Single nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotype differences.

BACKGROUND: Analyses of sequence variants of two distinct and highly inbred chicken lines allowed characterization of genomic variation that may be associated with phenotypic differences between breeds. These lines were the Leghorn, the major contributing breed to commercial white-egg production lines, and the Fayoumi, representative of an outbred indigenous and robust breed. Unique within- and between-line genetic diversity was used to define the genetic differences of the two breeds through the use of variant discovery and functional annotation. RESULTS: Downstream fixation test (F ST ) analysis and subsequent gene ontology (GO) enrichment analysis elucidated major differences between the two lines. The genes with high F ST values for both breeds were used to identify enriched gene ontology terms. Over-enriched GO annotations were uncovered for functions indicative of breed-related traits of pathogen resistance and reproductive ability for Fayoumi and Leghorn, respectively. CONCLUSIONS: Variant analysis elucidated GO functions indicative of breed-predominant phenotypes related to genomic variation in the lines, showing a possible link between the genetic variants and breed traits.

Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array.

BACKGROUND: Indigenous populations of animals have developed unique adaptations to their local environments, which may include factors such as response to thermal stress, drought, pathogens and suboptimal nutrition. The survival and subsequent evolution within these local environments can be the result of both natural and artificial selection driving the acquisition of favorable traits, which over time leave genomic signatures in a population. This study's goals are to characterize genomic diversity and identify selection signatures in chickens from equatorial Africa to identify genomic regions that may confer adaptive advantages of these ecotypes to their environments. RESULTS: Indigenous chickens from Uganda (n = 72) and Rwanda (n = 100), plus Kuroilers (n = 24, an Indian breed imported to Africa), were genotyped using the Axiom® 600 k Chicken Genotyping Array. Indigenous ecotypes were defined based upon location of sampling within Africa. The results revealed the presence of admixture among the Ugandan, Rwandan, and Kuroiler populations. Genes within runs of homozygosity consensus regions are linked to gene ontology (GO) terms related to lipid metabolism, immune functions and stress-mediated responses (FDR < 0.15). The genes within regions of signatures of selection are enriched for GO terms related to health and oxidative stress processes. Key genes in these regions had anti-oxidant, apoptosis, and inflammation functions. CONCLUSIONS: The study suggests that these populations have alleles under selective pressure from their environment, which may aid in adaptation to harsh environments. The correspondence in gene ontology terms connected to stress-mediated processes across the populations could be related to the similarity of environments or an artifact of the detected admixture.

The effect of hyperammonemia on myostatin and myogenic regulatory factor gene expression in broiler embryos.

Myogenesis is facilitated by four myogenic regulatory factors and is significantly inhibited by myostatin. The objective of the current study was to examine embryonic gene regulation of myostatin/myogenic regulatory factors, and subsequent manipulations of protein synthesis, in broiler embryos under induced hyperammonemia. Broiler eggs were injected with ammonium acetate solution four times over 48 h beginning on either embryonic day (ED) 15 or 17. Serum ammonia concentration was significantly higher (P<0.05) in ammonium acetate injected embryos for both ED17 and ED19 collected samples when compared with sham-injected controls. Expression of mRNA, extracted from pectoralis major of experimental and control embryos, was measured using real-time quantitative PCR for myostatin, myogenic regulatory factors myogenic factor 5, myogenic determination factor 1, myogenin, myogenic regulatory factor 4 and paired box 7. A significantly lower (P<0.01) myostatin expression was accompanied by a higher serum ammonia concentration in both ED17 and ED19 collected samples. Myogenic factor 5 expression was higher (P<0.05) in ED17 collected samples administered ammonium acetate. In both ED17 and ED19 collected samples, myogenic regulatory factor 4 was lower (P⩽0.05) in ammonium acetate injected embryos. No significant difference was seen in myogenic determination factor 1, myogenin or paired box 7 expression between treatment groups for either age of sample collection. In addition, there was no significant difference in BrdU staining of histological samples taken from treated and control embryos. Myostatin protein levels were evaluated by Western blot analysis, and also showed lower myostatin expression (P<0.05). Overall, it appears possible to inhibit myostatin expression through hyperammonemia, which is expected to have a positive effect on embryonic myogenesis and postnatal muscle growth.

