Commenced in January 2007
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Edition: International
Paper Count: 17

Search results for: genetic diversity

17 Cloning, Expression and Protein Purification of AV1 Gene of Okra Leaf Curl Virus Egyptian Isolate and Genetic Diversity between Whitefly and Different Plant Hosts

Authors: Dalia. G. Aseel

Abstract:

Begomoviruses are economically important plant viruses that infect dicotyledonous plants and exclusively transmitted by the whitefly Bemisia tabaci. Here, replicative form was isolated from Okra, Cotton, Tomato plants and whitefly infected with Begomoviruses. Using coat protein specific primers (AV1), the viral infection was verified with amplicon at 450 bp. The sequence of OLCuV-AV1 gene was recorded and received an accession number (FJ441605) from Genebank. The phylogenetic tree of OLCuV was closely related to Okra leaf curl virus previously isolated from Cameroon and USA with nucleotide sequence identity of 92%. The protein purification was carried out using His-Tag methodology by using Affinity Chromatography. The purified protein was separated on SDS-PAGE analysis and an enriched expected size of band at 30 kDa was observed. Furthermore, RAPD and SDS-PAGE were used to detect genetic variability between different hosts of okra leaf curl virus (OLCuV), cotton leaf curl virus (CLCuV), tomato yellow leaf curl virus (TYLCuV) and the whitefly vector. Finally, the present study would help to understand the relationship between the whitefly and different economical crops in Egypt.

Keywords: Begomovirus, AV1 gene, sequence, cloning, whitefly, okra, cotton, tomato, RAPD, phylogenetic tree and SDS-PAGE.

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16 Identification of 332G>A Polymorphism in Exon 3 of the Leptin Gene and Partially Effects on Body Size and Tail Dimension in Sanjabi Sheep

Authors: Roya Bakhtiar, Alireza Abdolmohammadi, Hadi Hajarian, Zahra Nikousefat, Davood, Kalantar-Neyestanaki

Abstract:

The objective of the present study was to determine the polymorphism in the leptin (332G>A) and its association with biometric traits in Sanjabi sheep. For this purpose, blood samples from 96 rams were taken, and tail length, width tail, circumference tail, body length, body width, and height were simultaneously recorded. PCR was performed using specific primer to amplify 463 bp fragment including exon 3 of leptin gene, and PCR products were digested by Cail restriction enzymes. The 332G>A (at 332th nucleotide of exon 3 leptin gene) that caused an amino acid change from Arg to Gln was detected by Cail (CAGNNNCTG) endonuclease, as the endonuclease cannot cut this region if G nucleotide is located in this position. Three genotypes including GG (463), GA (463, 360and 103 bp) and GG (360 bp and 103 bp) were identified after digestion by enzyme. The estimated frequencies of three genotypes including GG, GA, and AA for 332G>A locus were 0.68, 0.29 and 0.03 and those were 0.18 and 0.82 for A and G alleles, respectively. In the current study, chi-square test indicated that 332G>A positions did not deviate from the Hardy–Weinberg (HW) equilibrium. The most important reason to show HW equation was that samples used in this study belong to three large local herds with a traditional breeding system having random mating and without selection. Shannon index amount was calculated which represent an average genetic variation in Sanjabi rams. Also, heterozygosity estimated by Nei index indicated that genetic diversity of mutation in the leptin gene is moderate. Leptin gene polymorphism in the 332G>A had significant effect on body length (P<0.05) trait, and individuals with GA genotype had significantly the higher body length compared to other individuals. Although animals with GA genotype had higher body width, this difference was not statistically significant (P>0.05). This non-synonymous SNP resulted in different amino acid changes at codon positions111(R/Q). As leptin activity is localized, at least in part, in domains between amino acid residues 106-1406, it is speculated that the detected SNP at position 332 may affect the activity of leptin and may lead to different biological functions. Based to our results, due to significant effect of leptin gene polymorphism on body size traits, this gene may be used a candidate gene for improving these traits.

Keywords: Body size, Leptin gene, PCR-RFLP, Sanjabi sheep.

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15 Analysis of Genetic Variations in Camel Breeds (Camelus dromedarius)

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

Abstract:

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, cox1, neighbor-joining.

