Microsatellite DNA variation in sockeye salmon Oncorhynchus nerka (Walbaum, 1792) populations of eastern Kamchatka

The allelic variations of eight microsatellite loci (Ots107, Oki1a, Oki1b, One104, One109, OtsG68, OtsG85, and Oki6) were examined in sockeye salmon Oncorhynchus nerka (Walbaum) populations of eastern Kamchatka. Samples from river basins of the Karaginskiy and Olyutorskiy districts in the northern part of the investigated region are characterized by a smaller number of allelic variants and lower heterozygosity, compared to samples from the Kamchatka River basin. A fit to the Hardy-Weinberg distribution was found at most of the loci that were studied in all samples. The average differentiation between populations (st) over the eight loci was 2.93%, which corresponds to the statistical significance level. The most highly polymorphic loci proved to be the least differentiating between the analyzed samples.     

Comparative analysis of STR and SNP polymorphism in the populations of sockeye salmon (Oncorhynchus nerka) from Eastern and Western Kamchatka

Sockeye salmon samples from five largest lacustrine-riverine systems of Kamchatka Peninsula were tested for polymorphism at six microsatellite (STR) and five single nucleotide polymorphism (SNP) loci. Statistically significant genetic differentiation among local populations from this part of the species range examined was demonstrated. The data presented point to pronounced genetic divergence of the populations from two geographical regions, Eastern and Western Kamchatka. For sockeye salmon, the individual identification test accuracy was higher for microsatellites compared to similar number of SNP markers. Pooling of the STR and SNP allele frequency data sets provided the highest accuracy of the individual fish population assignment.     

Single nucleotide polymorphisms in chicken lmbr1 gene were associated with chicken growth and carcass traits

Lmbr1 is the key candidate gene controlling vertebrate limb development, but its effects on animal growth and carcass traits have never been reported. In this experiment, lmbr1 was taken as the candidate gene affecting chicken growth and carcass traits. T/C and G/A mutations located in exon 16 and one A/C mutation located in intron 5 of chicken lmbr1 were detected from Silky, White Plymouth Rock broilers and their F₂ crossing chickens by PCR-SSCP and sequencing methods. The analysis of variance (ANOVA) results suggests that T/C polymorphism of exon 16 had significant association with eviscerated yield rate (EYR), gizzard rate (GR), shank and claw rate (SCR) and shank girth (SG); A/C polymorphism of intron 5 was significantly associated with SCR, liver rate and head-neck weight (HNW), while both sites had no significant association with other growth and carcass traits. These results demonstrate that lmbr1 gene could be a genetic locus or linked to a major gene significantly affecting these growth and carcass traits in chicken. Supported by the State Major Basic Research Development Program (Grant No. G20000161) and Beijing Natural Science Foundation (Grant No. 5011002)     

The mucous coat on gill lamellae of rainbow trout (Oncorhynchus mykiss)

The existence of a layer of mucus covering the gill lamellae of healthy rainbow trout (Oncorhynchus mykiss) was investigated. Using cryo-scanning electron microscopy, a smooth, undulating, thin layer was observed which completely covered gill filaments and lamellae, thereby obscuring epithelial microridges. After processing cryopreserved gill arches in glutaraldehyde for conventional scanning electron microscopy, the layer was no longer present and epithelial microridges were clearly visible. The identity of this layer was investigated using cryopreserved gills which were treated in one of two ways. First, gills were incubated with a rabbit antiserum to gill mucus, with normal rabbit serum, or with phosphate-buffered saline. Following fixation in glutaraldehyde and processing, only the gill tissue incubated with the mucus-specific antiserum was still covered with the smooth layer. The layer was also retained on the gills of fish anesthetized in a solution containing mucusspecific antiserum and then processes in glutaraldehyde for conventional scanning electron microscopy. The tenacious nature of the mucous layer was demonstrated by its stability following exposure to formalin and a cationic detergent. Second, the presence of this layer was confirmed on gill tissue which was cryopreserved, followed by freeze-substitution and vapor fixation, and then examined by transmission electron microscopy.     

