Groenen M.A.M.,Wageningen University |
Megens H.-J.,Wageningen University |
Zare Y.,Wageningen University |
Warren W.C.,University of Washington |
And 6 more authors.
BMC Genomics | Year: 2011
Background: In livestock species like the chicken, high throughput single nucleotide polymorphism (SNP) genotyping assays are increasingly being used for whole genome association studies and as a tool in breeding (referred to as genomic selection). To be of value in a wide variety of breeds and populations, the success rate of the SNP genotyping assay, the distribution of the SNP across the genome and the minor allele frequencies (MAF) of the SNPs used are extremely important.Results: We describe the design of a moderate density (60k) Illumina SNP BeadChip in chicken consisting of SNPs known to be segregating at high to medium minor allele frequencies (MAF) in the two major types of commercial chicken (broilers and layers). This was achieved by the identification of 352,303 SNPs with moderate to high MAF in 2 broilers and 2 layer lines using Illumina sequencing on reduced representation libraries. To further increase the utility of the chip, we also identified SNPs on sequences currently not covered by the chicken genome assembly (Gallus_gallus-2.1). This was achieved by 454 sequencing of the chicken genome at a depth of 12x and the identification of SNPs on 454-derived contigs not covered by the current chicken genome assembly. In total we added 790 SNPs that mapped to 454-derived contigs as well as 421 SNPs with a position on Chr_random of the current assembly. The SNP chip contains 57,636 SNPs of which 54,293 could be genotyped and were shown to be segregating in chicken populations. Our SNP identification procedure appeared to be highly reliable and the overall validation rate of the SNPs on the chip was 94%. We were able to map 328 SNPs derived from the 454 sequence contigs on the chicken genome. The majority of these SNPs map to chromosomes that are already represented in genome build Gallus_gallus-2.1.0. Twenty-eight SNPs were used to construct two new linkage groups most likely representing two micro-chromosomes not covered by the current genome assembly.Conclusions: The high success rate of the SNPs on the Illumina chicken 60K Beadchip emphasizes the power of Next generation sequence (NGS) technology for the SNP identification and selection step. The identification of SNPs from sequence contigs derived from NGS sequencing resulted in improved coverage of the chicken genome and the construction of two new linkage groups most likely representing two chicken micro-chromosomes. © 2011 Groenen et al; licensee BioMed Central Ltd.
Swaggerty C.L.,U.S. Department of Agriculture |
Pevzner I.Y.,Cobb Vantress Inc. |
Kogut M.H.,U.S. Department of Agriculture
Poultry Science | Year: 2014
Salmonella is a leading cause of foodborne illness and can be transmitted through consumption of contaminated poultry; therefore, increasing a flock's natural resistance to Salmonella could improve food safety. Previously, we characterized the heterophil-mediated innate immune response of 2 parental broiler lines and F1 reciprocal crosses and showed that increased heterophil function and expression of pro-inflammatory mediators corresponds with increased resistance against diverse pathogens. A preliminary selection trial showed that individual sires had varying inherent levels of pro-inflammatory mediators and selection based on a high or low phenotype was passed onto progeny. Based on these results, we hypothesized selection of broilers for higher levels of the pro-inflammatory mediators IL- 6, CXCLi2, and CCLi2 would produce progeny with increased resistance against Salmonella Enteritidis. Peripheral blood leukocytes were isolated from 75 commercial broiler sires, screened, and 10 naturally high and low expressing sires were selected and mated to randomly selected dams to produce the first generation of "high" and "low" progeny. The mRNA expression of CXCLi2 and CCLi2 were significantly (P ≤ 0.02) higher in the high progeny and were more resistant to liver and spleen organ invasion by Salmonella Enteritidis compared with low progeny. Production of the second generation yielded progeny that had differences (P ≤ 0.03) in all 3 mediators and further improved resistance against Salmonella Enteritidis. Feed conversion ratio and percent breast meat yield were calculated and were equal, whereas the high birds weighed slightly, but significantly, less than the low birds. These data clearly demonstrate that selection based on a higher phenotype of key pro-inflammatory mediators is a novel means to produce broilers that are naturally more resistant to Salmonella, one of the most important foodborne pathogens affecting the poultry industry. © 2014 Poultry Science Association Inc.
