustering, 9 plants in the SP1 group were separated. Nine pairs of polymorphic primers were screened out frrom 64 pairs of primers. A total of 1 620 polymorphic loci were detected, with the average percentage of polymorphic loci(PPL) of 83.33%. The average Nei's gene diversity index(H) and Shannon's information index(I) were 0.192 2 and 0.305 2, respectively. After clustering, 4 plants in the SP1 group were screened out. According to the above results, plants No. 30, No. 66, and No. 89 in the SP1 group were subjected to greater mutagenic effect by the space environment and presented better growth and higher flower isoflavone content. Moreover, plant No. 30 showed the flower structure variation and flower weight two times of that in the CK group. These plants can be used as key materials for the subsequent experiments.

Genetic Diversity and Construction of Core Collection of Sterculia Germplasm

Amplification of 107 Sterculia accessions with 12 ISSR primers resulted in 235 bands, the percentage of polymorphic sites was 100%, with the average number of effective alleles (Ne) of 1.2464, the average Nei’s gene diversity index (H) of 0.1556, the average Shannon's information index (I) of 0.2563, and the average polymorphism information content (PIC) of 0.8594, indicating that the collected 107 accessions had high genetic diversity. The genetic diversity was unevenly distributed among Sterculia samples collected from different provinces, and the highest value was observed in samples from Guangdong Province, followed by those from Yunnan Province, and the lowest was from Guangxi Province. The core collection construction of the 107 Sterculia accessions was carried out by using the SCR and LDSS methods, respectively, and the results showed that the LDSS method was more suitable for Sterculia germplasm. Different core collections were constructed based on sampling proportions of 35, 30, 25, 20 and 15%, respectively, the t-test and principal coordinates analysis results showed that the genetic diversity of the original germplasm can be fully represented at a sampling proportion of 30%. Bangladesh J. Bot. 53(2): 319-325, 2024 (June)

Genetic diversity and population structure of Ethiopian basil (Ocimum basilicum L.) accessions using DArTseq markers

In Ethiopia, basil is the most widely used aromatic and medicinal herb. Despite being widely available across the nation and utilized for a variety of purposes for centuries, little is known about the degree of genetic variability in sweet basil. Thus, 62 basil accessions that were collected from various locations in Ethiopia were examined for genetic diversity and population structure, and genome-wide SNPs were created using genotyping by sequencing (GBS). The observed and expected heterozygosis are (0.01–0.02) and (0.13–0.33), respectively. The gene diversity index (GD) ranged from 0.13 to 0.29, with an overall mean of 0.13. Moreover, the polymorphic information content (PIC) varied from 0.23 to 0.37, with an average of 0.37. The Shannon index (I) ranged from 0.01 to 0.41, with an average of 0.12. A total variation of 90 % and 1 % within and among populations, respectively, was revealed using analysis of molecular variance (AMOVA). Furthermore, genetic variation showed a coefficient of gene differentiation of 0.01 and a gene flow value of 2.013 among populations. The 62 basil accessions were divided into two genetic groups according to STRUCTURE analysis, unweighted pair group method (UPGMA), discriminant analysis of principal components (DAPC), and principal coordinate analysis (PCoA). This research confirmed the diversity and population structure of the Ethiopian basil. Therefore, the variation pattern in their genetic diversity can serve as a basis for the selection, breeding, and maintenance of basil in Ethiopia.