Acid-base disequilibrium in the venous blood of rainbow trout (Oncorhynchus mykiss)

Acid-base equilibria/disequilibria were evaluated in vivo in post-branchial arterial blood and pre-branchial venous blood of freshwater rainbow trout (Oncorhynchus mykiss). This was accomplished using arterial and venous extracorporeal circuits in conjunction with a stopped-flow apparatus. After the abrupt stoppage of circulating post-branchial blood within the stopped-flow apparatus, pH increased slowly ([Delta]pH = +0.032 ± 0.004 pH units; n = 15), thus confirming the existence of an acid-base disequilibrium state in the arterial blood of rainbow trout. The slow downstream pH changes were unaffected by prior treatment of fish with the carbonic anhydrase inhibitor benzolamide (1.2 mg kg^-1; [Delta]pH = +0.032 ± 0.01 pH units; n = 5) but were eliminated after intra-vascular injection of 10 mg kg^-1 bovine carbonic anhydrase ([Delta]pH = -0.011 ± 0.003 pH units; n = 8). These results demonstrate that the acid-base disequilibrium in the arterial blood reflects a total absence of extracellular carbonic anhydrase activity. Similar stopped-flow experiments revealed the existence of a reduced, yet significant, acid-base disequilibrium in the venous blood circulating within the caudal vein ([Delta]pH = +0.004 ± 0.003 pH units; n = 15). Selective inhibition of extracellular carbonic anhydrase using benzolamide did not significantly influence the magnitude of the venous pH disequilibrium ([Delta]pH = +0.007 ± 0.007 pH units; n = 8) whereas intra-vascular injection of carbonic anhydrase eliminated the pH disequilibrium. These results demonstrate that extracellular carbonic anhydrase, although reported to be present within the skeletal muscle of rainbow trout, does not accelerate post-capillary pH changes in the venous circulation.     

Single nucleotide polymorphisms (SNPs) in the estrogen receptor gene and breast cancer susceptibility

In order to evaluate the role of inherited variation in the estrogen receptor (ESR1) gene in human breast cancer, we determined intronic sequences flanking each ESRI exon; identified multiple SNPs and length polymorphisms in the ESR1 coding sequence, splice junctions and regulatory regions; and genotyped families at high risk of breast cancer and population-based breast cancer patients and controls. Of 10 polymorphic sites in ESR1, four are synonymous SNPs, two are nonsynonymous SNPs and four are length polymorphisms; five are novel. No ESR1 polymorphisms were associated with breast cancer, either in the high-risk families or the case-control study. We therefore conclude that inherited genetic variation is not a mechanism by which the estrogen receptor is commonly involved in breast cancer development.     

Single nucleotide polymorphisms (SNPs) are inherited from parents and they measure heritable events

Single nucleotide polymorphisms (SNPs) are extensively used in case-control studies of practically all cancer types. They are used for the identification of inherited cancer susceptibility genes and those that may interact with environmental factors. However, being genetic markers, they are applicable only on heritable conditions, which is often a neglected fact. Based on the data in the nationwide Swedish Family-Cancer Database, we review familial risks for all main cancers and discuss the evidence for a heritable component in cancer. The available evidence is not conclusive but it is consistent in pointing to a minor heritable etiology in cancer, which will hamper the success of SNP-based association studies. Empirical familial risks should be used as guidance for the planning of SNP studies. We provide calculations for the assessment of familial risks for assumed allele frequencies and gene effects (odds ratios) for different modes of inheritance. Based on these data, we discuss the gene effects that could account for the unexplained proportion of familial breast and lung cancer. As a conclusion, we are concerned about the indiscriminate use of a genetic tool to cancers, which are mainly environmental in origin. We consider the likelihood of a successful application of SNPs in gene-environment studies small, unless established environmental risk factors are tested on proven candidate genes.     

The efficacy of two immunostimulants against Flavobacterium columnare infection in juvenile rainbow trout (Oncorhynchus mykiss)

Bacterium Flavobacterium columnare is the causative agent of columnaris disease in many wild and farmed fish species. Immunostimulants are used with success in aquaculture against many pathogens, but the ability to improve innate resistance to columnaris disease has not been studied. Fingerling rainbow trout were treated with two immunostimulants, yeast β-glucan and β-hydroxy-β-methylbutyrate (HMB). Selected innate immune function parameters, the production of reactive oxygen species (ROS) by whole blood and by isolated head kidney leukocytes, plasma lysozyme activity and complement bacteriolytic activity, were determined to assess the immune status of fish. The fish were then bath challenged with virulent F. columnare bacteria, and the mortality of fish was recorded. Given orally both stimulants raised the levels of immune function parameters, but did not improve survival in challenge at any concentration of the stimulants used. Intra peritoneal injection of β-glucan increased parameter values several fold, but no beneficial effect of injected glucan on survival was noted. As a control, antibiotic medication administered prior to and during the challenge infection prevented the mortality. Innate immune mechanisms, even when induced to high levels with immunostimulants, as evidenced here, were not able to increase resistance against F. columnare. This may be connected to the external character of the infection. The results from the treatments with β-glucan and HMB suggest that there is little prospect of preventing columnaris disease by means of immunostimulants in early life stage of rainbow trout. However, the efficacy of other immune stimulants remains open.     