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14 Genetic Characterization of Barley Genotypes via Inter-Simple Sequence Repeat

Authors: Mustafa Yorgancılar, Emine Atalay, Necdet Akgün, Ali Topal

Abstract:

In this study, polymerase chain reaction based Inter-simple sequence repeat (ISSR) from DNA fingerprinting techniques were used to investigate the genetic relationships among barley crossbreed genotypes in Turkey. It is important that selection based on the genetic base in breeding programs via ISSR, in terms of breeding time. 14 ISSR primers generated a total of 97 bands, of which 81 (83.35%) were polymorphic. The highest total resolution power (RP) value was obtained from the F2 (0.53) and M16 (0.51) primers. According to the ISSR result, the genetic similarity index changed between 0.64–095; Lane 3 with Line 6 genotypes were the closest, while Line 36 were the most distant ones. The ISSR markers were found to be promising for assessing genetic diversity in barley crossbreed genotypes.

Keywords: Barley, crossbreed, genetic similarity, ISSR.

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13 Genetic Diversity Based Population Study of Freshwater Mud Eel (Monopterus cuchia) in Bangladesh

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

Abstract:

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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12 Evaluation of Antioxidant Activity as a Function of the Genetic Diversity of Canna indica Complex

Authors: A. Rattanapittayapron, O. Vanijajiva

Abstract:

Canna indica is a prominent species complex in tropical and subtropical areas. They become indigenous in Southeast Asia where they have been introduced. At present, C. indica complex comprises over hundred hybrids, are cultivated as commercial horticulture. The species complex contains starchy rhizome having economic value in terms of food and herbal medicine. In addition, bright color of the flowers makes it a valuable ornamental plant and potential source for natural colorant. This study aims to assess genetic diversity of four varieties of C. indica complex based on SRAP (sequence-related amplified polymorphism) and iPBS (inter primer binding site) markers. We also examined phytochemical characteristics and antioxidant properties of the flower extracts from four different color varieties. Results showed that despite of the genetic variation, there were no significant differences in phytochemical characteristics and antioxidant properties of flowers. The SRAP and iPBS results agree with the more primitive traits showed by morphological information and phytochemical and antioxidant characteristics from the flowers. Since Canna flowers has long been used as natural colorants together with the antioxidant activities from the ethanol extracts in this study, there are likely to be good source for cosmetics additives.

Keywords: Canna indica, antioxidant activity, genetic diversity, SRAP, iPBS.

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11 Durian Marker Kit for Durian (Durio zibethinus Murr.) Identity

Authors: Emma K. Sales

Abstract:

Durian is the flagship fruit of Mindanao and there is an abundance of several cultivars with many confusing identities/ names. The project was conducted to develop procedure for reliable and rapid detection and sorting of durian planting materials. Moreover, it is also aimed to establish specific genetic or DNA markers for routine testing and authentication of durian cultivars in question. The project developed molecular procedures for routine testing. SSR primers were also screened and identified for their utility in discriminating durian cultivars collected. Results of the study showed the following accomplishments: 1. Twenty (29) SSR primers were selected and identified based on their ability to discriminate durian cultivars, 2. Optimized and established standard procedure for identification and authentication of Durian cultivars 3. Genetic profile of durian is now available at Biotech Unit Our results demonstrate the relevance of using molecular techniques in evaluating and identifying durian clones. The most polymorphic primers tested in this study could be useful tools for detecting variation even at the early stage of the plant especially for commercial purposes. The process developed combines the efficiency of the microsatellites development process with the optimization of non-radioactive detection process resulting in a user-friendly protocol that can be performed in two (2) weeks and easily incorporated into laboratories about to start microsatellite development projects. This can be of great importance to extend microsatellite analyses to other crop species where minimal genetic information is currently available. With this, the University can now be a service laboratory for routine testing and authentication of durian clones.

Keywords: DNA, SSR Analysis, genotype, genetic diversity, cultivars.

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10 RAPD Analysis of Genetic Diversity of Castor Bean

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

Abstract:

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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9 RAPD Analysis of the Genetic Polymorphism in the Collection of Rye Cultivars

Authors: L. Petrovičová, Ž. Balážová, Z. Gálová, M. Wójcik-Jagła, M. Rapacz

Abstract:

In the present study, RAPD-PCR was used to assess genetic diversity of the rye including landrances and new rye cultivars coming from Central Europe and the Union of Soviet Socialist Republics (SUN). Five arbitrary random primers were used to determine RAPD polymorphism in the set of 38 rye genotypes. These primers amplified altogether 43 different DNA fragments with an average number of 8.6 fragments per genotypes. The number of fragments ranged from 7 (RLZ 8, RLZ 9 and RLZ 10) to 12 (RLZ 6). DI and PIC values of all RAPD markers were higher than 0.8 that generally means high level of polymorphism detected between rye genotypes. The dendrogram based on hierarchical cluster analysis using UPGMA algorithm was prepared. The cultivars were grouped into two main clusters. In this experiment, RAPD proved to be a rapid, reliable and practicable method for revealing of polymorphism in the rye cultivars.

