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Pair-group Method (pair-group + method)
Kinds of Pair-group Method Selected AbstractsSequence-related amplified polymorphism, an effective molecular approach for studying genetic variation in Fasciola spp. of human and animal health significanceELECTROPHORESIS, Issue 2 2009Qiao-Yan Li Abstract In the present study, a recently described molecular approach, namely sequence-related amplified polymorphism (SRAP), which preferentially amplifies ORFs, was evaluated for the studies of genetic variation among Fasciola hepatica, Fasciola gigantica and the "intermediate" Fasciola from different host species and geographical locations in mainland China. Five SRAP primer combinations were used to amplify 120 Fasciola samples after ten SRAP primer combinations were evaluated. The number of fragments amplified from Fasciola samples using each primer combination ranged from 12 to 20, with an average of 15 polymorphic bands per primer pair. Fifty-nine main polymorphic bands were observed, ranging in size from 100 to 2000,bp, and SRAP bands specific to F. hepatica or F. gigantica were observed. SRAP fragments common to F. hepatica and the "intermediate" Fasciola, or common to F. gigantica and the "intermediate" Fasciola were identified, excised and confirmed by PCR amplification of genomic DNA using primers designed based on sequences of these SRAP fragments. Based on SRAP profiles, unweighted pair-group method with arithmetic averages clustering algorithm categorized all of the examined representative Fasciola samples into three groups, representing the F. hepatica, the "intermediate" Fasciola, or the F. gigantica. These results demonstrated the usefulness of the SRAP technique for revealing genetic variability between F. hepatica, F. gigantica and the "intermediate" Fasciola, and also provided genomic evidence for the existence of the "intermediate" Fasciola between F. hepatica and F. gigantica. This technique provides an alternative and a useful tool for the genetic characterization and studies of genetic variability in parasites. [source] Morphometric and genetic variation of small dwarf honeybees Apis andreniformis Smith, 1858 in ThailandINSECT SCIENCE, Issue 6 2007ATSALEK RATTANAWANNEE Abstract The small dwarf honey bee, Apis andreniformis, is a rare and patchily distributed Apis spp. and is one of the native Thai honey bees, yet little is known about its biodiversity. Thirty (27 Thai and 3 Malaysian) and 37 (32 Thai and 5 Malaysian) colonies of A. andreniformis were sampled for morphometric and genetic analysis, respectively. For morphometric analysis, 20 informative characters were used to determine the variation. After plotting the factor scores, A. andreniformis from across Thailand were found to belong to one group, a notion further supported by a cluster analysis generated dendrogram. However, clinal patterns in groups of bee morphometric characters were revealed by linear regression analysis. The body size of bees increases from South to North but decreases from West to East, although this may reflect altitude rather than longitude. Genetic variation was determined by sequence analysis of a 520 bp fragment of the mitochondrial cytochrome oxidase subunit b (cytb). DNA polymorphism among bees from the mainland of Thailand is lower than that from Phuket Island and Chiang Mai. Although two main different groups of bees were obtained from phylogenetic trees constructed by neighbor-joining and unweighted pair-group method using arithmetic averages programs, no clear geographic signal was present. Thus, while the minor group (B) contained all of the samples from the only island sampled (Phuket in the south), but not the southern mainland colonies, it also contained samples from the far northern inland region of Chiang Mai, other samples of which were firmly rooted in the major group (A). [source] Genetic differentiation and natural hybridization between the Sardinian endemic Maniola nurag and the European Maniola jurtinaJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 4 2007A. GRILL Abstract The Mediterranean island of Sardinia is known for its multitude of unique genetic lineages. We view one of them in a larger phylogeographic context. The endemic Sardinian Meadow Brown butterfly, Maniola nurag, is restricted to the mountainous areas of the island, whereas its widespread close relative, Maniola jurtina, also occurs on the coast. At intermediate altitudes the species' distributions overlap. There, a number of individuals exhibit phenotypic characteristics intermediate between the two species. We examined patterns of intra- and interpopulation variation in 10 M. nurag populations from Sardinia and 16 M. jurtina populations from Sardinia and continental Europe, as well as 17 intermediate individuals, sampled in 1999,2002, by means of allozyme markers, combining it with a morphometric analysis based on 18 wing-characters of 52 males. At the 15 loci studied (aldolase, aat-1, aat-2, g6pdh, gpd, idh-1, idh-2, mdh-1, mdh-2, mpi, me, leu-ala, pgi, pgm, and 6pgdh), 76 different alleles were detected, 63 of which were shared by M. nurag and M. jurtina. None of the loci was found to be alternatively fixed between the two species. In that respect, this study testifies to the difficulties that may