Level Of Genetic Similarity Research Articles

English

Genetic diversity among four indigenous breeds of sheep namely Mengali, Balochi, Beverigh and Harnai of Balochistan was detected by random amplified polymorphic DNA (RAPD) technique. Nineteen RAPD primers were initially applied and seventeen were chosen for further analysis, based on band pattern quality, reproducibility and presence of bands. An average of 92 RAPD fragments were obtained by using 17 primers and out of the 36 fragments (39.13%) illustrated monomorphism while, 56 bands (60.87%) were polymorphic in all the four sheep breeds. The number of bands amplified in all the sheep breeds ranged from 2 to 10. The highest number of polymorphic loci 40 was observed in the Mengali breed, while the lowest 28 was in Balochi. Further, 33 and 31 polymorphic loci were seen in Beverigh and Harnai breeds, respectively. The overall gene diversity was highest in the Mengali (0.1474) while the lowest in Balochi breed (0.0998). Results of genetic similarities showed closer proximity between Balochi and Beverigh (0.992), Balochi and Harnai (0.992), and between Beverigh and Harnai (0.996). The resemblance was observed between Mengali and Balochi (0.918), between Mengali and Beverigh breeds (0.931) and between Mengali and Harnai breeds (0.925). The high level of genetic similarity between Balochi, Beverigh and Harnai sheep indicated the close relationship that might be due to common habitat. Further the present study highlighted the presence of diversity among and within breeds that can be used in the selection or crossbreeding programs of sheep. The present study suggests that RAPD-PCR can effectively be used to determine the genetic distances among the sheep breeds.   Key words: Genetic distance, polymorphism, random amplified Polymorphic DNA.   &nbsp

Phylogenetics of selected Mentha species on the basis of rps8, rps11 and rps14 chloroplast genes

Mentha is a genus of family Lamiaecae, and is well known for its great medicinal and economic values. It is widely distributed over five continents (excluding Antarctica and South America) of the world. In order to construct the phylogeny and to investigate the genetic variability among seven Mentha species polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) (CAPS) marker technique was used. Three chloroplast genes rps8, rps11 and rps14 were used to amplify from the chloroplast genome of sevenMentha species. rps8 gene was tested on broad range of annealing temperatures but no amplification was observed while rps11 and rps14 regions of Mentha cpDNA were successfully amplified and subjected to PCR-RFLP. For restriction digestion of the amplified PCR product, twelve different restriction enzymes were used and the resulting restriction pattern was resolved on PAGE. Comparison of Nicotiana tabacum and Mentha rps11 andrps14 genes was also performed. The data was analyzed by using the software numerical taxonomy and multivariate analysis system (NTSYS) pc version 2.01 showing considerable level of genetic similarity among the Mentha species. It was also found that Eam1104I andAlw44I based PCR-RFLP of rps14 gene could serve as a specific marker for Mentha spicataidentification and differentiation. Key words: Mentha, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), chloroplast genes, rps, phylogenetic analysis.

Molecular characterization of the pathogenic plant fungus Rhizoctonia solani (Ceratobasidiaceae) isolated from Egypt based on protein and PCR-RAPD profiles

Twenty-one isolates of Rhizoctonia solani were categorized into three anastomosis groups consisting of AG-4-HG-I (eight isolates), AG-2-2 (nine isolates) and AG-5 (four isolates). Their pathogenic capacities were tested on cotton cultivar Giza 86. Pre-emergence damping-off varied in response to the different isolates; however, the differences were not significant. Soluble proteins of the fungal isolates were electrophoresed using SDS-PAGE and gel electrophoreses. A dendrogram of the protein banding patterns by the UPGMA of arithmetic means placed the fungal isolates into distinct groups. There was no evidence of a relationship between protein dendrogram, anastomosis grouping or level of virulence or geographic origin. The dendrogram generated from these isolates based on PCR analysis with five RAPD-PCR primers showed high levels of genetic similarity among the isolates from the same geographical locations. There was partially relationship between the genetic similarity and AGs or level of virulence or geographic origin based on RAPD dendrogram. These results demonstrate that RAPD technique is a useful tool in determining the genetic characterization among isolates of R. solani.