Atherosclerosis-susceptible and atherosclerosis-resistant pigeon aortic cells express different genes in vivo.

Spontaneous atherosclerosis in the White Carneau (WC-As) pigeon is inherited as a single gene disorder, and its progression closely mirrors the human disease. Representational difference analysis and microarray were used to identify genes that were differentially expressed between the susceptible WC-As and resistant Show Racer (SR-Ar) aortic tissue. The RNA extracted from 1-d-old squab aortas was used to make cDNA for each experiment. Fifty-six unique genes were found using representational difference analysis, with 25 exclusively expressed in the WC-As, 15 exclusive to the SR-Ar, and 16 nonexclusive genes having copy number variation between breeds. Caveolin and ß-actin were expressed in the WC-As, whereas the proteasome maturation protein and the transcription complex CCR4-NOT were exclusive to the SR-Ar. Microarray analysis revealed 48 genes with differential expression. Vascular endothelial growth factor and p53 binding protein were among the 17 genes upregulated in the WC-As. Thirty-one genes were upregulated in the SR-Ar including the transforming growth factor-ß signaling factor SMAD2 and heat shock protein 90. Genes representing several biochemical pathways were distinctly different between breeds. The most striking divergences were in cytoskeletal remodeling, proteasome activity, cellular respiration, and immune response. Actin cytoskeletal remodeling appears to be one of the first differences between susceptible and resistant breeds, lending support to the smooth muscle cell phenotypic reversion hypothesis of human atherogenesis.

Metabolic profiling of late-term turkey embryos by microarrays.

The last stages of embryonic development are crucial for turkeys as their metabolism shifts to accommodate posthatch survival and growth. To better understand the metabolic change that occurs during the perinatal period, focused microarray methodology was used to identify changes in the expression of key genes that control metabolism of turkey embryos from 20 d of incubation (E) until hatch (E28). Gene expression patterns were evaluated in liver, pectoral muscle, and hatching muscle and were associated with measured embryonic growth and tissue glycogen concentration. Within the studied period, the expression of 60 genes significantly changed in liver, 53 in pectoral muscle, and 51 in hatching muscle. Genes related to lipid metabolism (enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase, 3-hydroxymethylglutaryl-CoA reductase, acetyl-CoA carboxylase, lipoprotein lipase, and thyroxine deiodinase) had reduced expression between E22 and E26, corresponding to the period of expected limited oxygen supply. In contrast, genes related to opposing pathways in carbohydrate metabolism, such as glycolysis and gluconeogenesis (hexokinases, glucose-6 phosphatase, phosphofructokinases, glucose 1-6 phosphatase, pyruvate kinase, and phosphoenolpyruvate carboxykinase), or glycogenesis and glycogenolysis (glycogen synthase and glycogen phosphorylase) had rather static expression patterns between E22 and E26, indicating their enzymatic activity must be under posttranscriptional control. Metabolic survey by microarray methodology brings new insights into avian embryonic development and physiology.

Differential expression of genes characterizing myofibre phenotype.

Skeletal muscle is composed of metabolically heterogeneous myofibres that exhibit high plasticity at both the morphological and transcriptional levels. The objective of this study was to employ microarray analysis to elucidate the differential gene expression between the tonic-'red' anterior latissimus dorsi (ALD) muscle, the phasic-'white' posterior latissimus dorsi (PLD) and 'mixed'-phenotype biceps femoris (BF) in 1-week-and 19-week-old male turkeys. A total of 170 differentially expressed genes were identified in the muscle samples analysed (P < 0.05). Gene GO analysis software was utilized to identify top gene networks and metabolic pathways involving differentially expressed genes. Quantitative real-time PCR for selected genes (BAT2D, CLU, EGFR and LEPROT) was utilized to validate the microarray data. The largest differences were observed between ALD and PLD muscles, in which 32 genes were over-expressed and 82 genes were under-expressed in ALD1-PLD1 comparison, and 70 genes were over-expressed and 70 under-expressed in ALD19-PLD19 comparison. The largest number of genes over-expressed in ALD muscles, as compared to other muscles, code for extracellular matrix proteins such as dystroglycan and collagen. The gene analysis revealed that phenotypically 'red' BF muscle has high expression of glycolytic genes usually associated with the 'white' muscle phenotype. Muscle-specific differences were observed in expression levels of genes coding for proteins involved in mRNA processing and translation regulation, proteosomal degradation, apoptosis and insulin resistance. The current findings may have large implications in muscle-type-related disorders and improvement of muscle quality in agricultural species.

