Soya bean meal increases litter moisture and foot pad dermatitis in maize and wheat based diets for turkeys but maize and non-soya diets lower body weight.

1. A 2 × 2 factorial experiment was conducted to compare the effects of wheat or maize based diets differing in dietary electrolyte balance (DEB) on litter moisture and foot pad dermatitis (FPD) at 4, 8 and 12 weeks of age in heavy-medium turkeys. A second objective was to investigate the effects on foot pad dermatitis of the interaction between dietary composition and artificially increasing litter moisture by adding water to the litter. 2. High DEB diets contained soya as the main protein source whereas low DEB diets did not contain soya bean meal. Diets were formulated to be iso-caloric and iso-nitrogenous in each of 3 successive 4-week phases following recommended dietary compositions. DEB concentrations were 330, 290 and 250 mEq/kg in high DEB diets and 230, 200 and 180 mEq/kg in low DEB diets. 3. Litter moisture and mean FPD score were higher in turkeys fed on high DEB diets compared with low DEB diets whereas there was no difference between maize and wheat. 4. Food intake was similar and body weight was lower after litter moisture was artificially raised in the wet compared with the dry litter treatment and there was no interaction with dietary composition. 5. Mean body weight and feed intake were higher in turkeys fed on wheat compared with maize and in high DEB compared with low DEB diets at 12 weeks of age. 6. Lowering dietary DEB for turkeys may improve litter moisture and lower the prevalence of FPD in commercial turkey flocks.

Identification of a practical and reliable method for the evaluation of litter moisture in turkey production.

1. An experiment was conducted to compare 5 different methods for the evaluation of litter moisture. 2. For litter collection and assessment, 55 farms were selected, one shed from each farm was inspected and 9 points were identified within each shed. 3. For each device, used for the evaluation of litter moisture, mean and standard deviation of wetness measures per collection point were assessed. 4. The reliability and overall consistency between the 5 instruments used to measure wetness were high (α = 0.72). 5. Measurement of three out of the 9 collection points were sufficient to provide a reliable assessment of litter moisture throughout the shed. 6. Based on the direct correlation between litter moisture and footpad lesions, litter moisture measurement can be used as a resource based on-farm animal welfare indicator. 7. Among the 5 methods analysed, visual scoring is the most simple and practical, and therefore the best candidate to be used on-farm for animal welfare assessment.

Effect of crude protein concentration and dietary electrolyte balance on litter quality, foot pad dermatitis, growth performance and processing yields in two medium heavy turkey hybrids.

1. An experiment was conducted to investigate the effect of crude protein (CP) concentration and dietary electrolyte balance (DEB) on growth performance, processing yields, litter quality and foot pad dermatitis (FPD) in male turkeys from two commercial hybrids. Soya bean meal was replaced by vegetable protein sources selected for lower K concentrations to lower DEB in order to improve litter quality and subsequent quality of foot pads. 2. Effects of CP on litter friability and wetness were not consistent during the production period. FPD in turkeys fed on diets with low CP was significantly lower than FPD in turkeys fed on diets with high CP until 84 d. Growth performance was adversely affected at low CP. Processing yields were not affected by CP. 3. Litter was significantly dryer in pens of turkeys fed on diets with low DEB than in pens of turkeys fed on diets with high DEB. FPD in turkeys fed on diets with low DEB was significantly lower than in turkeys fed on diets with high DEB. Growth performance and processing yields were adversely affected at low DEB. 4. FPD in turkey hybrid A was higher than in turkey hybrid B at 28 d of age. Thereafter, no differences in FPD between turkey hybrids were observed. Growth performance and processing yields were not affected by turkey hybrid. 5. Overall, a significant interaction effect of CP × DEB was observed for FCR: in turkeys fed on the high DEB treatment, FCR of turkeys fed on the high CP diets was lower than FCR of turkeys fed on the low CP (LCP) diets whereas on the low DEB treatment, FCR was not affected by CP treatment. 6. It was concluded that litter quality can be improved and FPD may be decreased in turkeys fed on diets containing lower CP and DEB levels.