Genetic Diversity Assessment of Acid Lime (<i>Citrus aurantifolia</i> Swingle) Landraces in Nepal, Using SSR Markers

Acid lime (Citrus aurantifolia) is an important commercial fruits crop, cultivated in terai to high hills of Nepal. High variation of acid lime fruits are observed in existing landraces due to crossing within the other citrus species. Determination of genetic variation is important to the plant breeders for development of high yielding variety and hybrids. Therefore, an attempt has been made to study the genetic diversity of 62 acid lime landraces, collected from different altitudinal range in the eastern part of Nepal, using SSR markers. Twelve Simple Sequence Repeat (SSR) primer pairs were used to assess the genetic diversity of acid lime. The average genetic similarity level among the 62 accessions was 0.77, ranging from 0.54 to 1.0 and separated five major cluster groups. Total of 33 alleles were detected by eleven primer pairs and size of alleles ranged from 50 to 225. Average polymorphic information content (PIC) value was 0.50, whereas highest 0.75 and lowest 0.18 was observed in CAT01 and GT03 loci respectively. The results of the study clearly indicated that, SSR markers are highly polymorphic and more informative for the assessment of genetic diversity of acid lime landraces.

English

The regeneration capacity between the shoot tip and petiole explants that excised from two date palm (Phoenix dactylifera L.) cutivar namely Unknown and Ferhi was compared. It was noted that the shoot tip explants started to swill after several subculture when placed on Murashige and Skoog (MS) medium supplemented with 100 mg l-1 2, 4-D, 3 mg l-16-Benzyladenine (BA) and 3 g l-1 activated charcoal while embryogenic calli was induced by culturing the petiole explants on MS medium supplemented with 1 mgl-1 2, 4-D. The data indicate that callus induction efficiency decreased with increasing 2, 4-D in the culture media. The embryonic calli were transferred into shoot inducing medium containing 1 mgl-1 BA and 1 mgl-1naphthaleneacetic acid (NAA). The developed protocol for plant regeneration using petiole explant is repeatable and takes less time (four months) compared with the shoot tips as explants which take much time (3 years). Genetic similarity between the mother plants of the Unknown and Ferhi cultivars and several plants regenerated in vitro from both cultivars were examined by random amplification polymorphic DNA (RAPD) analysis using 10 random primers. Each primer generated a unique set of amplification products ranging in size from 200-2600 bp. The data indicate that the regenerated plants from the Unknown and Ferhi cultivars showed 36.2 and 37.8 % polymorphism and sharing 63.8 and 62.2% of similarities, respectively with their mother plants. The level of genetic similarity between regenerated plants and their mother plants as revealed by RAPD analysis indicate that this regeneration protocol is promising and can be used to produce transgenic date palm plants expressing economically important genes.   Key words: Date palm, somatic embryogenesis, genetic stability, RAPD anaysis.

Perspectives on Human Population Structure at the Cusp of the Sequencing Era

Human groups show structured levels of genetic similarity as a consequence of factors such as geographical subdivision and genetic drift. Surveying this structure gives us a scientific perspective on human origins, sheds light on evolutionary processes that shape both human adaptation and disease, and is integral to effectively carrying out the mission of global medical genetics and personalized medicine. Surveys of population structure have been ongoing for decades, but in the past three years, single-nucleotide-polymorphism (SNP) array technology has provided unprecedented detail on human population structure at global and regional scales. These studies have confirmed well-known relationships between distantly related populations and uncovered previously unresolvable relationships among closely related human groups. SNPs represent the first dense genome-wide markers, and as such, their analysis has raised many challenges and insights relevant to the study of population genetics with whole-genome sequences. Here we draw on the lessons from these studies to anticipate the directions that will be most fruitful to pursue during the emerging whole-genome sequencing era.