Direct fed microbial supplementation repartitions host energy to the immune system.

Direct fed microbials and probiotics are used to promote health in livestock and poultry; however, their mechanism of action is still poorly understood. We previously reported that direct fed microbial supplementation in young broilers reduced ileal respiration without changing whole-body energy expenditure. The current studies were conducted to further investigate the effects of a direct fed microbial on energy metabolism in different tissues of broilers. One hundred ninety-two 1-d-old broiler chicks (16 chicks/pen) were randomly assigned to 2 dietary groups: standard control starter diet (CSD) and CSD plus direct fed microbial (DFMD; 0.3%) with 6 pens/treatment. Body weight, feed consumption, whole-body energy expenditure, organ mass, tissue respiration rates, and peripheral blood mononuclear cell (PBMC) ATP concentrations were measured to estimate changes in energy metabolism. No differences in whole body energy expenditure or BW gain were observed; however, decreased ileal O(2) respiration (P < 0.05) was measured in DFMD fed broilers. In contrast, the respiration rate of the thymus in those broilers was increased (P < 0.05). The PBMC from DFMD fed broilers had increased ATP concentrations and exhibited increased ATP turnover (P < 0.01). To determine if the increased energy consumption by PBMC corresponded with an altered immune response, broilers were immunized with sheep red blood cells (SRBC) and assayed for differences in their humoral response. The DFMD-fed broilers had a faster rate of antigen specific IgG production (P < 0.05) and an increase in total IgA (P < 0.05). Collectively, these data indicate that supplementation with the direct fed microbial used in this study resulted in energy re-partitioning to the immune system and an increase in antibody production independent of changes in whole body metabolism or growth performance.

Genomic regions associated with antibody response to sheep red blood cells in the chicken.

F(1) and F(2) populations were generated by crossing two lines of chickens divergently selected from a common founder population for 32 generations for either high or low antibody response 5 days post-injection of a non-pathogenic antigen, sheep red blood cells (SRBCs). The number of loci with major effects on day 5 SRBC titers was estimated to be more than 7 in this population. There was a significant association between MHC haplotype and day 5 antibody titers as well as body weight at sexual maturity. A significant difference between reciprocal F(2) crosses for both 5- and 12-day antibody titers suggests that sex chromosome and/or parent of origin effects on autosomal loci have an important role in immune response. A single marker-trait association analysis on 1024 genetic markers and 128 F(2) individuals detected 11 genomic regions associated with antibody response traits and 17 regions associated with body weight gain. Several of the genomic regions identified as being associated with antibody response have been described previously, while novel regions associated with antibody response were identified on chromosomes 11 and 24. Based on the lack of overlap of the regions associated with body weight and antibody response, we conclude that while these phenotypes are inversely correlated in the selected lines, they are controlled by distinct genetic loci and may be reflective of intense selection pressure on loci affecting the partitioning of nutrients between the immune system and growth pathways.

Prehatch intestinal maturation of turkey embryos demonstrated through gene expression patterns.

