Activation tagging in plants: a tool for gene discovery

A significant limitation of classical loss-of-function screens designed to dissect genetic pathways is that they rarely uncover genes that function redundantly, are compensated by alternative metabolic or regulatory circuits, or which have an additional role in early embryo or gametophyte development. Activation T-DNA tagging is one approach that has emerged in plants to help circumvent these potential problems. This technique utilises a T-DNA sequence that contains four tandem copies of the cauliflower mosaic virus (CaMV) 35S enhancer sequence. This element enhances the expression of neighbouring genes either side of the randomly integrated T-DNA tag, resulting in gain-of-function phenotypes. Activation tagging has identified a number of genes fundamental to plant development, metabolism and disease resistance in Arabidopsis. This review provides selected examples of these discoveries to highlight the utility of this technology. The recent development of activation tagging strategies for other model plant systems and the construction of new more sophisticated vectors for the generation of conditional alleles are also discussed. These recent advances have significantly expanded the horizons for gain-of-function genetics in plants.     

Comparative studies on the feeding selectivity of silver carp Hypophthalmichthys molitrix and bighead carp Aristichthys nobilis

Silver carp and bighead carp exhibited size-selection for food particles in aquarium experiments, but did not select their preferred species of plankton actively when they were distributed evenly in the water. They also possessed the capacity of selection for feeding area. The removal rates (% g⁻¹ fish weight) of silver carp for smaller plankton (phytoplankton) were higher than those of bighead carp. The removal rates by the latter for bigger plankton (zooplankton) were higher than those of silver carp, but for plankton about 70 μm dia. the rates by the two species were almost equal.     

Genetic architecture of purple pigmentation and tagging of some loci to SSR markers in pearl millet, Pennisetum glaucum (L.) R. Br

This report describes the construction of integrated genetic maps in pearl millet involving certain purple phenotype and simple sequence repeat (SSR) markers. These maps provide a direct means of implementing DNA marker-assisted selection and of facilitating "map-based cloning" for engineering novel traits. The purple pigmentation of leaf sheath, midrib and leaf margin was inherited together 'en bloc' under the control of a single dominant locus (the 'midrib complex') and was inseparably associated with the locus governing the purple coloration of the internode. The purple panicle was caused by a single dominant locus. Each of the three characters (purple lamina, purple stigma and purple seed) was governed by two complementary loci. One of the two loci governing purple seed was associated with the SSR locus Xpsmp2090 in linkage group 1, with a linkage value of 22 cM, while the other locus was associated with the SSR locus Xpsmp2270 in linkage group 6, with a linkage value of 23 cM. The locus for purple pigmentation of the midrib complex was either responsible for pigmentation of the panicle in a pleiotropic manner or was linked to it very closely and associated with the SSR locus Xpsmp2086 in linkage group 4, with a suggestive linkage value of 21 cM. A dominant allele at this locus seems to be a prerequisite for the development of purple pigmentation in the lamina, stigma and seed. These findings suggest that the locus for pigmentation of the midrib complex might regulate the basic steps in anthocyanin pigment development by acting as a structural gene while other loci regulate the formation of color in specific plant parts.     

Preliminary studies on the genetic variability of six Hungarian common carp strains using microsatellite DNA markers

Genetic variation in six Hungarian common carp (Cyprinus carpio L.) strains was evaluated using 12 microsatellite loci. The domesticated (Tatai, Biharugrai and Szarvasi) strains were derived from fish farms. Two of wild strains (Tiszai and Dunai) were sampled from brood stocks maintained at fish farms for breeding, and Kis-Balatoni wild carp were sampled from the Small Balaton Lake. Pairwise Fst-values (0.013–0.161) were highly significant (p<0.0001), demonstrating differentiation among strains. The mean number of alleles ranged between 3.9 and 8.2. Overall mean observed heterozygosity was lower (0.557) than the mean expected heterozygosity (0.700). By strain, the only exception to this trend was the Dunai (Danubian), which showed higher mean observed heterozygosity (0.764) than expected (0.602). For five loci the Dunai strain showed extremely high levels of heterozygosity (1.00). Two wild strains exhibited a number of loci (Tiszai, 4; Dunai, 6) that were not in Hardy–Weinberg equilibrium. A relatively high number of private alleles overall (n=26), as well as differences in allele frequencies supported our ability to assign most individual fish (over 90%) to each strain.     

Modules for C-terminal epitope tagging of Tetrahymena genes

Although epitope tagging has been widely used for analyzing protein function in many organisms, there are few genetic tools for epitope tagging in Tetrahymena. In this study, we describe several C-terminal epitope tagging modules that can be used to express tagged proteins in Tetrahymena cells by both plasmid- and PCR-based strategies.     

