Analysis Of Molecular Variance Research Articles

Exploring cannabidiol variations, investigation of genetic diversity, population structure and unveiling male-specific genetic marker in industrial hemp (Cannabis sativa L.)

AbstractCannabis sativa played a pivotal role across different industries. Recently, industrial hemp, particularly in the case of Cannabidiol (CBD), gained attention for its therapeutic potential. This study evaluated cannabinoid variability and genetic diversity within 43 industrial hemp individuals, primarily Turkish, across various plant parts and growth stages, and inflorescences of females showed significant CBD content. The highest contents were observed in Turkish landraces (0.55–8.05% with an average of 3.26%), making them valuable genetic resources for high CBD. Genetic structure revealed distinct populations based on gender and influenced by geographical origin. Analysis of Molecular Variance showed 92% of genetic variation observed within populations and indicated a promising source of novel allelic diversity in the Turkish gene pool. Turkish females showed significant genetic diversity [No. of Different Alleles (Na) 1.507, No. of Effective Alleles (Ne) 1.226, Shannon’s Information Index (I) 0.258, and Percentage of Polymorphic Loc (%P) 74.91], exhibiting richer genetic variation than their international peers. Principal Coordinate Analysis unveiled gender-specific genetic differences, and admixture clusters shed light on genetic interactions and historical connections among diverse populations. Unweighted Pair-Group Method with Arithmetic Averaging highlighted unique genetic profiles and distinct genetic lineages. Genome-wide association study revealed a highly significant male-specific genetic marker explained 50% of the phenotypic variation. These findings inform future breeding strategies and conservation efforts and contribute to varietal identification methods, Marker-Assisted Selection, and efficient cultivar development in upcoming programs.

Genetic connectivity of the common octopus (Octopus insularis) along the southwestern Caribbean

AbstractOctopus insularis is a shallow‐water octopus distributed throughout the western Atlantic, the Gulf of Mexico and the Caribbean. To evaluate its phylogeographic pattern, mitochondrial markers (16S rRNA and COIII) and genome‐wide nuclear markers (SNP's) were analyzed in individuals from artisanal fishing in different locations of the Colombian Caribbean coast. Mitochondrial analyzes displayed novel haplotypes (16S = H2, H3 and H4; COIII = H2–H7) and haplotypes shared with distant geographic areas (16S = H1 COIII = H1). The COIII gene did not show genetic differentiation between the analyzed localities, while the 16S gene showed significant differences between Santa Marta and Isla Fuerte. COIII's demographic analysis indicated that the species' effective population size has remained constant. Inferences were made from next‐generation genomic data with restriction site‐associated DNA (ddRAD‐seq) and 6769 polymorphic loci. The pairwise FST test indicated that there are low but significant differences between localities; however, the general molecular analysis of variance (AMOVA) and the principal coordinate analysis showed a lack of spatial structure in the populations analyzed. The Mantel test found no correlation between genetic distance and geographic distance, and the genetic structure analyses showed the presence of one genetic stock. The information obtained in this study indicates the genetic connectivity of O. insularis in the southwestern Caribbean, the absence of putative biogeographic barriers that affect its gene flow, and the crucial role played by life history strategies (planktonic paralarvae) and oceanographic factors to define the current distribution of its genetic diversity in this region.

Morphological and genetic characterization of jackfruit (Artocarpus heterophyllus) in the Kayunga and Luwero districts of Uganda

