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Genetic Diversity Analysis (genetic + diversity_analysis)
Selected AbstractsGenetic Diversity of Landraces in Gossypium arboreum L. Race sinense Assessed with Simple Sequence Repeat MarkersJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 9 2006Wang-Zhen Guo Abstract Asiatic cotton (Gossypium arboreum L.) is an "Old World" cultivated cotton species, the sinense race of which is planted extensively in China. This species is still used in the current tetraploid cotton breeding program as an elite germplasm line, and is also used as a model for genomic research in Gossypium. In the present study, 60 cotton microsatellite markers, averaging 4.6 markers for each A-genome chromosome, were chosen to assess the genetic diversity of 109 accessions. These included 106 G. arboreum landraces, collected from 18 provinces throughout four Asiatic cotton-growing regions in China. A total of 128 alleles were detected, with an average of 2.13 alleles per locus. The largest number of alleles, as well as the maximum number of polymorphic loci, was detected in the A03 linkage group. No polymorphic alleles were detected on chromosome 10. The polymorphism information content for the 22 polymorphic microsatellite loci varied from 0.52 to 0.98, with an average of 0.89. Genetic diversity analysis revealed that the landraces in the Southern region had more genetic variability than those from the other two regions, and no significant difference was detected between landraces in the Yangtze and the Yellow River Valley regions. These findings are consistent with the history of sinense introduction, with the Southern region being the presumed center of origin for Chinese Asiatic cotton, and with subsequent northeastward extension to the Yangtze and Yellow River Valleys. Cluster analysis, based on simple sequence repeat data for 60 microsatellite loci, clearly differentiated Vietnamese and G. herbaceum landraces from the sinense landrace. No relationship between inter-variety similarity and geographical ecological region was observed. The present findings indicate that the Southern region landraces may have been directly introduced into the provinces in the middle and lower Yangtze River Valley, where Asiatic cotton was most extensively grown, and further race sinense crops were subsequently produced. (Managing editor: Ya-Qin Han) [source] Analyses of RAPD data for detection of host specialization in Sclerotinia homoeocarpaPLANT PATHOLOGY, Issue 2 2000T. Hsiang Upgma analysis, principal component analysis, genetic diversity analysis and genetic distance analysis of RAPD data were used to assess the extent of host specialization in 50 isolates of S. homoeocarpa from five turfgrass hosts. In upgma analysis and principal component analysis, the occurrence of host specialization was not readily apparent based on visual inspection. Genetic diversity analysis showed significant differentiation among isolates from different host species (GST = 0.34, P < 0.001). The strongest evidence for some degree of host specialization came from the statistical analysis of genetic distances among isolates. By grouping pairwise genetic distances between isolates based on their host species, and analysing for average distance within the same host species and among different host species, it was found that the average distance within species was less than among species (P < 0.0001). An analysis of molecular variance of the genetic distances among isolates found that 32.3% of the total variation was attributable to host species. It is concluded that these isolates of S. homoeocarpa showed a weak level of host specialization, which was not readily apparent by upgma or principal component analyses, but was revealed by genetic diversity analysis and statistical analysis of genetic distances among isolates. Inoculation tests on different host species and tests using a greater number of isolates are required to confirm the extent of specialization. [source] Genetic structure of the European polecat (Mustela putorius) and its implication for conservation strategiesJOURNAL OF ZOOLOGY, Issue 1 2006C. Pertoldi Abstract During the last century, the European polecat Mustela putorius populations in most of Europe declined and survived in fragmented patches, because of habitat alterations and direct persecution. To assess the genetic consequences of the demographic decline and to describe the spatial pattern of genetic diversity, 250 polecats sampled at seven localities from five European countries , Poland, Denmark (southern Denmark and northern Denmark), Spain, Belgium (eastern and western) and the Netherlands , were screened by means of nine microsatellite loci. Genetic diversity estimated by mean expected heterozygosity (HE) and allelic richness (AR) were moderately high within populations [range: 0.50 (northern Denmark) ,HE,0.64 (Poland) and 