The estimation of natural mortality in Irish Sea plaice, Pleuronectes platessa L., using tagging methods

This paper addresses the question as to whether natural mortality ( M ) can be estimated reliably in a heavily exploited fish population. Several methods, including a new opitimization technique based on Pope's cohort model, were used to estimate M from a large series of tagging experiments carried out on the Irish Sea plaice off North Wales and Ireland during the early 1960s, and off North Wales during 1979 and 1980. The assumptions underlying the new method were: (i) that the product of initial survival after tagging and the reporting rate of recaptures ( SB ) was constant for all experiments, and (ii) that the number of recoveries were log-normally distributed. Simulations showed that the estimator was robust to errors in input data. The SB values were low (0.37) but were more precise than the estimates of natural mortality for both sexes. The annual M values were 0.17 and 0.11 with standard errors 0.06 and 0.08 for males and females, respectively. The estimate of M for mature males was low, indicating a low M for older fish. The less precise estimate of M for females because of the inadequate dataset, and the higher M values obtained by applying traditional methods to the same dataset, indicated that a value of 0.2 is more appropriate for both sexes. Suggestions are made for designing and analysing tagging experiments to estimate M .     

Biochemical genetic comparison of the Chinese and European races of the common carp

An electrophoretic survey of the common carp revealed 33 loci. Nine were found to be polymorphic including two phosphoglucose isomerase loci, a phosphoglucomutase locus, three esterase loci, a lactate dehydrogenase locus, a malate dehydrogenase locus, and transferrin. Five of these polymorphic loci are reported for the first time, the two phosphoglucose isomerase loci, a phosphoglucomutase locus and two of the three esterase loci. Differences in allele frequencies between the European and Chinese races were found at most loci.     

Evaluation of VIE and PIT tagging methods for juvenile cyprinid fishes

Retention and mortality associated with visible implant elastomer (VIE) and passive integrated transponder (PIT) tagged juvenile chub [ Leuciscus cephalus (L.)], dace [ Leuciscus leuciscus (L.)] and roach [ Rutilus rutilus (L.)] were evaluated. PIT tag retention (96.6–100%) was higher than VIE over the 6-month duration of the experiment. VIE retention was significantly better in the head (96.3–98.8%) than in the fins (78.8–90.9%) the first month after tagging, but the opposite was found after 6 months (head = 21.5–57.5%; fins = 77.2–88.8%). Survival was not significantly different from controls for any treatment, except dace tagged with 23-mm PIT (significantly influenced by mass of fish at tagging) and sham PIT tagged dace, because of initial losses. PIT tags are recommended as the most suitable method for tagging individual juvenile chub, dace and roach based on high retention and survival. VIE implantation in the head (studies < 30 days) and fins (studies > 30 days) could provide a cheap, batch-marking alternative, provided retention rates are monitored.     

Social stress decreases marking behavior independently of testosterone in Mongolian gerbils

This study examined the endogenous androgen regulation of the marking behavior in Mongolian gerbils (Meriones unguiculatus). In the first experiment, developmental changes of fecal testosterone levels, ventral gland growth, and the marking frequency of male gerbils were investigated. From 9 weeks of age, marking frequency increased with increases in fecal testosterone levels and ventral gland size. The ventral gland size and marking frequency were significantly correlated to the fecal testosterone level. In the second experiment, we hypothesized that reduction in the marking frequency of subordinate males after social confrontations was controlled by a decrease in the circulating testosterone level, and we followed changes in marking frequency, endocrine status, and ventral gland size after social confrontations in which two adult male gerbils established their social ranks by fighting. As expected, marking frequency and ventral gland size were significantly related to social rank, that is, marking frequency was higher among dominant gerbils and lower among subordinates. In addition, fecal corticosterone levels among subordinates were higher than those of dominant animals. However, neither the fecal and plasma testosterone levels, nor testis size, differed between dominant and subordinate gerbils. These results revealed that endogenous androgen played a role in regulating marking behavior and ventral gland size during the developmental stage and that the reductions in marking frequency and ventral gland size occurring in subordinate males after social confrontations were not directly regulated by androgen changes.     

Development of silver carp (Hypophthalmichthys molitrix) and bighead carp (Aristichthys nobilis) genetic maps using microsatellite and AFLP markers and a pseudo-testcross strategy

Silver carp (Hypophthalmichthys molitrix) and bighead carp (Aristichthys nobilis) are two of the four most important pond-cultured fish species inhabiting the major river basins of China. In the present study, genetic maps of silver carp and bighead carp were constructed using microsatellite and AFLP markers and a two-way pseudo-testcross strategy. To create the maps, 60 individuals were obtained from a cross of a single bighead carp (female) and a single silver carp (male). The silver carp map consisted of 271 markers (48 microsatellites and 223 AFLPs) that were assembled into 27 linkage groups, of which 22 contained at least four markers. The total length of the silver carp map was 952.2 cM, covering 82.8% of the estimated genome size. The bighead carp map consisted of 153 markers (27 microsatellites and 126 AFLPs) which were organized into 30 linkage groups, of which 19 contained at least four markers. The total length of the bighead carp map was 852.0 cM, covering 70.5% of the estimated genome size. Eighteen microsatellite markers were common to both maps. These maps will contribute to discovery of genes and genetic regions controlling traits in the two species of carp.     

