Nei's Genetic Distance Research Articles

Comparative analysis of epigenetic variability in two pine species exposed to chronic radiation in the Chernobyl and Fukushima affected zones

Comparative analysis of epigenetic variability in two pine species affected as a result of the Chernobyl and Fukushima accidents is presented. The absorbed dose rate within the affected Chernobyl sites varies over a wider range (1.5–24.6 μGy/h) than within the Fukushima sites (3.5–6.5 μGy/h). It was shown that chronic irradiation can change the level of whole genome methylation in pine populations, but in different ways. The genomes of Japanese red pines are hypomethylated, and the degree of methylation and hydroxymethylation decreases with an increase in the level of radiation exposure. In contrast, the percentages of genome methylation and hydroxymethylation in Scots pine populations exceed the reference levels. The observed discrepancy in the patterns of genome-wide DNA methylation can be attributed partly to the design of the study (differences in the climate, radiation dose, age and species of the pines) which could affect the results. In the frame of IRAP analysis, a larger number of different bands was observed in the Chernobyl populations compared to the Japanese populations. Both the Japanese and Chernobyl populations are characterized by significant genetic variability. However, the main part of this variability is observed within populations. The dendrograms, based on presence/absence of IRAP fragments and Nei's genetic distances, revealed subdivisions of the Chernobyl and Japanese populations according to the level of radioactive contamination. Analysis of the results presented will improve our understanding of the mechanisms underlying the responses of pine trees to chronic radiation exposure.

Random Amplified Polymorphic DNA-Polymerase Chain Reaction Analysis of Four Koi Fish (Cyprinus carpio var. koi) Variants from Yogyakarta, Indonesia

Koi fish (Cyprinus carpio var. koi) is an ornamental fish with many hobbyists because of the beauty of its color pattern. Koi fish are widely cultivated around the world. Indonesia is a country that has many koi fish breeders and hobbyists. Crossbreeding between variants of koi fish can form a new variants. and provide a lot of genetic variation. This study aims to determine the variations and genetic relationships of koi fish that are widely cultivated in Indonesia. This study used 40 koi fish originating from fish farmers in the Special Region of Yogyakarta. Koi fish variants used are Kohaku, Showa, Sanke, and Shiro. This research uses amplification method with Polymerase Chain Reaction (PCR) with Random Amplified Polymorphic DNA (RAPD) marker which is OPA-1 and OPA-9. The results of the RAPD-PCR showed 14 bands from the OPA-1 primer and 5 bands from the OPA-9 primer with a total of 19 bands consisting of 18 polymorphic bands and 1 monomorphic band from the four samples of koi fish variants. The results of the polymorphism analysis showed that the polymorphisms of the Shiro variants is 63.16%, Showa 47.37%, Kohaku 36.84%, and Sanke 31.58%. Genetic distance calculation using the Nei genetic distance shows that the Kohaku variant has a close genetic distance to the Showa variant and the Sanke variant has a close genetic distance to the Shiro variant.

Impact of interpopulation distance on dominance variance and average heterosis in hybrid populations within species.

Interpopulation improvement for crosses of close populations in crops and livestock depends on the amount of heterosis and the amount of variance of dominance deviations in the hybrids. It has been intuited that the further the distance between populations, the lower the amount of dominance variation and the higher the heterosis. Although experience in speciation and interspecific crosses shows, however, that this is not the case when populations are so distant-here we confine ourselves to the case of not-too-distant populations typical in crops and livestock. We present equations that relate the distance between 2 populations, expressed as Nei's genetic distance or as correlation of allele frequencies, quadratically to the amount of dominance deviations across all possible crosses and linearly to the expected heterosis averaging all possible crosses. The amount of variation of dominance deviations decreases with genetic distance until the point where allele frequencies are uncorrelated, and then increases for negatively correlated frequencies. Heterosis always increases with Nei's genetic distance. These expressions match well and complete previous theoretical and empirical findings. In practice, and for close enough populations, they mean that unless frequencies are negatively correlated, selection for hybrids will be more efficient when populations are distant.