BackgroundJackfruit (Artocarpus heterophyllus) is an economically valuable fruit tree in Uganda. However, the production of jackfruit in Uganda is low. Additionally, because of deforestation, genetic erosion of the resource is predicted before its exploitation for crop improvement and conservation. As a prerequisite for crop improvement and conservation, 100 A. heterophyllus tree isolates from the Kayunga and Luwero districts in Uganda were characterized using 16 morphological and 10 microsatellite markers.ResultsThe results from the morphological analysis revealed variations in tree height, diameter at breast height (DBH), and crown diameter, with coefficient of variation (CV) values of 20%, 41%, and 33%, respectively. Apart from the pulp taste, variation was also observed in qualitative traits, including tree vigor, trunk surface, branching density, tree growth habit, crown shape, leaf blade shape, fruit shape, fruit surface, flake shape, flake color, flake flavor and pulp consistency/texture. Genotyping revealed that the number of alleles amplified per microsatellite locus ranged from 2 to 5, with an average of 2.90 and a total of 29. The mean observed (Ho) and expected (He) heterozygosity were 0.71 and 0.57, respectively. Analysis of molecular variance (AMOVA) indicated that 81% of the variation occurred within individual trees, 19% among trees within populations and 0% between the two populations. The gene flow (Nm) in the two populations was 88.72. The results from the ‘partitioning around medoids’ (PAM), principal coordinate analysis (PCoA) and genetic cluster analysis further revealed no differentiation of the jackfruit populations. The Mantel test revealed a negligible correlation between the morphological and genetic distances.ConclusionsBoth morphological and genetic analyses revealed variation in jackfruit within a single interbreeding population. This diversity can be exploited to establish breeding and conservation strategies to increase the production of jackfruit and hence boost farmers’ incomes. However, selecting germplasm based on morphology alone may be misleading.

Genetic Diversity, Linkage Disequilibrium, and Population Structure in a Common Bean Reference Collection

An in-depth understanding of the extent and pattern of genetic diversity and population structure in crop populations is of paramount importance for any crop improvement program to efficiently promote the translation of genetic diversity into genetic gain. A reference collection of 150 common bean genotypes selected from the International Center for Tropical Agriculture’s global core collection was evaluated using single-nucleotide polymorphism (SNP) markers to quantify the amount of genetic diversity, linkage disequilibrium, and population structure. The cultivars and landraces of the collection were diverse and originated from 14 countries, and wild accessions were used as controls for each gene pool. The collection was genotyped using an SNP array, generating a total of 5398 locus calls distributed across the entire bean genome. The SNP data quality was checked, and two datasets were generated. The first dataset (Dataset_1) comprised a set of 5108 SNPs and 150 genotypes after filtering for 10% missing alleles and an MAF < 0.05. The second dataset (Dataset_2) comprised a set of 2300 SNPs that remained after removing any null-allele SNPs and LD pruning for a criterion of r2 < 0.2. Dataset_1 was used for a principal coordinate analysis (PCoA), phylogenetic relationship determination, an analysis of molecular variance (AMOVA), and a discriminant analysis of principal components. Dataset_2 was used for a population structure analysis using STRUCTURE software and is proposed for a genome-wide association study (GWAS). The population structure analysis split the reference collection into two subpopulations according to an Andean or Mesoamerican gene pool. The Mesoamerican populations displayed higher genetic differentiation and tended to split into more groups that were somewhat aligned with common bean races. Andean beans were characterized by a larger average LD but lower LD percentage, a small average genetic distance between members of the population, and a higher major allele frequency, which suggested narrower genetic diversity compared to the Mesoamerican gene pool. In conclusion, the results indicated the presence of high genetic diversity, which is useful for a GWAS. However, the presence of significant linkage disequilibrium requires that genetic distance be considered as a co-factor for any further genetic studies. Overall, the molecular variation observed in the genotypes shows that this reference collection is valuable as a genebank-derived diversity panel which is useful for marker trait association studies.

Assessing Salinity Tolerance and Genetic Variation in Mung Bean (Vigna radiata) through CAAT Box and SCOT Marker Analysis

Vigna is a genus of approximately 100 wild species found in tropical and sub-tropical region. The three varieties of green gram (Vigna radiata L.) (VBN3, VBN6 & CO8) was widely cultivated in Tamil Nadu. Soil salinity is a significant issue in food production because excessive salt concentrations in soil inhibit plant development, delaying maturity and reducing crop yield or causing wilting. In the present study, we investigate the effective screening of saline tolerance in green gram, carried out the mechanism of physiological, biochemical and genetic variation using molecular markers of salinity stress of green gram under different concentration of NaCl (control, 50, 100, 150 and 200 mM). The result shows that, the salinity stress significantly reduced the physiological, biochemical and plant growth characteristics. Besides, the gene-targeted like Start Codon Targeted (SCoT) and CAAT box derived polymorphism (CBDP) markers were used to examine the genetic variability under saline stress of green gram. Herein, the SCoT and CBDP primers produced 54 and 90 polymorphic bands with an average of 5.7 and 7.8 bands per primer, respectively. The Analysis of Molecular Variance (AMOVA) and Principal Coordinate Analysis (PCoA) revealed genetic diversity within species was greater than between them, indicating that all of the saline-treated samples from the three varieties displayed genetic variation. The present study concludes that the increased concentration of NaCl reduced the plant growth and significantly affects the physiological, biochemical and genetic variation.

