Search results for: norovirus genetic diversity

Authors: Jean Pierre Kabue, Emma Meader, Afsatou Ndama Traore, Paul R. Hunter, Natasha Potgieter

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Norovirus is now considered the most common cause of outbreaks of nonbacterial gastroenteritis. Limited data are available for Norovirus strains in Africa, especially in rural and peri-urban areas. Despite the excessive burden of diarrhea disease in developing countries, Norovirus infections have been to date mostly reported in developed countries. There is a need to investigate intensively the role of viral agents associated with diarrhea in different settings in Africa continent. To determine the prevalence and genetic diversity of Norovirus strains circulating in the rural communities in the Limpopo Province, South Africa and investigate the genetic relationship between Norovirus strains, a cross-sectional study was performed on human stools collected from rural communities. Between July 2014 and April 2015, outpatient children under 5 years of age from rural communities of Vhembe District, South Africa, were recorded for the study. A total of 303 stool specimens were collected from those with diarrhea (n=253) and without (n=50) diarrhea. NoVs were identified using real-time one-step RT-PCR. Partial Sequence analyses were performed to genotype the strains. Phylogenetic analyses were performed to compare identified NoVs genotypes to the worldwide circulating strains. Norovirus detection rate was 41.1% (104/253) in children with diarrhea. There was no significant difference (OR=1.24; 95% CI 0.66-2.33) in Norovirus detection between symptomatic and asymptomatic children. Comparison of the median CT values for NoV in children with diarrhea and without diarrhea revealed significant statistical difference of estimated GII viral load from both groups, with a much higher viral burden in children with diarrhea. To our knowledge, this is the first study reporting on the differences in estimated viral load of GII and GI NoV positive cases and controls. GII.Pe (n=9) were the predominant genotypes followed by GII.Pe/GII.4 Sydney 2012 (n=8) suspected recombinant and GII.4 Sydney 2012 variants(n=7). Two unassigned GII.4 variants and an unusual RdRp genotype GII.P15 were found. With note, the rare GIIP15 identified in this study has a common ancestor with GIIP15 strain from Japan previously reported as GII/untypeable recombinant strain implicated in a gastroenteritis outbreak. To our knowledge, this is the first report of this unusual genotype in the African continent. Though not confirmed predictive of diarrhea disease in this study, the high detection rate of NoV is an indication of subsequent exposure of children from rural communities to enteric pathogens due to poor sanitation and hygiene practices. The results reveal that the difference between asymptomatic and symptomatic children with NoV may possibly be related to the NoV genogroups involved. The findings emphasize NoV genetic diversity and predominance of GII.Pe/GII.4 Sydney 2012, indicative of increased NoV activity. An uncommon GII.P15 and two unassigned GII.4 variants were also identified from rural settings of the Vhembe District/South Africa. NoV surveillance is required to help to inform investigations into NoV evolution, and to support vaccine development programmes in Africa.

Keywords: asymptomatic, common, outpatients, norovirus genetic diversity, sporadic gastroenteritis, South African rural communities, symptomatic

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Authors: M. F. Miah, A. Chakrabarty

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Two popular and highly valued fish, Stinging catfish (Heteropneustes fossilis) and Asian catfish (Clarias batrachus) are considered for observing genetic enhancement. Cross breeding was performed considering wild and farmed fish through inducing agent. Five RAPD markers were used to assess genetic diversity among parents and offspring of these two catfish for evaluating genetic enhancement in F1 generation. Considering different genetic data such as banding pattern of DNA, polymorphic loci, polymorphic information content (PIC), inter individual pair wise similarity, Nei genetic similarity, genetic distance, phylogenetic relationships, allele frequency, genotype frequency, intra locus gene diversity and average gene diversity of parents and offspring of these two fish were analyzed and finally in both cases higher genetic diversity was found in F1 generation than the parents.

Keywords: Heteropneustes fossilis, Clarias batrachus, cross breeding, genetic enhancement

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Authors: Mehdi Mohebodini, Iman Khalili-Baseri, Mehdi Behnamian, Sara Dezhsetan

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Diversity analysis at the molecular level using PCR-based markers is the efficient and rapid method of identifying the relationships and differences among the genotypes. In the present study, genetic diversity and relationships among 20 collected purslane accessions were evaluated using ISSR markers. The genotyping data were used to understand the relationships among the collected accessions and identify genetically diverse purslane accessions. The 25 primers gave a total of 92 bands, of which 62 were polymorphic (67.4%). The genetic diversity as estimated by Shannon’s information index was 0.55, revealing a quite high level of genetic diversity in the germplasm. The average number of an observed allele, effective allele, polymorphic information content (PIC) and Nei’s index were 2, 1.65, 0.37 and 0.37, respectively.