Genetic characteristics of Blastocystis sp. in cattle from Hebei Province, China

Blastocystis sp. is a protozoan parasite that infects the intestines of humans and animals, causing chronic diseases such as skin rashes, abdominal pain, and irritable bowel syndrome. A survey was conducted to determine the prevalence and genetic diversity of Blastocystis sp. infection in cattle, in Hebei Province, China. 2746 cattle fecal samples were collected from 11 cities in Hebei Province and analyzed using polymerase chain reaction targeting the Blastocystis sp. barcoding gene. MEGA, PhyloSuite, and PopART were used to analyze the subtype, sequence signature, pairwise genetic distance, and genetic diversity indices. The results showed that the Blastocystis sp. detection rate was 12.60% (346/2746). The infection rate in different herds was affected by region, age, breeding mode, and variety; that is, the infection rates in areas of southern Hebei, cattle under one year old, intensive raising, and dairy cattle were higher than the infection rates in northern Hebei, cattle over one year old, scatter feeding, and beef cattle. Seven Blastocystis subtypes were identified, namely, ST1, ST2, ST5, ST10, ST14, ST21, and ST26; ST10 was the dominant subtype, and ST14 was the second most common subtype. A total of 374 polymorphic and conserved sites were obtained, including 273 invariable (monomorphic) sites and 101 variable (polymorphic) sites, accounting for 27.01% of all nucleotides. The nucleotide diversity index (Pi) was 0.07749, and the haplotype (gene) diversity index (Hd) was 0.946. This study provides the first comprehensive information on the epidemiological situation of Blastocystis sp. infection in cattle from Hebei Province, China, and revealed rich genetic diversity of Blastocystis sp.

Microsatellite Markers: A Tool to Assess the Genetic Diversity of Yellow Mustard (Sinapis alba L.)

Microsatellite markers were used for the assessment of genetic diversity and genetic structure in a germplasm collection of yellow mustard, Sinapis alba L. The comprehensive collection of genetic resources represented 187 registered varieties, landraces, and breeding materials. Microsatellites generated 44 polymorphic alleles in 15 loci. Eleven of them were medium to highly polymorphic, and the high levels of observed heterozygosity (0.12–0.83) and Nei’s gene diversity index (0.11–0.68) indicated a high level of polymorphism. Based on PCoA and neighbor joining analyses, the genetic resources were divided into two groups. The range of genetic dissimilarity in the analysed collection was in the range of 0.00–1.00. The high level of dissimilarity between the accessions was documented by the high WAM value (33.82%). Bayesian clustering algorithms were performed in the STRUCTURE 2.3.4 software. The number of clusters was estimated at K = 2. The accessions were classified according to Q1/Q2 values. The low average values of the parameters Fst_1 (0.3482), Fst_2 (0.1916), and parameter alpha (0.0602) indicated substantial mating barriers between varieties and reproductive isolation due to the limited exchange of genetic resources between breeders. These results demonstrated the importance of extensive collections of genetic resources for the maintenance of genetic diversity and indicated considerable genetic differentiation among accessions.

Genetic characterization of superior durian (Durio zibethinus L.) accessions in Batang District, Central Java, Indonesia based on ISSR markers

Abstract. Amrullah MI, Rahayu ES, Puwantoyo E, Maharani RI, Solichin, Sriyadi, Hadiprasetya TY, Retnoningsih A. 2023. Genetic characterization of superior durian (Durio zibethinus L.) accessions in Batang District, Central Java, Indonesia based on ISSR markers. Biodiversitas 24: 4811-4819. Durian (Durio zibethinus L.) has the highest level of genetic diversity in the genus of Durio. The genetic diversity of D. zibethinus in Batang District, Central Java, Indonesia needs to be explored to obtain data on superior durian accessions that are adaptive in the area. This study aimed to analyze the genetic diversity of 40 superior durian accessions from 13 locations in Batang District using 10 Inter Simple Sequence Repeat (ISSR) primers. Genomic DNA was isolated from leaves using a modified CTAB method. PCR products were electrophoresed on 2% agarose and yielded 161 ISSR alleles with a percentage of 100% polymorphic alleles. The level of genetic diversity based on Nei's gene diversity and Shannon's Information index are 0.277 and 0.434, respectively. The durian accessions studied have a similarity coefficient of 0.22-0.86 and are divided into two main clusters. Siwatu 1 and Siwatu 2 accessions have the highest genetic similarity coefficient (0.86), while Butternuts and Watu Tembogo 1 accessions show the lowest genetic similarity coefficient (0.05). Specific alleles were found in 11 durian accessions. The molecular characterization results show the high genetic diversity of superior durian accessions in Batang District and add to the list of local superior durian accessions in Indonesia.

