Genetic Diversity Of Different Populations Research Articles

Batrachochytrium dendrobatidis strain affects transcriptomic response in liver but not skin in latitudinal populations of the common toad (Bufo bufo)

Batrachochytrium dendrobatidis (Bd) is a fungal pathogen that has decimated amphibian populations worldwide for several decades. We examined the changes in gene expression in response to Bd infection in two populations of the common toad, Bufo bufo, in a laboratory experiment. We collected B. bufo eggs in southern and northern Sweden, and infected the laboratory-raised metamorphs with two strains of the global panzoonotic lineage Bd-GPL. Differential expression analysis showed significant differences between infected and control individuals in both liver and skin. The skin samples showed no discernible differences in gene expression between the two strains used, while liver samples were differentiated by strain, with one of the strains eliciting no immune response from infected toads. Immune system genes were overexpressed in skin samples from surviving infected individuals, while in liver samples the pattern was more diffuse. Splitting samples by population revealed a stronger immune response in northern individuals. Differences in transcriptional regulation between populations are particularly relevant to study in Swedish amphibians, which may have experienced varying exposure to Bd. Earlier exposure to this pathogen and subsequent adaptation or selection pressure may contribute to the survival of some populations over others, while standing genetic diversity in different populations may also affect the infection outcome.

Study on the characteristics of genetic diversity of different populations of Guizhou endemic plant Rhododendron pudingense based on microsatellite markers

BackgroundRhododendron pudingense, firstly discovered in Puding county of Guizhou province in 2020, have adapted to living in rocky fissure habitat, which has important ornamental and economic values. However, the genetic diversity and population structure of this species have been rarely described, which seriously affects the collection and protection of wild germplasm resources.ResultsIn the present study, 13 pairs of primers for polymorphic microsatellite were used to investigate the genetic diversity of 65 R. pudingense accessions from six different geographic populations. A total of 254 alleles (Na) were obtained with an average of 19.5 alleles per locus. The average values of polymorphic information content (PIC), observed heterozygosity (Ho), and expected heterozygosity (He) were 0.8826, 0.4501, and 0.8993, respectively, These results indicate that the microsatellite primers adopted demonstrate good polymorphism, and the R. pudingense exhibits a high level of genetic diversity at the species level. The average genetic differentiation coefficient (Fst) was 0.1325, suggested that moderate divergence occurred in R. pudingense populations. The average values of genetic differentiation coefficient and gene flow among populations were 0.1165 and 3.1281, respectively. The analysis of molecular variance (AMOVA) indicated that most of the population differences (88%) were attributed to within-population variation. The PCoA results are consistent with the findings of the UPGMA clustering analysis, supporting the conclusion that the six populations of R. pudingense can be clearly grouped into two separate clusters. Based on Mantel analysis, we speculate that the PD population may have migrated from WM-1 and WM-2. Therefore, it is advised to protect the natural habitat of R. pudingense in situ as much as possible, in order to maximize the preservation of its genetic diversity.ConclusionsThis is the first comprehensive analysis of genetic diversity and population structure of R. pudingense in Guizhou province. The research results revealed the high genetic diversity and moderate population diferentiation in this horticulture plant. This study provide a theoretical basis for the conservation of wild resources of the R. pudingense and lay the foundation for the breeding or cultivation of this new species.

Evaluation of genetic diversity in different populations of six Salvia species using R-ISSR markers analysis

Evaluation of genetic diversity in different populations of six Salvia species using R-ISSR markers analysis

The seed oil of Paeonia ludlowii ameliorates Aβ25-35-induced Alzheimer's disease in rats.

Paeonia ludlowii, a plant of the Paeoniaceae family, has abundant genetic diversity in different populations, and the seed oil can be used in a diverse number of activities. However, its neuroprotective effect is not clear. We investigated the memory‐improving effects and associated mechanisms of Paeonia ludlowii seed oil (PLSO) on amyloid beta (Aβ)25–35‐induced Alzheimer's disease (AD) in rats. The Morris water maze test was undertaken, and subsequently, the content of malondialdehyde (MDA), superoxide dismutase (SOD), glutathione (GSH), and acetylcholinesterase (ACHE) in the hippocampus was detected by biochemical analyses. To further study PLSO, we examined the pathologic structure and apoptosis of hippocampal tissue by staining. Immunohistochemical analysis was used to detect expression of IBA‐1 and GFAP in the hippocampus. Detection of proinflammatory factors was achieved by reverse transcription–quantitative polymerase chain reaction and Western blotting. High‐dose PLSO inhibited expression of GFAP and IBA‐1. We demonstrated that high‐dose PLSO can regulate activation of glial cells and mediate apoptosis of hippocampal cells, and significantly improve learning and memory deficits in AD rats. PLSO could be developed as a nutritional supplement and sold as a drug for AD prevention and/or treatment.