Fragomeni B.O.,University of Georgia |
Misztal I.,University of Georgia |
Lourenco D.L.,University of Georgia |
Aguilar I.,Instituto Nacional Of Investigacion Agropecuaria |
And 2 more authors.
Frontiers in Genetics | Year: 2014
The purpose of this study was to determine if the set of genomic regions inferred as accounting for the majority of genetic variation in quantitative traits remain stable over multiple generations of selection. The data set contained phenotypes for five generations of broiler chicken for body weight, breast meat, and leg score. The population consisted of 294,632 animals over five generations and also included genotypes of 41,036 single nucleotide polymorphism (SNP) for 4,866 animals, after quality control. The SNP effects were calculated by a GWAS type analysis using single step genomic BLUP approach for generations 1-3, 2-4, 3-5, and 1-5. Variances were calculated for windows of 20 SNP. The top ten windows for each trait that explained the largest fraction of the genetic variance across generations were examined. Across generations, the top 10 windows explained more than 0.5% but less than 1% of the total variance. Also, the pattern of the windows was not consistent across generations. The windows that explained the greatest variance changed greatly among the combinations of generations, with a few exceptions. In many cases, a window identified as top for one combination, explained less than 0.1% for the other combinations. We conclude that identification of top SNP windows for a population may have little predictive power for genetic selection in the following generations for the traits here evaluated. © 2014 Fragomeni, Misztal, Lourenco, Aguilar, Okimoto and Muir.
Wideman Jr. R.F.,University of Arkansas |
Pevzner I.,Cobb Vantress Inc.
Poultry Science | Year: 2012
Bacterial chondronecrosis with osteomyelitis (BCO) and turkey osteomyelitis complex (TOC) are characterized by bacterial infection and necrotic degeneration within the tibiae and femora. Stress and immunosuppression have been implicated in the pathogenesis of BCO and TOC. Immunosuppressive doses of dexamethasone (DEX) trigger high incidences of TOC in turkey poults. The present study was conducted to determine if DEX injections or heat stress can trigger BCO and lameness in broilers. In 3 independent experiments, broilers were weighed and either remained uninjected or received repeated injections of 0.9% saline or DEX dissolved in saline (0.45 to 1.5 mg of DEX/kg of BW). Across all 3 experiments, the incidences of lameness were 0% for uninjected controls, 0 to 8% in salineinjected groups, and 24 to 68% in groups injected with 0.9 to 1.5 mg of DEX/kg of BW. Growth was inhibited by DEX injections regardless of whether the birds became lame or survived. When compared with salineinjected groups, DEX injections consistently increased the incidence of severe proximal tibial head necrosis in lame birds as well as in survivors. The DEX injections also triggered a subset of lesions that are not considered pathognomonic for BCO (for example, avascular femoral head necrosis and fatty necrosis of the tibiae). In a fourth experiment, repeated episodes of heat stress did not trigger lameness, although the subclinical incidence of tibial head necrosis was substantially higher at 28 and 35 d of age in heat-stressed broilers when compared with broilers reared under thermoneutral conditions. Accordingly, stress and immunosuppression must be considered contributing factors in the pathogenesis of tibial and femoral lesions associated with lameness in broilers. A subset of the lesions triggered by repeated DEX injections did not precisely mimic the pathogenesis of BCO in broilers, and DEX consistently inhibited growth whereas BCO is associated with rapid growth. These caveats must be acknowledged when DEX is used to trigger lameness in broilers. © 2012 Poultry Science Association Inc.
Kerstens H.H.D.,Wageningen University |
Crooijmans R.P.M.A.,Wageningen University |
Dibbits B.W.,Wageningen University |
Vereijken A.,Research and Technology Center |
And 2 more authors.
