Paul Hocking

Development of a high density 600K SNP genotyping array for chicken

BackgroundHigh density (HD) SNP genotyping arrays are an important tool for genetic analyses of animals and plants. Although the chicken is one of the most important farm animals, no HD array is yet available for high resolution genetic analysis of this species.ResultsWe report here the development of a 600 K Affymetrix® Axiom® HD genotyping array designed using SNPs segregating in a wide variety of chicken populations. In order to generate a large catalogue of segregating SNPs, we re-sequenced 243 chickens from 24 chicken lines derived from diverse sources (experimental, commercial broiler and layer lines) by pooling 10–15 samples within each line. About 139 million (M) putative SNPs were detected by mapping sequence reads to the new reference genome (Gallus_gallus_4.0) of which ~78 M appeared to be segregating in different lines. Using criteria such as high SNP-quality score, acceptable design scores predicting high conversion performance in the final array and uniformity of distribution across the genome, we selected ~1.8 M SNPs for validation through genotyping on an independent set of samples (n = 282). About 64% of the SNPs were polymorphic with high call rates (>98%), good cluster separation and stable Mendelian inheritance. Polymorphic SNPs were further analysed for their population characteristics and genomic effects. SNPs with extreme breach of Hardy-Weinberg equilibrium (P < 0.00001) were excluded from the panel. The final array, designed on the basis of these analyses, consists of 580,954 SNPs and includes 21,534 coding variants. SNPs were selected to achieve an essentially uniform distribution based on genetic map distance for both broiler and layer lines. Due to a lower extent of LD in broilers compared to layers, as reported in previous studies, the ratio of broiler and layer SNPs in the array was kept as 3:2. The final panel was shown to genotype a wide range of samples including broilers and layers with over 100 K to 450 K informative SNPs per line. A principal component analysis was used to demonstrate the ability of the array to detect the expected population structure which is an important pre-investigation step for many genome-wide analyses.ConclusionsThis Affymetrix® Axiom® array is the first SNP genotyping array for chicken that has been made commercially available to the public as a product. This array is expected to find widespread usage both in research and commercial application such as in genomic selection, genome-wide association studies, selection signature analyses, fine mapping of QTLs and detection of copy number variants.

Somatic sex identity is cell autonomous in the chicken.

In the mammalian model of sex determination, embryos are considered to be sexually indifferent until the transient action of a sex-determining gene initiates gonadal differentiation. Although this model is thought to apply to all vertebrates, this has yet to be established. Here we have examined three lateral gynandromorph chickens (a rare, naturally occurring phenomenon in which one side of the animal appears male and the other female) to investigate the sex-determining mechanism in birds. These studies demonstrated that gynandromorph birds are genuine male:female chimaeras, and indicated that male and female avian somatic cells may have an inherent sex identity. To test this hypothesis, we transplanted presumptive mesoderm between embryos of reciprocal sexes to generate embryos containing male:female chimaeric gonads. In contrast to the outcome for mammalian mixed-sex chimaeras, in chicken mixed-sex chimaeras the donor cells were excluded from the functional structures of the host gonad. In an example where female tissue was transplanted into a male host, donor cells contributing to the developing testis retained a female identity and expressed a marker of female function. Our study demonstrates that avian somatic cells possess an inherent sex identity and that, in birds, sexual differentiation is substantively cell autonomous.

Control of the development of the ovarian follicular hierarchy in broiler breeder pullets by food restriction during rearing

1. The increase in the numbers of yellow and of white ovarian follicles was studied from 10 weeks of age to sexual maturity in broiler breeder pullets fed ad libitum and on a restricted intake. The growth of follicles greater than 1 mm diameter commenced at 14 to 16 weeks of age in ad libitum birds and at 22 to 24 weeks in those which were restricted. 2. In a second experiment, groups of birds restricted from 4 d of age were transferred to ad libitum feeding at 2-week intervals and examined at first egg. The numbers of yellow follicles at first egg were not affected by restriction to 14 weeks of age but, thereafter, declined linearly with time on restriction. 3. In the second experiment there were no comparable responses in the numbers of white follicles or in the rates of atresia. 4. Food restriction to 22 weeks of age produced about half the response in numbers of yellow follicles as restriction continued to point of lay (27 to 32 weeks of age). In practical situations, the results suggest that food intake should be restricted up to the onset of lay and then increased in relation to the rise in egg production. 5. Atresia was greatest in white follicles 3.15 to 6.30 mm diameter and was less outside this range.