Genetic diversity and population structure of snap bean (Phaseolus vulgaris L.) from China revealed by microsatellite markers

AbstractSnap bean (Phaseolus vulgaris L.) is the vegetable form of common bean, and regarded as one of the most important and commonly consumed products in the world. In this study, 221 snap bean core accessions mostly from China were characterized the genetic diversity, gene pool identity, and relationships using 30 microsatellite markers, and concurrently evaluated for phenotype traits and phaseolin patterns. A total of 140 alleles were detected with an average of 4.67 per locus. The polymorphic information content ranged from 0.215 to 0.823, with an average of 0.488. Nei's genetic distances between accessions ranged from 0 to 0.9999, with an average of 0.6143. In those Chinese snap beans, structure analysis proved the existence of a high proportion of hybrid accessions except for identification of Andean and Mesoamerican gene pools. Neighbor‐joining clustering and principal coordinate analysis based microsatellite markers were similar in explaining the extent of diversity with both revealed Andean and Mesoamerican gene pools, which were divided into seven subgroups. Four of those subgroups, including one arising from introgression, were identified as belonging to the Andean gene pool, which likely represented Nueva Granada and Peru races. Other three subgroups were identified as belonging to the Mesoamerican gene pool, which likely represented the Mesoamerican race, owing to their close association with the control genotype. The diversity index of the qualitative traits was 0.80 to 1.88, with the average value of 1.20, while the diversity of the quantitative traits was ranked as 100‐seed weight (H′ = 1.98) > pod length (H′ = 1.90). Six principal components explained 69.13% of the total variation. Eight phaseolin patterns were identified in the 221 accessions. This study demonstrated the gene pool, as well as geographical, diversity of snap bean germplasms in China. The substantial diversity level is important for the utilization and conservation of snap bean, as well as future breeding programs.

Genetic Variability of Different Jordanian Almond Prunus Amygdalus L. Landraces Revealed by Morphological Traits and RAPD Markers

The relationship among six Jordanian almond landraces was studied using morphological traits and RAPD analyses. Across six almond landraces studied, nut shape, kernel size, nut length, nut size, and shell length That showed a high level of variation (CV>30%), while kernel length, shell width, internodes length, and nut width showed comparatively low values (CV<20%). Principal component analysis showed that the first five components explained all morphological variation among the landraces investigated. Kernel and nut traits were predominant in the first three components contributing to most of the total variation that existed among landraces. Euclidean distance was used to construct clusters from morphological data which allocated individuals into two main groups with a distance ranging from 5.5 to 10.14. Hajari, Hami Hallo, and Mukhmaly with small fruit sizes composed one main cluster, while the other three landraces (Oga, Fark, and Abu Dabos) with large fruit sizes composed the other main cluster. Out of 62 pre-screened RAPD primers, 12 with reproducible bands and maximum polymorphism were selected for diversity analysis. Seventy-one bands were scored with 28 of them being the polymorphic. Average value of polymorphism/primer ranged from 20% to 74.2%. Nei's genetic distance coefficient ranged from 0.5 to 0.85 with an average of 0.70. Molecular analysis revealed inconsistent separation among the landraces compared with that based on morphological traits. Although landraces found during the screening in the Ajloun area are limited in number, but considerable variation was observed both at morphological and DNA levels indicating that Jordanian almond landraces are rich and valuable genetic materials for almond improvement.

Infraspecific genetic diversity and seed fatty acid composition in Sesamum indicum L. populations (Pedaliaceae) in Iran