IPBS-полиморфизм редких реликтовых и исчезающих видов Allium, произрастающих на территории Казахстанского Алтая

Abstract. The purpose of the study. The estimation of genetic polymorphism of Kazakhstan populations of rare relict and endemic Allium species. The novelty of the research is the use of the modern molecular genetic iPBS (Inter- Primer Binding Site Polymorphism) method of DNA amplification to assess the genetic diversity of different populations of Allium sp., collected in their natural habitats in the Kazakhstan Altai. Methods. Samples of medicinal relict and endangered species A. ledebourianum, A. altaicum, A. microdiction were collected in the places of their natural growth in the territory of the Kazakhstan Altai. DNA was isolated from 3–5 day sterile seedlings using lysis STAB buffer with RNaseA. PBS primers were used to assess the genetic diversity of different populations of Allium spp. The amplification results obtained using different PBS primers were evaluated in the GenAlex 6.5 macro program for Excel. Results. The polymorphism of 16 genotypes of the rare relict and endangered Allium sp. was analyzed using 7 PBS primers. Clearly distinguishable amplicons were obtained, the number of which varied depending on the primer used. The dendrogram, based on UPGMA analysis, grouped the studied genotypes into 2 main clusters, one of which included samples from the A. altaicum population, and the second cluster included samples from the A. ledebourianum population. A. microdiction represented by one sample did not enter any cluster, and formed a basal branch in the dendrogram. The results of the study have revealed a high degree of iPBS polymorphism and genetic diversity in rare relict and endangered Allium sp. Practical significance. The use of the molecular genetic iPBS method allows to identify a high level of polymorphism, which can serve as a basis for the identification of various genotypes of the Allium sp., which will significantly supplement traditional preservation methods of natural populations of this genus.

Evaluation of Genetic Diversity in Antiaris toxicaria Lesch. from Sacred Groves of the Western Ghats, India

Antiaris toxicaria Lesch. is a deciduous tree belongs to the family Moraceae, is native to the Old World tropics. It is an important industrial forest plant for its veneer, plywood and medicinal values. In the present study, genetic diversity of different populations of A. toxicaria collected from sacred groves of the Western Ghats, India has been evaluated. Thirteen RAPD and ten ISSR primers produced a total of 175 and 143 reproducible bands, respectively. RPI 10 of RAPD primers used showed maximum (0.49) polymorphic information content (PIC), while UBC 809 (0.37) exhibits maximum PIC among ISSR primers. Nei’s genetic similarity showed that pairwise similarity coefficients ranged from 0.460 to 0.832 in RAPD analysis, whereas 0.550–0.842 in ISSR analysis. Understanding the genetic diversity among natural A. toxicaria populations will be useful for effective long-term conservation.

Genetic intraspecific diversity of Meloidogyne javanica parasitizing vegetables in southern Iran.

In order to investigate different species of root-knot nematodes associated with vegetable production in southern regions of Iran, 37 populations of the most predominant species, Meloidogyne javanica, were recovered. Morphological and morphometric studies were carried on the characters of females, males, J2s and perineal patterns. Species-specific Sequence Characterized Amplified Region (SCAR) primers confirmed morphological studies, and all these populations produced specific band in 670 bp using Fjav and Rjav primers. Genetic diversity of different populations was studied by Inter Simple Sequence Repeats (ISSR) and Random Amplified Polymorphic DNA (RAPD) markers implementing 10 primers for each approach. Results revealed a relatively low genetic diversity (the percentage of polymorphic bands were 19.08 and 24.60 for ISSR and RAPD, respectively). The analyses of molecular variance indicated that the variation resulted from genotypic variations within region and variances among regions are 81% and 19% for RAPD, and 86% and 14% for ISSR, respectively. On the other hand, FST and Nm values are 0.140 and 1.535 for ISSR while these values are 0.188 and 1.079 for RAPD. So it can be concluded that there is a great deal of gene flow between populations due to the movement of plant material contaminated with nematodes, which results in high mixing between populations. ISSR and RAPD datasets failed to group populations according to their geographic region. There were no pathotypes or other intraspecific biological entities observed in the species.

