No abstract

The zebrafish is an important model organism for neuro-anatomy and developmental genetics. It also offers opportunities for investigating the functional and evolutionary genetics of behaviour but these have yet to be exploited. The ecology of anti-predator behaviour has been widely studied in fish and has been shown to vary among populations and between wild and domesticated (laboratory) fish. Here, we utilise the strong behavioural differences present between a wild-derived strain of fish from Bangladesh and the laboratory strain AB. In total, 184 F2 fish were generated and tested for shoaling tendency and willingness to approach an unfamiliar object ('boldness'). Our results indicate the existence of QTL for boldness on chromosomes 9 and 16 and suggest another genomic region that influences anti-predator behaviour on chromosome 21. QTL for growth rate, weight and fat content, all of which are elevated in laboratory fish, were detected on chromosome 23. These initial results confirm the potential for QTL mapping of behavioural traits in zebrafish and also for dissecting the consequences of selection during domestication.

Background: Allergic rhinitis (AR) is recognized as a major health problem worldwide, and its prevalence depends on the age range of the subjects. The aims of this study were to determine the current prevalence of AR, effects of age on the prevalence of IgE sensitization to inhalant allergens, and serum total IgE levels in Japanese subjects. Methods: We conducted a survey of 1,540 subjects between 20 and 49 years of age in 2006 and 2007 and examined the prevalence of AR and sensitization to 7 common aeroallergens. We measured serum total IgE and specific IgE to 7 aeroallergens. AR was determined based on symptoms, predominantly in the nose and eyes, caused by aeroallergens as mentioned in a questionnaire and sensitization to any of the 7 aeroallergens as assessed by measurement of serum specific IgE. Results: The prevalence of AR was 44.2% (681 of the 1,540 subjects) and there was no difference among age decades. Of the 1,540 subjects, 1,073 (69.7%) were sensitized to at least 1 of the 7 aeroallergens. The most common allergen in AR was Japanese cedar pollen (89.6%, 610 of the 681 with AR) in all the age decades examined. The sensitization rate to mites was significantly higher in the younger subjects. Conclusion: Our data suggest that the prevalence of AR between 20 and 49 years of age has increased by nearly 10% during the last 10 years. Cedar pollen and mites were predominant allergen sources among the 7 aeroallergens in the Japanese population.

Copy number variations (CNVs) are universal genetic variations, and their association with disease has been increasingly recognized. We designed high-density microarrays for CNVs, and detected 3000–4000 CNVs (4–6% of the genomic sequence) per population that included CNVs previously missed because of smaller sizes and residing in segmental duplications. The patterns of CNVs across individuals were surprisingly simple at the kilo-base scale, suggesting the applicability of a simple genetic analysis for these genetic loci. We utilized the probabilistic theory to determine integer copy numbers of CNVs and employed a recently developed phasing tool to estimate the population frequencies of integer copy number alleles and CNV–SNP haplotypes. The results showed a tendency toward a lower frequency of CNV alleles and that most of our CNVs were explained only by zero-, one- and two-copy alleles. Using the estimated population frequencies, we found several CNV regions with exceptionally high population differentiation. Investigation of CNV–SNP linkage disequilibrium (LD) for 500–900 bi- and multi-allelic CNVs per population revealed that previous conflicting reports on bi-allelic LD were unexpectedly consistent and explained by an LD increase correlated with deletion-allele frequencies. Typically, the bi-allelic LD was lower than SNP–SNP LD, whereas the multi-allelic LD was somewhat stronger than the bi-allelic LD. After further investigation of tag SNPs for CNVs, we conclude that the customary tagging strategy for disease association studies can be applicable for common deletion CNVs, but direct interrogation is needed for other types of CNVs.

An empirical Bayes (EB) pairwise F ST estimator was previously introduced and evaluated for its performance by numerical simulation. In this study, we conducted coalescent simulations and generated genetic population structure mechanistically, and compared the performance of the EBF ST with Nei's G ST , Nei and Chesser's bias-corrected G ST (G ST_NC ), Weir and Cockerham's h (h WC ) and h with finite sample correction (h WC_F ). We also introduced EB estimators for Hedrick' G' ST and Jost' D. We applied these estimators to publicly available SNP genotypes of Atlantic herring. We also examined the power to detect the environmental factors causing the population structure. Our coalescent simulations revealed that the finite sample correction of h WC is necessary to assess population structure using pairwise F ST values. For microsatellite markers, EBF ST performed the best among the present estimators regarding both bias and precision under high gene flow scenarios (F ST 0:032). For 300 SNPs, EBF ST had the highest precision in all cases, but the bias was negative and greater than those for G ST_NC and h WC_F in all cases. G ST_NC and h WC_F performed very similarly at all levels of F ST . As the number of loci increased up to 10 000, the precision of G ST_NC and h WC_F became slightly better than for EBF ST for cases with F ST ! 0:004, even though the size of the bias remained constant. The EB estimators described the fine-scale population structure of the herring and revealed that 56% of the genetic differentiation was caused by sea surface temperature and salinity. The R package FINEPOP for implementing all estimators used here is available on CRAN.