Exploration of transcriptome SSR markers and its application in genetic diversity assessment of Asarum sieboldii

To explore the genetic diversity of Asarum sieboldii this study developed SSR markers based on transcriptome sequencing results and five populations of A.sieboldii from different regions were used as samples for genetic diversity assessment using software such as GenALEx 6.5, NTSYS 2.1, and Structure 2.3.4. The results showed that 16 SSR markers with high polymorphism and good repeatability were selected from the A.sieboldii transcriptome. Primers designed based on the flanking sequences of these markers successfully amplified 56 polymorphic fragments from 150 individual samples of the five A.sieboldii populations. On average, each primer amplified 3.5 polymorphic fragments, ranging from 2 to 8. The mean values of expected heterozygosity(H_e), Shannon's diversity index(I), Nei's gene diversity index(H), and the polymorphic information content(PIC) were 0.172, 0.281, 0.429, and 0.382, respectively. The mean population differentiation coefficient(F_(ST)) was 0.588, consistent with the analysis of molecular variance(AMOVA) results, which indicated greater genetic variation among A.sieboldii populations(69%) than that within populations(31%). The percentage of polymorphic loci(PPL) ranged from highest to lowest as SNJ>LN>SY>SZ>TB. Principal coordinate analysis(PCoA) and UPGMA clustering analysis further revealed genetic clustering of A.sieboldii individuals based on their geographical distribution, consistent with the results of the structure clustering analysis. In summary, the SSR markers developed from the transcriptome effectively assessed the genetic differentiation and population structure of natural A.sieboldii populations, revealing a relatively low genetic diversity in A.sieboldii, with genetic variation primarily observed at the population level and a correlation between population differentiation and geographic distance.

Genetic diversity assessment of some Iraqi Sheep breeds using micro satellite DNA markers

To assess genetic diversity among some Iraqi sheep breeds (Karadi, Jaff, and Awassi) randomly selected from three different locations of Sulaimani governorate (Jeshana, Halabjai Shahid and Kirkuk) respectively. A total of 150 blood samples were collected (50 animals per breed from both sexes) using 10 microsatellite markers, 7 were amplified and showed bands. Four primers were polymorphism and three were monomorphism. The results demonstrated that the total fragment number (TFN) for the 7 primes was 14 fragments. The overall polymorphic fragments number (PFN) was 6, the highest PFN found at locus OarJMP29 which had 3 bands, whereas the lowest PFN found at locus HUJ616, OarFCB20 and OarFCB304 which was 1 band. The overall mean percentage of polymorphic loci was 35.71 %. The OarJMP29 locus showed the highest polymorphism which was 100% and the lowest polymorphism was 0.0% for ILSTS5, MAF214, and OarJMP58 loci. In the current study mean value of number of alleles (Na) was 2 and effective number of alleles (Ne) was 1.5214. Nei’s gene diversity and Shannon index are respectively averaged of 0.3296, and 0.5063. The smallest genetic distance recorded between Jaff and Awassi which was 0.0554, while the farthest distance was observed between Karadi and Awassi 0.1168.The results of genetic identity showed that the Jaff and Awassi populations are more genetically alike (0.9461) while the Karadi and the Awassi populations were the least genetically identical (0.8898). The dendrogram tree separated the studied breeds into two clusters, the first one including Jaff and Awassi breeds, and the second cluster includes Karadi breed. Finally, moderate value for both of polymorphism and genetic diversity were observed among the studied sheep breeds, which will help in developing a suitable approach for the genetic improvement, utilization and conservation of Iraqi sheep breeds.

