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Hickey J.M.,University of New England of Australia | Hickey J.M.,Biometrics and Statistics Unit | Cleveland M.A.,Genus plc | Maltecca C.,North Carolina State University | And 3 more authors.
Methods in Molecular Biology | Year: 2013

Genotype imputation is a cost-effective way to increase the power of genomic selection or genome-wide association studies. While several genotype imputation algorithms are available, this chapter focuses on a heuristic algorithm, as implemented in the AlphaImpute software. This algorithm combines long-range phasing, haplotype library imputation, and segregation analysis and it is specifically designed to work with pedigreed populations. The chapter is organized in different sections. First the challenges related to genotype imputation in pedigreed populations are described, along with the specifics of the imputation algorithm used in AlphaImpute. In the second section, factors affecting the accuracy of genotype imputation using this algorithm are discussed. The different parameters that control AlphaImpute are detailed and examples of how to apply AlphaImpute are given. © Springer Science+Business Media, LLC 2013.


Morota G.,University of Wisconsin - Madison | Kranis A.,Aviagen | Kranis A.,Roslin Institute | Gianola D.,University of Wisconsin - Madison
BMC Genomics | Year: 2014

Background: Genome-wide association studies have been deemed successful for identifying statistically associated genetic variants of large effects on complex traits. Past studies have found enrichment of trait-associated SNPs in functionally annotated regions, while depletion was reported for intergenic regions (IGR). However, no systematic examination of connections between genomic regions and predictive ability of complex phenotypes has been carried out.Results: In this study, we partitioned SNPs based on their annotation to characterize genomic regions that deliver low and high predictive power for three broiler traits in chickens using a whole-genome approach. Additive genomic relationship kernels were constructed for each of the genic regions considered, and a kernel-based Bayesian ridge regression was employed as prediction machine. We found that the predictive performance for ultrasound area of breast meat from using genic regions marked by SNPs was consistently better than that from SNPs in IGR, while IGR tagged by SNPs were better than the genic regions for body weight and hen house egg production. We also noted that predictive ability delivered by the whole battery of markers was close to the best prediction achieved by one of the genomic regions.Conclusions: Whole-genome regression methods use all available quality filtered SNPs into a model, contrary to accommodating only validated SNPs from exonic or coding regions. Our results suggest that, while differences among genomic regions in terms of predictive ability were observed, the whole-genome approach remains as a promising tool if interest is on prediction of complex traits. © 2014 Morota et al.; licensee BioMed Central Ltd.


Wade A.J.,EW Group | French N.A.,Aviagen | Ireland G.W.,University of Manchester
Poultry Science | Year: 2014

Diseases such as avian influenza can destroy turkey flocks, potentially resulting in the loss of valuable or rare genetic material. Consequently, there is an urgent need to develop a means to archive such germplasm. Germline chimeras produced by intravascular transfer of primordial germ cells (PGC) have been reported in other avian species but not turkeys. This study examined the feasibility of both establishing an archive of frozen PGC, and producing germline chimeras by injecting the thawed PGC into host embryos. To meet these aims, the following experiments were performed: (1) PGC identification within turkey embryos; (2) development of an efficient method for isolation of turkey PGC; (3) demonstration that PGC can be cryopreserved, recovered, and retain viability; (4) reinjection into embryos and detection of injected PGC. Primordial germ cells were identified using periodic acid- Schiff reagent and the immunological marker OLP-1. Bloodstream PGC were isolated using Ficoll density gradient centrifugation with PGC recovery peaking at stages 13, 14, and 15 with 32 ± 4.9, 33 ± 6.4, and 26 ± 5.4 PGC recovered, respectively. Primordial germ cells were frozen using Dulbecco's modified Eagle medium, 20% fetal calf serum, and 10% dimethylsulfoxide and demonstrated 90 ± 1.7% viability after 3 mo frozen in liquid nitrogen. Freshly isolated and frozen thawed DiI- and Q-Tracker-labeled PGC repopulated stage 30 gonads after vascular transfer into ex ovo cultured embryos. The DiI-labeled cells repopulated gonads less frequently, with 36 ± 13.2% of gonads containing the DiI-labeled PGC, and 7 ± 3.8% of reinjected PGC reaching the gonads of positive embryos. The Q-tracker- labeled cells were detected more frequently in embryos, with 67 ± 21.1% having positive signals, and 44 ± 4.9% of reinjected Q-tracker-labeled PGC colonized the gonads of positive embryos. This study demonstrated the feasibility of using turkey PGC to archive turkey germplasm from different strains because frozen PGC reintroduced into host embryos can colonize the host gonads, suggesting the possibility of producing turkey germline chimeras. © 2014 Poultry Science Association Inc.