Sesamum indicum L. of the Pedaliaceae family is considered an economically important oil-bearing plant that has been cultivated for more than 5000 years. In this research, we examined genetic diversity and seed fatty acid composition in 11 Iranian populations of S. indicum. We extracted the nuclear DNA using the CTAB protocol and then amplified the genomes using 10 SCoT molecular primers. For the phytochemical study, the seed fatty acid methyl esters were subjected to a GC apparatus and their composition was determined. The data were then analyzed using PAST, POPGENE, Geno-Dive, and STRUCTURE software. We determined that the percentage of polymorphic loci was 62%. According to the AMOVA test and estimated genetic diversity parameters, high genetic differentiation occurred between the examined populations, which was followed by a low rate of gene flow and Hs. Based on the Nei's genetic distance and Structure analysis, the populations were divided into seven genotype groups. Most identified genotypes had homogeneous genetic structures indicating a limited genetic flow rate. The phytochemical evaluation revealed that a great part of the seed oils was composed of unsaturated fatty acids with linoleic and oleic acids as the main compounds. We detected palmitic acid as the major saturated fatty acid. The populations were divided into four chemotype groups based on the seed oil fatty acids composition. However, the population clustering patterns in the molecular genetic and seed fatty acid analyses were not identical. These results indicated that some environmental parameters strongly affect the seed oil fatty acids composition. We suppose that the populations under study are comprised of several genotypes or cultivars grown in various Iranian locations.

Implication of exon 4 TP53 Gene mutations in colorectal cancers in Senegalese patients

Background: Colorectal cancer (CRC) is a major cause of death in men and women, comprising about 10% of cancer deaths after breast and lung cancer. The most significant risk factors currently implicated in the etiology of this cancer are genetic, likely due to several mutations. Methods: The study explored the involvement of genetic factors in these pathologies; specifically, exon 4 of the TP53 gene was studied in 15 CRC patients and compared with 10 healthy individuals as controls. The position of the marker mutations was determined with the Mutation Surveyor software version 5.1.2. DnaSP version 5.10, MEGA version 7.014, and the program Arlequin version 3.1 were used to highlight the parameters of variability, differentiation, and the demo-genetic evolution of our study populations. The pathogenicity of the mutations was determined through Polyphen2, TAMISER, and ClinVar. Results: Our results showed the presence of a recurrent mutation of the TP53 gene in both tumor and healthy tissue where proline was replaced with arginine at codon 72. This mutation was predicted to be benign. The presence of this mutation in healthy tissue can be considered a relatively late event in colorectal tumorigenesis. In addition, the P47L, D49A, W53S, and D48G mutations appeared to be suspicious because they were predicted to be potentially damaging. This finding suggests the genes’ involvement in the pathology of CRCs in our study population. The cancer tissue sequences contained an average of 2.59 nucleotide differences that resulted in amino acid changes. The Nei genetic distance confirms this variability between tumor tissues. Conclusion: These results suggest that variants in exon 4 of the TP53 gene may contribute to the development of CRCs. These mutations could constitute molecular markers in CRC and possibly help in the development of early diagnosis

Genetic variation of Limnophora marginata Stein, 1904 (Diptera: Muscidae), associated with an altitudinal gradient in Pedro Moncayo Canton, Pichincha, Ecuador

Abstract. Aguilar KEV, Vivas AYS, Acosta-López C. 2023. Genetic variation of Limnophora marginata Stein, 1904 (Diptera: Muscidae), associated with an altitudinal gradient in Pedro Moncayo Canton, Pichincha, Ecuador. Biodiversitas 24: 269-275. Analyzing heterogeneity in insect populations is relevant to understanding its biology. Thus, we analyzed the genetic variability of two populations of “hunter-flies”, Limnophora marginata Stein, 1904 associated with an altitudinal gradient in the Tocachi and Jerusalem localities, in the Pedro Moncayo Canton, Ecuador, using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) of the mitochondrial Cytochrome oxidase I gene. Thirty alleles were detected from analysis with five restriction enzymes; the percentage of polymorphic loci was higher in Tocachi (96.67%) than in Jerusalem (80%). Haplotypes were generated with the corresponding alleles, resulting in a different haplotype for each analyzed individual. Several estimators were used to characterize the population structure. The Analysis of Molecular Variance (AMOVA) evidenced the existence of higher intra-population variability (94%) than inter-population (6%), showing similar information to that found through haplotype analysis. The Fst fixation index indicated that there is no genetic difference between populations (0.056, P<0.05). Nei's genetic distance and Nei's similarity index indicated that L. marginata populations did not show differences between populations. From the results we deduce that the evolutionary force that may be modelling the existent genetic variability may be gene flow, thus establishing a low inter-population genetic structure. The mitochondrial DNA Cytochrome oxidase I gene was an advantageous molecular marker to obtain results that established intra and inter population variability. The characteristics of the mitochondrial DNA were useful to successfully apply the PCR-RFLP technique. Our findings highlight the existence of ecosystem connectivity between L. marginata populations despite altitudinal and habitat differences.