Perhaps there were northern refugia in LGM? The phylogeographic structure of the thermophilic tree Carpinus betulus in the Carpathian region

Carpinus betulus L., the hornbeam, is a component of lowland and highland forests in Europe. By examining the postglacial migratory history of thermophilic tree species, the study aimed to unravel their putative glacial microrefugia in the Carpathian region. The present study points to the two distinct genetic AFLP groups of C. betulus in the Carpathian region that represent different genetic lineages based on Bayesian analysis. They differed in Nei's gene diversity index h, and the analysis of molecular variance AMOVA showed a percentage variation of the populations between the groups of 13.74 %. Principal coordinate analysis (PCoA) of 368 AFLP tree samples confirmed the presence of two genetic groups. Ninety-five populations underwent principal component analysis (PCA) to show the main correlations between genetic diversity indices and bioclimatic/climate variables (WorldClim and Carpatclim). The generalized logistic model (GLM) showed the significance of Nei's genetic index h in delimiting genetic groups. The results of population-genetic and multivariate analyses determined that the two genetic groups nowadays are spatially diffused and do not show a clear geographic pattern, pointing to a genetic melting pot. We found ecological links between genetic diversity and bioclimatic characteristics, especially the precipitation in the coldest quarter – Bio19. The refugial Maxent model indicates a significant contribution of the Bio7 variable (both linked with a continental type of climate) to the occurrence of the species during the LGM in Europe. We suggest the relict character of hornbeam populations in a specific climatic-terrain niche in the northern part of the Carpathian Basin.

The Genetic Diversity and Genetic Structure of the Germplasm Resources of the Medicinal Orchid Plant Habenaria dentata.

Habenaria dentata has medicinal and ornamental value, but the number of wild populations is decreasing dramatically. Thus, conducting research on its genetic diversity and structure is necessary to provide a basis for its conservation. This study aimed to explore the genetic diversity of the wild plant H. dentata and protect and optimize its wild resources. The genetic diversity of 133 samples from six wild populations of H. dentata was analyzed using Inter Simple Sequence Repeat molecular markers to provide a scientific basis for the screening of improved germplasm resources. The results showed that the average number of alleles was 1.765, the average number of effective alleles was 1.424, the average Nei's gene diversity index was 0.252, the average Shannon diversity index was 0.381, and the average percentage of polymorphic loci was 76.499%. The variation within the populations was 77.34%, and the variation between the populations was 22.66%. The gene flow was 1.705, which was greater than 1. The results of the cluster analysis showed that the six populations were mainly divided into four clusters and were not classified according to their geographical location. There was no significant correlation between the geographical location and genetic distance between the populations (r = 0.557, p > 0.05). The genetic diversity of H. dentata is high. Among the six wild populations, the genetic diversity of the Mulun population was the highest and this population can be used as a key protection unit. The study on the genetic diversity of H. dentata can not only reveal the reasons for the decrease in the number of individuals in the population to a certain extent, and put forward the protection strategy, but also provide a scientific basis for the breeding of excellent seed resources.

Genetic diversity analysis and fingerprints of Chrysanthemum×morifolium based on SSR molecular markers

The present study aims to explore the genetic diversity of germplasm resources of Chrysanthemum×morifolium (hereinafter, C.×morifolium) at the molecular level and to establish a fingerprint database of C.×morifolium varieties. We employed 12 pairs of primers with high levels of polymorphism, clear bands, and high degrees of reproducibility to analyze the SSR molecular markers and genetic diversity of 91 C.×morifolium materials and 14 chrysanthemum- related materials. With regard to constructing the fingerprints of the tested materials, we chose 9 pairs of core primers. The findings revealed that 12 primer pairs detected 104 alleles in 105 samples, ranging from 2 to 26. The average number of observed alleles (Na) per site was 9.25. The average number of effective alleles (Ne) per site was 2.745 6, with its range being 1.276 0 to 4.742 5. Shannon genetic diversity index (I) values ranged between 0.513 3 and 2.239 9 (M=1.209 0). Nei's gene diversity index (H) ranged between 0.216 3 and 0.789 1 (M=0.578 0). The observed heterozygosity (Ho) ranged between 0.223 3 and 0.895 2 (M=0.557 5). The expected heterozygosity (He) ranged between 0.217 4 and 0.793 3 (M=0.580 8). The polymorphism information content (PIC) ranged between 0.211 5 and 0.774 0 (M=0.532 9). The genetic similarity (GS) ranged between 0.228 5 and 1.000 0 (M=0.608 3). Cluster analysis revealed that when the genetic distance (GD) equals to 0.30, the tested materials can be classified into 2 groups. When the GD equals to 0.27, the first group can be divided into 6 subgroups; accordingly, 105 tested materials can be divided into 7 subgroups. The cophenetic correlation test was carried out based on the cluster analysis, and the corresponding results showed that the cluster map correlated with the genetic similarity coefficient (r=0.952 73). According to the results of Structure population analysis, we obtained the optimal population number, with the true number of populations (K) being 3 and the population being divided concerning Q≥0.5. Three subgroups, i.e., Q1, Q2 and Q3, included 34, 33 and 28 germplasms, respectively, and the remaining 10 germplasms were identified as the mixed population. During the experiment, 9 pairs of core primers were screened among the total of 12 for a complete differentiation regarding 105 tested materials, and the fingerprints of 91 C.×morifolium materials and 14 chrysanthemum-related materials were further constructed. Overall, there were significant genetic differences and rich genetic diversity among C.×morifolium materials, which would shed light on the garden application and variety selection fields of C.×morifolium. The fingerprint database of 105 C.×morifolium varieties and chrysanthemum-related species may provide technical support for future research regarding the identification and screening system of C.×morifolium varieties.

