The full exploration of gene-environment interactions requires model organisms with well-characterized ecological interactions in their natural environment, manipulability in the laboratory and genomic tools. The waterflea Daphnia magna is an established ecological and toxicological model species, central to the food webs of freshwater lentic habitats and sentinel for water quality. Its tractability and cyclic parthenogenetic life-cycle are ideal to investigate links between genes and the environment. Capitalizing on this unique model system, the STRESSFLEA consortium generated a comprehensive RNA-Seq data set by exposing two inbred genotypes of D. magna and a recombinant cross of these genotypes to a range of environmental perturbations. Gene models were constructed from the transcriptome data and mapped onto the draft genome of D. magna using EvidentialGene. The transcriptome data generated here, together with the available draft genome sequence of D. magna and a high-density genetic map will be a key asset for future investigations in environmental genomics.

BackgroundAlthough Daphnia is increasingly recognized as a model for ecological genomics and biomedical research, there is, as of yet, no high-resolution genetic map for the genus. Such a map would provide an important tool for mapping phenotypes and assembling the genome. Here we estimate the genome size of Daphnia magna and describe the construction of an SNP array based linkage map. We then test the suitability of the map for life history and behavioural trait mapping. The two parent genotypes used to produce the map derived from D. magna populations with and without fish predation, respectively and are therefore expected to show divergent behaviour and life-histories.ResultsUsing flow cytometry we estimated the genome size of D. magna to be about 238 mb. We developed an SNP array tailored to type SNPs in a D. magna F2 panel and used it to construct a D. magna linkage map, which included 1,324 informative markers. The map produced ten linkage groups ranging from 108.9 to 203.6 cM, with an average distance between markers of 1.13 cM and a total map length of 1,483.6 cM (Kosambi corrected). The physical length per cM is estimated to be 160 kb. Mapping infertility genes, life history traits and behavioural traits on this map revealed several significant QTL peaks and showed a complex pattern of underlying genetics, with different traits showing strongly different genetic architectures.ConclusionsThe new linkage map of D. magna constructed here allowed us to characterize genetic differences among parent genotypes from populations with ecological differences. The QTL effect plots are partially consistent with our expectation of local adaptation under contrasting predation regimes. Furthermore, the new genetic map will be an important tool for the Daphnia research community and will contribute to the physical map of the D. magna genome project and the further mapping of phenotypic traits. The clones used to produce the linkage map are maintained in a stock collection and can be used for mapping QTLs of traits that show variance among the F2 clones.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1033) contains supplementary material, which is available to authorized users.

Species in a common landscape often face similar selective environments. The capacity of organisms to adapt to these environments may be largely species specific. Quantifying shared and unique adaptive responses across species within landscapes may thus improve our understanding of landscape-moderated biodiversity patterns. Here we test to what extent populations of two coexisting and phylogenetically related fishes—three-spined and nine-spined stickleback—differ in the strength and nature of neutral and adaptive divergence along a salinity gradient. Phenotypic differentiation, neutral genetic differentiation and genomic signatures of adaptation are stronger in the three-spined stickleback. Yet, both species show substantial phenotypic parallelism. In contrast, genomic signatures of adaptation involve different genomic regions, and are thus non-parallel. The relative contribution of spatial and environmental drivers of population divergence in each species reflects different strategies for persistence in the same landscape. These results provide insight in the mechanisms underlying variation in evolutionary versatility and ecological success among species within landscapes.

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Studies monitoring changes in genetic diversity and composition through time allow a unique understanding of evolutionary dynamics and persistence of natural populations. However, such studies are often limited to species with short generation times that can be propagated in the laboratory or few exceptional cases in the wild. Species that produce dormant stages provide powerful models for the reconstruction of evolutionary dynamics in the natural environment. A remaining open question is to what extent dormant egg banks are an unbiased representation of populations and hence of the species' evolutionary potential, especially in the presence of strong environmental selection. We address this key question using the water flea Daphnia magna, which produces dormant stages that accumulate in biological archives over time. We assess temporal genetic stability in three biological archives, previously used in resurrection ecology studies showing adaptive evolutionary responses to rapid environmental change. We show that neutral genetic diversity does not decline with the age of the population and it is maintained in the presence of strong selection. In addition, by comparing temporal genetic stability in hatched and unhatched populations from the same biological archive, we show that dormant egg banks can be consulted to obtain a reliable measure of genetic diversity over time, at least in the multidecadal time frame studied here. The stability of neutral genetic diversity through time is likely mediated by the buffering effect of the resting egg bank.

Sugarcane juice was subjected following treatments viz. pasteurization at 808C for 10 min ? chemical treatments (KMS @ 150 ppm and citric acid @ 0.05%); pasteurization at 808C for 10 min ? chemical treatments (KMS @ 150 ppm and citric acid @ 0.05%) ? sterilization at 808C for 20 min. All the samples were packed in glass bottles, polyethylene Tetrapthelate (PET) bottles and low density polyethylene pouches (LDPE) and then irradiated at 0.25, 0.5 and 1.0 kGy and stored for 90 days at room and low temperature. Non-irradiated samples were taken as control. On treatment moisture content, ascorbic acid, viable bacterial count and viable yeast and mold count were decreased significantly (P [ 0.05) where as no significant effect was observed on reducing and total sugars in cane juice. Among the three packaging material used glass and PET was found to be at par in increasing the shelf life of sugarcane juice in comparison to LDPE pouches. On storage, ascorbic acid and total sugars were decreased significantly (P [ 0.05). Moisture content, viable bacterial count and viable yeast mold count were increased on storage. Irradiation and packaging material statistically showed no significant differences on organoleptic properties of juice but storage showed changes in sensory scores. Among all the treatments pasteurization at 808C for 10 min ? chemical treatments (KMS @ 150 ppm and citric acid @ 0.05%) ? sterilization at 808C for 20 min was found to be best in maintain the shelf life of juice up to 60 days at room temperature and 90 days at low temperature with 1.0 kGy irradiation doses. Among glass bottles, PET bottles and LDPE pouches, glass and PET were found to be best in maintaining the quality of juice.

We lack a thorough understanding of the origin and maintenance of standing genetic variation that enables rapid evolutionary responses of natural populations. Whole genome sequencing of a resurrected Daphnia population shows that standing genetic variation in over 500 genes follows an evolutionary trajectory that parallels the pronounced and rapid adaptive evolution of multiple traits in response to predator-driven natural selection and its subsequent relaxation. Genetic variation carried by only five founding individuals from the regional genotype pool is shown to suffice at enabling the observed evolution. Our results provide insight on how natural populations can acquire the genomic variation, through colonization by a few regional genotypes, that fuels rapid evolution in response to strong selection pressures. While these evolutionary responses in our study population involved hundreds of genes, we observed no evidence of genetic erosion.

Hypocholesterolemic effect of amaranth seeds was studied in male wistar strain albino rats as against Bengal gram. The results showed that liver weights were significantly higher in animals with hypercholesterolemia inducing diet. Contrarily, weights of other organs like brain, kidney, testes and spleen showed higher weights with amaranth and bengal gram diets. Serum lipid and TG (triglyceride) contents were lower and HDL-cholesterol fraction was higher and comparable with amaranth seed diet. Feeding with amaranth seed showed a definite hypocholesterolemic effect.