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New Genotypes (new + genotype)
Selected AbstractsSelection on apomictic lineages of Taraxacum at establishment in a mixed sexual,apomictic populationJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 4 2000De Kovel A species' mode of reproduction, sexual or asexual, will affect its ecology and evolution. In many species, asexuality is related to polyploidy. In Taraxacum, apomicts are triploid, and sexuals are diploid. To disentangle the effects of ploidy level and reproductive mode on life-history traits, we compared established apomictic Taraxacum genotypes with newly synthesized apomictic genotypes, obtained from diploid,triploid crosses. Diploid,triploid crossing is probably the way that most apomictic lineages originate. New genotypes had on average a much lower seed set than established genotypes. Established genotypes differed on average from new genotypes, in particular under shaded conditions: the established genotypes had longer leaves and flowered later. The differences between new and established triploids resembled the differences that have been found between sexual diploids and established apomictic triploids. We conclude that ploidy differences alone are not directly responsible for observed differences between sexual diploid and apomictic triploid dandelions. [source] A new genotype 2 subcluster identified among GBV-C strains circulating in the Lisbon metropolitan area of PortugalJOURNAL OF MEDICAL VIROLOGY, Issue 3 2010Cristina Branco Abstract The rate of infection by the GBV-C virus was investigated in a group of 214 individuals at high risk of infection with parenterally transmitted viruses, and all living in the Lisbon metropolitan area (Portugal). RNA was extracted from plasma samples, and a fragment of the 5,-UTR was amplified by RT-PCR, disclosing a high prevalence of infection (40.7%). Most probably due to similar modes of viral transmission, the majority of GBV-C (+) individuals were found to be coinfected with HIV and/or HCV. A genomic region covering part of the E1/E2 glycoprotein coding sequence was amplified from approximately half of the GBV-C positive samples (44/87). Phylogenetic analysis of nucleotide sequences showed segregation of Portuguese GBV-C strains with genotype 1 (G1, n,=,10) and genotype 2 (G2, n,=,24) references. Genotype 1 was significantly associated with the African descent of those infected. Curiously, some of the strains assigned to genotype 2 were shown to form a separate cluster (designated G2*) in both neighbor-joining and Bayesian phylogenetic trees, which was confirmed by multivariate principal coordinate analysis. However, analysis of the distribution of intra- and intergenotype genetic distances support the hypothesis that rather than corresponding to a new viral genotype, G2* is a geographical subcluster within the genotype 2 radiation. J. Med. Virol. 82:452,459, 2010. © 2010 Wiley-Liss, Inc. [source] Mumps virus strains isolated in Croatia in 1998 and 2005: Genotyping and putative antigenic relatedness to vaccine strainsJOURNAL OF MEDICAL VIROLOGY, Issue 5 2006antak Abstract Two mumps virus strains 9218/Zg98 and Du/CRO05 were isolated in two locations in Croatia in 1998 and 2005, respectively. Genetic characterization of these temporally distinct mumps virus isolates was carried out in order to determine their genotype and putative antigenic relatedness to mumps virus vaccine strains. Sequence analysis of the small hydrophobic (SH) gene revealed that isolate 9218/Zg98 shows less than 95% of similarity to any reference strain, thus representing a potential reference strain for a new genotype. Isolate Du/CRO05 clearly belongs to genotype G with the 97% of homology to the reference strain Glouc1/UK96. When compared to each other, the two Croatian strains have extremely low level of homology of only 89% indicating no relatedness between them. Putative antigenic properties of the HN protein of these two isolates were compared to different vaccine strains. The results reveal a higher level of homology of antigenic determinants to non-A genotype vaccine strains than to A genotype vaccine strain. J. Med. Virol. 78:638,643, 2006. © 2006 Wiley-Liss, Inc. [source] Novel TTV variants isolated in an epidemic of hepatitis of unknown etiologyJOURNAL OF MEDICAL VIROLOGY, Issue 1 2002Zhihua Liu Abstract TT virus (TTV) is a recently discovered single-stranded DNA virus that has been reported to be associated with elevated transminase levels in the patients with posttransfusion hepatitis of unknown etiology. TTV prevalence is very high in the common population and its pathogenicity remains unclear. In this study, we performed an epidemiological study to investigate the infection rate of TTV and its role in an epidemic of unknown-etiology hepatitis. Moreover, two TTV isolates named L01 and L02 were cloned from the serum of a patient with unknown-etiology hepatitis. Eighty-one subjects were included in the study and were divided into two groups: 18 in the case group and 63 in the control group. TTVDNA was detected by nested PCR from sera samples. The infection rates of TTV in case and control groups were 33.3 and 38.9%, respectively. There was no significant difference between the two groups. Homology analysis showed that L01 had a very poor homology with other TTV isolates and L02, and L02 was 75.5% identical to JA10. The result does not support TTV as a causative agent in this epidemic. The genetic divergence between L01 and other TTV isolates beyond genotype, so it represents a new genotype of TTV. J. Med. Virol. 