Genetic basis of leg health and its relationship with body weight in purebred turkey lines.

The aims of this study were to estimate the genetic parameters for leg and foot health and mobility in purebred turkey lines and their genetic correlations with BW. Traits were gait score (GS) as an overall measure of leg health, footpad dermatitis (FPD), and 2 skeletal leg health traits, namely, valgus and varus deformities (VVD) and tibial dyschondroplasia (TD). Data from 4 different lines, comprising 3 yr of phenotypic records and 4 yr of pedigree information per line, were used. The sex average BW for the lines at 18 wk ranged from 19.1 kg (line A) to 12.4 kg (line D). The prevalence of VVD ranged from 5.2 to 14.6% and for TD from 4.1 to 23.2%. The average score for FPD on a scale of 0 to 100 ranged from 48.5 to 61.1. Gait Score was scored on a scale of 1 to 5, standardized to a mean of 3 and SD of 1. Heritabilities were estimated at 0.08 to 0.13 for GS, 0.01 to 0.07 for VVD, 0.06 to 0.12 for TD, and 0.10 to 0.15 for FPD (all SE ≤ 0.02). Estimates of the genetic correlations between VVD and TD ranged from 0.03 to 0.21 (all SE ≤ 0.08), and estimates of these with GS ranged from 0.07 to 0.87 (all SE ≤ 0.09). The genetic correlations of FPD with GS ranged from 0.00 to 0.34 (all SE ≤ 0.04), and with the skeletal leg health traits from -0.06 to 0.33 (all SE ≤ 0.06). Body weight showed estimated genetic correlations ranging from 0.28 to 0.51 (all SE ≤ 0.06) with GS, -0.06 to 0.50 (all SE ≤ 0.13) with VVD/TD and 0.05 to 0.34 (all SE ≤ 0.05) with FPD. The results suggest that selection for improved leg health can be incorporated effectively in a commercial turkey breeding program using balanced breeding goals, in which production traits and leg health traits are considered simultaneously.

Gait in ducks (Anas platyrhynchos) and chickens (Gallus gallus) - similarities in adaptation to high growth rate.

Genetic selection for increased growth rate and muscle mass in broiler chickens has been accompanied by mobility issues and poor gait. There are concerns that the Pekin duck, which is on a similar selection trajectory (for production traits) to the broiler chicken, may encounter gait problems in the future. In order to understand how gait has been altered by selection, the walking ability of divergent lines of high- and low-growth chickens and ducks was objectively measured using a pressure platform, which recorded various components of their gait. In both species, lines which had been selected for large breast muscle mass moved at a slower velocity and with a greater step width than their lighter conspecifics. These high-growth lines also spent more time supported by two feet in order to improve balance when compared with their lighter, low-growth conspecifics. We demonstrate that chicken and duck lines which have been subjected to intense selection for high growth rates and meat yields have adapted their gait in similar ways. A greater understanding of which components of gait have been altered in selected lines with impaired walking ability may lead to more effective breeding strategies to improve gait in poultry.

The genomic architecture of resistance to Campylobacter jejuni intestinal colonisation in chickens.

BACKGROUND: Campylobacter is the leading cause of foodborne diarrhoeal illness in humans and is mostly acquired from consumption or handling of contaminated poultry meat. In the absence of effective licensed vaccines and inhibitors, selection for chickens with increased resistance to Campylobacter could potentially reduce its subsequent entry into the food chain. Campylobacter intestinal colonisation levels are influenced by the host genetics of the chicken. In the present study, two chicken populations were used to investigate the genetic architecture of avian resistance to colonisation: (i) a back-cross of two White Leghorn derived inbred lines [(61 x N) x N] known to differ in resistance to Campylobacter colonisation and (ii) a 9(th) generation advanced intercross (61 x N) line. RESULTS: The level of colonisation with Campylobacter jejuni following experimental infection was found to be a quantitative trait. A back-cross experiment using 1,243 fully informative single nucleotide polymorphism (SNP) markers revealed quantitative trait loci (QTL) on chromosomes 7, 11 and 14. In the advanced intercross line study, the location of the QTL on chromosome 14 was confirmed and refined and two new QTLs were identified located on chromosomes 4 and 16. Pathway and re-sequencing data analysis of the genes located in the QTL candidate regions identified potential pathways, networks and candidate resistance genes. Finally, gene expression analyses were performed for some of the candidate resistance genes to support the results. CONCLUSION: Campylobacter resistance in chickens is a complex trait, possibly involving the Major Histocompatibility Complex, innate and adaptive immune responses, cadherins and other factors. Two of the QTLs for Campylobacter resistance are co-located with Salmonella resistance loci, indicating that it may be possible to breed simultaneously for enhanced resistance to both zoonoses.