Characterization of the genetic diversity and population structure of the manakin genus Antilophia through the development and analysis of microsatellite markers

The two species of the genus Antilophia, Antilophia bokermanni and Antilophia galeata, are found in environments that are undergoing extensive modification, which may be provoking the loss of their genetic diversity. Nine polymorphic microsatellite loci were characterized and analyzed in each of these species. The distribution of allele frequencies revealed two clusters that reflected the distinct genetic profile of each species. Observed levels of heterozygosity were low for each species, with the lowest allelic diversity found in the critically endangered A. bokermanni. The set of loci described here, in contrast with other genetic markers that have been analyzed previously, effectively diagnosed the genetic diversity of different populations of the two species.

Correlation of genetic diversity between hosts and parasites in Entamoeba nuttalli isolates from Tibetan and rhesus macaques in China.

Entamoeba nuttalli infection is prevalent in captive and wild macaques. Recent studies have suggested that genotypes of E. nuttalli isolates are correlated with the geographical distribution of host macaques. Correlation of amoebic genotypes with genetic diversity of host macaques was analyzed in present study. Sixty fresh stool samples were obtained from wild Tibetan macaques living in Mount Huang (HS) of the An-hui Province in China. PCR analysis revealed that the most prevalent Entamoeba species was E. chattoni (E. polecki ST2) (86.7%) followed by E. nuttalli (58.3%) and E. coli (25%). Six E. nuttalli HS isolates were successfully cultured. The tRNA-linked short tandem repeat (STR) loci and serine-rich protein gene of E. nuttalli isolates from four different regions of China (Mount Long-hu, Gui-yang, Mount E-mei, and HS, the former three isolates were obtained in previous studies) were studied and high numbers of polymorphisms were detected. When genetic diversity of different populations of E. nuttalli isolates was compared with geographical distance, an r2 value of 0.919 was assigned by a Mantel test based on the tRNA-STR loci. In host macaques, the mtDNA HVS-I gene was also highly polymorphic in each of the genomes. Multiple regression analysis using E. nuttalli tRNA-STR loci genetic, macaque mtDNA HVS-I gene, and geographic distances showed an r2 value of 0.943, indicating that a higher relevance was demonstrated when geographic and host gene factors were considered. Analysis of genetic factor of host would benefit for better understanding of the evolution of E. nuttalli.

Molecular cytogenetic characterization, leaf anatomy and ultrastructure of the medicinal plant Potentilla alba L.

Potentilla alba L. is a valuable medicinal plant widely used in folk and traditional medicine and particularly promising in complex treatment of thyroid pathology. Natural resources of this species are insufficient due to ever-growing use in contemporary medicine. Comprehensive investigations of different P. alba populations are essential for the successful extension of P. alba plantings. Aiming for a better understanding of karyotype structure, chromosome behaviour in meiosis and developing new diagnostic characters, we performed molecular cytogenetic characterization and leaf structure and ultrastructure analyses of two introduced P. alba samples originating from different habitats. Based on chromosome morphology, distribution of 45S/5S rDNA and DAPI-banding patterns, all chromosomes in the karyotypes were identified and the P. alba chromosomal idiogram was constructed. Our findings confirmed P. alba karyotype stability and also revealed several diagnostic characters of this species: the features of cells of upper and lower leaf epidermis, the presence of calcium oxalate druses and three types of leaf indumentum, essential for evaluation of genetic diversity in different populations, validation of raw materials and further selection progress. The meiotic abnormalities were detected probably related to low pollen activity and indicated the advantages of vegetative propagation in the development of a P. alba plantation system.

English

English

Genetic diversity in different populations of Persicaria minor (Polygonaceae), a medicinal plant

Persicaria minor is an annual medicinal plant which grows in different regions of Iran. Antioxidative, antimicrobial, antiviral, anti-inflammatory and cytotoxic activities are reported in this plant. No investigation has been reported about population genetic structure of this valuable plant species in Iran. Therefore, genetic analysis of 11 populations of this species was carried out using ISSR markers for the first time. Genetic variability analysis revealed high genetic diversity within populations of this species. AMOVA test produced significant genetic difference among the studied populations. Mantel test revealed significant correlation between genetic distance and geographical distance of the populations. STRUCTURE analysis and K-means clustering showed population genetic fragmentation and the presence of two gene pools for this species. The results suggested that genetic divergence, gene flow and local adaptation have played an important role in diversification of P. minor.

