Genetical research最新文献_第6页

Mapping candidate genes for Drosophila melanogaster resistance to the parasitoid wasp Leptopilina boulardi. 黑腹果蝇对疏寄生蜂抗性候选基因定位。

Genetical research Pub Date : 2006-10-01 DOI: 10.1017/S001667230600841X

M Hita, E Espagne, F Lemeunier, L Pascual, Y Carton, G Periquet, M Poirie

引用次数: 24

QTL mapping of grain length in rice (Oryza sativa L.) using chromosome segment substitution lines. 利用染色体片段代换系定位水稻粒长QTL。

Genetical research Pub Date : 2006-10-01 DOI: 10.1017/S0016672306008408

Jiankang Wang, Xiangyuan Wan, Jose Crossa, Jonathan Crouch, Jianfeng Weng, Huqu Zhai, Jianmin Wan

{"title":"QTL mapping of grain length in rice (Oryza sativa L.) using chromosome segment substitution lines.","authors":"Jiankang Wang, Xiangyuan Wan, Jose Crossa, Jonathan Crouch, Jianfeng Weng, Huqu Zhai, Jianmin Wan","doi":"10.1017/S0016672306008408","DOIUrl":"https://doi.org/10.1017/S0016672306008408","url":null,"abstract":"Chromosome segment substitution (CSS) lines have the potential for use in QTL fine mapping and map-based cloning. The standard t-test used in the idealized case that each CSS line has a single segment from the donor parent is not suitable for non-idealized CSS lines carrying several substituted segments from the donor parent. In this study, we present a likelihood ratio test based on stepwise regression (RSTEP-LRT) that can be used for QTL mapping in a population consisting of non-idealized CSS lines. Stepwise regression is used to select the most important segments for the trait of interest, and the likelihood ratio test is used to calculate the LOD score of each chromosome segment. This method is statistically equivalent to the standard t-test with idealized CSS lines. To further improve the power of QTL mapping, a method is proposed to decrease multicollinearity among markers (or chromosome segments). QTL mapping with an example CSS population in rice consisting of 65 non-idealized CSS lines and 82 chromosome segments indicated that a total of 18 segments on eight of the 12 rice chromosomes harboured QTLs affecting grain length under the LOD threshold of 2.5. Three major stable QTLs were detected in all eight environments. Some minor QTLs were not detected in all environments, but they could increase or decrease the grain length constantly. These minor genes are also useful in marker-assisted gene pyramiding.","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"88 2","pages":"93-104"},"PeriodicalIF":0.0,"publicationDate":"2006-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0016672306008408","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26405978","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}

引用次数: 106

Comparative gene mapping in Arabidopsis lyrata chromosomes 6 and 7 and A. thaliana chromosome IV: evolutionary history, rearrangements and local recombination rates. 拟南芥6、7号染色体和拟南芥4号染色体的基因定位比较:进化史、重排和局部重组率。

Genetical research Pub Date : 2006-08-01 DOI: 10.1017/S0016672306008287

Akira Kawabe, Bengt Hansson, Alan Forrest, Jenny Hagenblad, Deborah Charlesworth

{"title":"Comparative gene mapping in Arabidopsis lyrata chromosomes 6 and 7 and A. thaliana chromosome IV: evolutionary history, rearrangements and local recombination rates.","authors":"Akira Kawabe, Bengt Hansson, Alan Forrest, Jenny Hagenblad, Deborah Charlesworth","doi":"10.1017/S0016672306008287","DOIUrl":"https://doi.org/10.1017/S0016672306008287","url":null,"abstract":"We have increased the density of genetic markers on the Arabidopsis lyrata chromosomes AL6 and AL7 corresponding to the A. thaliana chromosome IV, in order to determine chromosome rearrangements between these two species, and to compare recombination fractions across the same intervals. We confirm the two rearrangements previously inferred (a reciprocal translocation and a large inversion, which we infer to be pericentric). By including markers around the centromere regions of A. thaliana chromosomes IV and V, we localize the AL6 centromere, and can localize the breakpoints of these chromosome rearrangements more precisely than previously. One translocation breakpoint was close to the centromere, and the other coincided with one end of the inversion, suggesting that a single event caused both rearrangements. At the resolution of our mapping, apart from these rearrangements, all other markers are in the same order in A. lyrata and A. thaliana. We could thus compare recombination rates in the two species. We found slightly higher values in A. thaliana, and a minimum estimate for regions not close to a centromere in A. lyrata is 4-5 centimorgans per megabase. The mapped region of AL7 includes the self-incompatibility loci (S-loci), and this region has been predicted to have lower recombination than elsewhere in the genome. We mapped 17 markers in a region of 1.23 Mb surrounding these loci, and compared the approximately 600 kb closest to the S-loci with the surrounding region of approximately the same size. There were significantly fewer recombination events in the closer than the more distant region, supporting the above prediction, but showing that the low recombination region is very limited in size.","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"88 1","pages":"45-56"},"PeriodicalIF":0.0,"publicationDate":"2006-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0016672306008287","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26286609","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}