Genetic structure among and within populations of the serpentine endemic Heteropappus hispidus ssp. leptocladus (Compositae)

Heteropappus hispidus ssp. leptocladus is an edaphic endemic taxon that is confined to serpentine and limestone-derived soils and is allopatrically distributed in three regions of western Japan. In this study, we attempted to detect genomic signatures of seven H. hispidus ssp. leptocladus populations along with eight other subspecies populations using eight nuclear microsatellite loci. The Mantel test supported an isolation by distance model across all H. hispidus populations, thus implying the possibility of parallel evolution for each subspecies. Results from AMOVA recognized relatively larger differentiations in geographic distribution compared to intraspecific taxonomy. Relationships indicated by neighbor-joining phylogenetic tree analysis and population structure generally did not reflect an intraspecific taxonomy. Populations from limestone-derived soil harbored a homogeneous genetic structure with neighboring populations from serpentine-derived soils. These results suggest that the edaphic ecotype may have derived allopatrically while a lack of edaphic constraint existed between serpentine and limestone soils.     

Single nucleotide polymorphisms of Gcyc1 (Cycloidea) in Conandron ramondioides (Gesneriaceae) from Southeast China

Conandron ramondioides with actinomorphic flower in Gesneriaceae is an endemic species distributed in Taiwan, Southeast of China and Japan. Populations are usually small and isolated in typically fragmented habitat. Based on SNPs of Gcyc1 (Cycloidea), a TCP gene known in patterning the floral dorsoventral asymmetry, we have explored the molecular evolution and genetic differentiation of Gcyc1 at population level, and the population history of C. ramondioides populations distributed in SE China. Eighteen SNPs are detected in 774-bp of the gene, of which eleven are non-synonymous. However, morphological observation of flowers shows that there is no visible differentiation in shape and size across the dorsoventral axis within each whorl. None of the eighteen SNPs is by all shared the eleven populations. Population differentiation is significant. These results reveal that evolution of Gcyc1 at population level is well in accord with the neutral theory. Our study indicates that the SNPs of developmental genes are also useful molecular markers for exploring the genetic differentiation and population history in non-model organisms.     

Morphometric and genetic divergence among populations ofNeotinea ustulata (Orchidaceae) with different flowering phenologies

The terrestrial orchid speciesNeotinea ustulata has recently been split into two subspecies, differing remarkably in their flowering time, but only slightly in morphological characteristics, which makes their taxonomic status uncertain. We have analyzed morphometric and genetic differences between the early- and late-flowering populations in Central Europe. Our results on morphology are ambiguous. Indirect gradient analysis has not shown a distinct separation of early- and late-flowering individuals in the ordination space. However, according to MANOVA, populations of early- and late-flowering plants can be distinguished by plant height, leaf length, numbers of basal (rosette) and stem leaves and even better by certain ratios of these numbers. All genetic analyses, on the other hand, are definite and consistently distinguish two groups. Random amplified polymorphic DNA (RAPD) markers have shown that the early- and late-flowering populations differ significantly from one another. Principal coordinate analysis (PCoA) based on presence/absence matrix of RAPD bands separated the two groups, implying that the difference in flowering phenology could form an effective barrier to gene exchange. Partitioning of genetic diversity in analysis of molecular variance (AMOVA) has shown that the genetic divergence between the two groups, early- and late-flowering populations, is somewhat greater (33%) than the genetic variability among populations within particular group (23%). Using the Mantel test, we found that genetic differentiation coefficients between populations closely correspond to their geographic distribution. After elimination of the effect of sample origin from the model, direct gradient analysis (RDA) has shown that the early- and late-flowering groups differ significantly in their RAPD spectra. To conclude, our results indicate the presence of two genetically and phenologically distinct taxa, but the weak morphological differentiation supports the taxonomic rank of variety rather than subspecies.     

Expressed sequence tag-linked microsatellites as a source of gene-associated polymorphisms for detecting signatures of divergent selection in atlantic salmon (Salmo salar L.)

The prediction that selection affects the genome in a locus-specific way also affecting flanking neutral variation, known as genetic hitchhiking, enables the use of polymorphic markers in noncoding regions to detect the footprints of selection. However, as the strength of the selective footprint on a locus depends on the distance from the selected site and will decay with time due to recombination, the utilization of polymorphic markers closely linked to coding regions of the genome should increase the probability of detecting the footprints of selection as more gene-containing regions are covered. The occurrence of highly polymorphic microsatellites in the untranslated regions of expressed sequence tags (ESTs) is a potentially useful source of gene-associated polymorphisms which has thus far not been utilized for genome screens in natural populations. In this study, we searched for the genetic signatures of divergent selection by screening 95 genomic and EST-derived mini- and microsatellites in eight natural Atlantic salmon, Salmo salar L., populations from different spatial scales inhabiting contrasting natural environments (salt-, brackish, and freshwater habitat). Altogether, we identified nine EST-associated microsatellites, which exhibited highly significant deviations from the neutral expectations using different statistical methods at various spatial scales and showed similar trends in separate population samples from different environments (salt-, brackish, and freshwater habitats) and sea areas (Barents vs. White Sea). We consider these ESTs as the best candidate loci affected by divergent selection, and hence, they serve as promising genes associated with adaptive divergence in Atlantic salmon. Our results demonstrate that EST-linked microsatellite genome scans provide an efficient strategy for discovering functional polymorphisms, especially in nonmodel organisms.     