Keywords: Genetic diversity, polymorphism, RAPD markers, Secalecereale L.

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8 Methods for Distinction of Cattle Using Supervised Learning

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.

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7 Diversity Analysis of a Quinoa (Chenopodium quinoa Willd.) Germplasm during Two Seasons

Authors: M. Mhada, E. N. Jellen, S. E. Jacobsen, O. Benlhabib

Abstract:

The present work has been carried out to evaluate the diversity of a collection of 78 quinoa accessions developed through recurrent selection from Andean germplasm introduced to Morocco in the winter of 2000. Twenty-three quantitative and qualitative characters were used for the evaluation of genetic diversity and the relationship between the accessions, and also for the establishment of a core collection in Morocco. Important variation was found among the accessions in terms of plant morphology and growth behavior. Data analysis showed positive correlation of the plant height, the plant fresh and the dry weight with the grain yield, while days to flowering was found to be negatively correlated with grain yield. The first four PCs contributed 74.76% of the variability; the first PC showed significant variation with 42.86% of the total variation, PC2 with 15.37%, PC3 with 9.05% and PC4 contributed 7.49% of the total variation. Plant size, days to grain filling and days to maturity are correlated to the PC1; and seed size, inflorescence density and mildew resistance are correlated to the PC2. Hierarchical cluster analysis rearranged the 78 quinoa accessions into four main groups and ten sub-clusters. Clustering was found in associations with days to maturity and also with plant size and seed-size traits.

Keywords: Character association, Chenopodium quinoa, Diversity analysis, Morphotypic cluster, Multivariate analysis.

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6 Using Morphological and Microsatellite (SSR) Markers to Assess the Genetic Diversity in Alfalfa (Medicago sativa L.)

Authors: T. Cholastova, D. Knotova

Abstract:

Utilization of diverse germplasm is needed to enhance the genetic diversity of cultivars. The objective of this study was to evaluate the genetic relationships of 98 alfalfa germplasm accessions using morphological traits and SSR markers. From the 98 tested populations, 81 were locals originating in Europe, 17 were introduced from USA, Australia, New Zealand and Canada. Three primers generated 67 polymorphic bands. The average polymorphic information content (PIC) was very high (> 0.90) over all three used primer combinations. Cluster analysis using Unweighted Pair Group Method with Arithmetic Means (UPGMA) and Jaccard´s coefficient grouped the accessions into 2 major clusters with 4 sub-clusters with no correlation between genetic and morphological diversity. The SSR analysis clearly indicated that even with three polymorphic primers, reliable estimation of genetic diversity could be obtained.

Keywords: genetic diversity, Medicago sativa L., morphological traits, SSR markers

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5 Genetic Comparison of Two Different Arabian Oryx Populations in UAE Based on Microsatellite Analysis

Authors: Mohammed A. Khidhir, K. Praveen Kumar, Marwa Al-Aseer

Abstract:

This is a genetic comparison study of Arabian Oryx (Oryx leucoryx) population at two different locations (A &B) based on nuclear microsatellite DNA markers. Arabian Oryx is listed as vulnerable and endanger by the World Conservation Union (IUCN). Thirty microsatellite markers from bovine family were applied to investigate the genetic diversity of the Arabian Oryx and to set up a molecular inventory. Among 30 microsatellite markers used, 13 markers were moderately polymorphic. Arabian Oryx at location A has shown better gene diversity over location B. However, mean number of alleles were less than location B. Data of within population inbreeding coefficient indicates inbreeding at both locations (A&B). Based on the analysis of polymorphic microsatellite markers, the study revealed that Arabian Oryx need a genetically designed breeding program.