Predicted optimum ambient temperatures for broiler chickens to dissipate metabolic heat do not affect performance or improve breast muscle quality.

An experiment was conducted to test the hypothesis that muscle damage in fast-growing broiler chickens is associated with an ambient temperature that does not permit the birds to lose metabolic heat resulting in physiological heat stress and a reduction in meat quality. The experiment was performed in 4 climate chambers and was repeated in 2 trials using a total of 200 male broiler chickens. Two treatments compared the recommended temperature profile and a cool regimen. The cool regimen was defined by a theoretical model that determined the environmental temperature that would enable heat generated by the bird to be lost to the environment. There were no differences in growth rate or feed intake between the two treatments. Breast muscles from birds on the recommended temperature regimen were lighter, less red and more yellow than those from the cool temperature regimen. There were no differences in moisture loss or shear strength but stiffness was greater in breast muscle from birds housed in the cool compared to the recommended regimen. Histopathological changes in the breast muscle were similar in both treatments and were characterised by mild to severe myofibre degeneration and necrosis with regeneration, fibrosis and adipocyte infiltration. There was no difference in plasma creatine kinase activity, a measure of muscle cell damage, between the two treatments consistent with the absence of differences in muscle pathology. It was concluded that breast muscle damage in fast-growing broiler chickens was not the result of an inability to lose metabolic heat at recommended ambient temperatures. The results suggest that muscle cell damage and breast meat quality concerns in modern broiler chickens are related to genetic selection for muscle yields and that genetic selection to address breast muscle integrity in a balanced breeding programme is imperative.

Footpad dermatitis and pain assessment in turkey poults using analgesia and objective gait analysis.

The relationships between litter moisture, footpad dermatitis (FPD) and pain in medium-heavy turkey strains was studied by gait analysis in two medium-heavy with and without analgesia (betamethasone or bupivacaine). The relationship between FPD and litter moisture was linear above a breakpoint of 49% litter moisture, and there were no differences between the two breeds in susceptibility to FPD. Gait analysis showed higher impulse, single support time, stride time and stance time in breed A compared to breed B. Significant interactions between breed, litter and analgesic for impulse, single support time and stride time were associated with higher means for breed A given saline injection on wet litter. Data from betamethasone analgesia in Experiments 1 and 3 were combined for analysis. Peak vertical force was higher in saline- compared to betamethasone-treated birds. Compared to the wet (high FPD) litter treatments, birds on dry (low FPD) litter had greater speed and lower double support time and longer stride length. Turkeys kept on wet litter had a longer stride length compared to dry litter when given saline, whereas in betamethasone-treated birds the means were similar. There were no differences between birds with or without bupivacaine analgesia. Peak vertical force was higher in breed A than B and in birds with a low FPD compared to a high FPD score. It was concluded that breeds A and B did not differ in susceptibility to develop FPD when housed on wet litter but may have natural gait differences. Significant changes in gait parameters were associated with wet litter and with analgesic treatments. The results showed that FPD affected the gait of the turkeys and, combined with evidence of behavioural changes when given analgesia, suggest that footpad lesions are painful.

Behavioural assessment of pain in commercial turkeys (Meleagris gallopavo) with foot pad dermatitis.