Applicability of SCoT markers in unraveling genetic variation and population structure among sugar beet (Beta vulgaris L.) germplasm.

Sugar beet (Beta vulgaris L.) holds significant importance as a crop globally cultivated for sugar production. The genetic diversity present in sugar beet accessions plays a crucial role in crop improvement programs. During the present study, we collected 96 sugar beet accessions from different regions and extracted DNA from their leaves. Genomic DNA was amplified using SCoT primers, and the resulting fragments were separated by gel electrophoresis. The data were analyzed using various genetic diversity indices, and constructed a population STRUCTURE, applied the unweighted pair-group method with arithmetic mean (UPGMA), and conducted Principle Coordinate Analysis (PCoA). The results revealed a high level of genetic diversity among the sugar beet accessions, with 265 bands produced by the 10 SCoT primers used. The percentage of polymorphic bands was 97.60%, indicating substantial genetic variation. The study uncovered significant genetic variation, leading to higher values for overall gene diversity (0.21), genetic distance (0.517), number of effective alleles (1.36), Shannon's information index (0.33), and polymorphism information contents (0.239). The analysis of molecular variance suggested a considerable amount of genetic variation, with 89% existing within the population. Using STRUCTURE and UPGMA analysis, the sugar beet germplasm was divided into two major populations. Structure analysis partitioned the germplasm based on the origin and domestication history of sugar beet, resulting in neighboring countries clustering together. The utilization of SCoT markers unveiled a noteworthy degree of genetic variation within the sugar beet germplasm in this study. These findings can be used in future breeding programs with the objective of enhancing both sugar beet yield and quality.

Effects of past riverine connectivity on the population structure and species distribution of ‘Geophagus’ brasiliensis (Cichlidae) complex in a Neotropical hotspot

Abstract Once fishes and rivers are intrinsically connected, historical events such as river captures and the reconfiguration of palaeodrainages affect population structure and species distribution. However, direct evidence of these events remains limited. We aimed to directly infer putative connections between adjacent river basins to understand genetic and geographical patterns in populations and species of the ‘Geophagus’ brasiliensis complex. For that, we analysed 174 sequences of the mitochondrial gene cytochrome c oxidase subunit I (COI) from five species along 35 sites within and near a coastal basin in northeastern Brazil. Based on haplotype network, palaeodrainage reconstruction, geological inferences of river captures and analyses of molecular variance (AMOVAs), we tested how the genetic structure could be associated with variable patterns of habitat connectivity through time. In general, high levels of genetic variation were identified, including shared haplotypes among drainages for most species. AMOVA suggested that drainage rearrangements between adjacent basins were the main drivers of genetic diversification in the ‘G.’ brasiliensis complex. Our study refuted dispersal routes via the continental shelf, whereas eight putative river captures suggested historical connections that enabled gene flow among drainages until recent interruption. These results provide novel insights on the role of riverscape evolution on the biogeography of neotropical ichthyofauna.

Does the Artificial Enhancement and Release Activity Affect the Genetic Diversity of Marbled Rockfish Sebastiscus marmoratus in Zhoushan Waters?

Artificial enhancement and release activity is an important method in the restoration of fishery resources. In order to understand the possible genetic effect of hatchery-released populations on wild populations during the artificial enhancement and release activities of Sebastiscus marmoratus in Zhoushan waters, we utilized mitochondrial DNA control region sequences to examine the genetic diversity in four S. marmoratus populations, including one farmed population, one released population and two wild populations. A total of 68 haplotypes from 123 individuals were detected, including 3 shared haplotypes. Haplotype diversity ranged from 0.944 to 0.980, with a mean of 0.966. The nucleotide diversity ranged from 0.020 to 0.025, with a mean of 0.022. Analysis of Molecular Variance (AMOVA) indicated that the primary genetic variation occurs within populations and the index of genetic differentiation between populations (FST) among the four populations showed no differentiation. The results indicate that the current artificial enhancement and release has not impacted the S. marmoratus population in Zhoushan waters. Continued long-term monitoring is essential to protect the high-quality germplasm resources of S. marmoratus.