Time scales of divergence and speciation among natural populations and subspecies of Arabidopsis lyrata (Brassicaceae)

? Premise of the study: Plant populations that face new environments adapt and diverge simultaneously, and both processes leave footprints in their genetic diversity. Arabidopsis lyrata is an excellent species for studying these processes. Pairs of populations and subspecies of A. lyrata represent different stages of divergence. These populations are also known to be locally adapted and display various stages of emerging reproductive isolation. ? Methods: We used nucleotide diversity data from 19 loci to estimate divergence times and levels of diversity among nine A. lyrata populations. Traditional distance-based methods and model-based clustering analysis were used to supplement pairwise coalescence-based analysis of divergence. ? Key results: Estimated divergence times varied from 130000 generations between North American and European subspecies to 39000 generations between central European and Scandinavian populations. In concordance with previous studies, the highest level of diversity was found in Central Europe and the lowest in North America and a diverged Russian Karhum?ki population. Local adaptation among Northern and central European populations has emerged during the last 39000 generations. Populations that are reproductively isolated by prezygotic mechanisms have been separated for a longer time period of ～70000 generations but still have shared nucleotide polymorphism. ? Conclusions: In A. lyrata, reproductively isolated populations started to diverge ～70000 generations ago and more closely related, locally adapted populations have been separate lineages for ～39000 generations. However, based on the posterior distribution of divergence times, the processes leading to reproductive isolation and local adaptation are likely to temporally coincide.     

Estimation of protein digestibility—IV. Digestive proteinases from the pyloric caeca of coho salmon (Oncorhynchus kisutch) fed diets containing soybean meal

The goal of this study was to better understand why dietary soybean products are poorly utilized by salmonids. The influence of dietary intake on coho salmon fingerling weight gain and specific properties of pyloric caeca enzymes was investigated. Fingerlings were fed diets containing heated or unheated soybean meal (SBM) or Promoveal™, as 15–25% herring meal replacer, for 8–12 weeks. Fish fed to apparent satiation with diets containing heated SBM replacer gained more weight than those fed unheated SBM at the same level. Fish increased in body weight at the same rate when fed restricted rations containing either 15% SBM replacer that was variously heated up to 20 min, 15% Promoveal™ replacer or the herring meal basal diet. After the experimental diets were fed, digestive proteinases were isolated from the pyloric caeca. Yield of pyloric caeca enzymes (PCE), recovery of trypsin in PCE, soybean trypsin inhibitor (SBTI) sensitivity of PCE trypsin, specific activity of PCE trypsin and in vitro casein digestibility by PCE were determined for each dietary group. Weight gain vs in vitro casein digestibility by PCE was linear for animals fed unheated SBM to apparent satiation (r² = 0.71, P < 0.1) but not for animals fed either heated SBM to apparent satiation or variously heated SBM as 15% replacer at restricted levels. Trypsin from fish fed diets with heated or unheated SBM, but not Promoveal™ replacer, was less sensitive to SBTI than fish fed no SBM. For fish fed diets with variously heated SBM as 15% replacer, the SBTI activity of the SBM and SBTI inhibition of PCE trypsin were inversely related (r² = 0.88, P < 0.05). The yield of PCE was higher for fish fed 25% of heated SBM replacer than it was for diet groups fed less SBM. The yield of PCE trypsin was higher from animals fed 25% heated SBM replacer than those fed diets with a lower percentage of heated SBM replacer. Feeding coho fingerlings rations with SBM replacer appears to promote physiological compensation of PCE. Heat stable and/or heat-activated factor(s) and SBTI appear to cause the compensation of salmon digestive proteinases from coho salmon fed diets with SBM.     

Single nucleotide polymorphisms in exon 10 of the chinchilla growth hormone receptor (GHR) gene

The aim of this study was to detect SNPs in exon 10 of the chinchilla growth hormone receptor gene (GHR) by comparative sequencing. Sixty females of the same breed (Standard) were analysed. Four new SNPs were identified, which cause 3 amino acid substitutions in the intracellular domain of the receptor: G/C at position 135 bp (in relation to the total sequence of exon 10) (gln/his), CAG/AAA at 352 bp and 354 bp (gln/lys), and C/A at 641 bp (thr/asn).