Reproductive condition and occurrence of intersex in bighead carp and silver carp in the Missouri River

Little is known about the reproductive biology of the exotic bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix in the Missouri River. In order to fill this gap in understanding, herein is described the reproductive condition of these Asian carps. Evidence is presented which indicates that bighead and silver carp in the Missouri River have a protracted spawning period that extends from early spring through fall and some individual bighead and silver carp are spawning multiple times during a reproductive season. Although bighead and silver carps are successfully maturing and spawning in the Missouri River some reproductive abnormalities such as intersex, atresia, and sterility were observed. Knowledge of the reproductive activity of these invasive carps may be useful to resource managers tasked with their control. Furthermore, the reproductive abnormalities observed should be considered when evaluating the environmental condition of the Missouri River relative to supporting a healthy fish fauna.     

Construction of a genetic linkage map for silver carp (Hypophthalmichthys molitrix)

For silver carp (Hypophthalmichthys molitrix), a combined microsatellite (or simple sequence repeat) and amplified fragment length polymorphism (AFLP) sex average linkage map was constructed. A total of 483 markers (245 microsatellites and 238 AFLPs) were assigned to 33 linkage groups. The map spanned 1352.2 cM, covering 86.4% of the estimated genome size of silver carp. The maximum and average spaces between 420 loci were 21.5 cM and 3.2 cM, respectively. The length of linkage groups ranged from 3.6 cM to 98.5 cM with an average of 41.0 cM. The number of markers per group varied from 2 to 44 with an average of 14.6. The AFLP markers significantly improved the integrity of microsatellite-based linkage groups and increased the genome coverage and marker evenness. A genome-wide recombination suppression was observed in male. In an extreme case, six microsatellites co-segregated in male, but spanned a 45.1 cM region in female.     

草鱼、鲢和瓦氏黄颡鱼幼鱼感应流速的比较

在21±1℃水温下,使用自行制作的鱼类游泳行为测试槽,采用流速递增的方法测定了草鱼(Ctenopharyngodon idellus)(体长9.64±3.12 cm,体重20.97±16.71 g)、鲢(Hypophthalmichthys molitrix)(体长10.60±3.45 cm,体重24.37±18.61 g)和瓦氏黄颡鱼(Pelteobagrus vachelli)(体长11.54±1.46 cm,体重20.98±6.94 g)幼鱼个体的感应流速.结果表明:草鱼、鲢和瓦氏黄颡鱼幼鱼的感应流速分别是(8.21±0.68)、(6.74±0.84)和(33.11±3.06) cm·s-1,相对感应流速分别是(0.91±0.22)、(0.67±0.15)和(2.9±0.29) BL·s-1;鲢和草鱼幼鱼的感应流速差异不显著(P＞0.05),但瓦氏黄颡鱼比草鱼和鲢幼鱼感应流速大近4倍,差异显著(P＜0.05);因此,草鱼和鲢幼鱼较瓦氏黄颡鱼幼鱼对流速的感应更敏感.本实验结果可为设计鱼道、确定拖网速度等提供一定的科学指导.     

A comparison of four methods for detecting weak genetic structure from marker data

Genetic structure is ubiquitous in wild populations and is the result of the processes of natural selection, genetic drift, mutation, and gene flow. Genetic drift and divergent selection promotes the generation of genetic structure, while gene flow homogenizes the subpopulations. The ability to detect genetic structure from marker data diminishes rapidly with a decreasing level of differentiation among subpopulations. Weak genetic structure may be unimportant over evolutionary time scales but could have important implications in ecology and conservation biology. In this paper we examine methods for detecting and quantifying weak genetic structures using simulated data. We simulated populations consisting of two putative subpopulations evolving for up to 50 generations with varying degrees of gene flow (migration), and varying amounts of information (allelic diversity). There are a number of techniques available to detect and quantify genetic structure but here we concentrate on four methods: F(ST), population assignment, relatedness, and sibship assignment. Under the simple mating system simulated here, the four methods produce qualitatively similar results. However, the assignment method performed relatively poorly when genetic structure was weak and we therefore caution against using this method when the analytical aim is to detect fine-scale patterns. Further work should examine situations with different mating systems, for example where a few individuals dominate reproductive output of the population. This study will help workers to design their experiments (e.g., sample sizes of markers and individuals), and to decide which methods are likely to be most appropriate for their particular data.     