Keywords: Arabian oryx, Microsatellites

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4 Genetic Variation of Durum Wheat Landraces and Cultivars Using Morphological and Protein Markers

Authors: M. R. Naghavi, S. Rashidi Monfared, A. H. Ahkami, M. A. Ombidbakhsh

Abstract:

Knowledge of patterns of genetic diversity enhances the efficiency of germplasm conservation and improvement. In this study 96 Iranian landraces of Triticum turgidum originating from different geographical areas of Iran, along with 18 durum cultivars from ten countries were evaluated for variation in morphological and high molecular weight glutenin subunit (HMW-GS) composition. The first two principal components clearly separated the Iranian landraces from cultivars. Three alleles were present at the Glu-A1 locus and 11 alleles at Glu-B1. In both cultivars and landraces of durum wheat, the null allele (Glu-A1c) was observed more frequently than the Glu-A1a and Glu-A1b alleles. Two alleles, namely Glu-B1a (subunit 7) and Glu-B1e (subunit 20) represented the more frequent alleles at Glu-B1 locus. The results showed that the evaluated Iranian landraces formed an interesting source of favourable glutenin subunits that might be very desirable in breeding activities for improving pasta-making quality.

Keywords: Triticum turgidum var. durum, glutenin subunits, morphological characters.

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3 Efficiency of Floristic and Molecular Markers to Determine Diversity in Iranian Populations of T. boeoticum

Authors: M. R. Naghavi, M. Maleki, S. F. Tabatabaei

Abstract:

In order to study floristic and molecular classification of common wild wheat (Triticum boeoticum Boiss.), an analysis was conducted on populations of the Triticum boeoticum collected from different regions of Iran. Considering all floristic compositions of habitats, six floristic groups (syntaxa) within the populations were identified. A high level of variation of T. boeoticum also detected using SSR markers. Our results showed that molecular method confirmed the grouping of floristic method. In other word, the results from our study indicate that floristic classification are still useful, efficient, and economic tools for characterizing the amount and distribution of genetic variation in natural populations of T. boeoticum. Nevertheless, molecular markers appear as useful and complementary techniques for identification and for evaluation of genetic diversity in studied populations.

Keywords: T. boeoticum, diversity, floristic, SSRs.

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2 Cluster Algorithm for Genetic Diversity

Authors: Manpreet Singh, Keerat Kaur, Bhavdeep Singh

Abstract:

With the hardware technology advancing, the cost of storing is decreasing. Thus there is an urgent need for new techniques and tools that can intelligently and automatically assist us in transferring this data into useful knowledge. Different techniques of data mining are developed which are helpful for handling these large size databases [7]. Data mining is also finding its role in the field of biotechnology. Pedigree means the associated ancestry of a crop variety. Genetic diversity is the variation in the genetic composition of individuals within or among species. Genetic diversity depends upon the pedigree information of the varieties. Parents at lower hierarchic levels have more weightage for predicting genetic diversity as compared to the upper hierarchic levels. The weightage decreases as the level increases. For crossbreeding, the two varieties should be more and more genetically diverse so as to incorporate the useful characters of the two varieties in the newly developed variety. This paper discusses the searching and analyzing of different possible pairs of varieties selected on the basis of morphological characters, Climatic conditions and Nutrients so as to obtain the most optimal pair that can produce the required crossbreed variety. An algorithm was developed to determine the genetic diversity between the selected wheat varieties. Cluster analysis technique is used for retrieving the results.

Keywords: Genetic diversity, pedigree, nutrients.

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1 Coefficient of Parentage for Crop Hybridization

Authors: Manpreet Singh, Parvinder Singh Sandhu, Basant Raj Singh

Abstract:

Hybridization refers to the crossing breeding of two plants. Coefficient of Parentage (COP) is used by the plant breeders to determine the genetic diversity across various varieties so as to incorporate the useful characters of the two varieties to develop a new crop variety with particular useful characters. Genetic Diversity is the prerequisite for any cultivar development program. Genetic Diversity depends upon the pedigree information of the varieties based on particular levels. Pedigree refers to the parents of a particular variety at various levels. This paper discusses the searching and analyses of different possible pairs of varieties selected on the basis of morphological characters, Climatic conditions and Nutrients so as to obtain the most optimal pair that can produce the required crossbreed variety. An algorithm was developed to determine the coefficient of parentage (COP) between the selected wheat varieties. Dummy values were used wherever actual data was not available.

Keywords: Coefficient of Parentage, Morphological characters, Pedigree, Genetic Diversity.

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