Keywords: Portulaca oleracea L., genetic diversity, ISSR, germplasm

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Authors: Maletsema Alina Mofokeng, Hussein Shimelis, Mark Laing, Pangirayi Tongoona

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Sorghum is one of the most important cereal crops grown for food, feed and bioenergy. Knowledge of genetic diversity is important for conservation of genetic resources and improvement of crop plants through breeding. The objective of this study was to assess the level of genetic diversity among sorghum genotypes using microsatellite markers. A total of 103 accessions of sorghum genotypes obtained from the Department of Agriculture, Forestry and Fisheries, the African Centre for Crop Improvement and Agricultural Research Council-Grain Crops Institute collections in South Africa were estimated using 30 microsatellite markers. For all the loci analysed, 306 polymorphic alleles were detected with a mean value of 6.4 per locus. The polymorphic information content had an average value of 0.50 with heterozygosity mean value of 0.55 suggesting an important genetic diversity within the sorghum genotypes used. The unweighted pair group method with arithmetic mean clustering based on Euclidian coefficients revealed two major distinct groups without allocating genotypes based on the source of collection or origin. The genotypes 4154.1.1.1, 2055.1.1.1, 4441.1.1.1, 4442.1.1.1, 4722.1.1.1, and 4606.1.1.1 were the most diverse. The sorghum genotypes with high genetic diversity could serve as important sources of novel alleles for breeding and strategic genetic conservation.

Keywords: Genetic Diversity, Genotypes, Microsatellites, Sorghum

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Authors: Asma Afshari, Abdollah Jamshidi, Jamshid Razmyar, Mehrnaz Rad

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Clostridium perfringens is a serious pathogen which causes enteric diseases in domestic animals and food poisoning in humans. Spores can survive cooking processes and play an important role in the possible onset of disease. In this study RAPD-PCR and REP-PCR were used to examine the genetic diversity of 49isolates ofC. Perfringens type A from 3 different sources. The results of RAPD-PCR revealed the most genetic diversity among poultry isolates, while human isolates showed the least genetic diversity. Cluster analysis obtained from RAPD_PCR and based on the genetic distances split the 49 strains into five distinct major clusters (A, B, C, D, and E). Cluster A and C were composed of isolates from poultry meat, cluster B was composed of isolates from human feces, cluster D was composed of isolates from minced meat, poultry meat and human feces and cluster E was composed of isolates from minced meat. Further characterization of these strains by using (GTG) 5 fingerprint repetitive sequence-based PCR analysis did not show further differentiation between various types of strains. To our knowledge, this is the first study in which the genetic diversity of C. perfringens isolates from different types of meats and human feces has been investigated.

Keywords: C. perfringens, genetic diversity, RAPD-PCR, REP-PCR

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Authors: M. F. Miah, K. M. A. Zinnah, M. J. Raihan, H. Ali, M. N. Naser

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As genetic diversity is most important for existing, breeding and production of any fish; this study was undertaken for investigating genetic diversity of freshwater mud eel, Monopterus cuchia at population level where three ecological populations such as flooded area of Sylhet (P1), open water of Moulvibazar (P2) and open water of Sunamganj (P3) districts of Bangladesh were considered. Four arbitrary RAPD primers (OPB-12, C0-4, B-03 and OPB-08) were screened and RAPD banding patterns were analyzed among the populations considering 15 individuals of each population. In total 174, 138 and 149 bands were detected in the populations of P1, P2 and P3 respectively; however, each primer revealed less number of bands in each population. 100% polymorphic loci were recorded in P2 and P3 whereas only one monomorphic locus was observed in P1, recorded 97.5% polymorphism. Different genetic parameters such as inter-individual pairwise similarity, genetic distance, Nei genetic similarity, linkage distances, cluster analysis and allelic information, etc. were considered for measuring genetic diversity. The average inter-individual pairwise similarity was recorded 2.98, 1.47 and 1.35 in P1, P2 and P3 respectively. Considering genetic distance analysis, the highest distance 1 was recorded in P2 and P3 and the lowest genetic distance 0.444 was found in P2. The average Nei genetic similarity was observed 0.19, 0.16 and 0.13 in P1, P2 and P3, respectively; however, the average linkage distance was recorded 24.92, 17.14 and 15.28 in P1, P3 and P2 respectively. Based on linkage distance, genetic clusters were generated in three populations where 6 clades and 7 clusters were found in P1, 3 clades and 5 clusters were observed in P2 and 4 clades and 7 clusters were detected in P3. In addition, allelic information was observed where the frequency of p and q alleles were observed 0.093 and 0.907 in P1, 0.076 and 0.924 in P2, 0.074 and 0.926 in P3 respectively. The average gene diversity was observed highest in P2 (0.132) followed by P3 (0.131) and P1 (0.121) respectively.