Phenotypic and Genotypic Diversity of Roots Response to Salt in Durum Wheat Seedlings.

Soil salinity is a serious threat to food production now and in the near future. In this study, the root system of six durum wheat genotypes, including one highly salt-tolerant (J. Khetifa) used as a check genotype, was evaluated, by a high-throughput phenotyping system, under control and salt conditions at the seedling stage. Genotyping was performed using 11 SSR markers closely linked with genome regions associated with root traits. Based on phenotypic cluster analysis, genotypes were grouped differently under control and salt conditions. Under control conditions, genotypes were clustered mainly due to a root angle, while under salt stress, genotypes were grouped according to their capacity to maintain higher roots length, volume, and surface area, as J. Khetifa, Sebatel, and Azeghar. SSR analysis identified a total of 42 alleles, with an average of about three alleles per marker. Moreover, quite a high number of Private alleles in total, 18 were obtained. The UPGMA phenogram of the Nei (1972) genetic distance clusters for 11 SSR markers and all phenotypic data under control conditions discriminate genotypes almost into the same groups. The study revealed as the combination of high-throughput systems for phenotyping with SSR markers for genotyping it's a useful tool to provide important data for the selection of suitable parental lines for salt-tolerance breeding. Nevertheless, the narrow root angle, which is an important trait in drought tolerance, is not a good indicator of salt tolerance. Instated for salt tolerance is more important the amount of roots.

Gut Microbiome Composition of the Fire Ant Solenopsis invicta: an Integrated Analysis of Host Genotype and Geographical Distribution.

Gut symbiotic bacteria are known to be closely related to insect development, nutrient metabolism, and disease resistance traits, but the most important factors leading to changes in these communities have not been well clarified. To address this, we examined the associations between the gut symbiotic bacteria and the host genotype and geographical distribution of Solenopsis invicta in China, where it is invasive and has spread primarily by human-mediated dispersal. Thirty-two phyla were detected in the gut symbiotic bacteria of S. invicta. Proteobacteria were the most dominant group among the gut symbiotic bacteria. Furthermore, the Bray-Curtis dissimilarity matrices of the gut symbiotic bacteria were significantly positively correlated with the geographical distance between the host ant colonies, but this relationship was affected by the social form. The distance between monogyne colonies had a significant effect on the Bray-Curtis dissimilarity matrices of gut symbiotic bacteria, but the distance between polygyne colonies did not. Moreover, the Bray-Curtis dissimilarity matrices were positively correlated with Nei's genetic distance of the host but were not correlated with the COI-based genetic distance. This study provides a scientific basis for further understanding the ecological adaptability of red imported fire ants during invasion and dispersal. IMPORTANCE We demonstrated that gut microbiota composition and diversity varied among populations. These among-population differences were associated with host genotype and geographical distribution. Our results suggested that population-level differences in S. invicta gut microbiota may depend more on environmental factors than on host genotype.

Exploring Genetic Diversity and Population Structure of Turkish Black Sea Region Maize (Zea mays L.) Germplasm using SSR Markers

Plant landraces are heterogeneous plant populations that have adapted to local environmental conditions and serve as a source of genetic variations that can be used for the breeding perspectives. Studies regarding genetic diversity assessment are very important as they provide an opportunity for the scientific community to investigate novel genetic variations for the genetic improvement of crops. Maize is one of the most important cereal crops and provides daily calories to millions of people all over the world. This study aimed to investigate the genetic diversity and population structure of 32 local maize genotypes collected from the Black Sea Region of Turkey using SSR markers. Molecular characterization was performed using the 14 most polymorphic primers that yielded a total of 42 bands. An average of 3 alleles per SSR primer was detected, and the number of alleles varied from 1 (phi022) to 6 (umc1571). The unweighted pair-group method with arithmetic means (UPGMA) clustering divided maize accessions into three main populations. According to Nei's genetic distances, DZ-M-145 (Corum) and DZ-M-20 (Trabzon) genotypes were the closest (0.03) genetically related populations, while DZ-M-68 (Artvin) and DZ-M-55 (Rize) were the most genetically distant (0.63) populations. The study identified molecular genetic diversity not mentioned for maize plants from the Black Sea. On this occasion, new opportunities have been created for hybrid maize products.