引用次数: 31

Establishing interspecific mosaic genome lines between Drosophila ananassae and Drosophila pallidosa by means of parthenogenesis. 用孤雌生殖的方法建立褐果蝇和白果蝇种间镶嵌基因组系。

Genetical research Pub Date : 2006-08-01 DOI: 10.1017/S0016672306008299

Kyoichi Sawamura, Yoshihiko Tomimura, Hajime Sato, Hirokazu Yamada, Muneo Matsuda, Yuzuru Oguma

{"title":"Establishing interspecific mosaic genome lines between Drosophila ananassae and Drosophila pallidosa by means of parthenogenesis.","authors":"Kyoichi Sawamura, Yoshihiko Tomimura, Hajime Sato, Hirokazu Yamada, Muneo Matsuda, Yuzuru Oguma","doi":"10.1017/S0016672306008299","DOIUrl":"https://doi.org/10.1017/S0016672306008299","url":null,"abstract":"Strong sexual isolation exists between the closely related species Drosophila ananassae and D. pallidosa, but there is no obvious post-mating isolation; both sexes of the hybrids and their descendants appear to be completely viable and fertile. Strains exhibiting parthenogenesis have been derived from wild populations of both species. We intercrossed such strains and established iso-female lines after the second generation of parthenogenesis. These lines are clones, carrying homozygous chromosomes that are interspecific recombinants. We established 266 such isogenic lines and determined their genetic constitution by using chromosomal and molecular markers. Strong pseudo-linkage was seen between loci on the left arm of chromosome 2 and on the right arm of chromosome 3; the frequency of inheriting the two chromosome regions from the same species was significantly larger than expected. One possible cause of pseudo-linkage is female meiotic bias, so that chromosomes of the same species origin tend to be distributed to the same gamete. But this possibility is ruled out; backcross analysis indicated that the two chromosome regions segregated independently in female hybrids. The remaining possibility is elimination of low-fitness flies carrying the two chromosome regions from different species. Thus, genetic incompatibility was detected in the species pair for which no hybrid breakdown had previously been indicated. The 'interspecific mosaic genome' lines reported here will be useful for future research to identify genes involved in speciation and phenotypic evolution.","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"88 1","pages":"1-11"},"PeriodicalIF":0.0,"publicationDate":"2006-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0016672306008299","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26286184","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}

引用次数: 19

Upper limit of the rate and per generation effects of deleterious genomic mutations. 有害基因组突变率和每代效应的上限。

Genetical research Pub Date : 2006-08-01 DOI: 10.1017/S0016672306008329

Hong-Wen Deng, Jian Li, Michael E Pfrender, Jin-Long Li, Hongyi Deng

{"title":"Upper limit of the rate and per generation effects of deleterious genomic mutations.","authors":"Hong-Wen Deng, Jian Li, Michael E Pfrender, Jin-Long Li, Hongyi Deng","doi":"10.1017/S0016672306008329","DOIUrl":"https://doi.org/10.1017/S0016672306008329","url":null,"abstract":"Unbiased or upper limit estimates of the rate (U) of genomic mutations to mildly deleterious alleles are crucial in genetic and conservation studies and in human health care. However, only a few estimates of the lower bounds of U are available. We present a fairly robust estimation that yields an upper limit of U and a nearly unbiased estimate of the per generation fitness decline due to new deleterious mutations. We applied the approach to three species of the freshwater microcrustacean Daphnia and revealed that the upper limit of U for egg survivorship is 0.73 (SD = 0.30) in 14 D. pulicaria populations. For the first four clutches, per generation decline in fecundity due to deleterious mutations ranged from 2.2% to 7.8% in 20 D. pulex populations and from 1.1% to 5.1% in 8 D. obtusa populations. These results indicate the mutation pressure is high in natural Daphnia populations. The approach investigated here provides a potential way to quickly and conveniently characterize U and per generation effects of deleterious genomic mutations on fitness or its important components such as fecundity.","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"88 1","pages":"57-65"},"PeriodicalIF":0.0,"publicationDate":"2006-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0016672306008329","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26286610","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}