Some of the challenges faced by neonatal turkeys include weakness, reduced feed intake, impaired growth, susceptibility to disease, and mortality. These symptoms may be due to depleted energy reserves after hatch and an immature digestive system unable to replenish energy reserves from consumed feed. To better understand enteric development in turkeys just before hatch, a new method was used to identify the patterns of intestinal gene expression by utilizing a focused microarray. The duodenums of 24 turkey embryos were sampled on embryonic day (E)20, E24, E26, and hatch (E28). The RNA populations of 96 chosen genes were measured at each time point, from which 81 significantly changed (P < 0.01). These genes were clustered by gene expression pattern similarity into 4 groups. The expression pattern of hormone receptors revealed that intestinal tissues may be less responsive to growth hormone, insulin, glucagon, and triiodothyronine during the last 48 h before hatch, when developmental emphasis switches from cell proliferation to functional maturation. Based on gene expression patterns, we concluded that at hatch, poults should have the capacity to 1) digest disaccharides but not oligopeptides, due to increased expression of sucrase-isomaltase but decreased expression of aminopeptidases and 2) absorb monosaccharides and small peptides due to high expression of sodium-glucose cotransporter-4 and peptide transporter-1.

Genetic mapping of the sex-linked barring gene in the chicken.

The sex-linked barring gene of the chicken (Gallus gallus), first identified in 1908, produces an alternating pattern of white and black bars in the adult plumage. More recent studies have shown that melanocytes in the developing feather follicle of the Barred Plymouth Rock experience premature cell death, whereas initially it was thought that melanocytes remained viable in the region of the feather devoid of pigmentation but were simply inhibited from synthesizing melanin. In an attempt to reconcile these 2 different hypotheses at the molecular level, we have taken a gene mapping approach to isolate the sex-linked barring gene variant. We developed a mapping population consisting of 71 F2 chickens from crossing a single Barred Plymouth Rock female with a White Crested Black Polish male. Existing and novel microsatellite markers located on the chicken chromosome Z were used to genotype all individuals in our mapping population. Single marker association analysis revealed a 2.8-Mb region of the distal q arm of chicken chromosome Z to be significantly associated with the barring phenotype (P<0.001). Further analysis suggests that the causal mutation is located within a 355-kb region showing complete association with the barring phenotype and containing 5 known genes [micro-RNA 31 (miRNA-31), methylthioadenosine phosphorylase (MTAP), cyclin-dependent kinase inhibitor 2B (CDKN2B), tripartite motif 36 (TRIM36), and protein geranylgeranyltransferase type I, beta subunit (PGGT1B)], none of which have a defined role in normal melanocyte function. Although several of these genes or their homologs are known to be involved in processes that could potentially explain the barring phenotype, our results indicate that further work directed at fine-mapping this region is necessary to identify this novel mechanism of melanocyte regulation.

Focused microarrays as a method to evaluate subtle changes in gene expression.

Recent studies using microarray technologies for the chicken have reported information regarding the effects of specific experimental treatments on gene expression levels often resulting in large gene lists and limitations on the statistical significance levels detected. In most cases, with these limitations, along with thresholds of +/-2-fold differences in expression levels, that are used to create these gene lists, much of the biological information may have been overlooked. In this study, a focused 70-mer oligonucleotide microarray was developed to address the apparent limits of detection and issues with multiple testing resulting from the use of microarrays that include only a single spot (probe) for each gene. Gene expression was assayed across the development of the chicken embryonic heart from d 7 to 20 of incubation. When using a mixed-model approach and ANOVA with Bonferroni correction for multiple testing, including replicates within the focused array significantly increased the sensitivity with which differences could be detected across sample groups, as compared with single-spot data. By incorporating replication into the focused array, 50 genes were detected as being differentially expressed in the embryonic heart across the time points sampled. This compares with only 7 genes detected as being differentially expressed when a more typical, less statistically stringent single-spot analysis is conducted. Based on our observations, the use of focused microarrays allows for the thorough investigation of gene expression patterns, with detection of significant changes in gene expression of +/-7%. This limit of detection is far superior to that of real-time PCR, which is able to detect significant changes in expression from +/-33 to 55%, depending on the specific application. The ability to detect small differences in expression will allow investigators to identify subtle effects that have perhaps been overlooked in many prior assays, including single-spot arrays. Subtle shifts in gene expression are exactly those that occur during embryonic development, nutritional manipulation, and the initial stages of disease before clinical signs appear.

The expression patterns of hypoxia-inducing factor subunit alpha-1, heme oxygenase, hypoxia upregulated protein 1, and cardiac troponin T during development of the chicken heart.