English

Knowledge of the genetic variability of plantain cultivars in the Democratic Republic of the Congo (DRC) is limited. This study assessed genetic diversity and relationships in three plantain accessions differing in pseudostem color at seven microsatellite loci using SSR markers. DNA was extracted from banana leaves, and PCR was performed with unlabeled and fluorescent-labeled SSR primers and eventual capillary sequencing. Different population genetic analysis software was used to interpret the fragment analysis data. There was a high allelic power with a mean polymorphic information content of 0.83. A high average genetic diversity was indicated by Nei's Gene Diversity Index (h: 1.38) and the Shannon Information Index (I: 2.22). Pairwise genetic similarity between plantain genotypes averaged 0.82. A dendrogram grouped the 60 genotypes into three clusters. AMOVA showed high genetic variation within the population (98%) compared to the variation between populations, with no significant difference between the three cultivars regarding the color of the pseudostem. In contrast, these cultivars were closely related to each other. No correlation between the morphological and molecular characterization of cultivars was observed. We recommend a follow-up study with other plantain cultivars from other regions and large sample size for more representative data.   Key words: Characterization, microsatellites, genetic diversity, plantain cultivars.

Genetic Diversity and Population Structure in Türkiye Bread Wheat Genotypes Revealed by Simple Sequence Repeats (SSR) Markers.

Wheat genotypes should be improved through available germplasm genetic diversity to ensure food security. This study investigated the molecular diversity and population structure of a set of Türkiye bread wheat genotypes using 120 microsatellite markers. Based on the results, 651 polymorphic alleles were evaluated to determine genetic diversity and population structure. The number of alleles ranged from 2 to 19, with an average of 5.44 alleles per locus. Polymorphic information content (PIC) ranged from 0.031 to 0.915 with a mean of 0.43. In addition, the gene diversity index ranged from 0.03 to 0.92 with an average of 0.46. The expected heterozygosity ranged from 0.00 to 0.359 with a mean of 0.124. The unbiased expected heterozygosity ranged from 0.00 to 0.319 with an average of 0.112. The mean values of the number of effective alleles (Ne), genetic diversity of Nei (H) and Shannon's information index (I) were estimated at 1.190, 1.049 and 0.168, respectively. The highest genetic diversity (GD) was estimated between genotypes G1 and G27. In the UPGMA dendrogram, the 63 genotypes were grouped into three clusters. The three main coordinates were able to explain 12.64, 6.38 and 4.90% of genetic diversity, respectively. AMOVA revealed diversity within populations at 78% and between populations at 22%. The current populations were found to be highly structured. Model-based cluster analyses classified the 63 genotypes studied into three subpopulations. The values of F-statistic (Fst) for the identified subpopulations were 0.253, 0.330 and 0.244, respectively. In addition, the expected values of heterozygosity (He) for these sub-populations were recorded as 0.45, 0.46 and 0.44, respectively. Therefore, SSR markers can be useful not only in genetic diversity and association analysis of wheat but also in its germplasm for various agronomic traits or mechanisms of tolerance to environmental stresses.