引用次数: 4

Spatial genetic pattern in the land mollusc Helix aspersa inferred from a 'centre-based clustering' procedure. 从“基于中心的聚类”过程中推断的陆地软体动物螺旋的空间遗传模式。

Genetical research Pub Date : 2006-08-01 DOI: 10.1017/S0016672306008305

Annie Guiller, Alain Bellido, Alain Coutelle, Luc Madec

{"title":"Spatial genetic pattern in the land mollusc Helix aspersa inferred from a 'centre-based clustering' procedure.","authors":"Annie Guiller, Alain Bellido, Alain Coutelle, Luc Madec","doi":"10.1017/S0016672306008305","DOIUrl":"https://doi.org/10.1017/S0016672306008305","url":null,"abstract":"The present work provides the first broad-scale screening of allozymes in the land snail Helix aspersa. By using overall information available on the distribution of genetic variation between 102 populations previously investigated, we expect to strengthen our knowledge on the spread of the invasive aspersa subspecies in the Western Mediterranean. We propose a new approach based on a centre-based clustering procedure to cluster populations into groups following rules of geographical proximity and genetic similarity. Assuming a stepping-stone model of diffusion, we apply a partitioning algorithm which clusters only populations that are geographically contiguous. The algorithm used, which is actually part of leading methods developed for analysing large microarray datasets, is that of the k-means. Its goal is to minimize the within-group variance. The spatial constraint is provided by a list of connections between localities deduced from a Delaunay network. After testing each optimal group for the presence of spatial arrangement in the genetic data, the inferred genetic structure was compared with partitions obtained from other methods published for defining homogeneous groups (i.e. the Monmonier and SAMOVA algorithms). Competing biogeographical scenarios inferred from the k-means procedure were then compared and discussed to shed more light on colonization routes taken by the species.","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"88 1","pages":"27-44"},"PeriodicalIF":0.0,"publicationDate":"2006-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0016672306008305","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26286186","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}

引用次数: 14

The speciation history of the Drosophila nasuta complex. 纳苏塔果蝇复合体的物种形成史。

Genetical research Pub Date : 2006-08-01 DOI: 10.1017/S0016672306008330

Doris Bachtrog

{"title":"The speciation history of the Drosophila nasuta complex.","authors":"Doris Bachtrog","doi":"10.1017/S0016672306008330","DOIUrl":"https://doi.org/10.1017/S0016672306008330","url":null,"abstract":"The Drosophila nasuta subgroup of the immigrans species group is widely distributed throughout the South-East Asian region, consisting of morphologically similar species with varying degrees of reproductive isolation. Here, I report nucleotide variability data for five X-linked and two mtDNA loci in eight taxa from the nasuta subgroup, with deeper sampling from D. albomicans and its sister species D. nasuta. Phylogenetic relationships among these species vary among different genomic regions, and levels of genetic differentiation suggest that this species group diversified only about one million years ago. D. albomicans and D. nasuta share nucleotide polymorphisms and are distinguished by relatively few fixed differences. Patterns of genetic differentiation between this species pair are compatible with a simple isolation model with no gene flow. Nucleotide variability levels of species in the nasuta group are comparable to those in members of the melanogaster and pseudoobscura species groups, indicating effective population sizes on the order of several million. Population genetic analyses reveal that summaries of the frequency distribution of neutral polymorphisms in both D. albomicans and D. nasuta generally fit the assumptions of the standard neutral model. D. albomicans is of particular interest for evolutionary studies because of its recently formed neo-sex chromosomes, and our phylogenetic and population genetic analyses suggest that it might be an ideal model to study the very early stages of Y chromosome evolution.","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"88 1","pages":"13-26"},"PeriodicalIF":0.0,"publicationDate":"2006-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0016672306008330","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26286185","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}

