Genetical research最新文献

{"title":"Population genetic inference using a fixed number of segregating sites: a reassessment.","authors":"Sebastián E Ramos-Onsins,&nbsp;Sylvain Mousset,&nbsp;Thomas Mitchell-Olds,&nbsp;Wolfgang Stephan","doi":"10.1017/S0016672307008877","DOIUrl":"https://doi.org/10.1017/S0016672307008877","url":null,"abstract":"<p><p>Coalescent theory is commonly used to perform population genetic inference at the nucleotide level. Here, we examine the procedure that fixes the number of segregating sites (henceforth the FS procedure). In this approach a fixed number of segregating sites (S) are placed on a coalescent tree (independently of the total and internode lengths of the tree). Thus, although widely used, the FS procedure does not strictly follow the assumptions of coalescent theory and must be considered an approximation of (i) the standard procedure that uses a fixed population mutation parameter theta, and (ii) procedures that condition on the number of segregating sites. We study the differences in the false positive rate for nine statistics by comparing the FS procedure with the procedures (i) and (ii), using several evolutionary models with single-locus and multilocus data. Our results indicate that for single-locus data the FS procedure is accurate for the equilibrium neutral model, but problems arise under the alternative models studied; furthermore, for multilocus data, the FS procedure becomes inaccurate even for the standard neutral model. Therefore, we recommend a procedure that fixes the theta value (or alternatively, procedures that condition on S and take into account the uncertainty of theta) for analysing evolutionary models with multilocus data. With single-locus data, the FS procedure should not be employed for models other than the standard neutral model.</p>","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"89 4","pages":"231-44"},"PeriodicalIF":0.0,"publicationDate":"2007-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0016672307008877","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40850805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstracts from the Seventeenth Genetics Society's Mammalian Genetics and Development Workshop. November 9-10, 2006. London, United Kingdom.","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"89 3","pages":"181-8"},"PeriodicalIF":0.0,"publicationDate":"2007-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41068884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular genetic basis of flower colour variegation in Linaria.","authors":"Lisete Galego,&nbsp;Jorge Almeida","doi":"10.1017/S0016672307008786","DOIUrl":"https://doi.org/10.1017/S0016672307008786","url":null,"abstract":"<p><p>To identify transposons that may be of use for mutagenesis we investigated the genetic molecular basis of a case of flower colour variegation in Linaria, a close relative of the model species Antirrhinum majus. We show that this variegation is attributable to an unstable mutant allele of the gene encoding dihydroflavonol-4-reductase, one of the enzymes required for anthocyanin biosynthesis. This allele carries an insertion of a transposon belonging to the CACTA family (Tl1, Transposon Linaria 1) which blocks its expression thus conferring an ivory flower colour phenotype. Tl1 is occasionally excised in dividing epidermal cells to produce clonal patches of red tissue on the ivory background, and in cells giving rise to gametes to generate reversion alleles conferring a fully coloured phenotype. This finding may open the way for targeted transposon-mutagenesis in Linaria, and hence for using this genus in comparative genetic studies.</p>","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"89 3","pages":"129-34"},"PeriodicalIF":0.0,"publicationDate":"2007-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0016672307008786","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40993909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An intervarietal genetic linkage map of Indian bread wheat (Triticum aestivum L.) and QTL maps for some metric traits.","authors":"E Nalini,&nbsp;S G Bhagwat,&nbsp;N Jawali","doi":"10.1017/S0016672307008828","DOIUrl":"https://doi.org/10.1017/S0016672307008828","url":null,"abstract":"<p><p>Bread wheat (Triticum aestivum L.) exhibits very narrow genetic diversity and hence there is high relatedness among cultivated varieties. However, a population generated from an intervarietal cross, with the parents differing in a large number of traits, could lead to the generation of QTL maps which will be useful in practice. In this report a genetic linkage map of wheat is constructed using a cross between two Indian bread wheat varieties: Sonalika and Kalyansona. The linkage map consisted of 236 markers and spanned a distance of 3639 cM, with 1211.2 cM for the A genome, 1669.2 cM for the B genome, 192.4 cM for the D genome and 566.2 cM for unassigned groups. Linkage analysis defined 37 linkage groups of which 24 were assigned to 17 chromosomes. The genetic map was used to identify QTLs by composite internal mapping (CIM) for three metric traits, viz. culm length (CL), flag leaf length (FLL) and flag leaf breadth (FLB). Of 25 QTLs identified in this study, 15 have not been reported previously. Multitrait CIM (MCIM) analysis was carried out for traits that were significantly correlated such as FLB-FLL and CL-FLB-FLL. Detection of a large number of QTLs for the three traits analysed suggests that in parent cultivars that are not too diverse, the differences at genetic level detected as polymorphisms may be mostly associated with QTLs for the observed differences.