1.33,AR,7.80] as compared with other carnivores and mustelids. Bottleneck tests suggested that polecat populations in southern Denmark and Poland have declined recently and populations from northern Denmark and the Netherlands have expanded recently, whereas the remaining populations did not show any sign of demographic change. Recent demographic changes could suggest that some of the populations are still not in equilibrium, which could partly explain the relatively high genetic variability observed in polecat populations despite the drastic decline in population size observed in several European countries. A significant heterozygote deficiency [FIS=0.19; 0.01,95% confidence interval (CI),0.32] suggests substructuring within the total European sample. Partitioning of the genetic variation among sampling locations (FST=0.14; 0.06,95% CI,0.23) and pairwise FST between localities (range: 0.01,FST,0.37) without any correlation with the geographic distances between localities were found, suggesting a recent divergence and a restriction of gene flow between populations and the action of genetic drift. An assignment test showed that the Polish and the northern Danish populations were the most unique, whereas the other populations were partially admixed. Factorial component analysis tests indicate a subdivision of the total sample into two distinct groups: one including the samples from Poland and the two Danish localities and the second group comprising the remaining localities investigated. The observed pattern of genetic differentiation is suggested to be due to two main routes of recolonization after the last glacial period. To compare the results obtained with microsatellite data, the most variable region of the mitochondrial DNA (d-loop) was sequenced and different phylogenetic reconstructions and genetic diversity analyses based on nucleotide (,) and haplotype diversity (h) measures within populations were performed using a subsample of populations. The lack of well-defined geographical structure, as well as the reduced level of mitochondrial DNA variability (,: 0.00274±0.00038; h: 0.876±0.028) that was found, has been previously reported in several studies on different carnivores and supports the hypothesis of post-glacial recolonization from southern or eastern refugees of Europe as suggested by the microsatellite data. Implications for conservation strategies of the polecat at the European level are discussed. [source] Application of bovine microsatellite markers for genetic diversity analysis of European bison (Bison bonasus)JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 6 2006T. Roth Summary In this study, the cross-amplification of a commercial multiplex set of 11 cattle (Bos taurus) microsatellites was tested on a panel of 35 European bison (Bison bonasus) individuals. After polymerase chain reaction optimization, all loci cross-amplified successfully in investigated bisons. Number of alleles and observed and expected heterozygosity per locus are in the range of 2,4, 0.086,0.629 and 0.288,0.621 respectively. The availability of a heterologous set of multiplexed microsatellite markers derived from cattle opens an avenue for collecting profound genetic data for efficient conservation management strategies of the European bison. [source] Low genetic diversity and high genetic differentiation in the critically endangered Omphalogramma souliei (Primulaceae): implications for its conservationJOURNAL OF SYSTEMATICS EVOLUTION, Issue 2 2009Yuan HUANG Abstract Omphalogramma souliei Franch. is an endangered perennial herb only distributed in alpine areas of SW China. ISSR markers were applied to determine the genetic variation and genetic structure of 60 individuals of three populations of O. souliei in NW Yunnan, China. The genetic diversity at the species level is low with P=42.5% (percentage of polymorphic bands) and Hsp=0.1762 (total genetic diversity). However, a high level of genetic differentiation among populations was detected based on different measures (Nei's genetic diversity analysis: Gst=0.6038; AMOVA analysis: Fst=0.6797). Low level of genetic diversity within populations and significant genetic differentiation among populations might be due to the mixed mating system in which xenogamy predominated and autogamy played an assistant role in O. souliei. The genetic drift due to small population size and limited current gene flow also resulted in significant genetic differentiation. The assessment of genetic variation and differentiation of the endangered species provides important information for conservation on a genetic basis. Conservation strategies for this rare endemic species are proposed. [source] PERMANENT GENETIC RESOURCES: Isolation and characterization of microsatellite DNA loci from the southern flounder, Paralichthys lethostigmaMOLECULAR ECOLOGY RESOURCES, Issue 2 2008C. W. SHAO Abstract Paucity of