Oxygen is one of the critical determinants of appropriate embryonic and fetal development, including cardiogenesis. When the demand of tissues for oxygen exceeds oxygen supply, hypoxic conditions develop. In the developing embryo, hypoxia is associated with increased fetal mortality, cerebrovascular anomalies, cardiovascular dysfunction, and altered angiogenesis. Tissue hypoxia may elicit a broad range of responses, many of which are dependent upon hypoxia-inducible transcription factors. Three genes that are stimulated by hypoxia-hypoxia-inducing factor subunit alpha-1, heme oxygenase, hypoxia upregulated protein 1, and cardiac troponin T, which is responsible for binding tropomyosin to regulate calcium binding and contractility of heart muscle-were examined in the embryonic heart of the chicken to determine if expression patterns were altered throughout development. On embryonic day (E) 7, all 3 hypoxic-induced genes were expressed at their highest levels, followed by a decrease from E7 to E19 followed by an increase between internal (E19) and external pipping (E20). The cardiac troponin T exhibited a similar expression level for E7 and E15 with a similar significant increase at E19 and E20. During these periods of development, significant changes in the primary gas exchange organs occur. Based on our observation of upregulation of these hypoxia response genes, it appears that tissue hypoxia is likely a normal component of embryonic development in the chicken based on the upregulation of hypoxia response genes.

Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. III. Skeletal integrity.

Two unique chicken F(2) populations generated from a broiler breeder male line and 2 genetically distinct inbred (>99%) chicken lines (Leghorn and Fayoumi) were used for whole genome QTL analysis. Twelve phenotypic skeletal integrity traits (6 absolute and 6 relative traits) were measured or calculated, including bone mineral content, bone mineral density, tibia length, shank length, shank weight, and shank length:shank weight. All traits were also expressed as a percentage of BW at 8 wk of age. Birds were genotyped for 269 microsatellite markers across the entire genome. The QTL affecting bone traits in chickens were detected by the QTL express program. Significance levels were obtained using the permutation test. For the 12 traits, a total of 56 significant QTL were detected at the 5% chromosome-wise significance level, of which 14 and 10 were significant at the 5% genome-wise level for the broiler-Leghorn cross and broiler-Fayoumi cross, respectively. Phenotypic variation for each trait explained by all detected QTL across the genome ranged from 12.0 to 35.6% in the broiler-Leghorn cross and 2.9 to 31.3% in the broiler-Fayoumi cross. Different QTL profiles identified between the 2 related F(2) crosses for most traits suggested that genetic background is an important factor for QTL analysis. Study of associations of biological candidate genes with skeletal integrity traits in chickens will reveal new knowledge of understanding biological process of skeletal homeostasis. The results of the current study have identified markers for bone strength traits, which may be used to genetically improve skeletal integrity in chickens by MAS, and to identify the causal genes for these traits.

Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. IV. Metabolic traits.

The current study is a comprehensive genome analysis to detect QTL affecting metabolic traits in chickens. Two unique F(2) crosses generated from a commercial broiler male line and 2 genetically distinct inbred lines (Leghorn and Fayoumi) were used in the present study. The plasma glucagon, insulin, lactate, glucose, tri-iodothyronine, thyroxine, insulin-like growth factor I, and insulin-like growth factor II concentrations at 8 wk were measured in the 2 F(2) crosses. Birds were genotyped for 269 microsatellite markers across the entire genome. The program QTL Express was used for QTL detection. Significance levels were obtained using the permutation test. For the 10 traits, a total of 6 and 9 significant QTL were detected at a 1% chromosome-wise significance level, of which 1 and 6 were significant at the 5% genome-wise level for the broiler-Leghorn cross and broiler-Fayoumi cross, respectively. Most QTL for metabolic traits in the present study were detected in Gga 2, 6, 8, 9, 13, and Z for the broiler-Leghorn cross and Gga 1, 2, 4, 7, 8, 13, 17, and E47 for the broiler-Fayoumi cross. Phenotypic variation for each trait explained by all QTL across genome ranged from 2.73 to 14.08% in the broiler-Leghorn cross and from 6.93 to 21.15% in the broiler-Fayoumi cross. Several positional candidate genes within the QTL region for metabolic traits at the 1% chromosome-wise significance level are biologically associated with the regulation of metabolic pathways of insulin, triiodothyronine, and thyroxine.