Salas C.,University of Costa Rica | Ekmay R.,Dow AgroSciences | England J.,University of Arkansas | Cerrate S.,Aviagen | Coon C.N.,University of Arkansas
International Journal of Poultry Science | Year: 2013

Cotton seed meal (CSM) is an alternative ingredient in poultry diets but its use is limited due to the presence of gossypol and the potential effects of gossypol on digestibility of nutrients. Glandless cottonseed is available and contains very low gossypol but there has been a limited amount of poultry nutritional studies completed with glandless cottonseed meal (GCSM). The TMEn, proximate analysis, amino acid content and amino acid (AA) digestibility of a glandless (GCSM) and a commercial (CCSM) cottonseed meal were determined with broilers. Thirty 42-day old Cobb 500 male broilers were precision-fed 30g of CCSM, GCSM and glucose and excreta collected during a 48 h period. Glucose was fed to serve as a control (no nitrogen or AA content). The chemical composition, gossypol content, True metabolizable energy (TMEn) and digestibility coefficients for AA were calculated for both meals. The crude protein and fat content of GCSM was higher than the CCSM (54 and 51%, 6 and 2%, respectively). Both meals were similar in calcium, total phosphorus and phytic acid contents. The CCSM had a higher content of total and free gossypol (1.52 and 0.161%, respectively) when compared to GCSM (0.02 and .003%, respectively). The TMEn for the GCSM provided approximately one thousand kcal more per energy/ kg than the CCSM. The essential AA content (g/kg; 90% DM) was determined for both cottonseed meals and was generally higher for GCSM compared to CCSM but both types of CSM contained higher levels of key essential AA than reported values for AA in the literature. The most extreme differences were for methionine and cystine; % methionine content was approximately 2 fold higher than values in the literature and the % cystine was 74 to 93% higher. The true digestibility coefficients for essential AA ranged from the low of 73.9% for isoleucine to 91.8% for arginine, for CCSM; the amino acid digestibility coefficients for GCSM were all higher than 90% for the essential AAs. © Asian Network for Scientific Information, 2013.


Ewald S.J.,Auburn University | Kapczynski D.R.,U.S. Department of Agriculture | Livant E.J.,Auburn University | Suarez D.L.,U.S. Department of Agriculture | And 3 more authors.
Immunogenetics | Year: 2011

Myxovirus-resistance (Mx) proteins are produced by host cells in response to type I interferons, and some members of the Mx gene family in mammals have been shown to limit replication of influenza and other viruses. According to an early report, chicken Mx1 variants encoding Asn at position 631 have antiviral activity, whereas variants with Ser at 631 lack activity in experiments evaluating Mx1 complementary DNA (cDNA) expressed ectopically in a cell line. We evaluated whether the Mx1 631 dimorphism influenced pathogenesis of highly pathogenic avian influenza virus (HPAIV) infection in chickens of two commercial broiler lines, each segregating for Asn631 and Ser631 variants. Following intranasal infection with HPAIV strain A/Chicken/Queretaro/14588-19/1995 H5N2, chickens homozygous for Asn631 allele were significantly more resistant to disease based on early mortality, morbidity, or virus shedding than Ser631 homozygotes. Higher amounts of splenic cytokine transcripts were observed in the Ser631 birds after infection, consistent with higher viral loads seen in this group and perhaps contributing to their higher morbidity. Nucleotide sequence determination of Mx1 cDNAs demonstrated that the Asn631 variants in the two chicken lines differed at several amino acid positions outside 631. In vitro experiments with a different influenza strain (low pathogenicity) failed to demonstrate an effect of Mx1 Asn631 on viral replication suggesting that in vivo responses may differ markedly from in vitro, or that choice of virus strain may be critical in demonstrating effects of chicken Mx1. Overall, these studies provide the first evidence that Mx1 has antiviral effects in chickens infected with influenza virus. © 2011 Springer-Verlag.