High litter moisture alone is sufficient to cause footpad dermatitis in growing turkeys

1. Four randomised block experiments were conducted to determine the role of litter moisture, excreta and alternative bedding materials on the development of footpad dermatitis in growing turkeys. 2. Adding water to the litter increased external and histopathological scores independently of the presence of excreta. Fully developed lesions were induced by the application of water to dry litter in 2 to 4 d. 3. Footpad lesions were associated with discomfort during walking in one experiment and body weight was lower in birds on wet compared with dry litter. 4. Footpad lesions had virtually healed 15 d after transfer of the turkeys from wet to dry litter although histopathology assessment showed some residual tissue repair. 5. Long barley straw was associated with high footpad scores on wet and dry treatments. The footpad scores for turkeys on reprocessed cardboard chips were similarly high whereas scores were similar on paper litter and wood shavings whether dry or wet. 6. It was concluded that high litter moisture alone was sufficient to cause footpad dermatitis in young turkeys and that footpad dermatitis should be minimised by the maintenance of dry litter.

Ovarian follicular structure of white leghorns fed ad libitum and dwarf and normal broiler breeders fed ad libitum or restricted until point of lay

1. Yellow follicle numbers when the first egg was laid were 6.3, 9.0 and 12.4 for ad libitum reared Leghorns, sex-linked Dwarf (AL Dwarf) and Normal broiler breeders respectively. Multiple ovulation resulted in low egg production and a high proportion of defective egg shells in AL Dwarf and Normal broiler breeders during early lay. 2. Restricting the growth of broiler breeders during rearing by restricting food intake (R Dwarfs) reduced the number of yellow follicles to 6.8 and increased the rate of lay. 3. Atretic yellow follicles were common among broiler breeders but not in Leghorns or R Dwarfs when the first egg was laid. 4. Poor egg production in older broiler breeders was caused by birds with few or no developing yellow follicles, atresia in yellow follicles and the continued occurrence of multiple ovulations. 5. There was no relationship between the number of yellow follicles and the number of white follicles less than 5 mm diameter but atresia in white follicles 2 to less than 5 mm was negatively related to the number of yellow follicles. 7. No relationship was observed between abdominal fat weight and yellow follicle number, though birds which ate more had more yellow follicles. 8. The sex-linked dwarfing gene dw was associated with increased atresia among the white follicles and low numbers of yellow follicles compared with the Normal DW broiler breeder genotype.

Relationships between the degree of food restriction and welfare indices in broiler breeder females

1. Broiler breeder females were fed ad libitum, or according to a commercial food restriction programme or to gain 0.85, 0.70, 0.55, 0.40 or 0.25 of the body weight of ad libitum-fed birds. Several indices of the welfare of the birds were assessed at 3-weekly intervals to 18 weeks of age and related to body weight by regression analysis. Results for 6, 12 and 18 weeks of age are presented in detail. 2. Water intake was consistently higher in the 0.25, 0.40 and commercial restriction treatments. 3. There was a negative curvilinear relationship at each age group between body weight and the heterophil-lymphocyte ratio and plasma corticosterone concentration. 4. There was a positive relationship between the plasma concentration of creatine kinase and body weight at 12 and 18 weeks of age. The relationships between body weight and the plasma activity of alkaline phosphatase and aspartate transaminase changed with the age and there were no differences between treatments for lactate dehydrogenase. 5. The time spent resting increased with body weight at each age. The relationship between time spent preening and body weight changed with age whereas that for oral activities was similar among restricted birds at 6, and among all treatments at 12 weeks of age. At 18 weeks there was an increase in oral activities with decreasing body weight. 6. Fearfulness was positively related to body weight. The response of the comb to phytohaemagglutinin injection was similar in all treatments and the antibody titre to injections of sheep red blood cells was curvilinear. 7. A principal components analysis of all measured traits at 6, 12 and 18 weeks of age was conducted. Most of the variables were redundant but at least one from each of the different classes of welfare indices was retained at 6 and 12 weeks of age. 8. It was concluded that a body weight during rearing in the range of 0.5 to 0.85 of ad libitum might provide for optimum welfare of broiler breeder females.

Welfare assessment of broiler breeder and layer females subjected to food restriction and limited access to water during rearing

Abstract 1. A factorial experiment was conducted to assess the welfare at different ages of two strains of broiler breeder and one layer strain during rearing using a range of indicators. The birds were fed ad libitum or restricted and provided with free or limited access to water. 2. Food‐restricted birds spent a large proportion of time scratching and pecking the litter compared with birds fed ad libitum. 3. The heterophil/lymphocyte ratio and the proportion of basophils were raised at 8, 12 and 16 weeks, and the plasma concentrations of corticos‐terone were higher at 8 and 12 weeks of age in restricted birds compared with those fed ad libitum. 4. Creatine kinase activity was higher in broiler breeders fed ad libitum compared with layers and restricted broiler breeders. The activity of aspartate transaminase was higher in restricted layers compared with birds fed ad libitum and was similar in broiler breeders. 5. Plasma viscosity was lower in food‐restricted compared with ad libitum‐fed birds. 6. Limiti...