Characterization of the chicken small intestine type IIb sodium phosphate cotransporter.

Intestinal absorption and renal resorption play a critical role in overall phosphorus homeostasis in chickens. Using RNase-ligase-mediated rapid amplification of cDNA ends PCR, we obtained a cDNA from the broiler small intestine that encodes a type IIb Na-dependent phosphate transporter. The cDNA has an open reading frame of 2,022 bp and predicts a 674-amino acid protein with a molecular mass of approximately 74 kDa. Prediction of membrane spanning domains based on the hydrophilic and hydrophobic properties of the amino acids suggests 8 transmembrane domains, with both the NH(2) and COOH termini being intracellular. The Na-inorganic phosphate (Pi) IIb cotransporter has relative high homology with other type II Na-Pi cotransporters but low homology with the type I or type III Na-Pi cotransporters. Northern blot analysis demonstrated the presence of a single mRNA transcript present predominantly in the small intestine, with the highest expression in the duodenum, followed by the jejunum and ileum. In situ hybridization indicated that the Na-Pi cotransporter mRNA is expressed throughout the vertical cryptvillus axis of the small intestine. Reduction of P in the diet of chicks from hatch to 4 d of age resulted in a significant induction of Na-Pi cotransporter mRNA expression in the small intestine. Further study is needed to elucidate its physiological role in intestinal phosphate absorption in chickens.

Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. II. Body composition.

Two informative chicken F(2) populations based on crosses between a broiler breeder male line and dams from genetically distinct, highly inbred (>99%) chicken lines, the Leghorn G-B2 and Fayoumi M15.2, have been used for genome-wide linkage and QTL analysis. Phenotypic data on 12 body composition traits (breast muscle weight, breast muscle weight percentage, abdominal fat weight, abdominal fat weight percentage, heart weight, heart weight percentage, liver weight, liver weight percentage, spleen weight, spleen weight percentage, and drumstick weight, and drumstick weight percentage) were collected. Birds were genotyped for 269 microsatellite markers across the genome. The QTL Express program was used to detect QTL for body composition traits. Significant levels were obtained using the permutation test. For the twelve traits, a total of 61 (Gga 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 18, 24, and Z) and 45 (Gga 1, 2, 3, 4, 6, 7, 8, 9, 10, 12, 15, 17, and E46) significant QTL were detected at the 5% chromosome-wise significance level, of which 19 and 11 were significant at the 5% genome-wise level for the broiler-Leghorn cross and broiler-Fayoumi cross, respectively. Phenotypic variation for each trait explained by all QTL across the genome ranged from 3.22 to 33.31% in the broiler-Leghorn cross and 4.83 to 47.12% in broiler-Fayoumi cross. Distinct QTL profiles between the 2 crosses were observed for most traits. Cryptic alleles were detected for each trait. Potential candidate genes within the QTL region for body composition traits at the 1% chromosome-wise significance level were identified from databases for future association study. The results of the current study will increase the knowledge of genetic markers associated with body composition traits and aid the process of identifying causative genes. Knowledge of beneficial genetic variation can be incorporated in breeding programs to enhance genetic improvement through marker-assisted selection in chickens.

Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. I. Growth and average daily gain.