BMC Genomics | Year: 2011
Background: Variation within individual genomes ranges from single nucleotide polymorphisms (SNPs) to kilobase, and even megabase, sized structural variants (SVs), such as deletions, insertions, inversions, and more complex rearrangements. Although much is known about the extent of SVs in humans and mice, species in which they exert significant effects on phenotypes, very little is known about the extent of SVs in the 2.5-times smaller and less repetitive genome of the chicken.Results: We identified hundreds of shared and divergent SVs in four commercial chicken lines relative to the reference chicken genome. The majority of SVs were found in intronic and intergenic regions, and we also found SVs in the coding regions. To identify the SVs, we combined high-throughput short read paired-end sequencing of genomic reduced representation libraries (RRLs) of pooled samples from 25 individuals and computational mapping of DNA sequences from a reference genome.Conclusion: We provide a first glimpse of the high abundance of small structural genomic variations in the chicken. Extrapolating our results, we estimate that there are thousands of rearrangements in the chicken genome, the majority of which are located in non-coding regions. We observed that structural variation contributes to genetic differentiation among current domesticated chicken breeds and the Red Jungle Fowl. We expect that, because of their high abundance, SVs might explain phenotypic differences and play a role in the evolution of the chicken genome. Finally, our study exemplifies an efficient and cost-effective approach for identifying structural variation in sequenced genomes. © 2011 Kerstens et al; licensee BioMed Central Ltd.
Dorshorst B.,North Carolina State University |
Okimoto R.,Cobb Vantress Incorporated |
Ashwell C.,North Carolina State University
Journal of Heredity | Year: 2010
The Silkie chicken has been a model of melanoctye precursor and neural crest cell migration and proliferation in the developing embryo due to its extensive hyperpigmentation of dermal and connective tissues. Although previous studies have focused on the distribution and structure of the Silkie's pigment or the general mechanisms by which this phenotype presents itself, the causal genetic variants have not been identified. Classical breeding experiments have determined this trait to be controlled by 2 interacting genes, the sex-linked inhibitor of dermal melanin (Id) and autosomal fibromelanosis (Fm) genes. Genome-wide single nucleotide polymorphism (SNP)-trait association analysis was used to detect genomic regions showing significant association with these pigmentation genes in 2 chicken mapping populations designed to segregate independently for Id and Fm. The SNP showing the highest association with Id was located at 72.3 Mb on chromosome Z and 10.3-13.1 Mb on chromosome 20 showed the highest association with Fm. Prior to this study, the linkage group to which Fm belonged was unknown. Although the primary focus of this study was to identify loci contributing to dermal pigmentation in the Silkie chicken, loci associated with various other morphological traits segregating in these populations were also detected. A single SNP in a highly conserved cis-regulatory region of Sonic Hedgehog was significantly associated with polydactyly (Po). Genomic regions in association with silkie feathering or hookless (h), feathered legs (Pti), vulture hock (V), rose comb (R), and duplex comb (D) were also identified. © 2009 The American Genetic Association. All rights reserved.
Talaty P.N.,Purdue University |
Katanbaf M.N.,Cobb Vantress Inc. |
Hester P.Y.,Purdue University
Poultry Science | Year: 2010
Broilers selected for increased body size and breast muscle have imposed stress on the skeletal system, resulting in poorer walking ability. Our objectives were to determine the relationship between bone mineralization and gait score in 4 crosses of commercial broilers and to ascertain if mineralization of the toe is correlated to the tibia. Three chickens per pen each with good (gait score of 0 or 1) or poorer (gait score of 3) walking ability were killed and weighed. The left humerus, the left middle toe, and both drumsticks were collected for determination of bone mineral density (BMD), bone mineral content, and bone size traits using dual-energy x-ray absorptiometry. The BMD and bone size traits were similar among the 4 crosses of commercial broilers at 6 wk of age. However, gait scores differed among genotypes, with cross C having better gait scores than crosses A and B, but did not differ from cross D. The bone mineral content and bone size traits did not differ between birds with good walking ability as compared with those broilers of poorer walking ability. However, birds with poorer walking ability had higher BMD (P < 0.05) and BW (P < 0.001) than males with good walking ability. Within a cross, the correlation between gait score and BMD was not significant except for cross D birds. Broilers of cross D with better walking ability had decreased bone mineralization (r = 0.19, P = 0.03). The stronger correlation between gait score and BW for all crosses of commercial broilers (r = 0.38, P < 0.0001) suggests that the low association between gait score and bone mineralization for cross D was mainly due to BW. The BMD of the left toe was correlated to the BMD of the left tibia (r = 0.91, P < 0.0001) and right tibia (r = 0.87, P < 0.0001). In conclusion, bone mineralization was similar among crosses of meat-type chickens, and it had little influence on the gait score of male broilers. © 2010 Poultry Science Association Inc.