Molecular characterization and diversity analysis of some local potato (Solanum tuberosum L.) genotypes of Bangladesh by RAPD markers

Genetic identification of cultivars and varieties is useful in preserving endangered potato germplasm and planning for new breeding programs. Molecular characterization and genetic diversity of 10 local potato genotypes of Bangladesh were investigated with five RAPD primers, namely OPA-18, OPB-06, OPC-01, OPD-02 and OPW. Genomic DNA was extracted from young leaves and PCR reactions were performed with selected primers. The selected primers generated 33 distinct and differential amplified bands (size ranged from 131-1188 bp), out of which 28 were polymorphic. The percentage of polymorphic loci was valued from 33.33% to 100%. Gene frequency was ranged from 0.300 to 1 and gene diversity was from 0 to 0.70. The inter-varietal similarity indices was ranged from 42.45% to 92.67%. Pair-wise comparisons of Nei's genetic identity value was from 0.4848 to 0.9394. The highest Nei's genetic identity (0.9394) was observed in Sheel Bilati and SAU Promising Genotype-5 genotype pair. Nei's (1972) genetic distance was from 0.0625 to 0.7239. Dendrogram based on Nei's genetic distance using Unweighted Pair Group Method with Arithmetic Means (UPGMA) indicated the segregation of studied potato genotypes into two main clusters. It was found that RAPD markers are sensitive enough to identify genetic variation in a variety of germplasm, which will be helpful for choosing genetically unique germplasm in potato breeding programs. SAARC J. Agric., 20(2): 43-55 (2022)

Conservation Genetics of the Asian Giant Soft-Shelled Turtle (Pelochelys cantorii) with Novel Microsatellite Multiplexes.

To understand the genetic structure of the protected turtle species Pelochelys cantorii we used transcriptome data to design more than 30,000 tri- and tetranucleotide repeat microsatellite primer pairs, of which 230 pairs were used for laboratory experiments. After two screenings, only 10 microsatellite markers with good specificity, high amplification efficiency, and polymorphisms were obtained. Using the selected primers, two multiplex PCR systems were established to compare and analyze the genetic diversity of artificially assisted breeding generations from four parents (two females and two males) continuously bred over two years. A total of 25 alleles were detected among the 10 microsatellite loci of the offspring. The polymorphism information content (PIC) was 0.313-0.674, with an average of 0.401, among which two loci were highly polymorphic (PIC ≥ 0.5). The number of alleles was 2-5 and the number of effective alleles was 1.635-3.614. The observed heterozygosity was 0.341-0.813, with an average of 0.582, whereas the average expected heterozygosity was 0.389-0.725, with an average of 0.493. Moreover, on the basis of Nei's genetic distance and the Bayesian clustering algorithm, the 182 offspring were divided into two subgroups, and the results corresponded to the two maternal lines. This is the first study to investigate the molecular markers of P. cantorii, and the results obtained can be used to protect genetic resources and provide a genetic basis for the design of population recovery plans.