Ekmay R.D.,University of Arkansas | de Beer M.,Aviagen | Rosebrough R.W.,U.S. Department of Agriculture | Richards M.P.,U.S. Department of Agriculture | And 2 more authors.
Poultry Science | Year: 2010

A trial was conducted to determine the effects of different rearing feed regimens on plasma hormone and metabolite levels and hepatic lipid metabolism and gene expression on sexually mature broiler breeders. Cobb 500 birds were divided into 2 groups at 4 wk and fed either an everyday (ED) or skip-a-day (SKP) regimen. At 24 wk of age, all birds were switched over to an ED regimen. At 26.4 wk, breeder hens were randomly selected and killed at intervals after feeding. Livers were sampled from 4 hens at 4-h intervals for 24 h for a total of 28 samples per treatment. Blood was sampled from 4 hens per sampling time; sampling times were 0, 30, and 60 min and 2 and 4 h after feeding and then every 4 h up to 24 h for a total of 36 samples per treatment. Main feeding regimen, time, and interaction effects were analyzed. Significant interaction effects were found between time and feeding regimen for acetyl-coenzyme A carboxylase and malic enzyme mRNA expression. The peak for acetyl-coenzyme A carboxylase expression was higher in ED-reared birds, whereas the peak for malic enzyme expression was higher in SKP-reared birds. Overall, plasma levels of insulin-like growth factor-II were higher in SKP-reared birds. Overall, plasma corticosterone levels were also higher in SKP-reared birds and significant interaction effects between time and feeding regimen were seen. The expression of apolipoprotein A1 was significantly higher in ED-reared birds: significant interaction effects were also noted. Other researchers also found some of the differences observed in the present study in 16-wkold pullets. In summary, different feeding regimens alter metabolic responses, some of which carry over into sexual maturity. © 2010 Poultry Science Association Inc.


Gilbert E.R.,Virginia Polytechnic Institute and State University | Cox C.M.,Virginia Polytechnic Institute and State University | Williams P.M.,Virginia Polytechnic Institute and State University | McElroy A.P.,Virginia Polytechnic Institute and State University | And 6 more authors.
PLoS ONE | Year: 2011

Background: Coccidiosis is an intestinal disease caused by protozoal parasites of the genus Eimeria. Despite the advent of anti-coccidial drugs and vaccines, the disease continues to result in substantial annual economic losses to the poultry industry. There is still much unknown about the host response to infection and to date there are no reports of protein profiles in the blood of Eimeria-infected animals. The objective of this study was to evaluate the serum proteome of two genetic lines of broiler chickens after infection with one of three species of Eimeria. Methodology/Principal Findings: Birds from lines A and B were either not infected or inoculated with sporulated oocysts from one of the three Eimeria strains at 15 d post-hatch. At 21 d (6 d post-infection), whole blood was collected and lesion scoring was performed. Serum was harvested and used for 2-dimensional gel electrophoresis. A total of 1,266 spots were quantitatively assessed by densitometry. Protein spots showing a significant effect of coccidia strain and/or broiler genetic line on density at P<0.0520.01 (250 spots), P<0.0120.001 (248 spots), and P<0.001 (314 spots) were excised and analyzed by matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry. Proteins were identified in 172 spots. A total of 46 different proteins were identified. Of the spots with a corresponding protein identification, 57 showed a main effect of coccidia infection and/or 2-way interaction of coccidia infection×broiler genetic line at P≤0.001. Conclusions/Significance: Several of the metabolic enzymes identified in this study are potential candidates for early diagnostic markers of E. acervulina infection including malate dehydrogenase 2, NADH dehydrogenase 1 alpha subcomplex 9, and an ATP synthase. These proteins were detected only in Line A birds that were inoculated with E. acervulina. Results from this study provide a basic framework for future research aimed at uncovering the complex biochemical mechanisms involved in host response to Eimeria infection and in identifying molecular targets for diagnostic screening and development of alternative preventative and therapeutic methods. © 2011 Gilbert et al.


Howie J.A.,SAC | Avendano S.,Aviagen | Tolkamp B.J.,SAC | Kyriazakis I.,Northumbria University
Poultry Science | Year: 2011