Determination of variability in monosporidial lines of Tilletia indica by RAPD analysis

Genetic variability in 23 monosporidial lines developed from five isolates of Tilletia indica causing Karnal bunt of wheat isolated from four wheat growing states of India was determined by using 19 rapid amplified polymorphic DNA (RAPD) markers. Amplification profile generated with all the 19 primers produced 3–16 numbers of bands of 1.5–5 kb size. High level of polymorphism (95.2%) suggested wide range of variability. Maximum Jaccard's similarity coefficient (80%) was observed between KB2MsB and KB2MsC followed by KB5MsC and KB5MsE with 75% similarity, whereas it was minimum between KB3MsA and Kb4MsB (47%). The dendrogram derived from the fingerprint analysis with 19 RAPD primers by using UPGMA showed different levels of genetic similarity among monosporidial lines. At 35% genetic similarity, the monosporidial lines were grouped in two clusters. Some primers, viz., OPN-1, OPN-6, OPN-9, OPN-12, OPN-13, OPN-18, OPM-2, OPM-8, OPM-10, OPB-8, OPB-17 and OPB-20 showed 100% polymorphism. The RAPD fingerprint generated by OPN-1 and OPM-3 were analysed and showed high range of variation in genetic make-up of monosporidial lines.

Families and Genomes: The Next Generation

I thought this was about family relations and child development. Why are we reading and talking about genes? . Many of us who teach and study genetics and human behavior get questions like this from our students and our colleagues. My answer to this kind of question is informed by the ongoing work presented by Horwitz and Neiderhiser (2011), and it goes something like this: Our cultures and our genomes have coevolved for millennia. The continually changing products of this ongoing process include different versions of many genes (i.e., alleles) that covary and interact with variability in environments. Efforts to understand the impact of this ongoing process require consideration of family relationships. Successful reproduction and survival of offspring are ensured within the intense, lifelong social relationships formed in family groups, where individual differences between people develop. Over the course of the 20th century, theorists in every scientific discipline came to realize that they needed to incorporate genetic influences into conceptualizations of human functioning and behavior. Now we find ourselves living in the era of the genome. Every week, new discoveries are published that tell us something about genes and their influence on human functioning. So here is my question. As students and scholars of family and human development, will we be able to move family and developmental research and practice toward a more complete understanding of the role of genetics in family relations and child outcomes? We probably will succeed, if we take seriously the important and complex concepts, methods, and conclusions offered by Horwitz and Neiderhiser (201 1) in their review of behavioral genetic research on family relationships and child adjustment. They present the breadth and leading edge of genetically informative research addressing gene - environment interplay in marital and family relationships and outcomes in children. Their paper offers a clear and compelling message about what we know, and what lies ahead, for family and developmental scientists. Theories about gene - environment transactions are tested using quasi-experimental behavioral genetic studies based on different types of kin (e.g., adoptive and nonadoptive parent -child pairs, identical and fraternal twin siblings, full and half siblings) and molecular genetic studies that directly assess the structural variation in DNA and its associations with behaviors of interest. Gone are the days of simply estimating a heritability coefficient and arguing that this variable or that variable includes some kind of genetic influence. Now there are computational methods for considering gene - environment interplay between genetic and nongenetic factors. This includes the correlated and interacting effects highlighted by Horwitz and Neiderhiser. FAMILIES AND GENOMES Gene -environment interplay produces remarkable within-family variation in each individual's many personal attributes, as well as variation in each dyadic relationship. Paying attention to this within-family variability - rather than limiting the analysis to differences between families or groups - strengthens understanding of the bidirectional nature of family relationships and children's development in families (Reiss, Neiderhiser, Hetherington, & Plomin, 2000). Within families are substantial sibling differences in temperament and personality factors, cognitive and achievement skills, and many other individual difference attributes arising from genetic and nongenetic influences. Full siblings share 50% of their alleles identical by descent, on average, but there is noteworthy deviation from this average level of genetic similarity. The physical and behavioral similarity of siblings varies widely, due in part to variation in genetic similarity. But nongenetic factors matter, too, and are defined as nonshared environmental processes that enhance sibling differentiation. The behavioral genetic models described by Horwitz and Neiderhiser (201 1) generate mathematical constructs representing heritable and nonheritable influences. …

구제역 Asia1 백신의 방어 유전형 분석

Asia1/Shamir that has been recommended by World Reference Laboratory for foot-and-mouth disease (FMD) is used as a vaccine strain, and is being prepared in many countries including Korea. Although it is assumed that vaccine strain Asia1/Shamir has a wide antigenicity, sufficient molecular biological analysis has not been accomplished yet. Complete genome sequence analysis showed that the region with the most severe variations was 1D region of structural protein-coding sequence; particularly amino acid 141~157 residues in 1D region RGD sites for binding to susceptible cells. In addition, five amino acids in 1D region were identified as characteristic sites that are different from other known Asia1 viruses. Asia1/Shamir strain was shown to be genetically similar to group VI that had occurred in the Middle East, but showed low level of genetic similarity to the group V viruses that had occurred in the Southeast Asia and China. It is considered that, if these viruses, group I and II including group V are introduced into Korea, care would be paid in case of inoculating the vaccine strain Shamir available in Korea.