Keywords: genetic diversity, Monopterus cuchia, population, RAPD, Bangladesh

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Authors: Mohammad Sadegh Khavarinejad

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In this study, genetic diversity of 10 bread wheat genotypes by SSR and RAPD markers was evaluated. 11 primers were used included 6 RAPD primers and 5 SSR primers. RAPDs and SSRs could find 33 and 17 polymorphism respectively. In RAPDs, primers UBC 350 and UBC 109 and in SSRs, Primers Xgwm 469-6D and Xgwm120-2B showed genetic diversity among genotypes more than others.

Keywords: wheat, molecular markers, SSR, RAPD

Procedia PDF Downloads 398

Authors: Foluke E. Sola-Ojo, Ibraheem A. Abubakar, Semiu F. Bello, Isiaka H. Fatima, Sule Bisola, Adesina M. Olusegun, Adeniyi C. Adeola

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The domesticated pigeon, Columba livia domestica, has many valuable characteristics, including high nutritional value and fast growth rate. There is a lack of information on its genetic diversity in Nigeria; thus, the genetic variability in mitochondrial cytochrome oxidase subunit I (COI) sequences of 150 domestic pigeons from four different locations was examined. Three haplotypes (HT) were identified in Nigerian populations; the most common haplotype, HT1, was shared with wild and domestic pigeons from Europe, America, and Asia, while HT2 and HT3 were unique to Nigeria. The overall haplotype diversity was 0.052± 0.025, and nucleotide diversity was 0.026± 0.068 across the four investigated populations. The phylogenetic tree showed significant clustering and genetic relationship of Nigerian domestic pigeons with other global pigeons. The median-joining network showed a star-like pattern suggesting population expansion. AMOVA results indicated that genetic variations in Nigerian pigeons mainly occurred within populations (99.93%), while the Neutrality tests results suggested that the Nigerian domestic pigeons’ population experienced recent expansion. This study showed a low genetic diversity and population differentiation among Nigerian domestic pigeons consistent with a relatively conservative COI sequence with few polymorphic sites. Furthermore, the COI gene could serve as a candidate molecular marker to investigate the genetic diversity and origin of pigeon species. The current data is insufficient for further conclusions; therefore, more research evidence from multiple molecular markers is required.

Keywords: Nigeria pigeon, COI, genetic diversity, genetic variation, conservation

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Authors: Prachi Sharma, Mukesh Kumar Rana

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In the present study, the simple sequence repeat(SSR) markers have been used in analysis of genetic diversity of 37 genotypes of Triticum aestivum. The DNA was extracted using cTAB method. The DNA was quantified using the fluorimeter. The annealing temperatures for 27 primer pairs were standardized using gradient PCR, out of which 16 primers gave satisfactory amplification at temperature ranging from 50-62⁰ C. Out of 16 polymorphic SSR markers only 10 SSR primer pairs were used in the study generating 34 reproducible amplicons among 37 genotypes out of which 30 were polymorphic. Primer pairs Xgwm533, Xgwm 160, Xgwm 408, Xgwm 120, Xgwm 186, Xgwm 261 produced maximum percent of polymorphic bands (100%). The bands ranged on an average of 3.4 bands per primer. The genetic relationship was determined using Jaccard pair wise similarity co-efficient and UPGMA cluster analysis with NTSYS Pc.2 software. The values of similarity index range from 0-1. The similarity coefficient ranged from 0.13 to 0.97. A minimum genetic similarity (0.13) was observed between VL 804 and HPW 288, meaning they are only 13% similar. More number of available SSR markers can be useful for supporting the genetic diversity analysis in the above wheat genotypes.

Keywords: wheat, genetic diversity, microsatellite, polymorphism

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Authors: Rugang Tian

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In this study, we generated whole-genome sequence (WGS) data from110 native cattle. Together with whole-genome sequences from world-wide cattle populations, we estimated the genetic diversity and population genetic structure of different cattle populations. Our findings revealed clustering of cattle groups in line with their geographic locations. We identified noticeable genetic diversity between indigenous cattle breeds and commercial populations. Among all studied cattle groups, lower genetic diversity measures were found in commercial populations, however, high genetic diversity were detected in some local cattle, particularly in Rashoki and Mongolian breeds. Our search for potential genomic regions under selection in native cattle revealed several candidate genes related with immune response and cold shock protein on multiple chromosomes such as TRPM8, NMUR1, PRKAA2, SMTNL2 and OXR1 that are involved in energy metabolism and metabolic homeostasis.

Keywords: cattle, whole-genome, population structure, adaptation

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Authors: Fariborz Ahmadi, Reza Tati

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Genetic algorithm is a soft computing method that works on set of solutions. These solutions are called chromosome and the best one is the absolute solution of the problem. The main problem of this algorithm is that after passing through some generations, it may be produced some chromosomes that had been produced in some generations ago that causes reducing the convergence speed. From another respective, most of the genetic algorithms are implemented in software and less works have been done on hardware implementation. Our work implements genetic algorithm in hardware that doesn’t produce chromosome that have been produced in previous generations. In this work, most of genetic operators are implemented without producing iterative chromosomes and genetic diversity is preserved. Genetic diversity causes that not only do not this algorithm converge to local optimum but also reaching to global optimum. Without any doubts, proposed approach is so faster than software implementations. Evaluation results also show the proposed approach is faster than hardware ones.