Current selection goals in broiler breeding focus on the improvement of live performance traits, such as feed intake, BW, and feed conversion ratio (FCR). The use of electronic feeders allows measurement of feed intake of individuals housed in groups as well as the identification of different feeding behaviors. Feed intake can thus be split into underlying feeding behavior traits, allowing the estimation of genetic correlations and assessment of the genetic consequences of selecting for performance traits on feeding behavior traits. To investigate the genetic relationships between performance traits and feeding behavior, data of visits to feeders by birds from 4 lines of broilers that differed in selection focus on growth and FCR were analyzed. Visits were recorded electronically and grouped into meals using an existing model for estimating meal criteria. Mean individual feeding behavior traits were then calculated across the entire test period (2 to 5 wk of age). Records were available for between 14,000 and 18,000 birds/line. Analyzed feeding behavior traits were meals per day, meal size, visits per meal, meal duration, nonfeeding time in meal, time feeding per day, proportion of meal spent feeding, feeding rate, and ADFI. Analyzed performance traits were 35-d BW, total feed intake over the entire test period, and FCR. All feeding behavior traits showed moderate to high heritabilities (0.24 to 0.57) but low genetic correlations with performance traits (-0.20 to 0.18), except for ADFI, which was moderately correlated with total intake on test (0.57) and highly correlated with FCR (0.91). The low genetic correlations indicate that the difference in selection intensity among lines for these performance traits has had limited effect on feeding behavior. Different feeding strategies that would result in favorable breeding values for FCR were identified, adding opportunities for further improvements in feed efficiency within and across environments. © 2011 Poultry Science Association Inc.


Powell J.E.,Roslin Institute | Kranis A.,Aviagen | Floyd J.,Roslin Institute | Dekkers J.C.M.,Iowa State University | And 3 more authors.
Animal Genetics | Year: 2012

The performance of linear regression models in genome-wide association studies is influenced by how marker information is parameterized in the model. Considering the impact of parameterization is especially important when using information from multiple markers to test for association. Properties of the population, such as linkage disequilibrium (LD) and allele frequencies, will also affect the ability of a model to provide statistical support for an underlying quantitative trait locus (QTL). Thus, for a given location in the genome, the relationship between population properties and model parameterization is expected to influence the performance of the model in providing evidence for the position of a QTL. As LD and allele frequencies vary throughout the genome and between populations, understanding the relationship between these properties and model parameterization is of considerable importance in order to make optimal use of available genomic data. Here, we evaluate the performance of regression-based association models using genotype and haplotype information across the full spectrum of allele frequency and LD scenarios. Genetic marker data from 200 broiler chickens were used to simulate genomic conditions by selecting individual markers to act as surrogate QTL (sQTL) and then investigating the ability of surrounding markers to estimate sQTL genotypes and provide statistical support for their location. The LD and allele frequencies of markers and sQTL are shown to have a strong effect on the performance of models relative to one another. Our results provide an indication of the best choice of model parameterization given certain scenarios of marker and QTL LD and allele frequencies. We demonstrate a clear advantage of haplotype-based models, which account for phase uncertainty over other models tested, particularly for QTL with low minor allele frequencies. We show that the greatest advantage of haplotype models over single-marker models occurs when LD between markers and the causal locus is low. Under these situations, haplotype models have a greater accuracy of predicting the location of the QTL than other models tested. © 2011 Stichting International Foundation for Animal Genetics.


Gilbert E.R.,Virginia Polytechnic Institute and State University | Williams P.M.,Virginia Polytechnic Institute and State University | Ray W.K.,Virginia Polytechnic Institute and State University | Li H.,Shanxi Agricultural University | And 3 more authors.
Journal of Proteome Research | Year: 2010

The chicken small intestine undergoes structural and functional changes during the early posthatch period to accommodate the transition from a lipid-rich diet inside the egg to a carbohydrate- and protein-based diet. Many of the enterocyte brush-border membrane-associated proteins responsible for mediating changes in nutrient utilization are unknown. The objective of this study was to conduct a proteomic analysis of chicken small intestine during the early posthatch period. We isolated brush-border membrane at day of hatch and days 1, 3, 7, and 14 posthatch from the small intestine of 2 genetic lines of broilers that differ in growth performance, and performed 2D gel-electrophoresis. A total of 1693 spots were analyzed by matrix-assisted laser desorption/ionization-tandem time-of-flight mass spectrometry (MALDI-TOF/TOF). In total, 132 different proteins were identified and grouped according to biological function. Of these, there were 10 nutrient transporters, 9 digestive enzymes, and 17 proteins associated with cytoskeletal structure and microvilli organization. The remaining proteins were classified as basolateral membrane (3), endosomal/membrane trafficking (8), signaling (14), metabolic (33), degradative (5), stress-related (5), protein synthesis machinery/mitochondria/nucleus (19), immunologic (1), or unknown (8). Of the spots in which proteins were identified, there were 10 that showed an effect of broiler genetic line on protein spot density (P < 0.001) and 19 spots showing a correlation of broiler genetic line x age (P < 0.001). Identification of brush-border membrane-associated proteins is an important step in furthering our understanding of digestion and absorption in the chicken. © 2010 American Chemical Society.

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