</p>","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"89 3","pages":"165-79"},"PeriodicalIF":0.0,"publicationDate":"2007-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0016672307008828","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40993852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenotypic and genetic variations and correlations in multitrait developmental instability: a multivariate Bayesian model applied to Speckled Wood butterfly (Pararge aegeria) wing measurements.","authors":"Stefan Van Dongen,&nbsp;Willem Talloen","doi":"10.1017/S0016672307008816","DOIUrl":"https://doi.org/10.1017/S0016672307008816","url":null,"abstract":"<p><p>Phenotypic and genetic variation and covariation in developmental instability (DI) have been the subject of many debates. In this paper we develop and apply a statistical model in a Bayesian context to analyse different traits simultaneously in a multivariate model of DI. We apply the model to measurements of yellow spots on the front wing of the Speckled Wood butterfly (Pararge aegeria L.) in a full-sib breeding experiment. We estimated the posterior distribution of the broad-sense heritability of DI averaged across the five yellow spots, which had a median of 0.19 and a 95% credibility interval ranging between 0.04 and 0.64. Phenotypic and genetic correlations in DI could not be estimated accurately with the present sample size. Yellow spots 4 and 5 appeared to show some degree of developmental integration. The importance of this model and its possible extensions are discussed.</p>","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"89 3","pages":"155-63"},"PeriodicalIF":0.0,"publicationDate":"2007-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0016672307008816","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40993851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Triadic IBD coefficients and applications to estimating pairwise relatedness.","authors":"Jinliang Wang","doi":"10.1017/S0016672307008798","DOIUrl":"https://doi.org/10.1017/S0016672307008798","url":null,"abstract":"<p><p>Knowledge of the genetic relatedness among individuals is essential in diverse research areas such as behavioural ecology, conservation biology, quantitative genetics and forensics. How to estimate relatedness accurately from genetic marker information has been explored recently by many methodological studies. In this investigation I propose a new likelihood method that uses the genotypes of a triad of individuals in estimating pairwise relatedness (r). The idea is to use a third individual as a control (reference) in estimating the r between two other individuals, thus reducing the chance of genes identical in state being mistakenly inferred as identical by descent. The new method allows for inbreeding and accounts for genotype errors in data. Analyses of both simulated and human microsatellite and SNP datasets show that the quality of r estimates (measured by the root mean squared error, RMSE) is generally improved substantially by the new triadic likelihood method (TL) over the dyadic likelihood method and five moment estimators. Simulations also show that genotyping errors/mutations, when ignored, result in underestimates of r for related dyads, and that incorporating a model of typing errors in the TL method improves r estimates for highly related dyads but impairs those for loosely related or unrelated dyads. The effects of inbreeding were also investigated through simulations. It is concluded that, because most dyads in a natural population are unrelated or only loosely related, the overall performance of the new triadic likelihood method is the best, offering r estimates with a RMSE that is substantially smaller than the five commonly used moment estimators and the dyadic likelihood method.</p>","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"89 3","pages":"135-53"},"PeriodicalIF":0.0,"publicationDate":"2007-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0016672307008798","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40993850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic diversity of cultivated and wild-type peanuts evaluated with M13-tailed SSR markers and sequencing.","authors":"Noelle A Barkley,&nbsp;Rob E Dean,&nbsp;Roy N Pittman,&nbsp;Ming L Wang,&nbsp;Corley C Holbrook,&nbsp;Gary A Pederson","doi":"10.1017/S0016672307008695","DOIUrl":"https://doi.org/10.1017/S0016672307008695","url":null,"abstract":"<p><p>Thirty-one genomic SSR markers with a M13 tail attached were used to assess the genetic diversity of the peanut mini core collection. The M13-tailed method was effective in discriminating almost all the cultivated and wild accessions. A total of 477 alleles were detected with an average of 15.4 alleles per locus. The mean polymorphic information content (PIC) score was 0.687. The cultivated peanut (Arachis hypogaea L.) mini core produced a total of 312 alleles with an average of 10.1 alleles per locus. A neighbour-joining tree was constructed to determine the interspecific and intraspecific relationships in this data set. Almost all the peanut accessions in this data set classified into subspecies and botanical varieties such as subsp. hypogaea var. hypogaea, subsp. fastigiata var. fastigiata, and subsp. fastigiata var. vulgaris clustered with other accessions with the same classification, which lends further support to their current taxonomy. Alleles were sequenced from one of the SSR markers used in this study, which demonstrated that the repeat motif is conserved when transferring the marker across species borders. This study allowed the examination of the diversity and phylogenetic relationships in the peanut mini core which has not been previously reported.