Keywords: hardware, genetic algorithm, computer science, engineering

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Authors: Zia Amjad, Salem Safar Alghamdi

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This experiment was carried out at student educational farm College of Food and Agriculture, KSU, kingdom of Saudi Arabia; in order to characterize 154 Vicia faba, characterization, PCA, ago-morphological diversity. Icia faba L. accessions were based on ipove and ibpgr descriptors. 24 agro-morphological characters including 11 quantitative and 13 qualitative were observed for genetic variation. All the results were analyzed using multivariate analysis i.e. principle component analysis. First 6 principle components with eigenvalue greater than one; accounted for 72% of available Vicia faba genetic diversity. However, first three components revealed more than 10% of genetic diversity each i.e. 22.36%, 15.86%, and 10.89% respectively. PCA distributed the V. faba accessions into different groups based on their performance for the characters under observation. PC-1 which represented 22.36% of the genetic diversity was positively associated with stipule spot pigmentation, intensity of streaks, pod degree of curvature and to some extent with 100 seed weight. PC-2 covered 15.86 of the genetic diversity and showed positive association for average seed weight per plant, pod length, number of seeds per plant, 100 seed weight, stipule spot pigmentation, intensity of streaks (same as in PC-1), and to some extent for pod degree of curvature and number of pods per plant. PC-3 revealed 10.89% of genetic diversity and expressed positive association for number of pods per plant and number of leaflets per plant.

Keywords: Vicia faba, characterization, PCA, ago-morphological diversity

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Authors: Zia Amjad, Salem S. Alghamdi

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This experiment was carried out at student educational farm College of Food and Agriculture, KSU, kingdom of Saudi Arabia; in order to characterize 154 V. faba accessions based on UPOV and IBPGR descriptors. 24 agro-morphological characters including 11 quantitative and 13 qualitative were observed for genetic variation. All the results were analyzed using multivariate analysis i.e. principle component analysis (PCA). First six principle components (PC) had Eigen-value greater than one; accounted for 72% of available V. faba genetic diversity. However first three components revealed more than 10% of genetic diversity each i.e. 22.36%, 15.86% and 10.89% respectively. PCA distributed the V. faba accessions into different groups based on their performance for the characters under observation. PC-1 which represented 22.36% of the genetic diversity was positively associated with stipule spot pigmentation, intensity of streaks, pod degree of curvature and to some extent with 100 seed weight. PC-2 covered 15.86 of the genetic diversity and showed positive association for average seed weight per plant, pod length, number of seeds per plant, 100 seed weight, stipule spot pigmentation, intensity of streaks (same as in PC-1) and to some extent for pod degree of curvature and number of pods per plant. PC-3 revealed 10.89% of genetic diversity and expressed positive association for number of pods per plant and number of leaflets per plant.

Keywords: agro morphological characterization, diversity, vicia faba, PCA

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Authors: S. Sokel, M. Kale

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Norovirus (NoV) infection is effective and contagious in humans and many animals such as calves, pigs, dogs, cats, monkeys. There is not enough evidence about the zoonotic transmission of NoV between humans and animals. However, the fact that contamination of foods and environment by animal/human waste happens in indirect way leads to consideration of the agent as a zoonotic character. In our study, we aim to search the presence of NoV infection, which is a major public health problem, in possessed dogs showing diarrhea symptoms, to detect its genotype and to study nutrition and life conditions. We searched the existence of human NoV GI, GII and GIV in the stool of 128 pet dogs in Burdur Province with diarrhoea in various sex, age and breed by using Real-Time PCR method. Human NoV GII was found in only 5 of the 128 dog stool samples (3.91%). In the study, it was determined that the owners of the dogs with NoV GII are middle aged or elderly people most of whom are male and that there were no children in their houses. As these dogs are treated like the owner’s child, it is assumed that they could be transmitted with NoV GII as a result of close interaction with their owner.

Keywords: dog, human, norovirus, Real-Time PCR, stool

Procedia PDF Downloads 115

Authors: Masoud Sheidaei, Fahimeh Koohdar

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Date palms are economically important tree plants with high nutrition and medicinal values. More than 400 date palm cultivars are cultivated in many regions of Iran, but no report is available on landscape genetics and species distribution modeling of these trees from the country. Therefore, the present study provides a detailed insight into the genetic diversity and structure of date palm populations in Iran and investigates the effects of geographical and climatic variables on the structuring of genetic diversity in them. We used different computational methods in the study like, spatial principal components analysis (sPCA), redundancy analysis (RDA), latent factor mixed model (LFMM), and Maxent and Dismo models of species distribution modeling. We used a combination of different molecular markers for this study. The results showed that both global and local spatial features play an important role in the genetic structuring of date palms, and the genetic regions associated with local adaptation and climatic variables were identified. The effects of climatic change on the distribution of these taxa and the genetic regions adaptive to these changes will be discussed.