Two experiments were conducted to investigate the differences in susceptibility to foot pad dermatitis (FPD) of two medium-heavy lines of turkeys, and whether FPD is painful, by detailed analysis of behaviour in birds with and without analgesic treatment (betamethasone). Turkeys housed on dry litter in the first experiment generally had more frequent bouts of different behaviours that were of shorter duration than birds on wet litter. T-patterns (behavioural sequences) were more frequent, varied and complex on dry than on wet litter. Betamethasone-injected birds of line B, but not breed A, had shorter resting and longer standing durations on wet litter than saline-injected birds. In the second experiment, turkeys on wet litter given saline stood less and rested more than all other treatment groups, suggesting that they experienced pain that was alleviated in birds receiving betamethasone. Turkeys on dry litter had more frequent, varied and complex patterns of behaviour than turkeys on wet litter and birds kept on intermediate litter wetness. Betamethasone provision increased pattern variety regardless of litter treatment. Turkeys with low FPD scores transferred to wet litter and given saline injections had a longer total duration of resting and shorter duration of standing compared to betamethasone-treated birds. Low FPD birds transferred to wet litter had a similar number of patterns and total pattern occurrence as high FPD birds transferred to dry litter. Betamethasone increased pattern variety and frequency compared to saline injections whereas overall pattern complexity was similar. It was concluded that wet litter affects the behaviour of turkey poults independently of FPD and that betamethasone may also change the behaviour of turkeys. There was some evidence from analgesic treatment and T-pattern analyses that FPD was painful. However, there was no evidence of differences in susceptibility to FPD of the two commercial hybrids.

Identification and characterisation of alternative transcriptional variants of PDGFRL in two lines of commercial poultry.

The platelet-derived growth factor (PDGF) family of genes and their receptors are involved in angiogenesis and steroid hormone production. A putative member of the family, platelet-derived growth factor receptor-like (PDGFRL), has been implicated in steroid-based feedback mechanisms within the chicken reproductive system. Three potential variants of PDGFRL were identified in the chicken, supported by in silico prediction and EST sequencing. The three potential transcripts have been further verified and the 5' terminal regions sequenced in this research. The sum of expression of all three transcripts in broiler breeders (the parents of broiler chickens) has been shown to be consistent with total expression of the gene. However, cumulative expression of the three transcripts in a range of tissues in egg layers was significantly short of total expression, indicating the existence of potential additional variants. Two additional variants were subsequently identified in egg layer cerebellum tissue and the 5' terminal regions sequenced. Sequence analysis of the three initial variants suggests that only one variant, which was the most abundant in broiler breeders and the majority of egg layer tissues, had a functional signal peptide. Although 5' RACE identified two additional transcripts in egg layers, the most likely protein translations indicated that these variants possessed no functional signal peptide, suggesting that, if they have a function, it is not a traditional one.

Maternal genealogical patterns of chicken breeds sampled in Europe.

The aim of this study was to investigate the maternal genealogical pattern of chicken breeds sampled in Europe. Sequence polymorphisms of 1256 chickens of the hypervariable region (D-loop) of mitochondrial DNA (mtDNA) were used. Median-joining networks were constructed to establish evolutionary relationships among mtDNA haplotypes of chickens, which included a wide range of breeds with different origin and history. Chicken breeds which have had their roots in Europe for more than 3000 years were categorized by their founding regions, encompassing Mediterranean type, East European type and Northwest European type. Breeds which were introduced to Europe from Asia since the mid-19th century were classified as Asian type, and breeds based on crossbreeding between Asian breeds and European breeds were classified as Intermediate type. The last group, Game birds, included fighting birds from Asia. The classification of mtDNA haplotypes was based on Liu et al.'s (2006) nomenclature. Haplogroup E was the predominant clade among the European chicken breeds. The results showed, on average, the highest number of haplotypes, highest haplotype diversity, and highest nucleotide diversity for Asian type breeds, followed by Intermediate type chickens. East European and Northwest European breeds had lower haplotype and nucleotide diversity compared to Mediterranean, Intermediate, Game and Asian type breeds. Results of our study support earlier findings that chicken breeds sampled in Europe have their roots in the Indian subcontinent and East Asia. This is consistent with historical and archaeological evidence of chicken migration routes to Europe.