Siegel P.B.,Virginia Polytechnic Institute and State University |
Gustin S.J.,Cobb Vantress Inc |
Katanbaf M.N.,Cobb Vantress Inc
Journal of Applied Poultry Research | Year: 2011
Breeding programs designed for broiler production have resulted in a chicken that, when fully fed, grows rapidly and has a body conformation that enhances yield at market weight. Compared with chickens bred for high egg production, the motor ability of broilers has been compromised and is of increasing concern in broiler breeding and production. Broilers with intermediate gait scores of 2, 3, and 4 were provided choices among diets containing different doses of a nonsteroidal anti-inflammatory drug (carprofen). Broilers with no identifiable gait abnormality (score of 1) or unable to walk (score of 5) were excluded from the study. The hypothesis that broilers with higher gait scores, if experiencing pain, would prefer diets with higher doses of carprofen was rejected because no differences were observed in feed consumption among treatment groups. Although males and females responded similarly, there was an interaction of sex with left-right preference for feeder location. © 2011 Poultry Science Association, Inc.
Rekaya R.,University of Georgia |
Sapp R.L.,Cobb Vantress Inc |
Wing T.,Cobb Vantress Inc |
Aggrey S.E.,University of Georgia
Poultry Science | Year: 2013
A multiple trait linear-threshold model was used to analyze data for BW, residual feed intake, breast meat yield (BMY), conformation score (CS), area (AR), tibial dyschondroplasia, valgus, varus, and rotated tibia. Leg soundness traits were considered as binary responses. At the liability scale, the model included the fixed effects of flock-week of hatch, and sex of the bird and the genetic additive effect, and the error terms as random. The random maternal effect was included in the model only for BW. A full Bayesian implementation of the model was straightforward even though large number of traits and missing records were present. As expected, binary traits have the lowest heritability. Heritability ranged from 0.12 for tibial dyschondroplasia to 0.44 for BMY. Genetic correlations between BW and conformation traits were moderate to high. Residual feed intake was negatively correlated with BW (-0.15), AR (-0.13), BMY (-0.04), and CS (-0.12). Genetic correlation between leg soundness traits were generally low and negative with the exception of the correlation between valgus and varus (-0.70) and between varus and rotated tibia (-0.39). Genetic correlations between BW, BMY, CS, and AR with leg soundness traits were in general negative and low in magnitude. Thus, selecting for improved leg soundness will have minimal effect on BW and carcass traits. Furthermore, genetic improvement in residual feed intake will result in improvements in carcass traits. Simultaneous genetic improvement in leg soundness and innovative husbandry practices should improve broiler welfare without significant adverse effects on production efficiency. © 2013 Poultry Science Association Inc.
Katanbaf M.N.,Cobb Vantress Inc |
Hardiman J.W.,Cobb Vantress Inc
Poultry Science | Year: 2010
Primary breeders are well aware that selecting for better health and well-being along with economic traits such as faster growth rate, higher levels of meat yield, and improved efficiency of feed utilization are critical to balanced long-term genetic progress of their pure lines as well as to increased production efficiency of broiler products for the broiler industry. Cobb collects and selects on over 50 phenotypic observations per pedigree candidate at various ages. Over 50% of these collections are involved with evaluation of each bird's health, welfare, and fitness. Some examples of these traits are various chick defects, various broiler age skeletal and leg abnormalities, feather cover, various physiological measures of heart and lung functions, and specific causes of mortality. Large pedigree populations, massive data collection infrastructure, integration of better technologies in evaluation of phenotypes, and sophisticated data analysis capability have allowed geneticists to perform selections that are balanced for both economic and welfare traits. Cobb's internal as well as worldwide sponsored research has facilitated geneticists to make science-based breeding decisions. Each pedigree line per product available to primary breeders exhibits their own unique characteristics that are enhanced by selective breeding and positioned in special mating schemes to produce the product and welfare performance that our customers demand. Additionally, most if not all primary breeding companies now offer different products for different markets that exhibit varying levels of performance and behavior to fit customer needs. Future expansion of these products and creation of new products by breeding companies will be in large dictated by both our customers and consumers.© 2010 Poultry Science Association Inc.