Keywords: adaptive genetic regions, genetic diversity, isolation by distance, populations divergence

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Authors: Nadir Ali Rind, Özlem Aksoy, Muhammad Umar Dahot, Salih Dikilitaş, Muhammad Rafiq, Burçak Tütünoğlu

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Melia azedarach L. is freshly fruited small to medium sized tree native to China and North western India. It is growing in Pakistan and Turkey in various areas facing great environmental changes to maintain its survival. The species is valued for its high quality wood, medicinal, ornamental and shade purposes. The present work was aimed to estimate the genetic variation among the populations of Melia azedarach L. leaf samples that were collected from five different locations of Turkey and three different areas of Pakistan. These populations were chosen on the random bases by applying RAPD primers in order to construct a dendogram using UPGMA method to show genetic diversity. After that appropriate conservation strategies were suggested. 14 primers producing polymorphic and monomorphic bands were analyzed. Genetic distances were calculated for all the species studied by RAPD-PCR methods. According to the results the lowest genetic identity values and the highest genetic polymorphic values were determined. It is observed that there was a clear split among populations from different areas in Turkey and Pakistan. These differences may be due to eco-geographical association with genetic variation and should be conserved to retain the genetic variation of the species.

Keywords: melia azedarach L., genetic diversity, conservation, RAPD-PCR, medicinal plant

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Authors: M. Vivodík, Ž. Balážová, Z. Gálová

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The aim of this work was to detect genetic variability among the set of 40 castor genotypes using 8 RAPD markers. Amplification of genomic DNA of 40 genotypes, using RAPD analysis, yielded in 66 fragments, with an average of 8.25 polymorphic fragments per primer. Number of amplified fragments ranged from 3 to 13, with the size of amplicons ranging from 100 to 1200 bp. Values of the polymorphic information content (PIC) value ranged from 0.556 to 0.895 with an average of 0.784 and diversity index (DI) value ranged from 0.621 to 0.896 with an average of 0.798. The dendrogram based on hierarchical cluster analysis using UPGMA algorithm was prepared and analyzed genotypes were grouped into two main clusters and only two genotypes could not be distinguished. Knowledge on the genetic diversity of castor can be used for future breeding programs for increased oil production for industrial uses.

Keywords: dendrogram, polymorphism, RAPD technique, Ricinus communis L.

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Authors: Ibrahim Ilker Ozyigit, Ertugrul Filiz, Seda Birbilener, Semsettin Kulac, Zeki Severoglu

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In this study, we have performed genetic diversity analysis of Tilia tomentosa genotypes by using randomly amplified polymorphic DNA (RAPD) primers. A total of 28 genotypes, including 25 members from the urban ecosystem and 3 genotypes from forest ecosystem as outgroup were used. 8 RAPD primers produced a total of 53 bands, of which 48 (90.6 %) were polymorphic. Percentage of polymorphic loci (P), observed number of alleles (Na), effective number of alleles (Ne), Nei's (1973) gene diversity (h), and Shannon's information index (I) were found as 94.29 %, 1.94, 1.60, 0.34, and 0.50, respectively. The unweighted pair-group method with arithmetic average (UPGMA) cluster analysis revealed that two major groups were observed. The genotypes of urban and forest ecosystems showed a high genetic similarity between 28% and 92% and these genotypes did not separate from each other in UPGMA tree. Also, urban and forest genotypes clustered together in principal component analysis (PCA).

Keywords: Tilia tomentosa, genetic diversity, urban ecosystem, RAPD, UPGMA

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Authors: Ilian Badjakov, Ivayla Dincheva, Violeta Kondakova, Rossitza Batchvarova

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In this study, we present our initial results on the assessment of genetic diversity among wild Bulgarian berry accessions (Rubus idaeus L. Fragaria Vesca L., Vaccinium vitis-idaea L., Vaccinium myrtillus L.) using Random Amplified Polymorphic DNA (RAPDs) markers. Leaves and fruits were collected from two natural habitats - the Balkan Mountain and the Mountain of Orpheus - Rhodope Mountain. All accessions were screened for their polymorphism using five RAPD primers. The phylogenetic distances calculated from RAPD data ranged from 0.29 to 0.82 thus indicating that a high level of gene diversity is present in the selected genotypes. In order to characterize further the structure and grouping of berry accessions, a dendrogram deriving from UPGMA cluster analysis based on the genetic similarity (GS) coefficient matrix was designed. RAPD analysis provided to be efficient for discrimination of accessions within the same species with similar morphological characters