引用次数: 31

Targeted reduction of the DNA methylation level with 5-azacytidine promotes excision of the medaka fish Tol2 transposable element. 靶向降低DNA甲基化水平的5-氮杂胞苷促进medaka鱼Tol2转座元件的切除。

Genetical research Pub Date : 2006-06-01 DOI: 10.1017/S0016672306008184

Atsuo Iida, Atsuko Shimada, Akihiro Shima, Naofumi Takamatsu, Hiroshi Hori, Kosei Takeuchi, Akihiko Koga

{"title":"Targeted reduction of the DNA methylation level with 5-azacytidine promotes excision of the medaka fish Tol2 transposable element.","authors":"Atsuo Iida, Atsuko Shimada, Akihiro Shima, Naofumi Takamatsu, Hiroshi Hori, Kosei Takeuchi, Akihiko Koga","doi":"10.1017/S0016672306008184","DOIUrl":"https://doi.org/10.1017/S0016672306008184","url":null,"abstract":"The Tol2 element of the medaka fish Oryzias latipes is a member of the hAT (hobo/Activator/Tam3) transposable element family. There is evidence for rapid expansion in the genome and throughout the species in the past but a high spontaneous transposition rate is not observed with current fish materials, suggesting that the Tol2 element and its host species have already acquired an interactive mechanism to control the transposition frequency. DNA methylation is a possible contributing factor, given its involvement with many other transposable elements. We therefore soaked embryos in 5-azacytidine, a reagent that causes reduction in the DNA methylation level, and examined amounts of PCR products reflecting the somatic excision frequency, obtaining direct evidence that exposure promotes Tol2 excision. Our results thus suggest that methylation of the genome DNA is a factor included in the putative mechanisms of control of transposition of the Tol2 element.","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"87 3","pages":"187-93"},"PeriodicalIF":0.0,"publicationDate":"2006-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0016672306008184","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26123948","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}

引用次数: 22

Multiplicative background correction for spotted microarrays to improve reproducibility. 倍增背景校正斑点微阵列，以提高再现性。

Genetical research Pub Date : 2006-06-01 DOI: 10.1017/S0016672306008196

Dabao Zhang, Min Zhang, Martin T Wells

{"title":"Multiplicative background correction for spotted microarrays to improve reproducibility.","authors":"Dabao Zhang, Min Zhang, Martin T Wells","doi":"10.1017/S0016672306008196","DOIUrl":"https://doi.org/10.1017/S0016672306008196","url":null,"abstract":"We propose a simple approach, the multiplicative background correction, to solve a perplexing problem in spotted microarray data analysis: correcting the foreground intensities for the background noise, especially for spots with genes that are weakly expressed or not at all. The conventional approach, the additive background correction, directly subtracts the background intensities from foreground intensities. When the foreground intensities marginally dominate the background intensities, the additive background correction provides unreliable estimates of the differential gene expression levels and usually presents M-A plots with fishtails or fans. Unreliable additive background correction makes it preferable to ignore the background noise, which may increase the number of false positives. Based on the more realistic multiplicative assumption instead of the conventional additive assumption, we propose to logarithmically transform the intensity readings before the background correction, with the logarithmic transformation symmetrizing the skewed intensity readings. This approach not only precludes the fishtails and fans in the M-A plots, but provides highly reproducible background-corrected intensities for both strongly and weakly expressed genes. The superiority of the multiplicative background correction to the additive one as well as the no background correction is justified by publicly available self-hybridization datasets.","PeriodicalId":12777,"journal":{"name":"Genetical research","volume":"87 3","pages":"195-206"},"PeriodicalIF":0.0,"publicationDate":"2006-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1017/S0016672306008196","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26123949","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}

引用次数: 11

Genetic mapping of allometric scaling laws. 异速标度定律的遗传作图。

Genetical research Pub Date : 2006-06-01 DOI: 10.1017/S0016672306008172

Fei Long, Ying Qing Chen, James M Cheverud, Rongling Wu

引用次数: 19