</p>","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"89 2","pages":"93-106"},"PeriodicalIF":0.0,"publicationDate":"2007-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0016672307008695","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26863238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantitative and molecular genetic variation in sympatric populations of Medicago laciniata and M. truncatula (Fabaceae): relationships with eco-geographical factors.","authors":"Mounawer Badri,&nbsp;Houcine Ilahi,&nbsp;Thierry Huguet,&nbsp;Mohamed Elarbi Aouani","doi":"10.1017/S0016672307008725","DOIUrl":"https://doi.org/10.1017/S0016672307008725","url":null,"abstract":"<p><p>Medicago laciniata is restricted to south of the Mediterranean basin and it extends in Tunisia from the inferior semi-arid to Saharan stages, whereas M. truncatula is a widespread species in such areas. The genetic variability in four Tunisian sympatric populations of M. laciniata and M. truncatula was analysed using 19 quantitative traits and 20 microsatellites. We investigated the amplification transferability of 52 microsatellites developed in M. truncatula to M. laciniata. Results indicate that about 78.85% of used markers are valuable genetic markers for M. laciniata. M. laciniata displayed significantly lower quantitative differentiation among populations (QST=0.12) than did M. truncatula (QST=0.45). However, high molecular differentiations, with no significant difference, were observed in M. laciniata (FST=0.48) and M. truncatula (FST=0.47). Several quantitative traits exhibited significantly smaller QST than FST for M. laciniata, consistent with constraining selection. For M. truncatula, the majority of traits displayed no statistical difference in the level of QST and FST. Furthermore, these traits are significantly associated with eco-geographical factors, consistent with selection for local adaptation rather than genetic drift. In both species, there was no significant correlation between genetic variation at quantitative traits and molecular markers. The site-of-origin explains about 5.85% and 11.27% of total quantitative genetic variability among populations of M. laciniata and M. truncatula, respectively. Established correlations between quantitative traits and eco-geographical factors were generally more moderate for M. laciniata than for M. truncatula, suggesting that the two species exhibit different genetic bases of local adaptation to varying environmental conditions. Nevertheless, no consistent patterns of associations were found between gene diversity (He) and environmental factors in either species.</p>","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"89 2","pages":"107-22"},"PeriodicalIF":0.0,"publicationDate":"2007-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0016672307008725","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26863239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selection responses of means and inbreeding depression for female fecundity in Drosophila melanogaster suggest contributions from intermediate-frequency alleles to quantitative trait variation.","authors":"Brian Charlesworth, Takahiro Miyo, Helen Borthwick","doi":"10.1017/S001667230700866X","DOIUrl":"10.1017/S001667230700866X","url":null,"abstract":"<p><p>The extent to which quantitative trait variability is caused by rare alleles maintained by mutation, versus intermediate-frequency alleles maintained by balancing selection, is an unsolved problem of evolutionary genetics. We describe the results of an experiment to examine the effects of selection on the mean and extent of inbreeding depression for early female fecundity in Drosophila melanogaster. Theory predicts that rare, partially recessive deleterious alleles should cause a much larger change in the effect of inbreeding than in the mean of the outbred population, with the change in inbreeding effect having an opposite sign to the change in mean. The present experiment fails to support this prediction, suggesting that intermediate-frequency alleles contribute substantially to genetic variation in early fecundity.</p>","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"89 2","pages":"85-91"},"PeriodicalIF":0.0,"publicationDate":"2007-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26739366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenotypic effects induced by knock-down of the period clock gene in Bombyx mori.","authors":"Federica Sandrelli,&nbsp;Silvia Cappellozza,&nbsp;Clara Benna,&nbsp;Alessio Saviane,&nbsp;Antonio Mastella,&nbsp;Gabriella M Mazzotta,&nbsp;Stephane Moreau,&nbsp;Mirko Pegoraro,&nbsp;Alberto Piccin,&nbsp;Mauro A Zordan,&nbsp;Luciano Cappellozza,&nbsp;Charalambos P Kyriacou,&nbsp;Rodolfo Costa","doi":"10.1017/S0016672307008713","DOIUrl":"https://doi.org/10.1017/S0016672307008713","url":null,"abstract":"<p><p>The lepidopteran Bombyx mori is an insect of considerable scientific and economic importance. Recently, the B. mori circadian clock gene period has been molecularly characterized. We have transformed a B. mori strain with a construct encoding a period double-strand RNA in order to knock-down period gene expression. We observe that this post-transcriptional silencing produces a small but detectable disruption in the egg-hatching rhythm, as well as a reduction in egg-to-adult developmental time, without altering silk production parameters. Thus we show that both circadian and non-circadian phenotypes can be altered by changing per expression, and, at a practical level, these results suggest that per knock-down may provide a suitable strategy for improving the efficiency of rearing, without affecting silk productivity.</p>","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"89 2","pages":"73-84"},"PeriodicalIF":0.0,"publicationDate":"2007-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0016672307008713","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26863237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}