arise when trying to identify hybrids from genotypic data. Levels of genetic variation in island populations (M. jurtina: HO = 0.137,0.189; M. nurag: HO = 0.141,0.270) were comparable to those of mainland M. jurtina (HO = 0.141,0.236). A Bayesian admixture analysis supported the hypothesis of mixed (hybrid) ancestry of individuals occurring at intermediate altitudes. Similarly, neighbour-joining and unweighted pair-group method with arithmetic averaging (UPGMA) analyses, as well as morphometrics hinted at the existence of a Maniola -hybrid zone in Sardinia at intermediate altitudes. We discuss the results in the light of the phylogeography of other Sardinian taxa with the aim to reach a general understanding of the biogeographic history of this island's endemic species. [source] Assessment of Genetic Variation Within Indian Mustard (Brassica juncea) Germplasm Using Random Amplified Polymorphic DNA MarkersJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 4 2008Muhammad Ayub Khan Abstract Genetic diversity among 45 Indian mustard (Brassica juncea L.) genotypes comprising 37 germplasm collections, five advance breeding lines and three improved cultivars was investigated at the DNA level using the random amplified polymorphic DNA (RAPD) technique. Fifteen primers used generated a total of 92 RAPD fragments, of which 81 (88%) were polymorphic. Of these, 13 were unique to accession ,Pak85559'. Each primer produced four to nine amplified products with an average of 6.13 bands per primer. Based on pairwise comparisons of RAPD amplification products, Nei and Li's similarity coefficients were calculated to evaluate the relationships among the accessions. Pairwise similarity indices were higher among the oilseed accessions and cultivars showing narrow ranges of 0.77,0.99. An unweighted pair-group method with arithmetic averages cluster analysis based on these genetic similarities placed most of the collections and oilseed cultivars close to each other, showing a low level of polymorphism between the accessions used. However, the clusters formed by oilseed collections and cultivars were comparatively distinct from that of advanced breeding lines. Genetically, all of the accessions were classified into a few major groups and a number of individual accessions. Advanced breeding lines were relatively divergent from the rest of the accessions and formed independent clusters. Clustering of the accessions did not show any pattern of association between the RAPD markers and the collection sites. A low level of genetic variability of oilseed mustard was attributed to the selection for similar traits and horticultural uses. Perhaps close parentage of these accessions further contributed towards their little diversity. The study demonstrated that RAPD is a simple and fast technique to compare the genetic relationship and pattern of variation among the gene pool of this crop. [source] Genetic Relationship of Pyrenophora graminea, P. teres f. maculata and P. teres f. teres Assessed by RAPD AnalysisJOURNAL OF PHYTOPATHOLOGY, Issue 2 2007J. Bakonyi Abstract Barley-pathogenic Pyrenophora isolates are P. graminea (PG), P. teres f. maculata (PTM) and P. teres f. teres (PTT), which cause foliar leaf stripe, spot blotch and net blotch lesions, respectively. However, the species are often indistinguishable by morphological and cultural characteristics. Random amplified polymorphic DNA (RAPD) analysis has been used to study the genetic relationship amongst 11 PG, 9 PTM and 23 PTT isolates from distant geographical locations. Using seven primers, 55 (52.38%) polymorphic DNA bands were detected out of 105 different fragments amplified in the three pathogens. Genotypic diversity was high as all but two PTT strains had distinct multilocus RAPD fingerprints. Unweighted pair-group method with arithmetic average (UPGMA) clustering separated the isolates into three main clusters, corresponding to the three pathogens studied. No clear geographical substructuring was found. Nei's gene diversity analysis detected only small differences (max. 6.6%) in band frequencies but considerable levels of differentiation were observed among the pathogen species/forms. However, the variability among the Pyrenophora species/forms (max. 42.0%) was less than within species/forms (max. 58%). Nei's unbiased genetic distance values were in agreement with UPGMA clustering and gene diversity analysis: the two forms of P. teres showed higher divergence from one another (D = 0.132) than the distance found between PG and PTM (D = 0.094). The results suggest that the present taxonomical classification of these morphological taxa may not correspond to their phylogenetic relationship and that there is a very close genetic relationship amongst barley-pathogenic Pyrenophora species, but genetic exchanges between them could be infrequent. [source] Genetic diversity in hazelnut (Corylus avellana L.) cultivars from Black Sea countries assessed using SSR markersPLANT BREEDING, Issue 4 2010K. Gürcan With 6 figures and 6 tables Abstract European hazelnut (Corylus avellana L.) is an important crop in Turkey, Georgia and Azerbaijan, where cultivars were selected from the native vegetation. Accessions from Turkey have been assigned to the Black Sea group, and cultivars from Georgia and Azerbaijan have a similar