Genetic history of esophageal cancer group in southwestern China revealed by Y‐chromosome STRs and genomic evolutionary connection analysis

Genetic and environmental factors play crucial roles in the development of esophageal cancer (EC) and contribute uniquely or cooperatively to human cancer susceptibility. Sichuan is located in the interior of southwestern China, and the northern part of Sichuan is one of the regions with a high occurrence of EC. However, the factors influencing the high incidence rate of EC in the Sichuan Han Chinese population and its corresponding genetic background and origins are still poorly understood. Here, we utilized genome-wide single nucleotide polymorphisms (SNPs) and Y-chromosome short tandem repeats (Y-STRs) to characterize the genetic structure, connection, and origin of cancer groups and general populations. We generated Y-STR-based haplotype data from 214 Sichuan individuals, including the Han Chinese EC population and a control group of Han Chinese individuals. Our results, obtained from Y-STR-based population statistical methods (analysis of molecular variance (AMOVA), principal component analysis (PCA), and phylogenetic analysis), demonstrated that there was a genetic substructure difference between the EC population in the high-incidence area of northern Sichuan Province and the control population. Additionally, there was a strong genetic relationship between the EC population in the northern Sichuan high-incidence area and those at high risk in both the Fujian and Chaoshan areas. In addition, we obtained high-density SNP data from saliva samples of 60 healthy Han Chinese individuals from three high-prevalence areas of EC in China: Sichuan Nanchong, Fujian Quanzhou, and Henan Xinxiang. As inferred from the allele frequency of SNPs and sharing patterns of haplotype segments, the evolutionary history and admixture events suggested that the Han population from Nanchong in northern Sichuan Province shared a close genetic relationship with the Han populations from Xinxiang in Henan Province and Quanzhou in Fujian Province, both of which are regions with a high prevalence of EC. Our study illuminated the genetic profile and connection of the Northern Sichuan Han population and enriched the genomic resources and features of the Han Chinese populations in China, especially for the Y-STR genetic data of the Han Chinese EC population. Populations living in different regions with high incidences of EC may share similar genetic backgrounds, which offers new insights for further exploring the genetic mechanisms underlying EC.

Differences in Albizia odoratissima genetic diversity between Hainan Island and mainland populations in China.

This study aimed at exploring unique population genetic characteristics of Albizia odoratissima (Linn. f) Benth on Hainan Island to provide a scientific basis for its rational utilization and protection. It analyzed the genetic diversity and structure of 280 individuals from 10 subpopulations of A. odoratissima from Hainan Island and Baise City using 16 expression sequence markers - simple sequence repeat markers. The genetic diversity of Hainan population (I = 0.7290, He = 0.4483) was lower than that of the Baise population (I = 0.8722, He = 0.5121). Compared with the Baise population (Nm = 2.0709, FST = 0.1077), the Hainan Island population (Nm = 1.7519, FST = 0.1249) exhibited lower gene flow and higher degree of genetic differentiation. Molecular variance and genetic differentiation analyses showed that the main variation originated from individuals within the subpopulation. There were significant differences in the genetic structure between Hainan and Baise populations. It grouped according to geographical distance, consistent with the Mantel test results (R2 = 0.77, p = 0.001). In conclusion, the genetic diversity of the island A. odoratissima population was lower than that distributed on land, the two populations exhibited obvious genetic structure differences. Both the degrees of inbreeding and genetic differentiation were higher in the island population than in the land population.