A genome scan was used to detect chromosomal regions and QTL that control quantitative traits of economic importance in chickens. Two unique F(2) crosses generated from a commercial broiler male line and 2 genetically distinct inbred lines (Leghorn and Fayoumi) were used to identify QTL affecting BW and daily average gain traits in chickens. Body weight at 2, 4, 6, and 8 wk was measured in the 2 F(2) crosses. Birds were genotyped for 269 microsatellite markers across the entire genome. Linkage distance among microsatellite markers was estimated by the CRIMAP program. The program QTL Express was used for QTL detection. Significance levels were obtained using the permutation test. For the 8 traits, a total of 18 and 13 significant QTL were detected at a 1% chromosome-wise significance level, of which 17 and 10 were significant at the 5% genome-wise level for the broiler-Leghorn cross and broiler-Fayoumi cross, respectively. Highly correlated growth traits showed similar QTL profiles within each cross but different QTL profiles between the 2 crosses. Most QTL for growth traits in the current study were detected in Gga 1, 2, 4, 7, and 14 for the broiler-Leghorn cross and Gga 1, 2, 4, 5, 8, and 13 for the broiler-Fayoumi cross. Potential candidate genes within the QTL region for growth traits at 1% chromosome-wise significance level were discussed. The results in the current study lay the foundations for fine mapping these traits in the advanced intercross lines and provide a start point for identification causative genes responsible for growth traits in chickens.

The relationship of body composition, feed intake, and metabolic hormones for broiler breeder females.

Three hundred twenty Cobb 500 broiler breeder pullets at 21 wk of age were selected from a flock fed according to Cobb Breeder Management Guide specifications. One hundred sixty pullets at 21 wk of age were switched to ad libitum feeding, and the remaining 160 pullets continued to be control-fed. The pullets were photostimulated at 22 wk and maintained until 36.5 wk. Plasma samples were obtained, BW was determined, and hens were killed for determination of body composition at the following periods: 24 h prior to photostimulation, 2.5 wk after photostimulation, 24 h after first egg, and 36.5 wk following peak egg production. Compared with ad libitum-fed breeders, the restricted breeders had a higher percentage carcass protein and lower percentage carcass fat at all sampling periods. Total egg numbers were greater, and abnormal eggs were less for the restricted pullets compared with the ad libitum-fed pullets at 36.5 wk. Carcass percentage fat of ad libitum-fed pullets was positively related to plasma glucagon, insulin-like growth factor-II (IGF-II), and 17beta-estradiol but negatively related to plasma insulin, insulin/glucagon M ratio, insulin-like growth factor-I (IGF-I), thyroxine (T4), and triiodothyronine (T3). Carcass percentage fat of feed-restricted pullets was negatively related to IGF-I, IGF-II, and T4. The T4 was the most important hormone for predicting the percentage carcass fat in ad libitum-fed pullets, and IGF-I was the most important hormone for predicting the percentage carcass fat in feed-restricted pullets. The percentage carcass protein for ad libitum-fed breeders was positively correlated to IGF-I, T4, T3, insulin/glucagon M ratio, and insulin. Carcass percentage protein for feed-restricted breeders was positively correlated to IGF-I, IGF-II, T4, and glucagon. Stepwise regressions for predicting percentage carcass protein for breeders fed by both systems shows that T3 and IGF-I concentrations were the most important for ad libitum-fed breeders, whereas IGF-II and T4 were best for feed-restricted breeders. The hormone status of breeders may be a key indicator to help predict the body composition and thus support management decisions for maintaining optimum production.

Integration of microsatellite-based genetic maps for the turkey (Meleagris gallopavo).

Integration of turkey genetic maps and their associated markers is essential to increase marker density in support of map-based genetic studies. The objectives of this study were to integrate 2 microsatellite-based turkey genetic maps--the Roslin map and the University of Minnesota (UMN) map--by genotyping markers from the Roslin study on the mapping families of the UMN study. A total of 279 markers was tested, and 240 were subsequently screened for polymorphisms in the UMN/Nicholas Turkey Breeding Farms (NTBF) mapping families. Of the 240 markers, 89 were genetically informative and were used for genotyping the F2 offspring. Significant genetic linkages (log of odds > 3.0) were found for 84 markers from the Roslin study. BLASTn comparison of marker sequences with the draft assembly of the chicken genome found 263 significant matches. The combination of genetic and in silico mapping allowed for the alignment of all linkage groups of the Roslin map with those of the UMN map. With the addition of the markers from the Roslin map, 438 markers are now genetically linked in the UMN/NTBF families, and more than 1700 turkey sequences have now been assigned to likely positions in the chicken-genome sequence.