Human metapneumovirus and human bocavirus associated with respiratory infection in Apulian population

We have studied the occurrence of hBoV, hMPV and InfA-B in an Apulian population with respiratory tract infections. During influenza season 2008–2009, 116 oropharingeal swabs were collected from patients affected by Influenza-Like Illness (ILI). The PCR products of hMPV M and HBoV NP-1 genes were sequenced. 78 out of 116 samples were positive for at least one respiratory virus; hBoV was detected in 53, hMPV in 22 and InfA-B in 41 out of 116 swabs. A high rate of hBoV infection in adult (18.9%) and elderly (26.4%) subjects was found. The co-infection rate was higher for hMPV (18/22 cases, 81.8%) compared to hBoV (26/53 cases, 49.1%), and InfA-B (25/41 cases, 61.0%). Co-infections were common in children. hBoV positive samples shared a high level of genetic similarity with the hBoV1 genotype, and hMPV positive samples clustered with A2 subgroup. Our results suggest that hBoV and hMPV play a role in ILI.

A case study of Eucalyptus globulus fingerprinting for breeding

• Introduction Tree genetic improvement programs usually lack, in general, pedigree information. Since molecular markers can be used to estimate the level of genetic similarity between individuals, we genotyped a sample of a Portuguese Eucalyptus globulus breeding population—a reference population of 125 individuals—with 16 microsatellites (SSR).

Indirect evidence for the genetic determination of short stature in African Pygmies

Central African Pygmy populations are known to be the shortest human populations worldwide. Many evolutionary hypotheses have been proposed to explain this short stature: adaptation to food limitations, climate, forest density, or high mortality rates. However, such hypotheses are difficult to test given the lack of long-term surveys and demographic data. Whether the short stature observed nowadays in African Pygmy populations as compared to their Non-Pygmy neighbors is determined by genetic factors remains widely unknown. Here, we study a uniquely large new anthropometrical dataset comprising more than 1,000 individuals from 10 Central African Pygmy and neighboring Non-Pygmy populations, categorized as such based on cultural criteria rather than height. We show that climate, or forest density may not play a major role in the difference in adult stature between existing Pygmies and Non-Pygmies, without ruling out the hypothesis that such factors played an important evolutionary role in the past. Furthermore, we analyzed the relationship between stature and neutral genetic variation in a subset of 213 individuals and found that the Pygmy individuals' stature was significantly positively correlated with levels of genetic similarity with the Non-Pygmy gene-pool for both men and women. Overall, we show that a Pygmy individual exhibiting a high level of genetic admixture with the neighboring Non-Pygmies is likely to be taller. These results show for the first time that the major morphological difference in stature found between Central African Pygmy and Non-Pygmy populations is likely determined by genetic factors.

Genetic variation among highly endangered Bacopa monnieri (L.) Pennell from Southern India as detected using RAPD analysis

Randomly amplified polymorphic DNA (RAPD) fingerprinting approach was applied to assess genetic diversity in different accessions of rejuvenating and intellect-promoting ancient ayurvedic medicinal herb Bacopa monnieri (L.) Pennell collected from four Southern Indian states, along with in vitro micropropagated samples maintained in the laboratory for 5 years. With the 10 analyzed primers, 110 distinct bands, in the size range of 250–870 bp were observed, and among which 14 (12.72%) were polymorphic. Among the random primers used, only OPD 02 generated highest percentage of polymorphism with 30.77. Whereas OPD 08 generated a maximum of 18 amplified bands, but with only 1% polymorphism. Cluster analysis done on the basis of similarity co-efficient generated from RAPD profiles indicated all the accessions were divided into two sub-groups based on genetic distances under one major cluster. Major cluster is only the lone loose group of the Bm.2 collected from Kerala (KER) and in vitro micropropagated plant (IVMP) maintained in the lab. The other sub-group consisted of Bm.1 and Bm.3 collected from Tamil Nadu (TN) and Andhra Pradesh (AP) respectively, which are genetically similar and showed similarity with accessions from Karnataka Bm.4 (KK). These two sub-groups were joined together at 0.66 genetic distance level. Overall, the levels of genetic similarity within the accessions varied from 0.24 to 0.80, the matrix ranged from 0.36 to 0.80, with a mean value of 0.68 indicating genetic similarity at low level.