Decoding genetic diversity and population structure of Brassica species by inter primer binding site (iPBS) retrotransposon markers

AbstractMarker-assisted breeding serves as a potent tool for screening target germplasm, assessing genetic diversity, and determining breeding potential of a crop. Therefore, inter primer binding site (iPBS)-retrotransposons marker system was employed to evaluate a collection of 33 Brassica genotypes, including 10 Brassica juncea, 5 B. oleracea, 7 Sinapis alba, 5 B. nigra, and 6 B. rapa, were utilized to evaluate their genetic diversity and variations 10 polymorphic primers that generated a total of 144 bands. Various diversity indices were calculated in the studied germplasm, including polymorphism information content (0.13–0.30), effective number of alleles (1.217–1.689), Shannon’s information index (0.244–0.531), and gene diversity (0.148–0.370). These indices collectively affirmed substantial genetic variations within the germplasm. Molecular variance analysis revealed that the majority (62%) of genetic variations were present within populations. The Brassica accessions were categorized into three populations utilizing a model-based structure algorithm. Evaluation of diversity indices based on the structure indicated that populations III and II exhibited higher diversity. Principal coordinate analysis and neighbor-joining analysis further corroborated the three distinct populations, confirming the reliability of the STRUCTURE analysis. Notably, the genetic distance assessment identified BN1 and BN3 from B. nigra species and the genotypes BO1 and BO3 from B. oleracea as genetically diverse mustard accessions. The extensive genetic diversity observed within the Brassica germplasm underscores its significance as a valuable genetic resource for comprehensive Brassica breeding programs. Moreover, these accessions hold promise as suitable candidates for heterosis breeding initiatives aimed at improving mustard production.

Broad-scale genetic assessment of Southern Ground-Hornbills (Bucorvus leadbeateri) to inform population management

The Southern Ground-hornbill (SGH) (Bucorvus leadbeateri) is considered an umbrella species for biodiversity conservation in savannah biomes since they require large territories and significant protection measures that help to conserve a wide range of biodiversity with similar savanna and grassland requirements. Declines of the species are attributed to low reproductive rates coupled with multiple anthropogenic threats, including secondary poisoning, and persecution. Little is known about connectivity and population structure of SGH populations in Africa, south of the equator. Knowledge of population differentiation is needed to ensure that targeted conservation management plans can be implemented to slow population declines and ensure survival of the species. To inform a long-term conservation strategy, we investigated the broad-scale population structure of Southern Ground-hornbill across their sub-equatorial range. Our study based on 16 microsatellite loci identified moderate variation (average of 5.889 alleles per locus and a mean observed heterozygosity of 0.546) similar to other long-lived avian species. In contrast, mitochondrial DNA sequences analysis identified low diversity (Hd = 0.3313, π = 0.0015). A Bayesian assignment approach, principal component analysis, analysis of molecular variance and phylogenetic analysis identified weak to moderate population structuring across long distances and mitochondrial data showed a shallow phylogeny. Restriction to long-distance dispersal was detected that could not be attributed to isolation by distance, suggesting that other factors, such as their dispersal biology, are shaping the observed genetic differentiation. Although our study does not support the designation of populations as independent conservation units, we advocate that population management should continue to follow the Precautionary Principle (mixing founders from the same range state, rather than allowing mixing of founders from the extremes of the range) until there is scientific certainty. Following further research, if no independent conservation units are detected, then the global captive population can contribute to reintroductions across the range. In the wild, populations at the edge of the species range may need additional management strategies and gene flow should be promoted between neighbouring populations.

A panel of tetranucleotide STR markers as an alternative approach to forensic DNA identification of wolf and dog.

Commercial panels of microsatellite (STR) loci are focused on the use of DNA of the domestic dog (Canis lupus familiaris) and are often inapplicable for genotyping the DNA of the gray wolf (Canis lupus lupus). We propose a CPlex test system, including one hexa- and 12 tetranucleotide autosomal STR loci, as well as two sex loci, that is equally efficient in DNA identification of biological samples of the wolf and the dog. Analysis of molecular variance between samples revealed significant differentiation values (FST = 0.0784, p < 0.001), which allows to use the panel to differentiate wolf and dog samples. Population subdivision coefficients (θ-values) were calculated for each of the 13 STR loci of the developed test system. It was shown that the values of the genotype frequency for dogs and wolves, without and with considering the θ-value, differ by three orders of magnitude (for dogs 8.9 × 10-16 and 2.1 × 10-14 and for wolves 1.9 × 10-15 and 4.5 × 10-14, respectively). The use of population subdivision coefficients will allow to identify the most reliable results of an expert identification study and the power of exclusion provided by the STR loci of the CPlex test system makes it possible to achieve a reliable level of evidence in forensic DNA analysis of both wolves and dogs. The test system has been validated for use in forensic identification of the dog and wolf based on biological traces found at crime scenes, as well as for individual identification and establishing biological relationship of animals of these species.