67:113,117, 2002. © 2002 Wiley-Liss, Inc. [source] Population changes in Phytophthora infestans in Taiwan associated with the appearance of resistance to metalaxyl,PEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 9 2002Kenneth L Deahl Abstract In recent years, late blight, caused by Phytophthora infestans (Mont) De Bary, has increased in severity in many parts of the world, and this has been associated with migrations which have introduced new, arguably more aggressive, populations of the pathogen. In Taiwan, late blight has been endemic on outdoor tomato crops grown in the highlands since the early 1900s, but recent epidemics have been more damaging. To ascertain the present status of the Taiwanese population of P infestans, 139 isolates of the pathogen collected and maintained by the Asian Vegetable Research and Development Center (AVRDC) were characterized using mating type, metalaxyl sensitivity, allozyme genotype, mitochondrial haplotype and RFLP fingerprinting. Up to 1997, all isolates were found to belong to the old clonal lineage of P infestans (US-1 and variants), but in isolates from 1998 a new genotype appeared, and by 2000 this had apparently completely displaced the old population. This new genotype was an A1 mating type and has the dilocus allozyme genotype 100/100/111, 100/100 for the loci coding for glucose-6-phosphate isomerase and peptidase, respectively. These characters, together with RG57 fingerprinting, indicated that these isolates belonged to the US-11 clonal lineage, a minority (11%) being a previously unreported variant of US-11. Whereas metalaxyl-resistant isolates were not detected in the old population, 96% of the new genotypes proved resistant, with the remainder being intermediate in sensitivity. It may be inferred from this sudden, marked change in the characteristics of the Taiwanese P infestans that a new population of the pathogen was introduced around 1997,98 and that this may well have already been metalaxyl-resistant when it arrived, although a role for in situ selection cannot be excluded. © 2002 Society of Chemical Industry [source] Orange, yellow and white-cream: inheritance of carotenoid-based colour in sunflower pollenPLANT BIOLOGY, Issue 1 2010M. Fambrini Abstract Inheritance of pollen colour was studied in sunflower (Helianthus annuus L.) using three distinct pollen colour morphs: orange, yellow and white-cream. Orange is the most common colour of sunflower pollen, while the yellow morph is less frequent. These two types were observed in the inbred lines F11 and EF2L, respectively. White-cream pollen is a rare phenotype in nature, and was identified in a mutant, named white-cream pollen, recovered in the R2 generation of an in vitro regenerated plant. The F11 inbred line was used as starting material for in vitro regeneration. The carotenoid content of these three pollen morphs differed, and was extremely reduced in white-cream pollen. The phenotype of F1 populations obtained by reciprocal crosses revealed that the orange trait was dominant over both white-cream and yellow. Segregation of F2 populations of both crosses, orange × yellow and orange × white-cream, approached a 3:1 ratio, indicating the possibility of simple genetic control. By contrast, a complementation cross between the two lines with white-cream and yellow pollen produced F1 plants with orange pollen. The F2 populations of this cross-segregated as nine orange: four white-cream: four yellow. A model conforming to the involvement of two unlinked genes, here designated Y and O, can explain these results. Accessions with yellow pollen would have the genotype YYoo, the white-cream pollen mutant would have yyOO and the accession with orange pollen would have YYOO. Within F2 populations of the cross white-cream × yellow a new genotype, yyoo, with white-cream pollen was scored. The results of the cross yyoo × YYoo produced only F1 plants with yellow pollen, supporting a recessive epistatic model of inheritance between two loci. In this model, yy is epistatic on O and o. In F2 populations, the distributions of phenotypic classes suggested that the genetic control of carotenoid content is governed by major genes, with large effects segregating in a background of polygenic variation. These three pollen morphs can provide insight into the sequence in which genes act, as well into the biochemical pathway controlling carotenoid biosynthesis in anthers and the transfer of these different pigments into pollenkitt. [source] Microevolution in agricultural environments: how a traditional Amerindian farming practice favours heterozygosity in cassava (Manihot esculenta Crantz, Euphorbiaceae)ECOLOGY LETTERS, Issue 2 2005Benoît Pujol Abstract We demonstrate a novel case of selection for heterozygosity in nature, involving inadvertent human selection on a population of domesticated plants. Amerindian farmers