Plasticity genes and plasticity costs: a new approach using an Arabidopsis recombinant inbred population

Earlier flowering is triggered by vernalization in some but not all Arabidopsis ecotypes, often reflecting allelic variation at the FRIGIDA (FRI) locus. Using a recombinant inbred (RI) population polymorphic at FRI, we examined fitness consequences of variation for plasticity. Flowering and fitness were scored for 68 RI genotypes following full and partial vernalization treatments. Within-environment and mixed-model anovas estimated variance components for a genotype effect and a G x E term, respectively. Selection analyses examined whether delayed bolting increases fitness; a plasticity costs analysis asked whether increased plasticity lowers fitness. We also explored whether trait QTL had environment-specific effects, colocated in the immediate vicinity of FRI, or overlapped with fitness QTL. Selection may favor fri alleles and constitutive early flowering, especially in conditions that only partially vernalize plants. Plasticity costs, detected only after partial vernalization and only marginally significant, were nonetheless consistent with FRI-FLC function. We discuss how information about QTL with environment-specific effects, fitness QTL, and knowledge about plasticity genes can improve interpretation of selection or plasticity cost analyses.     

Prediction of IBD based on population history for fine gene mapping

A novel multiple regression method (RM) is developed to predict identity-by-descent probabilities at a locus L (IBD_L), among individuals without pedigree, given information on surrounding markers and population history. These IBD_L probabilities are a function of the increase in linkage disequilibrium (LD) generated by drift in a homogeneous population over generations. Three parameters are sufficient to describe population history: effective population size (Ne), number of generations since foundation (T), and marker allele frequencies among founders (p). IBD_L are used in a simulation study to map a quantitative trait locus (QTL) via variance component estimation. RM is compared to a coalescent method (CM) in terms of power and robustness of QTL detection. Differences between RM and CM are small but significant. For example, RM is more powerful than CM in dioecious populations, but not in monoecious populations. Moreover, RM is more robust than CM when marker phases are unknown or when there is complete LD among founders or Ne is wrong, and less robust when p is wrong. CM utilises all marker haplotype information, whereas RM utilises information contained in each individual marker and all possible marker pairs but not in higher order interactions. RM consists of a family of models encompassing four different population structures, and two ways of using marker information, which contrasts with the single model that must cater for all possible evolutionary scenarios in CM.     

Photoperiodic flowering of Arabidopsis: integrating genetic and physiological approaches to characterization of the floral stimulus

In many plants the transition from vegetative growth to flowering is controlled by environmental cues. One of these cues is day length or photoperiod, which synchronizes flowering of many species with the changing seasons. Recently, advances have been made in understanding the molecular mechanisms that confer photoperiodic control of flowering and, in particular, how inductive events occurring in the leaf, where photoperiod is perceived, are linked to floral evocation that takes place at the shoot apical meristem. We discuss recent data obtained using molecular genetic approaches on the function of regulatory proteins that control flowering time in Arabidopsis thaliana. These data are compared with the results of physiological analyses of the floral transition, which were performed in a range of species and directed towards identification of the transmitted floral singals.     

Natural genetic variation in Arabidopsis: tools, traits and prospects for evolutionary ecology

BACKGROUND: The model plant Arabidopsis thaliana (Arabidopsis) shows a wide range of genetic and trait variation among wild accessions. Because of its unparalleled biological and genomic resources, the potential of Arabidopsis for molecular genetic analysis of this natural variation has increased dramatically in recent years. SCOPE: Advanced genomics has accelerated molecular phylogenetic analysis and gene identification by quantitative trait loci (QTL) mapping and/or association mapping in Arabidopsis. In particular, QTL mapping utilizing natural accessions is now becoming a major strategy of gene isolation, offering an alternative to artificial mutant lines. Furthermore, the genomic information is used by researchers to uncover the signature of natural selection acting on the genes that contribute to phenotypic variation. The evolutionary significance of such genes has been evaluated in traits such as disease resistance and flowering time. However, although molecular hallmarks of selection have been found for the genes in question, a corresponding ecological scenario of adaptive evolution has been difficult to prove. Ecological strategies, including reciprocal transplant experiments and competition experiments, and utilizing near-isogenic lines of alleles of interest will be a powerful tool to measure the relative fitness of phenotypic and/or allelic variants. CONCLUSIONS: As the plant model organism, Arabidopsis provides a wealth of molecular background information for evolutionary genetics. Because genetic diversity between and within Arabidopsis populations is much higher than anticipated, combining this background information with ecological approaches might well establish Arabidopsis as a model organism for plant evolutionary ecology.     