Some notes on the combinatorial properties of haplotype tagging

Tagging haplotypes with a small number of genetic markers is becoming an increasingly interesting and important problem. Surprisingly little work has been done to characterize the mathematical framework of this problem. In this paper we present a mathematical frame, based on Boolean algebras, that adequately describe the structure of a set of genetic bi-allelic markers and the corresponding set of haplotypes. We derive a number of results that relate the number of markers required to tag a set of haplotypes to the set of markers themselves.     

Mini-transposon Tn5gfp constructs for differential tagging of microorganisms

Recently thegfp (green fluorescent protein) gene from the jellyfishAequoria victoria has been widely used as a reporter gene. In this study mini-transposons, named as mini-Tn5gfp, were constructed by subcloning thegfp gene into a transposon Tn5. To improve the expression level of thegfp gene, tandom array ofgfp gene was obtained. The constructs were successfully used in tagging target microorganisms by transposition. The level of GFP expression was found to be closely correlated with the copy number of the gfp transposed. These constructs will facillitate not only efficient tagging of whole organism but also genetic marking of target genes by transposition.     

Choosing appropriate genetic markers and analytical methods for testing landscape genetic hypotheses

Landscape genetics and phylogeography both examine population‐level microevolutionary processes, such as population structure and gene flow, in the context of environmental and geographic variation. They differ in terms of the spatial and temporal scales they typically investigate, meaning that different genetic markers and analytical methods are better suited for testing the different hypotheses typically posed by each discipline. In a recent comment, Bohonak & Vandergast (2011) argue that I overlooked the value of mtDNA for landscape genetics in an article I published last year in Molecular Ecology (Wang 2010) and that a gap between landscape genetics and phylogeography, which I outlined, does not exist. Here, I clarify several points in my original article and summarize the commonly held viewpoint that different genetic markers are appropriate for drawing inferences at different temporal scales.     

Amine-reactive isobaric tagging reagents: requirements for absolute quantification of proteins and peptides

Amine-reactive isobaric tagging reagents such as iTRAQ (isobaric tags for relative and absolute quantitation) have recently become increasing popular for relative protein quantification, cell expression profiling, and biomarker discovery. This is due mainly to the possibility of simultaneously identifying and quantifying multiple samples. The principles of iTRAQ may also be applied to absolute protein quantification with the use of synthetic peptides as standards. The prerequisites that must be fulfilled to perform absolute quantification of proteins by iTRAQ have been investigated and are described here. Three samples of somatropin were quantified using iTRAQ and synthetic peptides as standards, corresponding to a portion of the protein sequence. The results were compared with those obtained by quantification of the same protein solutions using double exact matching isotope dilution mass spectrometry (IDMS). To obtain reliable results, the appropriate standard peptides needed to be selected carefully and enzymatic digestion needed to be optimized to ensure complete release of the peptides from the protein. The kinetics and efficiency of the iTRAQ derivatization reaction of the standard peptides and digested proteins with isobaric tagging reagents were studied using a mixture of seven synthetic peptides and their corresponding labeled peptides. The implications of incomplete derivatization are also presented.     

Dispersal in a stream dwelling salmonid: Inferences from tagging and microsatellite studies

We used both direct (mark-recapture) andindirect (microsatellite analysis)methodologies to investigate dispersal betweentwo putative populations of brook charr (Salvelinus fontinalis) in Freshwater River,Cape Race, Newfoundland, Canada. Over a 5-yearstudy period, mark-recapture data revealed somemovement by fish, but the proportion ofrecaptured fish migrating from one populationarea to another was low (0–4.1%).Additionally, during sampling periods in thespawning seasons, no fish was found in thealternate population area to that of its firstcapture. Despite this pattern of limitedmovement, microsatellite analysis based onsixteen polymorphic loci provided no evidenceof genetic differentiation. Indirect estimatesof dispersal parameters varied greatly betweendifferent methods of analysis. While use of acoalescent-based model yielded estimatedmigration rates congruent with the results ofthe mark-recapture study, other methodsresulted in much higher estimates of migrationbetween the populations. In particular, thelack of genetic differentiation coupled withlikely violations of the assumed island modelprevented generation of meaningful estimates ofdispersal using F_st. The disparitiesbetween migration rates estimated from themark-recapture work and from the differentindirect methods highlight the difficulties ofusing indirect methods to estimate dispersal onan ecological timescale. However,mark-recapture methods can fail to detecthistorical or episodic movement that isimportant in an evolutionary context, and wetherefore argue that a combination of directand indirect methods can provide a morecomplete picture of dispersal than eitherapproach alone.