propagate cassava (Manihot esculenta) clonally by cuttings. Seedlings also appear spontaneously in fields, and farmers allow them to grow, later using some for cuttings. These ,volunteers' contribute new genotypes. However, many are inbred, whereas multiplied clones are highly heterozygous. We demonstrate the selective retention of heterozygous volunteers. When farmers weeded fields, they killed small volunteers, but retained large ones. Plant size and heterozygosity were correlated, and both increased after weeding. The process we document allows maintenance of genotypically diverse and heterozygous clonal stocks. Demonstrating heterosis in nature usually requires large sample sizes, but novel features of our system allowed escape of this constraint. Traditional agroecosystems offer unusual opportunities for the microevolutionary studies required to give on-farm conservation of genetic resources a solid scientific basis. [source] A statistical model for unwarping of 1-D electrophoresis gelsELECTROPHORESIS, Issue 22 2005Chris Glasbey Professor Abstract A statistical model is proposed which relates density profiles in 1-D electrophoresis gels, such as those produced by pulsed-field gel electrophoresis (PFGE), to databases of profiles of known genotypes. The warp in each gel lane is described by a trend that is linear in its parameters plus a first-order autoregressive process, and density differences are modelled by a mixture of two normal distributions. Maximum likelihood estimates are computed efficiently by a recursive algorithm that alternates between dynamic time warping to align individual lanes and generalised-least-squares regression to ensure that the warp is smooth between lanes. The method, illustrated using PFGE of Escherichia coli O157 strains, automatically unwarps and classifies gel lanes, and facilitates manual identification of new genotypes. [source] Genetic diversity in Nordic and Baltic populations of Chondrostereum purpureum: a potential herbicide biocontrol agentFOREST PATHOLOGY, Issue 6 2008H. Vartiamäki Summary We analysed genetic variation in the natural populations of a potential herbicide biocontrol agent, Chondrostereum purpureum, in Nordic and Baltic countries using random amplified microsatellite markers. The results showed high genetic diversity among the populations of this fungus, but almost a complete lack of local differentiation. The results implicate that any local strain from the area can be used as a biocontrol agent without a fear of introducing new genotypes to treatment areas. [source] Direct DNA delivery into zebrafish embryos employing tissue culture techniquesGENESIS: THE JOURNAL OF GENETICS AND DEVELOPMENT, Issue 1 2001Raquel Sussman Abstract Summary: The production of transfected fish embryos requires expertise in injecting the fertilized eggs and/or expensive equipment for electroporation or microprojectiles. This article demonstrates that by exposure to DNA constructs conjugated with transfecting reagents dechorionated Danio rerio embryos are capable of acquiring extracellular DNA and expressing reporter genes. Embryos incubated with pCMVluc complexed with GeneJammer or GenePORTER expressed luciferase 24,48 h after exposure. pCMVGFP DNA mixed with the same agents generated embryos that exhibited differential patterns of expression of green fluorescent protein (GFP). Embryonic development varied depending on the procedure employed and the reporter gene utilized. Expression of the luciferase gene did not interfere with the subsequent development of the embryos. In contrast, the embryos expressing a high level of GFP were affected, probably due to a very active promoter. These results demonstrate the ease of obtaining transfected fish embryos, which facilitate the mass production of new genotypes and extend the procedure to laboratories with limited resources. genesis 31:1,5, 2001. © 2001 Wiley-Liss, Inc. [source] Selection on apomictic lineages of Taraxacum at establishment in a mixed sexual,apomictic populationJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 4 2000De Kovel A species' mode of reproduction, sexual or asexual, will affect its ecology and evolution. In many species, asexuality is related to polyploidy. In Taraxacum, apomicts are triploid, and sexuals are diploid. To disentangle the effects of ploidy level and reproductive mode on life-history traits, we compared established apomictic Taraxacum genotypes with newly synthesized apomictic genotypes, obtained from diploid,triploid crosses. Diploid,triploid crossing is probably the way that most apomictic lineages originate. New genotypes had on average a much lower seed set than established genotypes. Established genotypes differed on average from new genotypes, in particular under shaded conditions: the established genotypes had longer leaves and flowered later. The differences between new and established triploids resembled the differences that have been found between sexual diploids and established apomictic triploids. We conclude that ploidy differences alone are not directly responsible for observed differences between sexual diploid and apomictic triploid dandelions. [source] Population genetic structure of Plasmopara viticola in the Western