Light sheet microscopy with acoustic sample confinement

Contactless sample confinement would enable a whole host of new studies in developmental biology and neuroscience, in particular, when combined with long-term, wide-field optical imaging. To achieve this goal, we demonstrate a contactless acoustic gradient force trap for sample confinement in light sheet microscopy. Our approach allows the integration of real-time environmentally controlled experiments with wide-field low photo-toxic imaging, which we demonstrate on a variety of marine animal embryos and larvae. To illustrate the key advantages of our approach, we provide quantitative data for the dynamic response of the heartbeat of zebrafish larvae to verapamil and norepinephrine, which are known to affect cardiovascular function. Optical flow analysis allows us to explore the cardiac cycle of the zebrafish and determine the changes in contractile volume within the heart. Overcoming the restrictions of sample immobilisation and mounting can open up a broad range of studies, with real-time drug-based assays and biomechanical analyses

Mapping of quantitative trait loci for flesh colour and growth traits in Atlantic salmon (Salmo salar)

<p>Abstract</p> <p>Background</p> <p>Flesh colour and growth related traits in salmonids are both commercially important and of great interest from a physiological and evolutionary perspective. The aim of this study was to identify quantitative trait loci (QTL) affecting flesh colour and growth related traits in an F2 population derived from an isolated, landlocked wild population in Norway (Byglands Bleke) and a commercial production population.</p> <p>Methods</p> <p>One hundred and twenty-eight informative microsatellite loci distributed across all 29 linkage groups in Atlantic salmon were genotyped in individuals from four F2 families that were selected from the ends of the flesh colour distribution. Genotyping of 23 additional loci and two additional families was performed on a number of linkage groups harbouring putative QTL. QTL analysis was performed using a line-cross model assuming fixation of alternate QTL alleles and a half-sib model with no assumptions about the number and frequency of QTL alleles in the founder populations.</p> <p>Results</p> <p>A moderate to strong phenotypic correlation was found between colour, length and weight traits. In total, 13 genome-wide significant QTL were detected for all traits using the line-cross model, including three genome-wide significant QTL for flesh colour (Chr 6, Chr 26 and Chr 4). In addition, 32 suggestive QTL were detected (chromosome-wide P < 0.05). Using the half-sib model, six genome-wide significant QTL were detected for all traits, including two for flesh colour (Chr 26 and Chr 4) and 41 suggestive QTL were detected (chromosome-wide P < 0.05). Based on the half-sib analysis, these two genome-wide significant QTL for flesh colour explained 24% of the phenotypic variance for this trait.</p> <p>Conclusions</p> <p>A large number of significant and suggestive QTL for flesh colour and growth traits were found in an F2 population of Atlantic salmon. Chr 26 and Chr 4 presented the strongest evidence for significant QTL affecting flesh colour, while Chr 10, Chr 5, and Chr 4 presented the strongest evidence for significant QTL affecting growth traits (length and weight). These QTL could be strong candidates for use in marker-assisted selection and provide a starting point for further characterisation of the genetic components underlying flesh colour and growth.</p

Genetic Networks Controlling Structural Outcome of Glucosinolate Activation across Development

Most phenotypic variation present in natural populations is under polygenic control, largely determined by genetic variation at quantitative trait loci (QTLs). These genetic loci frequently interact with the environment, development, and each other, yet the importance of these interactions on the underlying genetic architecture of quantitative traits is not well characterized. To better study how epistasis and development may influence quantitative traits, we studied genetic variation in Arabidopsis glucosinolate activation using the moderately sized Bayreuth×Shahdara recombinant inbred population, in terms of number of lines. We identified QTLs for glucosinolate activation at three different developmental stages. Numerous QTLs showed developmental dependency, as well as a large epistatic network, centered on the previously cloned large-effect glucosinolate activation QTL, ESP. Analysis of Heterogeneous Inbred Families validated seven loci and all of the QTL×DPG (days post-germination) interactions tested, but was complicated by the extensive epistasis. A comparison of transcript accumulation data within 211 of these RILs showed an extensive overlap of gene expression QTLs for structural specifiers and their homologs with the identified glucosinolate activation loci. Finally, we were able to show that two of the QTLs are the result of whole-genome duplications of a glucosinolate activation gene cluster. These data reveal complex age-dependent regulation of structural outcomes and suggest that transcriptional regulation is associated with a significant portion of the underlying ontogenic variation and epistatic interactions in glucosinolate activation

Comparative mapping reveals quantitative trait loci that affect spawning time in coho salmon (Oncorhynchus kisutch)

Spawning time in salmonids is a sex-limited quantitative trait that can be modified by selection. In rainbow trout (Oncorhynchus mykiss), various quantitative trait loci (QTL) that affect the expression of this trait have been discovered. In this study, we describe four microsatellite loci associated with two possible spawning time QTL regions in coho salmon (Oncorhynchus kisutch). The four loci were identified in females from two populations (early and late spawners) produced by divergent selection from the same base population. Three of the loci (OmyFGT34TUF, One2ASC and One19ASC) that were strongly associated with spawning time in coho salmon (p < 0.0002) were previously associated with QTL for the same trait in rainbow trout; a fourth loci (Oki10) with a suggestive association (p = 0.00035) mapped 10 cM from locus OmyFGT34TUF in rainbow trout. The changes in allelic frequency observed after three generations of selection were greater than expected because of genetic drift. This work shows that comparing information from closely-related species is a valid strategy for identifying QTLs for marker-assisted selection in species whose genomes are poorly characterized or lack a saturated genetic map

An assessment of the spatial scale of local adaptation in brown trout (Salmo trutta L.): footprints of selection at microsatellite DNA loci

Local adaptation is considered a paradigm in studies of salmonid fish populations. Yet, little is known about the geographical scale of local adaptation. Is adaptive divergence primarily evident at the scale of regions or individual populations? Also, many salmonid populations are subject to spawning intrusion by farmed conspecifics that experience selection regimes fundamentally different from wild populations. This prompts the question if adaptive differences between wild populations and hatchery strains are more pronounced than between different wild populations? We addressed these issues by analyzing variation at 74 microsatellite loci (including anonymous and expressed sequence tag- and quantitative trait locus-linked markers) in 15 anadromous wild brown trout (Salmo trutta L.) populations, representing five geographical regions, along with two lake populations and two hatchery strains used for stocking some of the populations. FST-based outlier tests revealed more outlier loci between different geographical regions separated by 522±228 km (mean±s.d.) than between populations within regions separated by 117±79 km (mean±s.d.). A significant association between geographical distance and number of outliers between regions was evident. There was no evidence for more outliers in comparisons involving hatchery trout, but the loci under putative selection generally were not the same as those found to be outliers between wild populations. Our study supports the notion of local adaption being increasingly important at the scale of regions as compared with individual populations, and suggests that loci involved in adaptation to captive environments are not necessarily the same as those involved in adaptive divergence among wild populations