Unexpected consequences of genetic selection in broilers and turkeys: problems and solutions.

1. Genetic theory leads to the expectation that unexpected consequences of genetic selection for production traits will inevitably occur and that these changes are likely to be undesirable. 2. Both artificial selection for production efficiency and "natural" selection for adaptation to the production environment result in selection sweeps that increase the frequencies of rare recessive alleles that have a negative effect on fitness. 3. Fitness is broadly defined as any trait that affects the ability to survive, reproduce and contribute to the next generation, such as musculoskeletal disease in growing broiler chickens and multiple ovulation in adult broiler parents. 4. Welfare concerns about the negative effects of genetic selection on bird welfare are sometimes exaggerated but are nevertheless real. Breeders have paid increasing attention to these traits over several decades and have demonstrated improvement in pedigree flocks. There is an urgent need to monitor changes in commercial flocks to ensure that genetic change is accompanied by improvements in that target population. 5. New technologies for trait measurement, whole genome selection and targeted genetic modification hold out the promise of efficient and rapid improvement of welfare traits in future breeding of broiler chickens and turkeys. The potential of targeted genetic modification for enhancing welfare traits is considerable, but the goal of achieving public acceptability for the progeny of transgenic poultry will be politically challenging.

Supplementary biotin decreases tibial bone weight, density and strength in riboflavin-deficient starter diets for turkey poults.

1. Growth and skeletal responses to different dietary concentrations of riboflavin and biotin were compared in turkey poults from hatch to 21 d of age. The birds were fed on a turkey starter diet with different concentrations of supplementary riboflavin (0, 20 and 40 mg/kg) and biotin (0, 0.3 and 0.6 mg/kg) in a factorial design. 2. Poults fed on diets with no supplementary riboflavin had poor gait scores, decreased times to sit and higher rates of culling compared to poults fed on the control diet (20 mg riboflavin and 0.3 mg biotin/kg [corrected] diet). Histologically, riboflavin deficiency was associated with a peripheral neuropathy similar to that described previously in chicks and, unexpectedly, in growth plate abnormalities. 3. Tibiae of poults fed on the control diet were larger, more dense, stronger and stiffer than the diets with no supplementary riboflavin. 4. Increasing supplementary biotin in poults fed on diets with no supplementary riboflavin was associated with a decrease in tibia weight, density, strength and stiffness. 5. The results demonstrated that riboflavin deficiency in fast-growing turkey poults was associated with growth retardation, growth plate disturbance and peripheral nerve dysfunction leading to an inability to walk.

Traditional and commercial turkeys show similar susceptibility to foot pad dermatitis and behavioural evidence of pain.

1. An experiment was conducted to compare the development and clinical significance of foot pad dermatitis (FPD) in 4 lines of turkey poults kept on wet or dry litter for 6 d. 2. Turkeys kept on wet litter were less active and expressed fewer unique sequences of behaviour than poults kept on dry litter, suggesting that high FPD scores are associated with pain during movement. 3. Heavier lines of turkeys had higher mean foot scores that developed earlier, than those in a traditional line, but the effect was relatively small and not statistically significant after 6 d, whereas there were large differences between individuals within line. 4. Body weight gains were greater, and feed intake was lower in the commercial lines kept on dry litter compared with wet litter. There were no differences in water intake between poults kept on wet or dry litter.

The use of conditioned place preference to determine broiler preferences for quantitative or qualitative dietary restriction.