polymorphic molecular markers in southern flounder (Paralichthys lethostigma) has been a major limitation in genetic improvement of this important economic fish. Hence, we constructed a repeat-enriched genomic library from P. lethostigma. A total of 39 new microsatellites were identified, for which 33 primer pairs were designed. After validating and scoring, 10 of these loci were polymorphic in a test population with the range of alleles from two to nine per locus. The observed and expected heterozygosities ranged from 0.2500 to 0.9000 and from 0.4469 to 0.8514, respectively. These polymorphic microsatellites will be useful for genetic diversity analysis and linkage map construction for P. lethostigma. [source] Characterization of microsatellite markers for rough fescue species (Festuca spp.)MOLECULAR ECOLOGY RESOURCES, Issue 3 2006YONG-BI FU Abstract One major challenge in genetic diversity analysis of minor grass species is the lack of informative molecular markers. A set of 210 simple sequence repeat (SSR) markers developed from wheat and barley were evaluated for their transferability to three rough fescue species [Festuca altaica Trinius, F. campestris (Rydb.) and F. hallii (Vassey) Piper]. Twelve SSR primer pairs displayed scorable polymorphism among and within the species. The number of alleles per primer pair ranged from three to 17 with an average of 8.3 for all the species and greatly varied for each species. About 82% of SSR variation resided within the species. Festuca hallii was genetically most distinct among the three species. [source] Analyses of RAPD data for detection of host specialization in Sclerotinia homoeocarpaPLANT PATHOLOGY, Issue 2 2000T. Hsiang Upgma analysis, principal component analysis, genetic diversity analysis and genetic distance analysis of RAPD data were used to assess the extent of host specialization in 50 isolates of S. homoeocarpa from five turfgrass hosts. In upgma analysis and principal component analysis, the occurrence of host specialization was not readily apparent based on visual inspection. Genetic diversity analysis showed significant differentiation among isolates from different host species (GST = 0.34, P < 0.001). The strongest evidence for some degree of host specialization came from the statistical analysis of genetic distances among isolates. By grouping pairwise genetic distances between isolates based on their host species, and analysing for average distance within the same host species and among different host species, it was found that the average distance within species was less than among species (P < 0.0001). An analysis of molecular variance of the genetic distances among isolates found that 32.3% of the total variation was attributable to host species. It is concluded that these isolates of S. homoeocarpa showed a weak level of host specialization, which was not readily apparent by upgma or principal component analyses, but was revealed by genetic diversity analysis and statistical analysis of genetic distances among isolates. Inoculation tests on different host species and tests using a greater number of isolates are required to confirm the extent of specialization. [source] Interspecies and intergenus transferability of barley and wheat D-genome microsatellite markersANNALS OF APPLIED BIOLOGY, Issue 3 2010A. Castillo A selection of 147 wheat D-genome and 130 barley genomic simple sequence repeat (gSSR) markers were screened for their utility in Hordeum chilense, as an alien donor genome for cereal breeding. Fifty-eight wheat D-genome and 71 barley PCR primer pairs consistently amplified products from H. chilense. Nineteen wheat D-genome and 20 barley gSSR markers were polymorphic and allowed wide genome coverage of the H. chilense genome. Twenty-three of the wheat D-genome and 11 barley PCR primer pairs were suitable for studying the introgressions of H. chilense into wheat, amplifying H. chilense products of distinct size. In 88% of the markers tested, H. chilense products were maintained in the expected homeologous linkage group, as revealed by the analysis of wheat/H. chilense addition lines. Twenty-nine microsatellite markers (eight gSSRs and 21 expressed sequence tags-SSRs) uniformly distributed across the genome were tested for their utility in genetic diversity analysis within the species. Three genetic clusters are reported, in accordance with previous morphological and amplified fragment length polymorphism data. These results show that it is possible to discriminate the three previously established germplasm groups with microsatellite markers. The reported markers represent a valuable resource for the genetic characterisation of H. chilense, for the analysis of its genetic variability, and as a tool for wheat introgression. This is the first intraspecific study in a collection of H. chilense germplasm using microsatellite markers. [source] | ||||||||||||||||||||||