Start codon-targeted marker evaluation of genetic relationship and population structure in southern Nigerian fluted pumpkin (Telfairia occidentalis Hook F.) collection

AbstractFluted pumpkin (Telfairia occidentalis Hook F.) is an underutilized indigenous leafy vegetable with enormous prospects for food security in sub-Saharan Africa. However, relatively little is known about genetic relationships and population structure in the species. In this study, 32 landraces of fluted pumpkin collected across three southern geographical regions in Nigeria were assessed for genetic diversity and population structure using 8 start codon-targeted (SCoT) makers. The polymorphic information content of the SCoT markers ranged from 0.48 in SCoT36 to 0.94 in SCoT28, with an average of 0.77. Hierarchical cluster dendrogram based on Ward's method and principal component analysis grouped the landraces into four clusters without affiliation to provenance. Overall, the mean values of the population genetic diversity parameters – Nei's gene diversity (H) and Shannon's information index (I) showed values of 0.28 ± 0.01 and 0.43 ± 0.02, respectively, implying a narrow genetic base for the landraces. The result was further corroborated by a very close Nei's genetic distance and identity among populations of the landraces. Furthermore, the south-west population exhibited the higher genetic diversity (H = 0.31 ± 0.02 and I = 0.45 ± 0.03). Population structure analysis inferred three subpopulations for the accessions with varying degrees of allelic admixture. An analysis of molecular variance revealed that almost all the genetic variation occurred within (99%) than between (1%) populations. The findings shed light on the genetic diversity of southern Nigerian fluted pumpkin and have significant implications for the characterisation, conservation, exploitation and improvement of the species.

Analysis of genetic diversity and structure of Mongolian horse using microsatellite markers

Mongolian horses are one of the oldest horse breeds, and are very important livestock in Mongolia as they are used in various fields such as transportation, food (milk, meat), and horse racing. In addition, research and preservation on pure Mongolian breeds are being promoted under the implementation of the new Genetics of Livestock Resources' act in Mongolia. However, despite the implementation of this act, genetic research on Mongolian horses using microsatellites (MS) has not progressed enough. Therefore, this study was conducted to analyze the genetic polymorphism of five breeds (Gobi shankh, Tes, Gal shar, Darkhad, and Undurshil) using 14 MS markers recommended by International Society for Animal Genetics (ISAG). The mean number of alleles (MNA) was 8.29, expected heterozygosity frequency (HExp) was 0.767, observed heterozygosity frequency (HObs) was 0.752, and polymorphism information content (PIC) was 0.729. The Nei's genetic distance analysis showed that the genetic distance between Gobi shankh and Darkhad horses was the farthest, and the other three breeds, Tes, Gal shar, and Undurshil were found to be close to each other. Similarly, the principal coordinate analysis (PCoA) and factorial correspondence analysis (FCA) showed that the Gobi shankh and Darkhad horses were genetically distinct from other breeds. On the other hand, it appears that Tes, Gal shar, and Undurshil horses, which are genetically similar, most likely interbred with each other. Therefore, it is expected that these results will help the conservation of genetic resources in Mongolia and the establishment of policies related to Mongolian horses.

Genetic diversity and population structure of Venturia inaequalis isolates in apple orchards from Turkey

Apple scab caused by Venturia inaequalis is one of the major diseases of apple orchards worldwide. Genetic variability in pathogen populations present new strategies for management the disease and breeding studies. In this study aimed to evaluate genetic diversity and population structure of 81 V. inaequalis isolates obtained from six provinces of Turkey. Twenty-six iPBS and 20 ISSR primers were investigated for their ability to produce polymorphic bands among the pathogen isolates. The mean percentage of polymorphic bands per primer was 85.48 and 84.87 for iPBS and ISSR markers, respectively. The dendrogram derived from UPGMA cluster analysis based on the combined dataset of iPBS and ISSR markers classified the isolates into two main groups with a genetic similarity of 69%, which no relationship between distribution and geographical origin of the isolates. The dendrogram of Nei's genetic distances Isparta and Sivas populations clustered separately other populations. STRUCTURE analysis showed four populations (K = 4) with the highest mean value of Ln likelihood (−3067.0). The average genetic differentiation (GST) among all populations was 0.105. The overall gene flow (NM) was high level of 4.260. The analysis of molecular variance (AMOVA) showed that 96% of the variation was between the isolates within populations, compared to only 4% was among populations. iPBS marker based on the LTR retrotransposons has been tried for the first time to evaluate intraspecific variation among the isolates of V. inaequalis. Both iPBS and ISSR markers were useful, informative and reliable tools for investigating the genetic diversity of V. inaequalis. The results obtained from the present study provide detailed information about population genetic structure of V. inaequalis in Turkey. These study also will provide new approaches for plant breeders and disease management strategies.