phenotype. Genetic diversity was investigated in 88 accessions from these three countries and compared with cultivars from Spain and Italy using 12 microsatellite loci. A high level of genetic diversity (He = 0.71, Ho = 0.70) was observed in the Black Sea accessions. Six Turkish accessions in the US hazelnut collections were found to be synonyms of cultivars in the Turkish collection in Giresun. An unweighted pair-group method using arithmetic average dendrogram and principal component analysis of 109 unique accessions showed a tendency to form subgroups by country of origin, and high diversity within each subgroup. A moderate shift in allelic frequencies (FST = 0.114,0.131) was seen between accessions from the Black Sea and the Spanish-Italian accessions. Simple sequence repeat analysis identified the putative parents of two Turkish cultivars. [source] Genetic relationships of sesame germplasm collection as revealed by inter-simple sequence repeatsPLANT BREEDING, Issue 3 2002D. H. Kim Abstract Inter-simple sequence repeats (ISSR) polymorphism was used to determine genetic relationships among 75 Sesamum indicum L. accessions of Korean and exotic sesame. Fourteen reliable ISSR primers were selected for the assessment of genetic diversity, yielding 79 amplification products. Of these polymerase chain reaction products, 33% revealed polymorphism among the 75 accessions. Genetic distances ranged from 0 to 0.255, with a mean genetic distance of 0.0687. The 75 accessions were divided into seven groups on the basis of unweighted pair-group method with arithmetic averages (UPGMA) cluster analysis. The largest group consisted of 25 Korean cultivars, eight Korean breeding lines and 17 world-wide accessions. The other groups included 25 accessions, several of which contained useful traits. The dendrogram did not indicate any clear division among sesame accessions based on their geographical origin. However, all Korean sesame cultivars except ,Namsankkae' were clustered in the same group, indicating a narrow gene pool. Some of the Korean breeding lines were spread along the dendrogram, showing enlargement of genetic diversity. The genetic diversity data uncovered in this study can be used in future breeding programmes. [source] Phylogenetic analysis for the Seoul National University (Minnesota) miniature pig by mitochondrial DNA sequence polymorphismANIMAL SCIENCE JOURNAL, Issue 2 2010Su-Cheong YEOM ABSTRACT Seoul National University (SNU) miniature pigs are originated from the Minnesota miniature pig. This study was conducted to investigate the maternal origin of SNU (Minnesota) miniature pigs and their phylogenetic relationships by analyzing the mitochondrial DNA (mtDNA) D-loop (control region) sequence. Two mtDNA D-loop sequences of the SNU miniature pigs were identified. On an unweighted pair-group method with an arithmetic mean (UPGMA) phylogenetic tree analysis, the large white was the pig breed closest to the SNU miniature pig, and the pairwise distance analysis showed the same result. While mtDNA sequences of 4 pig breeds which were used to establish Minnesota miniature pig were not known, our result might be different from the history of the Minnesota miniature pig development. In conclusion, we thought that some haplotypes of the Minnesota miniature pig maternally were originated from the Large white pig, or that wild pigs had similar mtDNA sequences to the Large white pig, and all SNU miniature pigs were derived from this colony. [source] Combined definition of seed transfer guidelines for ecological restoration in the French PyreneesAPPLIED VEGETATION SCIENCE, Issue 1 2010S. Malaval Abstract Question: Can genetic tools combined with phytogeography help to define local plants and how geographically close the source population should be to the restoration site? Location: Subalpine and alpine French Pyrenees. Methods: The main phytogeographic boundaries in the French Pyrenees described by different authors were studied and this geographic pattern was compared with the results of genetic analysis for the four Pyrenean plants studied (Trifolium alpinum, Festuca eskia, Festuca gautieri and Rumex scutatus), based on random amplified polymorphic DNA (RAPD) marker analysis, unweighted pair-group method with arithmetic averages (UPGMA) analysis and Mantel correlograms comparing geographic and genetic distances. Results: The genetic analysis allowed definition of two main evolutionarily significant units (ESUs) for the plants under study. Although the limit between the two zones was slightly variable according to the species considered, an eastern and a western ESU was consistently observed. This delineation was concordant with the main phytogeographic boundaries of the French Pyrenees. Conclusion: RAPD markers and associated Mantel correlograms can be useful to draw ESUs for individual species when the sampling intensity is relatively dense, and similarities were revealed between species sharing the same distribution range. This delineation allowed integration of infraspecific plant variation in the management of natural resources for revegetation in the Pyrenees. Nevertheless, caution is needed for the establishment of seed pools in order to maximize genetic diversity in each of the pools during collection and production. [source] | ||||||||||