Parasitism and pathogenicity of Radopholus similis to Ipomoea aquatica, Basella rubra and Cucurbita moschata and genetic diversity of different populations

Ten populations of Radopholus similis from different ornamental hosts were tested for their parasitism and pathogenicity to water spinach (Ipomoea aquatic), malabar spinach (Basella rubra), and squash (Cucurbita moschata) in pots. The results showed all three plants were new hosts of R. similis. Growth parameters of plants inoculated with nematodes were significantly lower than those of healthy control plants. All R. similis populations were pathogenic to the three plants, but pathogenicity differed among populations from different hosts. The same R. similis populations also showed different pathogenic effects in the three different plants. RadN5 population from Anthurium andraeanum had the highest pathogenicity to the three studied plants. RadN1 from A. andraeanum had the lowest pathogenicity to squash and RadN7 from Chrysalidocarpus lutesens had the lowest pathogenicity to water spinach and malabar spinach. R. similis is usually associated with root tissues, but here we report that it could be found to move and feed in the stem bases of all three studied plants. Sequence and phylogenetic analyses of DNA markers of the 18S rRNA, 28S rRNA, ITS rRNA, and mitochondrial DNA gene sequences of ten R. similis populations revealed significant genetic diversity. RadN5 and RadN6 populations from anthurium showed a close genetic relationship and could be distinguished from other populations by PCR-RFLP. At the same time, RadN5 and RadN6 populations were the most pathogenic to three studied plants. These results confirm the existence of large biological variability and molecular diversity among R. similis populations from the same or different hosts, and these characteristics are related to pathogenic variability.

Genetic diversity of different populations of lilyturf revealed by RSAP analysis

Restriction site amplification polymorphism (RSAP) markers were employed to access the genetic diversity and relationship of 120 lilyturf germplasms from different geographical origins. Sixteen RSAP primer pairs generated 326 polymorphic bands, of which 318 (97.55%) were polymorphic. The value of polymorphism information content (PIC) ranged from 0.87 to 0.95 with an average of 0.92. These results indicated there was abundant genetic diversity among samples. The results of data analysis on 20 population showed that the value of percentage of polymorphic locus (PPL), Nei's gene diversity (H) and Shannon's information index (I) were 19.94%-85.58%, 0.082 6-0.210 7, 0.120 6-0.328 1 respectively. The most abundant genetic diversity was found in the O. japonicus population from Zhejiang and the least in the Liriope minor population. The genetic distance among 20 population was 0.024 6-0.286 8, of which the minimum genetic distance was 0.024 6 between population I and population 13 while the maximum 0.286 8 between population 5 and population 15. Coefficient of genetic differentiation among natural populations was 0.115 3 (Gst). And the gene differentiation contributed to 43.07% of the total genetic variation among populations and to 56.93% within populations. The total gene flow (Nm) was 0.660 9. UPMGA clustering analysis was basically similar to of the principle coordinate analysis (PCA). The 120 samples were classified into four major groups, which were basically corresponded with the genetic relationships based on morphological traits. The results of UPMGA and PCA were also consistent with geographical origins.

Genetic diversity of different populations and improved growth in the F1 hybrids in the swimming crab (Portunus trituberculatus).

The swimming crab, Portunus trituberculatus, is widely distributed throughout the coastal waters of Asian-Pacific nations and is an important economic species in this region. The aquaculture of swimming crabs has been plagued by problems associated with low growth rates, poor flesh quality, and weak disease resistance. To overcome these problems, selective breeding programs have been suggested as a means of genetically improving these traits in stock populations. In this study, we evaluated the genetic differentiation of 3 different geographical populations (Zhoushan: S; Laizhou Bay: L; and Haizhou Bay: H) using 8 polymorphic microsatellite loci. Nine strains of first filial generation were obtained, with 3 geographically populations as parental stock. We assessed the growth and survival rates of the F1 generation to identify new strains or breeds showing improvements in these economically important traits. Our results indicated that pairwise FST among populations was significantly higher than 0 (P = 0.0000) for every population pair, ranging from 0.0810 to 0.1083 for 3 different geographical populations. We observed significant heterosis for the growth and viability (survival) traits, although some strains (crossbred combinations) showed evidence of hybrid weakness in some growth measurements. One particular strain ("SL") outperformed other combinations, displaying the greatest extent of heterosis over the growth and viability (survival) traits. These results indicate that hybridization may be used to increase the performance of P. trituberculatus in aquaculture.