Genetic characterization of Nigerian indigenous pig using polyacrilamide gel electrophoresis

The genetic structure of Nigerian indigenous pigs (NIP) and crossbred pigs were investigated using polyacrylamide gel electrophoresis. A total of 79 NIP blood samples were collected from three different locations within South-western Nigeria namely, Igbara Odo, Ekiti State (33 samples), Ogbooro, Oyo State (30 samples), and Institute of Agricultural Research and Training (IAR&T), Oyo State (16 samples). In addition, 41 crossbred pig blood samples were collected from the Teaching and Research Farm (T&R Farm), Obafemi Awolowo University, Ile-Ife. The blood serum samples obtained from the pigs were subjected to Sodium dodecyl sulphate (12%) SDS-PAGE gel electrophoresis. A total of 19 protein loci were scored for the NIP and 16 for crossbred samples. The SDS-PAGE electrophoretic profiles were analysed using PAST package (2005) to determine genetic similarity coefficients and construct phylogenetic dendrograms using Nei’s standard genetic distance. Ogbooro NIP samples showed a very high level of genetic similarity (91%) while IAR&T was 87% whereas Igbara Odo was 56%. The T&R Farm crossbred pigs showed 81%. The total local pig samples from the three locations gave a high genetic similarity coefficient of 84% confirming their genetic relatedness. The high genetic similarity observed in the indigenous pig samples in Ogbooro indicated a level of inbreeding of pig stocks in this locality which can be conserved as a genetic resource for breeding programmes for pure NIP in the future. Key words: Animal genetic resources, conservation, Nigeria indigenous pig, electrophoresis

Genetic Relationship of Wickham and IRRDB 1981 Rubber Population Based on RAPD Markers Analysis

Rubber hand pollination in Indonesian Rubber Research Institute program currently uses Wickham population which genetic analysis showed that genetic diversity of this population is narrow. The development of breeding activity has made the genetic base narrower by inbreeding. In order to solve this problem can use a new genetic resource that is the rubber germplasm IRRDB 1981 population. The genetic relationship between these populations is important to choose parents to avoid closely related genotypes in hand pollination. Therefore RAPD analysis was carried out using four selected primers i.e. OPH-03, OPH-05, OPH-18 and OPN-06. The result showed that Wickham and IRRDB 1981 population were separated into two different big groups with genetic similarity value of 0.64, and those big groups were separated further into many small sub groups with some genetic similarity level. The genetic similarity matrix showed that Wickham and IRRDB 1981 population has a range of genetic similarity 0.37– 0.98. The highest genetic similarity was found between RRIM 600 and PN 621, while the lowest was between BPM 1 and RRIC 100. Value in this matrix showed the genetic diversity between each clone. Based on this result, rubber genotypes of Wickham population could be crossed with genotypes of IRRDB 1981 population by choosing genotypes that have low genetic similarity.

Genetic variability among Coleus sp studied by RAPD banding pattern analysis

AbstractGenetic improvement of the medicinal plants depends upon the existence, nature and extent of the genetic variability available for manipulation. Genetic analysis with RAPD markers has been extensively used to determine genetic diversity among Coleus sp and to identify the best quality for human consumption for its medicinal purpose. The objectives of the present study were to assess molecular variation among C.amboinicus, C.aromaticus and C.forskohlii. and to determine the level of genetic similarity among them. We performed random amplification of polymorphic DNA (RAPD) analysis on three strains of Coleus sp. Random primers were used for the PCR. Electrophoresis on denaturing acrylamide gels improved RAPD reproducibility and increased the band number. The primer OPW 6 and OPW 7 gave reproducible results and the band profiles.