Keywords: Bulgarian wild berries, genetic diversity, RAPD, UPGMA

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Authors: Asim Mehmood, Abdul Karim, Muhammad J. Jaskani, Faisal S. Awan, Muhammad W. Sajid

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Guava (Psidium guajava L.) is an important commercial fruit crop of Pakistan. It is an allogamous crop having 25-40% cross pollination which on the one hand leads to clonal degradation and on the other hand can add variations to generated new cultivars. Morpho-genetic characterization of 37 guava accessions was carried out for study of the genetic diversity among guava accessions located in province Punjab, Pakistan. For morphological analysis, 17 morphological traits were studied, and strong positive correlation was found among the 7 morphological traits which included thickness of outer flesh in relation to core diameter, fruit length, fruit width, fruit juiciness, fruit size, fruit sweetness and number of seeds. For genetic characterization, 18 microsatellites were used, and the sizes of reproducible and scorable bands ranged from 150 to 320 bp. These 18 primer pairs amplified a total of 85 alleles in P. guajava, with an average total number of 4.7 alleles per locus and no more than two displayed bands (nuclear SSR loci). The phylogenetic tree based on the morphological and genetic traits showed the diversity of these 37 guava genotypes into two major groups. These results indicated that Pakistani guava is quite diverse and a more detail study is needed to define the level of genetic variability.

Keywords: Psidium guajava L, genetic diversity, SSR markers, polymorphism, dendrogram

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Authors: Monisha Isaac

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Use of molecular markers for selecting plants with desired traits has been started long back. Due to their heritable characteristics, they are useful for identification and characterization of specific genotypes. The study involves various types of molecular markers used to select multiple desired characters in plants, their properties, and advantages to improve crop productivity in adverse climatological conditions for the purpose of providing food security to fast-growing global population. The study shows that genetic similarities obtained from molecular markers provide more accurate information and the genetic diversity can be better estimated from the genetic relationship obtained from the dendrogram. The information obtained from markers assisted characterization is more suitable for the crops of economic importance like sugarcane.

Keywords: molecular markers, crop productivity, genetic diversity, genotype

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Authors: Somayeh Akrami, Habib Onsori, Elham Tahmassebian

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Species of Anemone narcissiflora is belonged to Anemone genus of Ranunculaceae family. This species has two subspecies named narcissiflora and willdenowii which the latest is recorded in Iran in 2010. Some samples of A. narcissiflora is gathered from kuhkamar-zonouz region of East -Azerbaijan province, Iran to study the genetic diversity of the species by using RAPD molecular markers, and estimation of genetic diversity were evaluated with the using 10mer RAPD primers by PCR-RAPD method. 39 polymorphic bands were produced from the six primers used in this technique that the maximum band is related to the RP1 primer, the lowest band is related to the RP7 and the average band for all primers were 6.5 polymorphic bands. Cluster analysis of samples in done by UPGMA method in NTSYSpc 2.02 software. Dendrogram resulting from migrating bands showed that the studied samples can be divided into two groups. The first group includes samples with 1-2 flowers and the second group consists of two sub-groups which the first subgroup consists of samples with 3-5 flowers, and the second subgroup consists of samples with 6-7 flowers. The results of the comparison and analysis of the data obtained from RAPD technique and similarity matrix represents the genetic variation between collected samples. This study shows that RAPD markers can determine the polymorphisms between different genotypes of A. narcissiflora and their hybrids. So RAPD technique can serve as a suitable molecular method to determine the genetic diversity of samples.

Keywords: Anemone narcissiflora, genetic diversity, RAPD-PCR

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Authors: Hamid Mustafa, Huson J. Heather, Kim Eiusoo, McClure Matt, Khalid Javed, Talat Nasser Pasha, Afzal Ali1, Adeela Ajmal, Tad Sonstegard

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Genetic differences associated with speciation, breed formation or local adaptation can help to preserve and effective utilization of animals in selection programs. Analyses of population structure and breed diversity have provided insight into the origin and evolution of cattle. In this study, we used a high-density panel of SNP markers to examine population structure and diversity among ten Pakistani indigenous cattle breeds. In total, 25 individuals from three cattle populations, including Achi (n=08), Bhagnari (n=04) and Cholistani (n=13) were genotyped for 777, 962 single nucleotide polymorphism (SNP) markers. Population structure was examined using the linkage model in the program STRUCTURE. After characterizing SNP polymorphism in the different populations, we performed a detailed analysis of genetic structure at both the individual and population levels. The whole-genome SNP panel identified several levels of population substructure in the set of examined cattle breeds. We further searched for spatial patterns of genetic diversity among these breeds under the recently developed spatial principal component analysis framework. Overall, such high throughput genotyping data confirmed a clear partitioning of the cattle genetic diversity into distinct breeds. The resulting complex historical origins associated with both natural and artificial selection have led to the differentiation of numerous different cattle breeds displaying a broad phenotypic variety over a short period of time.