Cape Province of South AfricaMOLECULAR PLANT PATHOLOGY, Issue 6 2007TREVOR KOOPMAN SUMMARY Plasmopara viticola populations in South Africa were studied for two consecutive grape growing seasons, in an organically managed and a conventional fungicide-sprayed vineyard. Three to four samplings in each season were genotyped with four microsatellite markers (GOB, CES, ISA and BER). Population differentiation (Fst) between the conventional fungicide-sprayed vineyard and organically managed vineyard was low (0.004 and 0.016) in both growing seasons, suggesting one metapopulation. However, differences in the relative contribution of the predominant and new genotypes to epidemics in the two vineyards suggested that fungicide applications may have selected for reduced pathogen diversity. In both years and vineyards, sexual (oosporic) reproduction and/or migration occurred throughout the year and contributed between 12 and 74% to the epidemic. Hardy,Weinberg analyses suggest that South African P. viticola populations are randomly mating. Epidemics in both years and vineyards were dominated by one or two genotypes that each contributed between 14 and 67% to the epidemic through asexual reproduction. The remaining genotypes showed low levels of asexual reproduction, with most genotypes never being able to reproduce asexually. However, for some genotypes asexual reproduction was important, as it enabled survival of the genotypes from one season to the next. In total, ten genotypes were able to survive asexually or vegetatively from one season to the next. The populations were further characterized by the presence of a high frequency of isolates that most likely have elevated ploidy levels. [source] Population changes in Phytophthora infestans in Taiwan associated with the appearance of resistance to metalaxyl,PEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 9 2002Kenneth L Deahl Abstract In recent years, late blight, caused by Phytophthora infestans (Mont) De Bary, has increased in severity in many parts of the world, and this has been associated with migrations which have introduced new, arguably more aggressive, populations of the pathogen. In Taiwan, late blight has been endemic on outdoor tomato crops grown in the highlands since the early 1900s, but recent epidemics have been more damaging. To ascertain the present status of the Taiwanese population of P infestans, 139 isolates of the pathogen collected and maintained by the Asian Vegetable Research and Development Center (AVRDC) were characterized using mating type, metalaxyl sensitivity, allozyme genotype, mitochondrial haplotype and RFLP fingerprinting. Up to 1997, all isolates were found to belong to the old clonal lineage of P infestans (US-1 and variants), but in isolates from 1998 a new genotype appeared, and by 2000 this had apparently completely displaced the old population. This new genotype was an A1 mating type and has the dilocus allozyme genotype 100/100/111, 100/100 for the loci coding for glucose-6-phosphate isomerase and peptidase, respectively. These characters, together with RG57 fingerprinting, indicated that these isolates belonged to the US-11 clonal lineage, a minority (11%) being a previously unreported variant of US-11. Whereas metalaxyl-resistant isolates were not detected in the old population, 96% of the new genotypes proved resistant, with the remainder being intermediate in sensitivity. It may be inferred from this sudden, marked change in the characteristics of the Taiwanese P infestans that a new population of the pathogen was introduced around 1997,98 and that this may well have already been metalaxyl-resistant when it arrived, although a role for in situ selection cannot be excluded. © 2002 Society of Chemical Industry [source] Anthocyanin profile of Spanish Vitis vinifera L. red grape varieties in danger of extinctionAUSTRALIAN JOURNAL OF GRAPE AND WINE RESEARCH, Issue 3 2007S. GÓMEZ-ALONSO Abstract This paper reports on a study of the anthocyanin fraction in berry skins of ten minority red and pink grapevine varieties from Castilla-La Mancha (Spain) and two traditional varieties from this growing region, Tempranillo and Garnacha Tinta, as references. These varieties were correctly identified beforehand by analysing six microsatellite regions recommended by the GENRES 081 project; five varieties were identified with genotypes identical to those described previously, and five new genotypes not described for any variety according to the literature consulted. Grape skin extracts of each variety were analysed by HPLC-UV-Vis, and four perfectly differentiated anthocyanin profiles were obtained. In six out of ten varieties (Churriago, Unknown 1, Unknown 2, Ariño, Brujidera and Moravia Agria) the major anthocyanin was malvidin-3-glucoside (39%). Tinto Velasco contained more than 29% delphinidin-3-glucoside, Gordera Roja and Teta de Vaca Tinta more than 40% peonidin-3-glucoside, and Rojal more than 29% cyanidin-3-glucoside. Results of this work point out the existence of unusual anthocyanic profiles in several of these indigenous varieties, and highlight the necessity of studying the effects of variety on other flavonoids and their impact on wine colour. [source] | |||||||||||||