The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies

Background

Urothelial bladder cancer is a highly heterogeneous disease. Cancer cell lines are useful tools for its study. This is a comprehensive genomic characterization of 40 urothelial bladder carcinoma (UBC) cell lines including information on origin, mutation status of genes implicated in bladder cancer (FGFR3, PIK3CA, TP53, and RAS), copy number alterations assessed using high density SNP arrays, uniparental disomy (UPD) events, and gene expression.

Results

Based on gene mutation patterns and genomic changes we identify lines representative of the FGFR3-driven tumor pathway and of the TP53/RB tumor suppressor-driven pathway. High-density array copy number analysis identified significant focal gains (1q32, 5p13.1-12, 7q11, and 7q33) and losses (i.e. 6p22.1) in regions altered in tumors but not previously described as affected in bladder cell lines. We also identify new evidence for frequent regions of UPD, often coinciding with regions reported to be lost in tumors. Previously undescribed chromosome X losses found in UBC lines also point to potential tumor suppressor genes. Cell lines representative of the FGFR3-driven pathway showed a lower number of UPD events.

Conclusions

Overall, there is a predominance of more aggressive tumor subtypes among the cell lines. We provide a cell line classification that establishes their relatedness to the major molecularly-defined bladder tumor subtypes. The compiled information should serve as a useful reference to the bladder cancer research community and should help to select cell lines appropriate for the functional analysis of bladder cancer genes, for example those being identified through massive parallel sequencing.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1450-3) contains supplementary material, which is available to authorized users.     

水稻产量相关QTL研究现状

产量是最为复杂的数量性状,对它的遗传机理了解甚微。近15年来,许多学者利用随机分离群体定位了许多影响水稻产量及其组分的QTL,即以QTL定位的方法对产量潜力进行遗传剖析。试验证明上位性效应对产量及其组分性状遗传变异起着重要作用,但目前大多数QTL研究仍侧重于发掘和克隆单个主效QTL,然而对单一基因／QTL的深入了解还不足以诠释复杂性状遗传基础的全貌,还没有为育种家提供足够的可应用于分子标记辅助育种的遗传信息并用于提高水稻产量。笔者认为今后的数量性状研究尚需加强复杂性状QTL遗传网络的发掘,在改良水稻品种性状的同时发展并完善QTL研究。     

Genetics of drought adaptation in Arabidopsis thaliana: I. Pleiotropy contributes to genetic correlations among ecological traits

We examined patterns of genetic variance and covariance in two traits (i) carbon stable isotope ratio delta13C (dehydration avoidance) and (ii) time to flowering (drought escape), both of which are putative adaptations to local water availability. Greenhouse screening of 39 genotypes of Arabidopsis thaliana native to habitats spanning a wide range of climatic conditions, revealed a highly significant positive genetic correlation between delta13C and flowering time. Studies in a range of C3 annuals have also reported large positive correlations, suggesting the presence of a genetically based trade-off between mechanisms of dehydration avoidance (delta13C) and drought escape (early flowering). We examined the contribution of pleiotropy by using a combination of mutant and near-isogenic lines to test for positive mutational covariance between delta13C and flowering time. Ecophysiological mutants generally showed variation in delta13C but not flowering time. However, flowering time mutants generally demonstrated pleiotropic effects consistent with natural variation. Mutations that caused later flowering also typically resulted in less negative delta13C and thus probably higher water use efficiency. We found strong evidence for pleiotropy using near-isogenic lines of Frigida and Flowering locus C, cloned loci known to be responsible for natural variation in flowering time. These data suggest the correlated evolution of delta13C and flowering time is explained in part by the fixation of pleiotropic alleles that alter both delta13C and time to flowering.     

