No abstract

The Japanese quail has several advantages as a laboratory animal for biological and biomedical investigations. In this study, the draft genome of the Japanese quail was sequenced and assembled using next-generation sequencing technology. To improve the quality of the assembly, the sequence reads from the Japanese quail were aligned against the reference genome of the chicken. The final draft assembly consisted of 1.75 Gbp with an N50 contig length of 11,409 bp. On the basis of the draft genome sequence obtained, we developed 100 microsatellite markers and used these markers to evaluate the genetic variability and diversity of 11 lines of Japanese quail. Furthermore, we identified Japanese quail orthologs of spermatogenesis markers and analyzed their expression using in situ hybridization. The Japanese quail genome sequence obtained in the present study could enhance the value of this species as a model animal.

Organisms living outside the tropics measure the changes in the length of the day to adapt to seasonal changes in the environment. Animals that breed during spring and summer are called long-day breeders, while those that breed during fall are called short-day breeders. Although the influence of thyroid hormone in the regulation of seasonal reproduction has been known for several decades, its precise mechanism remained unknown. Recent studies revealed that the activation of thyroid hormone within the mediobasal hypothalamus plays a key role in this phenomenon. This localized activation of the thyroid hormone is controlled by thyrotropin (thyroid-stimulating hormone) secreted from the pars tuberalis of the pituitary gland. Although seasonal reproduction is a rate-limiting factor in animal production, genes involved in photoperiodic signal transduction pathway could emerge as potential targets to facilitate domestication.

To cope with seasonal changes in the environment, organisms adapt their physiology and behavior. Although color perception varies among seasons, the underlying molecular basis and its physiological significance remain unclear. Here we show that dynamic plasticity in phototransduction regulates seasonal changes in color perception in medaka fish. Medaka are active and exhibit clear phototaxis in conditions simulating summer, but remain at the bottom of the tank and fail to exhibit phototaxis in conditions simulating winter. Mate preference tests using virtual fish created with computer graphics demonstrate that medaka are more attracted to orange-red-colored model fish in summer than in winter. Transcriptome analysis of the eye reveals dynamic seasonal changes in the expression of genes encoding photopigments and their downstream pathways. Behavioral analysis of photopigment-null fish shows significant differences from wild type, suggesting that plasticity in color perception is crucial for the emergence of seasonally regulated behaviors.

No abstract

Background: The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research. Results: We have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics, gene content and chromosomal organisation, the quail genome shows high similarity to the chicken genome. We demonstrate the utility of this genome through three diverse applications. First, we identify selection signatures and candidate genes associated with social behaviour in the quail genome, an important agricultural and domestication trait. Second, we investigate the effects and interaction of photoperiod and temperature on the transcriptome of the quail medial basal hypothalamus, revealing key mechanisms of photoperiodism. Finally, we investigate the response of quail to H5N1 influenza infection. In quail lung, many critical immune genes and pathways were downregulated after H5N1 infection, and this may be key to the susceptibility of quail to H5N1. Conclusions: We have produced a high-quality genome of the quail which will facilitate further studies into diverse research questions using the quail as a model avian species.

1. The advantages and disadvantages of various housing systems for laying hens were compared as a pilot study for work in commercial conditions. 2. At 16 weeks of age, 284 hens were introduced into one of 6 housing systems: two types of conventional cages (small: SC; large: LC), furnished cages (small: SF; large: LF), and non-cage systems (single-tiered aviary: SA; free-range: FR). 3. We evaluated the welfare, egg production, and immune response of the birds in these housing systems, built in the same location, for 18 months. For welfare evaluation, we examined their ethology, physiology, anatomy, production, and physical condition. 4. The non-cage systems, especially FR, had a low score for freedom from pain, injury, and disease, together with other disadvantages, such as pale eggs and increased feed intake for production. However, the score for freedom to express normal behaviour was high and immune response was good in the non-cage systems. 5. In the furnished cages, behaviour was more diverse in SF than in LF, and in SF immune response was comparable with the non-cage systems. 6. For freedom from fear and distress, the non-cage systems had high scores for some indicators such as TI duration, H/L ratio and claw length, while aggressive pecking and feather pecking was worse in the housing systems with large group sizes.

1. The objective of the present study was to examine the behaviour of laying hens in single-tiered aviaries with and without outdoor areas with particular reference to the proportion of each behaviour and the ways it changed. 2. In all, 144 interbred cross layers (WL/RIR cross-breed) were used. At the age of 16 weeks, the hens were divided at random into two groups and moved to single-tiered aviary (SA) and free-range systems (FR, SA with in addition an outdoor range area covered with clover) with 18 hens per pen. Behavioural observations were conducted before, during and after access to the range. 3. All behaviours using the beak (eating, grazing, drinking, preening, aggressive pecking, feather pecking, litter pecking, object pecking and mate pecking) were recorded as pecking behaviour. 4. While most of the FR hens spent their time outside foraging, the proportion of hens eating, preening, litter pecking, object pecking, aggressive pecking and feather pecking was higher in SA than in FR hens. 5. The proportion of hens performing pecking behaviour of all types was very similar in SA (61.7 +/- 2.0%) and in FR (64.0 +/- 0.8%). The proportion of hens performing overall pecking behaviour increased as pre-laying sitting decreased. 6. The proportion of hens feather pecking decreased in FR during access to range and a similar tendency was found for aggressive pecking. 7. In conclusion, the total proportion of hens pecking was almost the same regardless of whether an outdoor area was provided or not, but the incidence of different types of pecking behaviour differed between SA and FR. The risk of feather pecking in FR may be lower when an outdoor grazing area is provided, although further testing on a larger scale would be essential.