Keywords: Pakistan, cattle, genetic diversity, population structure

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Authors: Yasser M. Saad, Amr A. El Hanafy, Saleh A. Alkarim, Hussein A. Almehdar, Elrashdy M. Redwan

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Camels are substantial providers of transport, milk, sport, meat, shelter, security and capital in many countries, particularly in Saudi Arabia. Inter simple sequence repeat technique was used to detect the genetic variations among some camel breeds (Majaheim, Safra, Wadah, and Hamara). Actual number of alleles, effective number of alleles, gene diversity, Shannon’s information index and polymorphic bands were calculated for each evaluated camel breed. Neighbor-joining tree that re-constructed for evaluated these camel breeds showed that, Hamara breed is distantly related from the other evaluated camels. In addition, the polymorphic sites, haplotypes and nucleotide diversity were identified for some camelidae cox1 gene sequences (obtained from NCBI). The distance value between C. bactrianus and C. dromedarius (0.072) was relatively low. Analysis of genetic diversity is an important way for conserving Camelus dromedarius genetic resources.

Keywords: camel, genetics, ISSR, neighbor-joining

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Authors: Masoud Sheidaei, Melica Tabasi, Fahimeh Koohdar, Mona Sheidaei

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Juglans regia L. is an economically important species of edible nuts. Iran is known as a center of origin of genetically rich walnut germplasm and expected to be found a large diversity within Iranian walnut populations. A detailed population genetic of local populations is useful for developing an optimal strategy for in situ conservation and can assist the breeders in crop improvement programs. Different phylogenetic studies have been carried out in this genus, but none has been concerned with genetic changes associated with geographical divergence and the identification of adaptive SNPs. Therefore, we carried out the present study to identify discriminating ITS nucleotides among Juglans species and also reveal association between ITS SNPs and geographical variables. We used different computations approaches like DAPC, CCA, and RDA analyses for the above-mentioned tasks. We also performed population genetics analyses for population effective size changes associated with the species expansion. The results obtained suggest that latitudinal distribution has a more profound effect on the species genetic changes. Similarly, multiple analytical approaches utilized for the identification of both discriminating DNA nucleotides/ SNPs almost produced congruent results. The SNPs with different phylogenetic importance were also identified by using a parsimony approach.

Keywords: Persian walnut, adaptive SNPs, data analyses, genetic diversity

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Authors: Reza Talebi

Abstract:

Wheat (Triticum aestivum) is one of the most important food staples in Iran. Understanding genetic variability among the landrace wheat germplasm is important for breeding. Landraces endemic to Iran are a genetic resource that is distinct from other wheat germplasm. In this study, 60 Iranian landrace wheat accessions were characterized AFLP and ISSR markers. Twelve AFLP primer pairs detected 128 polymorphic bands among the sixty genotypes. The mean polymorphism rate based on AFLP data was 31%; however, a wide polymorphism range among primer pairs was observed (22–40%). Polymorphic information content (PIC value) calculated to assess the informativeness of each marker ranged from 0.28 to 0.4, with a mean of 0.37. According to AFLP molecular data, cluster analysis grouped the genotypes in five distinct clusters. .ISSR markers generated 68 bands (average of 6 bands per primer), which 31 were polymorphic (45%) across the 60 wheat genotypes. Polymorphism information content (PIC) value for ISSR markers was calculated in the range of 0.14 to 0.48 with an average of 0.33. Based on data achieved by ISSR-PCR, cluster analysis grouped the genotypes in three distinct clusters. Both AFLP and ISSR markers able to showed that high level of genetic diversity in Iranian landrace wheat accessions has maintained a relatively constant level of genetic diversity during last years.

Keywords: wheat, genetic diversity, AFLP, ISSR

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Authors: Sa’adu Mafara Abubakar, Muhammad Nuraddeen Danjuma, Adewole Tomiwa Adetunji, Richard Mundembe, Salisu Mohammed, Francis Bayo Lewu, Joseph I. Kiok

Abstract:

Pearl millet is the most drought tolerant of all domesticated cereals, is cultivated extensively to feed millions of people who mainly live in hash agroclimatic zones. It serves as a major source of food for more than 40 million smallholder farmers living in the marginal agricultural lands of Northern Nigeria. Pearl millet grain is more nutritious than other cereals like maize, is also a principal source of energy, protein, vitamins, and minerals for millions of poorest people in the regions where it is cultivated. Pearl millet has recorded relatively little research attention compared with other crops and no sufficient work has analyzed its genetic diversity in north-western Nigeria. Therefore, this study was undertaken with the objectives to analyze the genetic diversity of pearl millet accessions using SSR marker and to analyze the extent of evolutionary relationship among pearl millet accessions at the molecular level. The result of the present study confirmed diversity among accessions of pearl millet in the study area. Simple Sequence Repeats (SSR) markers were used for genetic analysis and evolutionary relationship of the accessions of pearl millet. To analyze the level of genetic diversity, 8 polymorphic SSR markers were used to screen 69 accessions collected based on three maturity periods. SSR markers result reveal relationships among the accessions in terms of genetic similarities, evolutionary and ancestral origin, it also reveals a total of 53 alleles recorded with 8 microsatellites and an average of 6.875 per microsatellite, the range was from 3 to 9 alleles in PSMP2248 and PSMP2080 respectively. Moreover, both the factorial analysis and the dendrogram of phylogeny tree grouping patterns and cluster analysis were almost in agreement with each other that diversity is not clustering according to geographical patterns but, according to similarity, the result showed maximum similarity among clusters with few numbers of accessions. It has been recommended that other molecular markers should be tested in the same study area.