基于染色体片段置换系的野生稻粒宽QTL qGW8的精细定位与遗传分析

利用以栽培稻9311为受体、普通野生稻为供体的染色体单片段置换系CSSL182,检测到一个与粒宽相关的QTL。CSSL182与受体亲本9311粒型性状差异显著,且只在8号染色体有一个野生稻导入片段。构建CSSL182/9311的F2次级分离群体,将粒宽QTL初定位在8号染色体的标记RM447和RM264之间,贡献率达22.49,将该QTL命名为qGW8。随后进一步设计区间内多态性分子标记引物,检测F2群体的2000株分离个体以及F2：3群体交换单株,结合后代表型验证,最终将qGW8精细定位到8号染色体10kb区间内。该区间内含有3个候选基因,基因测序发现这3个基因在双亲之间均含有丰富的变异。对双亲籽粒颖壳细胞电镜扫描观察发现,CSSL182的颖壳细胞宽度比9311减少16.7%。这一结果表明qGW8中来自野生稻的等位基因通过改变颖壳细胞形状影响粒型。     

New tools for the high throughput characterization of rat genomic DNA samples

Linkage studies and positional cloning projects for the identification of disease related genes require the genetic characterization of large numbers of genomic DNA samples. The application of spotting robots enables the production of high density filters representing several thousand DNA probes. To take full advantage of the potential of these filters we have established a new, hybridization based Interspersed Repetitive Sequence (IRS-)marker system for the rat genome. This marker panel was shown to be useful for rapid genotyping of many multigenic crosses as well as high throughput characterization of large insert genomic libraries.     

Natural variation involving deletion alleles of FRIGIDA modulate temperature‐sensitive flowering responses in Arabidopsis thaliana

Ambient temperature is one of the major environmental factors that modulate plant growth and development. There is extensive natural genetic variation in thermal responses of plants exemplified by the variation exhibited by the accessions of Arabidopsis thaliana. In this work we have studied the enhanced temperature response in hypocotyl elongation and flowering shown by the Tsu‐0 accession in long days. Genetic mapping in the Col‐0 × Tsu‐0 recombinant inbred line (RIL) population identified several QTLs for thermal response including three major effect loci encompassing candidate genes FRIGIDA (FRI), FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT). We confirm and validate these QTLs. We show that the Tsu‐0 FRI allele, which is the same as FRI‐Ler is associated with late flowering but only at lower temperatures in long days. Using transgenic lines and accessions, we show that the FRI‐Ler allele confers temperature‐sensitive late flowering confirming a role for FRI in photoperiod‐dependent thermal response. Through quantitative complementation with heterogeneous inbred families, we further show that cis‐regulatory variation at FT contributes to the observed hypersensitivity of Tsu‐0 to ambient temperature. Overall our results suggest that multiple loci that interact epistatically govern photoperiod‐dependent thermal responses of A. thaliana.     

一个基于熵的精细定位数量性状位点的指数

针对数量性状位点的精细定位,本文采用群体的极端样本,利用稠密的标记位点,通过比较标记的熵和条件熵,给出了一个基于熵的指数。该指数是标记基因和性状位点间连锁不平衡系数的函数,它不依赖于标记基因的频率。该指数对应我们之前提出的数量性状位点精细定位的哈迪-温伯格不平衡(HWD)指数,但在精细定位数量性状位点时,本文提出的指数的效能要高于哈迪-温伯格不平衡(HWD)指数。通过计算机模拟,文章调查了不同遗传参数下该指数的性质。模拟结果表明该指数用作精细定位是有效的。     

AtMap1: a DNA microarray for genomic deletion mapping in Arabidopsis thaliana

We have designed a novel tiling array, AtMap1, for genomic deletion mapping. AtMap1 is a 60-mer oligonucleotide microarray consisting of 42 497 data probes designed from the genomic sequence of Arabidopsis thaliana Col-0. The average probe interval is 2.8 kb. The performance of the AtMap1 array was assessed using the deletion mutants mag2-2, rot3-1 and zig-2. Eight of the probes showed threefold lower signals in mag2-2 than Col-0. Seven of these probes were located in one region on chromosome 3. We considered these adjacent probes to represent one deletion. This deletion was consistent with a reported deleted region. The other probe was located near the end of chromosome 4. A newly identified deletion around the probe was confirmed by PCR. We also detected the responsible deletions for rot3-1 and zig-2. Thus we concluded that the AtMap1 array was sufficiently sensitive to identify a deletion without any a priori knowledge of the deletion. An analysis of the result of hybridization of Ler and previously reported polymorphism data revealed that the signal decrease tended to depend on the overlap size of sequence polymorphisms. Mutation mapping is time-consuming, laborious and costly. The AtMap1 array removes these limitations.     