Phytochemical and genetic marker (SCoT and CBDP) based study of genetic diversity and population structure in natural populations of Cannabis sativa L.: A high-value sustainable biodiversity of North-Indian Himalaya

Cannabis sativa is a versatile, sustainable cash crop grown in vast agro-climatic zones of India. The present study used comprehensive datasets involving phytochemical and molecular genotyping to characterize forty-two wild cannabis accessions collected from fourteen geographical locations of the North Indian Himalayas. Two gene-targeted dominant molecular markers, i.e., start codon targeted (SCoT) polymorphism and CAAT-box derived polymorphism (CBDP), were used for molecular genotyping to evaluate genetic assortment and interrelatedness among and within wild inhabitants of C.sativa. Multiple t-tests indicated significant differences among the studied cannabis populations for the phytochemical traits. Five major cannabinoids were identified in Indian Cannabis sativa germplasm, and most of the populations were of drug/marijuana types. The considerable diversity in drug types was observed at the chemical and genetic levels. Twenty-six SCoT and twenty-one CBDP markers generated a sum of 134, and 80 alleles averaged with 3.08 and 6.65 alleles per primer, respectively. The average polymorphic information content (PIC) and resolving power per primer indicated both SCoT and CBDP as ideal markers system for genetic diversity study in Cannabis sativa. The population diversity analysis based on SCoT, CBDP, and cumulative marker dataset revealed a high genetic differentiation (Gst>0.15), and a low estimated gene flow (Nm<1.0) between the studied populations. The highest gene diversity (H) and Shannon diversity Index (I) were observed for the population of Matiyal location (Pop3) using SCoT and cumulative marker dataset. However, Population 7 (Pop7) of location Kanatal was found to be highly diverse using the CBDP marker dataset. The multivariate analyses, i.e., Neighbour-joining tree based phenetic analysis, Principal Coordinate Analysis (PCoA), and Structure, revealed that there was no individual geographical location based grouping among the cannabis populations using both markers data set individually and their cumulative datasets. However, the allocation of accessions in common groups corresponding to their geographical locations was maximum in the case of Analysis with a cumulative marker data set. Analysis of molecular variance (AMOVA) also demonstrated a maximum percentage of molecular variation at the intra-population level (77–86%) rather than the inter-population level (14–23%). Altogether, our data suggest that both SCoT and CBDP markers are the ideal markers to study the genetic relationship among geographically different populations of C.sativa, and populations identified as highly diverse can be utilized as parents in Indian cannabis breeding programs.

Genetic diversity and haplotype analysis of Leishmania tropica identified in sand fly vectors of the genera Phlebotomus and Sergentomyia using next-generation sequencing technology.

Next-generation sequencing (NGS) was used to investigate the genetic diversity of Leishmania tropica in the sand fly vector, targeting the internal transcribed spacer 1 (ITS1) of the genus Leishmania. Bioinformatics analyses were conducted using Galaxy, MEGA version X, DnaSP ver. 6.12.03, and PopART 1.7 software for NGS analysis, phylogenetic tree, genetic diversity, and haplotype networking, respectively. A total of 307 engorged sand flies were trapped, with an overall Leishmania infection rate of 9.4 (29/307) and 6.8% by NGS and ITS1-PCR, respectively. Two Leishmania-infectedsand fly genera were identified: Phlebotomus (10.2%, 26/254) and Sergentomyia (5.7% (3/53). The phylogenetic tree showed two clusters, cluster I included the four study sequences along with 25 GenBank-retrieved DNA sequences. Cluster II consisted of three sequences from Iran and Pakistan. The genetic diversity analysis for the 29 L. tropica sequences showed high haplotype (gene) diversity index (Hd) (0.62 ± 0.07) but low nucleotide diversity index (π) (0.04 ± 0.01). Tajima's D, a neutrality test, is more negative in cluster I (D = - 2.0) than in total population (D = - 1.83), but both are equally significant (P < 0.001), indicating that observed variation in cluster I and whole population is less frequent than expected. The median-joining haplotype network produced a total of 11 active haplotypes. In conclusion, L. tropica from sand flies in Palestine is monophyletic that assembled in one main phylogroup and one haplotype.