Using a reference population yardstick to calibrate and compare genetic diversity reported in different studies: an example from the brown bear

In species with large geographic ranges, genetic diversity of different populations may be well studied, but differences in loci and sample sizes can make the results of different studies difficult to compare. Yet, such comparisons are important for assessing the status of populations of conservation concern. We propose a simple approach of using a single well-studied reference population as a 'yardstick' to calibrate results of different studies to the same scale, enabling comparisons. We use a well-studied large carnivore, the brown bear (Ursus arctos), as a case study to demonstrate the approach. As a reference population, we genotyped 513 brown bears from Slovenia using 20 polymorphic microsatellite loci. We used this data set to calibrate and compare heterozygosity and allelic richness for 30 brown bear populations from 10 different studies across the global distribution of the species. The simplicity of the reference population approach makes it useful for other species, enabling comparisons of genetic diversity estimates between previously incompatible studies and improving our understanding of how genetic diversity is distributed throughout a species range.

English

Acridotheres tristis is a widely distributed species of Pakistan but no genetic data of this species is available in the literature. In this study, we applied 8 selected RAPD markers from a total of 20 tested markers, to decipher the genetic structure and genetic diversity of different populations. The RAPD markers revealed total polymorphism at P = 87.73%. The overall Nei’s genetic diversity (H) and Shannon’s index (S) levels were high and remained at H = 0.369 and S = 0.540. The genetic distances (D) between populations were also observed to be high. These distances ranged from D = 0.137 between Dera Gahzi Khan and Khanewal to D = 0.273 between Gujranwala and Khanewal. This study will be useful in conservation plans in future under changing environmental scenario.   Key words: Acridotheres tristis, genetic diversity, genetic distance, RAPD markers.

Genetic diversity of <I>Macrobrachium nipponense</I> on a regional scale in the Yangtze River

Oriental river prawn (Macrobrachium nipponense) is one of the most important freshwater prawns for aquaculture in China. However,M. nipponense farming recently declined due to genetic retrogression. Its genetic diversity of different populations in the Yangtze River with microsatellite markers was investgated in order to give support to conservation and utilization of wild resources of M. nipponense. Twenty polymorphic microsatellite markers were applied to investigate the genetic diversity of 6 M. nipponense populations in the Yangtze River. The sampling sites included Chongqing,Wanzhou,Yichang,Wuhan,Jiujiang and Jiangyin. The average number of alleles (A) and effective numbers of alleles (Ne) in 6 populations were 5.25 and 3.462 2 respectively. The mean PIC value of 20 microsatellite loci was 0.589 4. Expected heterozygosity (He) of 6 populations was as follows:Jiangyin (0.630 8),Jiujiang (0.609 6),Yichang (0.594 5),Wuhan (0.593 4),Wanzhou (0.584 4) and Chongqing (0.582 1),and their mean value was 0.629 6. The analysis of molecular variance (AMOVA) indicated that almost majority of the variance in the M. nipponense was within populations (93.08%) ,and 6.92%was among populations. The FST values between populations were 0.025 3-0.083 8(P0.05),which showed the genetic divergence between populations in the Yangtze River was intermediate but lower than that in the lakes. It was probably because running water promoted the exchanges between populations. Hardy-Weinberg equilibrium analysis indicated that deficiency of heterozygote existed in all of 6 populations,which was probably because of rare allele deficiency or null alleles. The genetic distances among populations ranged from 0.062 0 to 0.180 9. The UPGMA tree showed that Jiangyin stock formed an independent clade and resident 5 populations formed another one in which Jiujiang and Wuhan populations clustered at first.

Genetic Diversity in Different Populations of Matricaria chamomilla L. Growing in Southwest of Iran, Based on Morphological and RAPD Markers

Genetic Diversity in Different Populations of Matricaria chamomilla L. Growing in Southwest of Iran, Based on Morphological and RAPD Markers

Genetic Diversity of Amaranthus Species from the Indo-Gangetic Plains Revealed by RAPD Analysis Leading to the Development of Ecotype-Specific SCAR Marker

Genetic diversity and relationships among 6 Amaranthus species from 8 phytogeographic regions of the Indo-Gangetic plains were analyzed using a random amplified polymorphic DNA (RAPD) marker. RAPD primers yielded a total of 262 amplicons, ranging from approximately 250 to approximately 3000 bp in size with an average of 13.1 amplicons per primer, of which 254 amplicons (96.94%) were polymorphic. The genetic similarity coefficient among all the Amaranthus species ranged from 0.16 to 0.97 with a mean similarity coefficient of 0.56, indicating that variation existed in the genetic diversity of different populations. In the unweighted pair group method with arithmetic average dendrogram, populations of the same species clustered together. A unique 1371-bp RAPD band specific for Amaranthus gangeticus (syn. tricolor) of a particular phytogeographic region was converted to a sequenced characterized amplified region (SCAR) marker. The translated marker sequence showed homology with hemagglutinin protein. This SCAR marker is potentially useful for germplasm conservation and identification of amaranth ecotype.