Community Dynamics of Pelagic Bacteria in The High Mountain Lake Sulzata—Rila Mountain, Bulgaria

ABSTRACTThis study analyzed the temporal dynamics in the abundance and composition of pelagic bacterial communities inhabiting Sulzata Lake (2 500 m a.s.l.), a lake of glacial origin situated in Rila National Park (Rila Mountain, Bulgaria). Epifluorescence microscopic counting and amplified rDNA restriction analysis (ARDRA) were used to monitor the succession of planktonic bacterial communities. Sulzata Lake was well abundant in bacteria (on average (69.13±81.1) X 105 cells ml−1), as their number fluctuated drastically depending on the values of environmental determinants. ARDRA analysis yielded high bacterial diversity resulting in different band patterns. The observed changes in ARDRA profiles were a consequence of strongly fluctuating population sizes under the fluctuation of environmental determinants causing changes in the rate of dominance, hence in the bacterial diversity (H': 0.69–2.07) and low levels of genetic similarity (0-65%) between the pelagic bacterial communities. The diversity of different ecotypes increases adaptation fitness which guarantees stability and drives the evolution of an ecosystem under extreme and extremely variable conditions.

Genetic evaluation of the mating system in the blue-and-yellow macaw (Ara ararauna, Aves, Psittacidae) by DNA fingerprinting

More than 90% of birds are socially monogamous, although genetic studies indicate that many are often not sexually monogamous. In the present study, DNA fingerprinting was used to estimate the genetic relationships between nestlings belonging to the same broods to evaluate the mating system in the socially monogamous macaw, Ara ararauna. We found that in 10 of 11 broods investigated, the nestlings showed genetic similarity levels congruent with values expected among full-sibs, suggesting that they shared the same parents. However, in one brood, the low genetic similarity observed between nestlings could be a result of intraspecific brood parasitism, intraspecific nest competition or extra-pair paternity. These results, along with available behavioral and life-history data, imply that the blue-and-yellow macaw is not only socially, but also genetically monogamous. However, the occurrence of eventual cases of extra-pair paternity cannot be excluded.

Spatial and genetic structure of a Melittis sarmatica Klok. (Lamiaceae) metapopulation located in the Volkovysk Upland (Belarus)

The spatial and genetic structure of the metapopulation of Melittis sarmatica Klok. from the Volkovysk Upland (Grodno region, Belarus) has been studied. The use of the RAPD method for genetic analysis of the similarity of populations revealed the exchange of genetic information between metapopulation components. We also revealed the most stable connections within the metapopulation, the key and problem elements of its structure, and some genetically separate groups. A negative linear dependence between the level of genetic similarity of populations and the distance between them was observed.

Novel hemotrophic mycoplasma identified in naturally infected California sea lions (Zalophus californianus)

The hemoplasmas are the trivial name for a group of erythrocyte-parasitizing, non-cultivable in vitro bacteria of the genus Mycoplasma that have been described in several mammalian hosts worldwide. This study is the first report of hemoplasmas in marine mammals. EDTA anticoagulated whole blood samples from 137 California sea lions (Zalophus californianus) and 20 northern elephant seals (Mirounga angustirostris) admitted to the Marine Mammal Center (Sausalito, CA; www.marinemammalcenter.org) or live captured in Oregon were collected during 2008. Hemoplasma-specific genomic DNA was detected in blood samples from 12.4% California sea lions tested using PCR. Hemoplasma PCR positive blood specimens also were tested in reverse transcription polymerase chain reaction (RT-PCR) using the hemoplasma-specific primers for the 16S and 23S rRNA genes. The RT-PCR showed the presence the hemoplasmal rRNA, strongly suggesting the presence of potentially viable hemoplasmas in the bloodstream of the animals. BLAST search and phylogenetic analysis of the 16S rRNA sequences of the hemoplasma from California sea lions revealed that the organism is a novel hemoplasma species with only 92.1% of its nucleotide similarity to the 16S rRNA gene of the previously described hemoplasma species of alpacas, Candidatus Mycoplasma haemolamae. Thus, due to low level of genetic similarity of the hemoplasma to other described hemoplasmas and the mammalian host in which the hemoplasma was detected we propose that this novel hemoplasma species has been given the provisional name Candidatus Mycoplasma haemozalophi sp. nov.