Genetic diversity between local landraces and current breeding lines of pepper in China

Based on 22 qualitative traits, 13 quantitative traits, and 27 molecular markers (26 SSR and 1 InDel), in the current study we compared the diversity and population structure of 94 local landraces and 85 current breeding lines of pepper in China. The results showed that the Shannon Diversity indices of 9 qualitative traits and 8 quantitative traits in current breeding lines were greater than those of landraces, of which 11 were fruit organ-related traits. Compared with current breeding lines, the mean values of Gene Diversity index and Polymorphism Information content of local landraces were higher by 0.08 and 0.09, respectively. Population structure and phylogenetic tree analysis showed that the 179 germplasm resources could be divided into two taxa, dominated by local landraces and current breeding lines, respectively. The above results indicated that the diversity of quantitative traits of current breeding lines were higher than that of local landraces, especially traits related to fruit organs, but the genetic diversity based on molecular markers was lower than that of local landraces. Therefore, in the future breeding process, we should not only focus on the selection of target traits, but also strengthen the background selection based on molecular markers. Moreover, the genetic information of other domesticated species and wild species will be transferred to the breeding lines through interspecific crosses to expand the genetic background of the breeding material.

Identification and analysis of the genetic integrity of different types of rice resources through SSR markers

Seed aging is the key factor leading to the loss of genetic integrity. In this study, the seeds of Dongxiang wild rice, Xianggu, 9194 and Nipponbare were kept in a plant incubator with constant temperature and humidity for artificial aging treatment. The genetic integrity of germplasm resources with different germination gradients were analyzed using 44 SSR markers. The results suggested that different accessions could be ranked in order of aging resistance from highest to lowest as common wild rice > Xianggu > 9194 > Nipponbare. In order to maintain the genetic diversity of rice, the population size for reproduction and regeneration should be between 60 and 140. After aging, the number of polymorphic alleles, the number of specific single plant, the ratio of polymorphic bands, the number of alleles, the number of effective alleles, gene diversity index and Shannon index of different accessions all decreased with the decrease of germination rate. The germination rate of 60% was the critical value to maintain genetic integrity. Besides, the genetic integrity of eighteen SSR markers was rapidly lost or significantly increased. The regions of these markers were closely related to seed viability or genetic integrity. This study provides a theoretical basis for determining the population size for reproduction and regeneration and the critical value of germination rate of rice resources.

Genetic structure analysis and genetic fingerprinting of pomegranate cultivars (Punica granatum L.) by using SCoT molecular markers

AbstractGenetic diversity and genetic relatedness among 50 genotypes from eight countries, including Iran, Afghanistan, Turkmenistan, Syria, Lebanon, India, Yemen, and the United States located in two continents of Asia and the America, were assessed using SCoT markers. A total of 213 bands were produced; 100% of them were polymorphic; the average polymorphism information content (PIC) was 0.39. The mean Nei's gene diversity and Shannon's index were 0.33 and 0.49, respectively. Analysis of molecular variance suggested significant genetic differences within pomegranate populations. 99% of variance occurs within the populations, whereas 1% of the variation was recorded among the populations of pomegranate. Cluster analysis using SCoT markers able to group genotypes based on their geographical origins. Based on cluster analysis, the genotypes studied were divided into two main groups. The first group included most Asian genotypes, while American genotypes along with some Asian genotypes were in the second group. In the first group, Iranian genotypes were grouped with genotypes from Afghanistan and India. In the second group, the genotypes belonging to the America were in the same group as most of the genotypes of Turkmenistan. According to the present study, SCoT markers can be used to evaluate genetic diversity, identification and DNA fingerprinting pomegranate genotypes of different origins. This information can be used in breeding programs and the management of pomegranate collections.