Variability of Scots pine (Pinus sylvestris L.) plus trees in the Middle and Upper Volga Region with the use of ISSR markers.

One of the serious issues in forest breeding is how to reduce the variability level in breeding populations of forest tree species that is a set of selected plus trees. The problem is that variability is jeopardized by the risk of losing the genetic diversity of future artificial forests, as well as emerging inbreeding depression in the seed plus trees progeny. DNA markers are an effective tool to study variability, identify features of the genetic structure and degree of plant differentiation. The research focuses on assessing the level of the genetic diversity and the degree of differentiation of plus trees of various geographic origin with the use of ISSR markers. We used six ISSR primers to study 270 plus trees grown in the Penza region, the Chuvash Republic, the Republic of Tatarstan and the Mari El Republic. The samples of plus trees under study were characterized by different levels of genetic diversity. Two hundred fifteen PCR fragments were identified for six ISSR primers in total, while the number of amplified fragments varied from 186 to 201 in different plus trees samples. The genetic variability varied within the following limits: 95.7-96.9 %, polymorphic loci; 1.96-1.97, the number of alleles per locus; 1.31-1.48, the number of effective alleles per locus: finally, 0.291-0.429, Shannon's index; 0.205-0.298, the expected heterozygosity. According to the analysis of molecular variance (AMOVA), 82 % of the variability of ISSR markers is typical for the plus tree samples, while only 18 % is variability among the compared groups of trees from different geographical zones. The dendrogram generated by UPGMA showed that the plus trees grown in the Penza region, the Chuvash Republic and the Republic of Tatarstan are similar in term of the genetic structure of plus trees, while the plus gene pool of Scots pine from the Mari El Republic stands alone. The results of the research prove that the level of genetic diversity, the structure of genetic variability, and the nature of differentiation of plus trees are consistent with those previously elicited for natural populations of Scots pine in the Middle and Upper Volga region.

Ecology, genetic diversity, and population structure among commercial varieties and local landraces of Capsicum spp. grown in northeastern states of India.

Northeastern states of India are known for unique landraces of Capsicum spp. with geographical indications. However, little information is available about these valuable landraces of chillies. Surveys and collections were carried out in niche areas to find out their ecology and diversity through morphological traits and molecular analysis using microsatellite markers. Our result characterized the ecology of niche areas as cool (11.0°C-20.7°C) and humid (>60% relative humidity) climates for dalle-chilli (Capsicum annuum L.); mild-warm (12.2°C-28.6°C) and humid for king-chilli (C. chinense Jacq.); and cool to warm (11.3°C-33.1°C) and humid for bird's eye chilli (C. frutescens L.) during the crop period. The canonical correspondence analysis has shown the significant impact of temperature on the agro-morphological traits and distribution of the landraces in their niche areas. A wide variability was observed for different quantitative traits and yield attributing characters (fruit length, diameter, weight, and yield), showing high heritability (97.0%-99.0%), and genetic advance as a percentage of the mean (119.8%-434.0%). A total of 47 SSR markers used for the molecular analysis generated 230 alleles, ranging from 2 (HPMSE-7) to 10 (HPMSE-5), with an average of 4.89 alleles per locus. The average polymorphism information content was also high (0.61) and ranged from 0.20 (HPMSE-7) to 0.85 (CAMS-91). The observed average heterozygosity was lower than the expected value. Analysis of molecular variance has shown significant variation within (69%) and between (31%) of the populations of Capsicum spp. Based on Nei's genetic distance, bird's eye chilli and king-chilli were found to be closer to each other, whereas dalle-chilli, a tretraploid species, was closer to hot pepper (C. annuum). However, the flower size of dalle-chilli was large and found closer to king-chilli in color and differs from C. chinense due to the presence of calyx teeth. For quality traits, landraces king-chilli, dalle-chilli, and bird's eye chilli have shown 2.8, 2.0, and 1.4 times higher average capsaicin and 0.46, 0.25, and 0.22 times higher average oleoresin content over the hot pepper, respectively. The knowledge of ecology and diversity can be used in identifying new areas for production, selection of elite lines, conservation, and crop improvement.