Dipylidium caninum draft genome - a new resource for comparative genomic and genetic explorations of flatworms

Here, we present a draft genome of the tapeworm Dipylidium caninum (family Dipylidiidae) and compare it with other cestode genomes. This draft genome of D. caninum is 110 Mb in size, has a repeat content of ~13.4% and is predicted to encode ~10,000 protein-coding genes. We inferred excretory/secretory molecules (representing the secretome), other key groups of proteins (including peptidases, kinases, phosphatases, GTPases, receptors, transporters and ion-channels) and predicted potential intervention targets for future evaluation. Using 144 shared single-copy orthologous sequences, we investigated the genetic relationships of cestodes for which nuclear genomes are available. This study provides first insights into the molecular biology of D. caninum and a new resource for comparative genomic and genetic explorations of this and other flatworms.     

High‐precision genetic mapping of behavioral traits in the diversity outbred mouse population

Historically our ability to identify genetic variants underlying complex behavioral traits in mice has been limited by low mapping resolution of conventional mouse crosses. The newly developed Diversity Outbred (DO) population promises to deliver improved resolution that will circumvent costly fine‐mapping studies. The DO is derived from the same founder strains as the Collaborative Cross (CC), including three wild‐derived strains. Thus the DO provides more allelic diversity and greater potential for discovery compared to crosses involving standard mouse strains. We have characterized 283 male and female DO mice using open‐field, light–dark box, tail‐suspension and visual‐cliff avoidance tests to generate 38 behavioral measures. We identified several quantitative trait loci (QTL) for these traits with support intervals ranging from 1 to 3 Mb in size. These intervals contain relatively few genes (ranging from 5 to 96). For a majority of QTL, using the founder allelic effects together with whole genome sequence data, we could further narrow the positional candidates. Several QTL replicate previously published loci. Novel loci were also identified for anxiety‐ and activity‐related traits. Half of the QTLs are associated with wild‐derived alleles, confirming the value to behavioral genetics of added genetic diversity in the DO. In the presence of wild‐alleles we sometimes observe behaviors that are qualitatively different from the expected response. Our results demonstrate that high‐precision mapping of behavioral traits can be achieved with moderate numbers of DO animals, representing a significant advance in our ability to leverage the mouse as a tool for behavioral genetics .     

Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis

High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1–8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species.     

ASSIMILATOR: a new tool to inform selection of associated genetic variants for functional studies

MOTIVATION: Fine-mapping experiments from genome-wide association studies (GWAS) are underway for many complex diseases. These are likely to identify a number of putative causal variants, which cannot be separated further in terms of strength of genetic association due to linkage disequilibrium. The challenge will be selecting which variant to prioritize for subsequent expensive functional studies. A wealth of functional information generated from wet lab experiments now exists but cannot be easily interrogated by the user. Here, we describe a program designed to quickly assimilate this data called ASSIMILATOR and validate the method by interrogating two regions to show its effectiveness. AVAILABILITY: http://www.medicine.manchester.ac.uk/musculoskeletal/research/arc/genetics/bioinformatics/assimilator/.     

Standing genetic variation in FRIGIDA mediates experimental evolution of flowering time in Arabidopsis