Genetic Diversity of Philippine Native Pigs (Sus scrofa L.) from Quezon and Marinduque Based on Morphological and Microsatellite Markers

Nine microsatellite markers recommended by the Food and Agriculture Organization were used to measure the genetic diversity of Quezon and Marinduque native pig populations – with a total of 37 and 40 individuals, respectively. All markers were discovered to be polymorphic, with a mean number of alleles per locus of 10. Marinduque native pigs were found to have a mean effective number of alleles (EA), mean observed heterozygosity (HO), mean expected heterozygosity (HE), and mean polymorphic information content (PIC) of 5.005 ± 0.547, 0.673 ± 0.040, 0.780 ± 0.024, and 0.76 ± 0.03, respectively. By contrast, Quezon native pigs had mean EA, mean HO, mean HE, and mean PIC values of 5.280 ± 0.787, 0.634 ± 0.044, 0.773 ± 0.035, and 0.75 ± 0.04, respectively. Between the two populations, the heterozygosity (HE > HO) and positive values of FIS (0.1714) and FIT (0.1868) indicated a low number of heterozygotes, suggesting the possibility of inbreeding. The test of Hardy-Weinberg equilibrium (HWE) showed that three loci each in the Quezon and Marinduque native pig populations deviated from HWE. Although morphological analysis revealed significant differences in snout shape, head profile, ear type, and all morphometric traits, a low level of genetic differentiation between the two populations was observed (FST = 0.0186; Nei genetic distance = 0.130; Nei unbiased genetic distance = 0.082). Overall, these findings imply that further studies on the genetic improvement and conservation of Philippine native pigs are required for the development of signature pig breeds across the country.

Assessment of the genetic variations of sago palm Metroxylon sagu in three regions of Sarawak, Malaysia using amplified fragment length polymorphism (AFLP) marker

BackgroundSago palm (Metroxylon sagu) is an important staple crop in the rural area of Sarawak, Malaysia. The palms grow well in the rough, swampy peat, from low flooded areas to uplands and acidic to neutral soils. Among the starch-producing crops, this palm is the most productive and promising, where it can store a significant amount of carbohydrate in the trunk. Due to the lack of molecular study of sago palm, the work described here aimed to develop molecular markers for identifying M. sagu and accessing the genetic variations of sago palm in different locations of Sarawak.ResultsAmplified fragment length polymorphism was employed to determine the genetic variations of sago palm between fifteen populations collected from three different locations: Mukah, Pusa and Samarahan. Based on 35,016 polymorphic fragments generated from 32 primer combinations, polymorphic information content (PIC), marker index (MI) and resolving power (RP) averaged 0.269, 0.005157 and 51.52039 per primer combination, respectively, were obtained, signifying the effectiveness and accuracy of the AFLP marker. Mukah showed higher diversity (I = 0.428, H = 0.232), while Pusa showed the lowest (I = 0.367, H = 0.240). The average value of the Shannon information index was 0.404. AMOVA showed 99% of the variation was found within the population. The Mantel test was performed with 9999 permutations. A significantly positive correlation (r = 0.220, p = 0.010) was observed between the genetic divergence of the population (Nei genetic distance) with the geographical distance.ConclusionsOur study considered AFLP is as an effective and reliable method to assess the genetic variations and the identification of M. sagu.Graphical

A comprehensive genomic study, mutation screening, phylogenetic and statistical analysis of SARS-CoV-2 and its variant omicron among different countries