Genetic characterization of Zeyheria tuberculosa progenies and evaluation for formation of a seed orchard

Zeyheria tuberculosa, a native species of Brazil known for its significant potential in silviculture and genetic improvement, holds prominence among various species. In this study, our objective was to assess the diversity, genetic structure, and feasibility of establishing a seedling seed orchard (SSO) for this species. A total of 71 progenies were collected from different locations and were used in our experiment in Ijaci - MG. We genotyped 92 individuals (nine families with eight individuals, two families with seven individuals, and one family with six individuals), specifically selecting those with the highest predicted genetic values, using ten ISSR primers. The molecular markers employed effectively detected polymorphism (PIC = 0.44). The population exhibited moderate to high genetic diversity, as evidenced by observed (AO = 2.00) and effective alleles (AE = 1.61), Nei's diversity index (H* = 0.35), and Shannon's diversity index (I* = 0.52). Molecular variance analysis indicated significant genetic differentiation between the progenies (Φst = 0.19), yet the majority of the variation was observed within them (80.1%). Employing a Bayesian approach, we identified the formation of two distinct genetic groups, further confirming the non-genetic structure of the population. These findings affirm the potential of the Z. tuberculosa progenies to contribute to the establishment of a seedling seed orchard, supporting genetic improvement strategies and the conservation of the species' genetic diversity.

GENETIC CHARACTERIZATION OF RELICT ENDEMIC LIQUIDAMBAR ORIENTALIS (ALTINGIACEAE) POPULATIONS

Liquidambar orientalis, a relict endemic species, is distributed in the south-west of Turkey. The natural spread areas of the species have been decreasing since the early 1900s. This poses a great threat to the future and genetic diversity of the species. In this study, the genetic diversity of a total of 190 individuals in ten populations was examined with ten polymorphic ISSR primers. Data analysis was performed using POPGENE ver. 1.32 and GenAlEx 6.503 softwares. According to the results of the analysis, a total of 271 loci were identified. For the ten populations, the rate of polymorphic loci ranged from 21.03% to 34.69%. The mean number of observed alleles (Na) and mean number of effective alleles (Ne) were found as 1.98 ± 0.13 and 1.47 ± 24 0.37, respectively. Nei's genetic diversity values (h) ranged from 0.07 ± 0.15 to 0.12 ± 0.18. According to the results of Molecular Analysis of Variance (AMOVA) and POPGENE ver. 1.32 analysis, it was determined that the main contribution to the genetic variance originated from among the populations. In addition, the gene flow level (NM) was found to be low with a value of 0.27 per generation.

Genetic diversity and morpho-physiological assessment of drought tolerance in rapeseed (Brassica napus L.) cultivars

AbstractWater deficit is one of the most important abiotic stresses constraining crop production in rapeseed. Understanding the mechanisms of adaptation to this stress is essential for the development and production of drought-tolerant genotypes. For this reason, this research study aims to investigate the importance of genetic diversity in identifying genotypes with a high degree of drought tolerance through assessing effectiveness of inter simple sequence repeat (ISSR) markers on 14 genotypes of rapeseed in a factorial design. Morphological and physiological characteristics were studied after the early stages of growth; in order to evaluate the genetic diversity among genotypes, 18 different ISSR markers were used. A total of 106 clear and scalable loci were amplified, of which 60 bands (56.6%) were polymorphic. The highest polymorphism information content belonged to marker number 9 with the amount of 0.365 (85.7%). Gene variation ranged from 0.081 to 0.365 and the rapeseed genotypes were divided into three groups by cluster analysis (unweighted pair group method with arithmetic mean method). The analysis of molecular variance showed that 70% of the total variation was observed within populations and 30% of this variation occurred among populations. In addition, t-test was used for comparing oil content percentage among different genotypes in control and stress levels. Adriana had the highest amount of seed oil with 36.47%, whereas Karaj 2 had the lowest amount with 27.28 and Cooper had the highest decrease in oil content percentage under stress conditions. Overall, the genotypes Likord, Hyola 401 and Sarigol 32 were identified as the most drought-tolerant.