1. Calcium propionate (CAP) may improve the welfare of feed restricted broiler breeders by improving their satiety when included within the feed ration. However, the evidence for this is mixed. 2. This study used a closed economy conditioned place preference (CPP) task and aimed to identify whether broilers (as a model for broiler breeders) preferred an environment associated with quantitative food restriction (QFR) or an environment associated with a diet quality-adjusted by the inclusion of CAP. Birds taught to associate different environments with QFR and ad libitum (AL) access to feed were used to validate the methodology. 3. The two treatment groups were (1) QFR/AL (n = 12) in which birds alternated every 2 d between QFR and ad libitum access to food, and (2) QFR/CAP (n = 12) in which birds alternated every 2 d between QFR and QFR + calcium propionate (increased from 3-9% over the study period). Birds were taught to associate one diet option with vertical stripes and the other with horizontal black and white stripes. Each bird was tested twice for a CPP (once per diet). 4. QFR/AL birds showed a significant preference for the pen associated with ad libitum access to feed, but only when tested hungry (i.e. fed QFR on day of testing). QFR/CAP birds did not show a preference under either hunger state. 5. Reasons for the failure of QFR/CAP birds to show a preference are unclear but could include a lack of preference or failure to learn the task. 6. The existence of state-dependent effects indicates that care is needed in the design of future CPP studies and that the effect of calcium propionate and level of hunger on ability to learn a CPP needs further investigation.

Changes in ovarian function and egg production in commercial broiler breeders through 40 weeks of lay.

1. Egg production, body weight, feed intake and mortality were recorded in over 78 000 broiler breeder hens in 4 commercial flocks housed in 16 houses from early lay though 40 weeks of lay. A total of 420 hens were sampled at regular intervals throughout the laying period to determine the changes in body weight and the numbers of yellow follicles, paired follicles and hierarchical positions with time in the ovary throughout lay to relate ovarian function to productivity. Average egg weight was recorded weekly from one flock. 2. A quadratic equation fitted the changes in time for the number of yellow follicles, body weight, feed intake and mortality; a linear equation described the decline in the number positions in the hierarchy and there was a linear decline in the logistic scale of the proportions of yellow follicles developing as pairs of similar weight. Egg production was described by a cubic equation and egg weight by a line plus exponential model. 3. The average number of yellow follicles declined from 7·2 to 5·4 and the number of hierarchical positions from 6 to 5 from 4 to 40 weeks after photostimulation. The proportion of follicles developing as pairs of similar weight was over 25% at the onset of lay and declined to less than 10% from 20 weeks after photostimulation, representing a substantial loss of potential productivity. 4. Body weight and egg production were similar to the breeder's targets whereas average egg weight and mortality were higher than expected. 5. The relationship defining ovarian function will facilitate the development of an improved model of egg production in broiler breeder hens.

Many quantitative trait loci for feather growth in an F(2) broiler × layer cross collocate with body weight loci.

1. A genome-wide scan of 467 F(2) progeny of a broiler x layer cross was conducted to identify quantitative trait loci (QTL) affecting the rate of growth of the tail, wing and back feathers, and the width of the breast feather tract, at three weeks of age. 2. Correlations between the traits ranged from 0·36 to 0·61. Males had longer tail and wing feathers and shorter back feathers than females. Breast feather tract width was greater in females than males. 3. QTL effects were generally additive and accounted for 11 to 45% of sex average feather lengths of the breeds, and 100% of the breast feather tract width. Positive and negative alleles were inherited from both lines, whereas the layer allele was larger than the broiler allele after adjusting for body weight. 4. A total of 4 genome-significant and 4 suggestive QTL were detected. At three or 6 weeks of age, 5 of the QTL were located in similar regions as QTL for body weight. 5. Analysis of a model with body weight at three weeks as a covariate identified 5 genome significant and 6 suggestive QTL, of which only two were coincident with body weight QTL. One QTL for feather length at 148 cM on GGA1 was identified at a similar location in the unadjusted analysis. 6. The results suggest that the rate of feather growth is largely controlled by body weight QTL, and that QTL specific for feather growth also exist.

Characterization of the genetic diversity, structure and admixture of British chicken breeds.