BackgroundWith the rapid development of the genomic sequence data for the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants Delta (B.1.617.2) and Omicron (B.1.1.529), it is vital to successfully identify mutations within the genome. ObjectiveThe main objective of the study is to investigate the full-length genome mutation analysis of 157 SARS-CoV-2 and its variant Delta and Omicron isolates. This study also provides possible effects at the structural level to understand the role of mutations and new insights into the evolution of COVID-19 and evaluates the differential level analysis in viral genome sequence among different nations. We have also tried to offer a mutation snapshot for these differences that could help in vaccine formulation. This study utilizes a unique and efficient method of targeting the stable genes for the drug discovery approach. MethodsComplete genome sequence information of SARS-CoV-2, Delta, and Omicron from online resources were used to predict structure domain identification, data mining, and screening; employing different bioinformatics tools. BioEdit software was used to perform their genomic alignments across countries and a phylogenetic tree as per the confidence of 500 bootstrapping values was constructed. Heterozygosity ratios were determined in-silico. A minimum spanning network (MSN) of selected populations was determined by Bruvo's distance role-based framework. ResultsOut of all 157 different strains of SARS-CoV-2 and its variants, and their complete genome sequences from different countries, Corona nucleoca and DUF5515 were observed to be the most conserved domains. All genomes obtained changes in comparison to the Wuhan-Hu-1 strain, mainly in the TRS region (CUAAAC or ACGAAC). We discovered 596 mutations in all genes, with the highest number (321) found in ORF1ab (QHD43415.1), or TRS site mutations found only in ORF7a (1) and ORF10 (2). The Omicron variant has 30 mutations in the Spike protein and has a higher alpha-helix shape (23.46%) than the Delta version (22.03%). T478 was also discovered to be a prevalent polymorphism in Delta and Omicron variations, as well as genomic gaps ranging from 45 to 65aa. All 157 sequences contained variations and conformed to Nei's Genetic distance. We discovered heterozygosity (Hs) 0.01, mean anticipated Hs 0.32, the genetic diversity index (GDI) 0.01943989, and GD within population 0.01266951. The Hedrick value was 0.52324978, the GD coefficient was 0.52324978, the average Hs was 0.01371452, and the GD coefficient was 0.52324978. Among other countries, Brazil has the highest standard error (SE) rate (1.398), whereas Japan has the highest ratio of Nei's gene diversity (0.01). ConclusionsThe study's findings will assist in comprehending the shape and kind of complete genome, their streaming genomic sequences, and mutations in various additions of SARS-CoV-2, as well as its different variant strains like Omicron. These results will provide a scientific basis to design the vaccines and understand the genomic study of these viruses.

Genetic diversity of wild zebrafish Danio rerio populations available in Bangladesh

The morphometric and genetic variations of 4 wild populations of zebrafish ( Danio rerio ) in Bangladesh were studied using DNA barcoding and RAPD (Random Amplified Polymorphic DNA). The zebrafish populations were as ZMS (zebrafish from the Brahmaputra river, Mymensingh), ZFP (zebrafish from the Kumar river, Faridpur), ZKH (zebrafish from the Moyurriver, Khulna) and ZMG (zebrafish from the Aarial Beel, Munshiganj). The morphometric variations were insignificant to establish the genetic structure and diversity of these populations. Therefore, the genetic variation was analyzed with DNA barcoding and RAPD techniques. FishF1 and FishR1 primers were used for barcoding with amplification of Cytochrome Oxidase C subunit 1(COI) gene region and OPA03, OPA04 and OPF01 primers were used for RAPD analysis. In DNA barcoding analysis, the database provided species matches of 100% sequence similarity for these 4 wild fish populations with D. rerio . The overall sequence alignment similarity among these populations was 99.40%. The neighbor-joining phylogenetic tree was constructed from these COI barcode sequences also revealed genetic relationships and diversity among these populations. In RAPD analysis, a total number of 112 bands were found where 22 bands were polymorphic, indicated 19.64% polymorphism among these 4 wild populations. The percent polymorphic loci and genetic distance varied within a range of 14.00–26.67 and 0.2877–1.6094 respectively. Nei's genetic similarity among these 4 populations across all the primers ranged from 0.2000 to 0.7500. The Dendrogram based on Nei's genetic distance showed 3 clusters indicating the ZFP population is the maximum genetically diversified among them however; the ZMS and ZKH populations were in the same cluster. The knowledge of the molecular variation of wild zebrafish could be helpful for planning more effective and efficient managing strategies for this model species and also provide a significant contribution to zebrafish research all over the world.