Unraveling the genetic diversity of Ceiba pubiflora (Malvaceae) in isolated limestone outcrops: Conservation strategies.

Seasonally Dry Tropical Forests (SDTFs) located on limestone outcrops are vulnerable to degradation caused by timber logging and limestone extraction for cement production. Some of these forests represent the last remnants of native vegetation cover, functioning as isolated islands. Ceiba pubiflora (Malvaceae) is a tree frequently found on limestone outcrops in the central region of Brazil. This study aimed to evaluate the genetic diversity and identify suitable populations for the establishment of Management Units (MUs) for conservation. Inter-simple sequence repeat markers were employed to assess the genetic diversity in ten populations sampled from the Caatinga, Cerrado, and Atlantic Forest biomes. The species exhibited substantial genetic diversity (HT = 0.345; PLP = 97.89%). Populations SAH, JAN, and MON demonstrated elevated rates of polymorphic loci (> 84.2%) along with notable genetic diversity (He > 0.325). Additionally, these populations were the primary contributors to gene flow. The analysis of molecular variance (AMOVA) indicated that most genetic variation occurs within populations (91.5%) than between them. In the Bayesian analysis, the ten populations were clustered into five groups, revealing the presence of at least three barriers to gene flow in the landscape: 1) the Central Plateau or Paranã River valley; 2) near the Espinhaço mountains or the São Francisco River valley; and 3) around the Mantiqueira mountain range, Chapada dos Veadeiros plateau, and disturbed areas. A positive and statistically significant correlation was observed between genetic (θB) and geographic distances (r = 0.425, p = 0.008). Based on these findings, we propose the establishment of Management Units in Minas Gerais state, encompassing the (1) southern region (MIN population), (2) central region (SAH population), and (3) north region (MON population), as well as in Goiás state, covering the (4) Central Plateau region. These units can significantly contribute to preserving the genetic diversity of these trees and protecting their habitat against ongoing threats.

Epidemiological investigation of Entamoeba in wild rhesus macaques in China: a novel ribosomal lineage and genetic differentiation of Entamoeba nuttalli

Wild rhesus macaques are a potential source of zoonotic parasites for humans, and Entamoeba spp. are common intestinal parasites. To investigate the prevalence of Entamoeba in wild rhesus macaques in China and explore the genetic differentiation of the potentially pathogenic species Entamoeba nuttalli, a total of 276 fecal samples from five populations at high altitudes (HAG, 2,800–4,100 m above sea level) and four populations at low altitudes (LAG, 5–1,000 m above sea level) were collected. PCR methods based on the ssrRNA gene were used to detect Entamoeba infection. Genotyping of E. nuttalli was performed based on six tRNA-linked short tandem repeat (STR) loci for further genetic analyses. The results revealed that Entamoeba infection (69.2%) was common in wild rhesus macaques in China, especially in LAG which had a significantly higher prevalence rate than that in HAG (P < 0.001). Three zoonotic species were identified: Entamoeba chattoni (60.9%) was the most prevalent species and distributed in all the populations, followed by Entamoeba coli (33.3%) and Entamoeba nuttalli (17.4%). In addition, a novel Entamoeba ribosomal lineage named RL13 (22.8%) was identified, and phylogenetic analysis revealed a close genetic relationship between RL13 and Entamoeba. hartmanni. Genotyping of E. nuttalli obtained 24 genotypes from five populations and further analysis showed E. nuttalli had a high degree of genetic differentiation (FST > 0.25, Nm < 1) between the host populations. The result of analysis of molecular variance (AMOVA) revealed that observed genetic differences mainly originate from differences among populations (FST = 0.91). Meanwhile, the phylogenetic tree showed that these genotypes of E. nuttalli were clustered according to geographical populations, indicating a significant phylogeographic distribution pattern. Considering the potential pathogenicity of E. nuttalli, attention should be paid to its risk of zoonotic transmission.