The characterization of livestock genetic diversity can inform breed conservation initiatives. The genetic diversity and genetic structure were assessed in 685 individual genotypes sampled from 24 British chicken breeds. A total of 239 alleles were found across 30 microsatellite loci with a mean number of 7.97 alleles per locus. The breeds were highly differentiated, with an average F(ST) of 0.25, similar to that of European chicken breeds. The genetic diversity in British chicken breeds was comparable to that found in European chicken breeds, with an average number of alleles per locus of 3.59, ranging from 2.00 in Spanish to 4.40 in Maran, and an average expected heterozygosity of 0.49, ranging from 0.20 in Spanish to 0.62 in Araucana. However, the majority of breeds were not in Hardy-Weinberg Equilibrium, as indicated by heterozygote deficiency in the majority of breeds (average F(IS) of 0.20), with an average observed heterozygote frequency of 0.39, ranging from 0.15 in Spanish to 0.49 in Cochin. Individual-based clustering analyses revealed that most individuals clustered to breed origin. However, genetic subdivisions occurred in several breeds, and this was predominantly associated with flock supplier and occasionally by morphological type. The deficit of heterozygotes was likely owing to a Wahlund effect caused by sampling from different flocks, implying structure within breeds. It is proposed that gene flow amongst flocks within breeds should be enhanced to maintain the current levels of genetic diversity. Additionally, certain breeds had low levels of both genetic diversity and uniqueness. Consideration is required for the conservation and preservation of these potentially vulnerable breeds.

Complex traits analysis of chicken growth using targeted genetical genomics.

Dissecting the genetic control of complex trait variation remains very challenging, despite many advances in technology. The aim of this study was to use a major growth quantitative trait locus (QTL) in chickens mapped to chromosome 4 as a model for a targeted approach to dissect the QTL. We applied a variant of the genetical genomics approach to investigate genome-wide gene expression differences between two contrasting genotypes of a marked QTL. This targeted approach allows the direct quantification of the link between the genotypes and the genetic responses, thus narrowing the QTL-phenotype gap using fewer samples (i.e. microarrays) compared with the genome-wide genetical genomics studies. Four differentially expressed genes were localized under the region of the QTL. One of these genes is a potential positional candidate gene (AADAT) that affects lysine and tryptophan metabolism and has alternative splicing variants between the two genotypes. In addition, the lysine and glycolysis metabolism pathways were significantly enriched for differentially expressed genes across the genome. The targeted approach provided a complementary route to fine mapping of QTL by characterizing the local and the global downstream effects of the QTL and thus generating further hypotheses about the action of that QTL.

Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens.

Extensive phenotypic variation is a common feature among village chickens found throughout much of the developing world, and in traditional chicken breeds that have been artificially selected for traits such as plumage variety. We present here an assessment of traditional and village chicken populations, for fine mapping of Mendelian traits using genome-wide single-nucleotide polymorphism (SNP) genotyping while providing information on their genetic structure and diversity. Bayesian clustering analysis reveals two main genetic backgrounds in traditional breeds, Kenyan, Ethiopian and Chilean village chickens. Analysis of linkage disequilibrium (LD) reveals useful LD (r(2) ≥ 0.3) in both traditional and village chickens at pairwise marker distances of ~10 Kb; while haplotype block analysis indicates a median block size of 11-12 Kb. Association mapping yielded refined mapping intervals for duplex comb (Gga 2:38.55-38.89 Mb) and rose comb (Gga 7:18.41-22.09 Mb) phenotypes in traditional breeds. Combined mapping information from traditional breeds and Chilean village chicken allows the oocyan phenotype to be fine mapped to two small regions (Gga 1:67.25-67.28 Mb, Gga 1:67.28-67.32 Mb) totalling ~75 Kb. Mapping the unmapped earlobe pigmentation phenotype supports previous findings that the trait is sex-linked and polygenic. A critical assessment of the number of SNPs required to map simple traits indicate that between 90 and 110K SNPs are required for full genome-wide analysis of haplotype block structure/ancestry, and for association mapping in both traditional and village chickens. Our results demonstrate the importance and uniqueness of phenotypic diversity and genetic structure of traditional chicken breeds for fine-scale mapping of Mendelian traits in the species, with village chicken populations providing further opportunities to enhance mapping resolutions.