Simultaneous mapping of epistatic QTL in chickens reveals clusters of QTL pairs with similar genetic effects on growth

We used simultaneous mapping of interacting quantitative trait locus (QTL) pairs to study various growth traits in a chicken F2 intercross. The method was shown to increase the number of detected QTLs by 30 % compared with a traditional method detecting QTLs by their marginal genetic effects. Epistasis was shown to be an important contributor to the genetic variance of growth, with the largest impact on early growth (before 6 weeks of age). There is also evidence for a discrete set of interacting loci involved in early growth, supporting the previous findings of different genetic regulation of early and late growth in chicken. The genotype-phenotype relationship was evaluated for all interacting QTL pairs and 17 of the 21 evaluated QTL pairs could be assigned to one of four clusters in which the pairs in a cluster have very similar genetic effects on growth. The genetic effects of the pairs indicate commonly occurring dominance-by-dominance, heterosis and multiplicative interactions. The results from this study clearly illustrate the increase in power obtained by using this novel method for simultaneous detection of epistatic QTL, and also how visualization of genotype-phenotype relationships for epistatic QTL pairs provides new insights to biological mechanisms underlying complex traits.

Differential leucocyte responses to various degrees of food restriction in broilers, turkeys and ducks.

1. White blood cell responses of broilers, turkeys and ducks were examined at regular intervals after being subjected to various degrees of food restriction. 2. Restricted-fed broilers showed increases in heterophil and basophil numbers, together with a corresponding decrease in lymphocytes. The heterophil/lymphocyte ratio was raised. There were no differences between broiler strains. 3. After only one week of feeding restricted diets, heterophils were significantly raised in selected and unselected 2-week-old ducks. At 21 weeks of age, those ducks receiving 50% of food required to achieve their ad libitum-fed body weight had raised heterophils. 4. Ducks receiving food to achieve 25% of ad libitum-fed birds produced a marked basophilia, but no heterophilia. 5. After two weeks of food restriction, turkeys responded with significant heterophil/lymphocyte ratios following two degrees of restricted feeding. 6. It was concluded that in some poultry, a heterophilia may be the response to mild to moderate stress but a basophilia may result after severely stressing birds.

Effects of low dietary protein and different allocations of food during rearing and restricted feeding after peak rate of lay on egg production, fertility and hatchability in female broiler breeders

1. A 3 × 2 × 2 factorial experiment was conducted with boiler breeder females to determine the effects of body weight gain (three levels) and conventional or lower crude protein concentrations in the rations during rearing, and restricted or ad libitum feeding after the peak rate of lay on egg production, fertility, hatchability, mortality and food consumption. 2. Compared with ad libitum feeding, conventional food restriction resulted in a decrease in average daily food consumption of 0.6 during rearing, 0.2 during early lay and an increase of 0.4 after the peak rate of egg production. Mortality was decreased by more than half. 3. Restricted birds had higher total and settable egg production, fewer defective or damaged eggshells and higher fertility and hatchability than those fed ad libitum . The modified (more generous) rearing programme resulted in lower rates of egg production and higher rates of mortality compared with the conventional food restriction programme. 4. Low-protein rearing rations were associated with higher rates of food intake, higher mortalities and lower rates of egg production than the conventional protein rations. There were no differences in the fertility or hatchability of eggs between birds fed on the two concentrations of dietary crude protein. 5. Ad libitum feeding post-peak was associated with higher rates of mortality to 60 weeks of age. Postpeak feeding had little effect on the rate of lay or egg weight in conventionally restricted birds fed high protein rations or in birds fed ad libitum . Restricted feeding post-peak decreased the rate of lay and egg weight in birds on the modified restriction programme and in conventionally restricted birds fed on the low protein rations. There was no effect of post-peak feeding on fertility or hatchability of eggs. 6. The total numbers of saleable chicks per kg food consumed were 1.83, 1.72 and 0.52 for conventional, modified and ad libitum feeding during rearing; 1.56 and 1.15 for restricted and ad libitum feeding post-peak: there were no differences associated with protein concentrations of rations fed during rearing.