Keywords: pearl millet, genetic diversity, simple sequence repeat (SSR)

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Authors: Abdullah M. Alzahrani

Abstract:

The unicellular alga Chlorella vulgaris was isolated from Al-Asfar Lake, which is located in the Al-Ahsa province of Saudi Arabia. Two different isolates were sub-cultured under laboratory conditions. The wild type was grown under a regular concentration of copper, whereas the other isolate was grown under a progressively increasing copper concentration. An Inter Simple Sequence Repeats (ISSR) analysis was performed using DNA isolated from the wild type and tolerant strains. The sum of the scored bands of the wild type was 155, with 100 (64.5%) considered to be polymorphic bands, whereas the resistant strain displayed 147 bands, with 92 (62.6%) considered to be polymorphic bands. The sum of the scored bands of a mixed sample was 117 bands, of which only 4 (3.4%) were considered to be polymorphic. The average Nei's genetic diversity (h) and Shannon-Weiner diversity indices (I) were 0.3891 and 0.5394, respectively. These results clearly indicate that the adaptation to a high level of copper in Chlorella vulgaris is not merely physiological but rather driven by modifications at the genomic level.

Keywords: chlorella vulgaris, copper tolerance, genetic diversity, green algae

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Authors: Radoslav Židek, Veronika Šidlová, Radovan Kasarda, Birgit Fuerst-Waltl

Abstract:

Machine learning represents a set of topics dealing with the creation and evaluation of algorithms that facilitate pattern recognition, classification, and prediction, based on models derived from existing data. The data can present identification patterns which are used to classify into groups. The result of the analysis is the pattern which can be used for identification of data set without the need to obtain input data used for creation of this pattern. An important requirement in this process is careful data preparation validation of model used and its suitable interpretation. For breeders, it is important to know the origin of animals from the point of the genetic diversity. In case of missing pedigree information, other methods can be used for traceability of animal´s origin. Genetic diversity written in genetic data is holding relatively useful information to identify animals originated from individual countries. We can conclude that the application of data mining for molecular genetic data using supervised learning is an appropriate tool for hypothesis testing and identifying an individual.

Keywords: genetic data, Pinzgau cattle, supervised learning, machine learning

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Authors: Naser B. Almari, Salem S. Alghamdi, Muhammad Afzal, Mohamed Helmy El Shal

Abstract:

Wheat landraces are a rich genetic resource for boosting agronomic qualities in breeding programs while also providing diversity and unique adaptation to local environmental conditions. These genotypes have grown increasingly important in the face of recent climate change challenges. This research aimed to look at the genetic diversity of Saudi Durum wheat landraces using morpho-phenological and molecular data. The principal components analysis (PCA) analysis recorded 78.47 % variance and 1.064 eigenvalues for the first six PCs of the total, respectively. The significant characters contributed more to the diversity are the length of owns at the tip relative to the length of the ear, culm: glaucosity of the neck, flag leaf: glaucosity of the sheath, flag leaf: anthocyanin coloration of auricles, plant: frequency of plants with recurved flag leaves, ear: length, and ear: shape in profile in the PC1. The significant wheat genotypes contributed more in the PC1 (8, 14, 497, 650, 569, 590, 594, 598, 600, 601, and 604). The cluster analysis recorded an 85.42 cophenetic correlation among the 22 wheat genotypes and grouped the genotypes into two main groups. Group, I contain 8 genotypes, however, the 2nd group contains 12 wheat genotypes, while two genotypes (13 and 497) are standing alone in the dendrogram and unable to make a group with any one of the genotypes. The second group was subdivided into two subgroups. The genotypes (14, 602, and 600) were present in the second sub-group. The genotypes were grouped into two main groups. The first group contains 17 genotypes, while the second group contains 3 (8, 977, and 594) wheat genotypes. The genotype (602) was standing alone and unable to make a group with any wheat genotype. The genotypes 650 and 13 also stand alone in the first group. Using the Mantel test, the data recorded a significant (R2 = 0.0006) correlation (phenotypic and genetic) among 22 wheat durum genotypes.

Keywords: durum wheat, PCA, cluster analysis, SRAP, genetic diversity

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