The role of standing genetic variation in adaptive evolution remains unclear. Although there has been much progress in identifying candidate genes that underlie adaptive traits, we still lack direct evidence that natural allelic variation in these genes can actually mediate adaptive evolution. In this study, we investigate the role of natural allelic variation in two candidate flowering time genes, in response to selection for early flowering in Arabidopsis thaliana : FRIGIDA ( FRI ) and FLOWERING LOCUS C ( FLC ). We performed artificial selection for early flowering under 'spring-' and 'winter-annual' growth conditions using an outbred population of A. thaliana produced by intermating 19 natural accessions. FRI and FLC are involved in A. thaliana 's response to winter conditions, and nonfunctional and weak alleles at these loci are know to reduce flowering time, particularly under spring-annual conditions. Our results provide direct evidence that natural allelic variation in FRI can provide rapid and predictable adaptive evolution in flowering time under spring-annual conditions. We observed a strong response to selection, in terms of reducing flowering time, in both growth conditions (~2 standard deviation reduction). Concomitantly, the frequency of functional FRI alleles under spring-annual conditions was reduced by 68%, in agreement with predicted changes. No significant changes in allele frequencies were observed in FRI in the winter-annual growth condition or in FLC for either growth conditions. These results indicate that changes in flowering time are mediated by different genetic factors under spring- and winter-annual growth conditions, and that other loci must also be contributing to the response to selection.     

CAUT lines: a novel resource for studies of cell autonomy in Arabidopsis

Plant development is critically dependent on the interactions between clonally unrelated cell layers. The cross-talk between layers can be addressed by studies of cell autonomy. Cell autonomy is a property of genetic mosaics composed of cells of differing genotypes. Broadly, if the phenotype of a mutant tissue reflects only its genotype and is unaffected by the presence of wild-type tissue, the trait is cell-autonomous. Conversely, if the phenotype of a mutant tissue reflects that of wild-type tissue in the mosaic, the trait is non-autonomous. Here we report a novel, versatile and robust method for studies of cell autonomy in Arabidopsis. Cell autonomy (CAUT) lines consist of a collection of homozygous stocks, each containing one of 76 mapped T-DNA inserts, each of which corrects the yellow ch-42 mutant to green ( CH-42 ) by complementation. This has the effect of translocating the colour marker to 76 new locations around the genome. X-irradiation of heterozygous CAUT line seeds results in yellow sectors, with loss of the CH-42 transgene and adjacent wild-type genes. This property can be used to remove the wild-type copy of developmental genes in appropriate heterozygotes, resulting in yellow ( ch-42 ) sectors that are hemizygous for the trait of interest. Such sectors can provide insight into cell autonomy. Experiments using the ap1 , ap3 , ag and clv1 mutants show that CAUT lines are useful in the study of cell autonomy.     

Molecular markers: a potential resource for ginger genetic diversity studies

Ginger is an economically important and valuable plant around the world. Ginger is used as a food, spice, condiment, medicine and ornament. There is available information on biochemical aspects of ginger, but few studies have been reported on its molecular aspects. The main objective of this review is to accumulate the available molecular marker information and its application in diverse ginger studies. This review article was prepared by combing material from published articles and our own research. Molecular markers allow the identification and characterization of plant genotypes through direct access to hereditary material. In crop species, molecular markers are applied in different aspects and are useful in breeding programs. In ginger, molecular markers are commonly used to identify genetic variation and classify the relatedness among varieties, accessions, and species. Consequently, it provides important input in determining resourceful management strategies for ginger improvement programs. Alternatively, a molecular marker could function as a harmonizing tool for documenting species. This review highlights the application of molecular markers (isozyme, RAPD, AFLP, SSR, ISSR and others such as RFLP, SCAR, NBS and SNP) in genetic diversity studies of ginger species. Some insights on the advantages of the markers are discussed. The detection of genetic variation among promising cultivars of ginger has significance for ginger improvement programs. This update of recent literature will help researchers and students select the appropriate molecular markers for ginger-related research.     

Power studies in the estimation of genetic parameters and the localization of quantitative trait loci for backcross and doubled haploid populations

A statistical model for doubled haploids and backcrosses based on the interval-mapping methodology has been used to carry out power studies to investigate the effects of different experimental designs, heritabilities of the quantitative trait, and types of gene action, using two test statistics, the F of Fisher-Snedecor and the LOD score. The doubled haploid experimental design is more powerful than backcrosses while keeping actual type I errors similar to nominal ones. For the doubled haploid design, individual QTLs, showing heritabilities as low as 5% were detected in about 90% of the cases using only 250 individuals. The power to detect a given QTL is related to its contribution to the heritability of the trait. For a given nominal type I error, tests using F values are more powerful than with LOD scores. It seems that more conservative levels should be used for the LOD score in order to increase the power and obtain type I errors similar to nominal ones.