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ABSTRACT: 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.
Poultry Science 03/2007; 86(2):255-66. · 1.73 Impact Factor
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ABSTRACT: 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.
Poultry Science 03/2007; 86(2):267-76. · 1.73 Impact Factor
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ABSTRACT: A chicken 13K cDNA microarray was used to profile global gene expression after Salmonella enteritidis (SE) challenge of young chickens. Two F8 advanced intercross lines (AIL), broiler by Leghorn, and broiler by Fayoumi, were studied. Day-old chicks were orally inoculated with SE, and spleens were harvested at day 7 or 8 post-inoculation. The SE bacteria burden in the spleen was quantified. The 20% high and 20% low SE burden birds within each AIL and harvest time were studied by microarray. The loop design was used for pair-comparison between high and low SE burden challenged birds and unchallenged birds, within each AIL and harvest time. The signal intensity of each gene was globally normalized and expressed on the natural log scale. A mixed model including line, treatment, time, array (random effect), dye, and all two-way interactions among treatment, time, and line was used to identify differentially expressed candidate genes at the 1% significance level. The results suggest that genetics, time, and interaction between genetics and time play important roles in gene regulation of SE infection and colonization in chickens. The differentially expressed genes identified in the current study are candidates for detailed hypothesis-driven investigation of genes determining resistance to SE in chickens.
Cytogenetic and Genome Research 02/2007; 117(1-4):131-8. · 1.53 Impact Factor
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ABSTRACT: 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.
Poultry Science 11/2006; 85(10):1700-11. · 1.73 Impact Factor
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ABSTRACT: 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.
Poultry Science 10/2006; 85(10):1712-21. · 1.73 Impact Factor
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ABSTRACT: Very low density apolipoprotein-II (apoVLDL-II) is a major constituent of very low density lipoprotein and is involved in lipid transportation in chickens. The current study was designed to investigate the associations of an apoVLDL-II gene polymorphism on chicken growth and body composition traits. The Iowa Growth and Composition Resource Population was established by crossing broiler sires with dams from 2 unrelated highly inbred lines (Leghorn and Fayoumi). The F1 birds were intercrossed, within dam line, to produce 2 related F2 populations. Body weight and body composition traits were measured in the F2 population. Primers for the 5'-flanking region in apoVLDL-II were designed from database chicken genomic sequence. Single nucleotide polymorphisms (SNP) between parental lines were detected by DNA sequencing, and PCR-RFLP methods were then developed to genotype SNP in the F2 population. There was no polymorphism in the 492 bp sequenced between broiler and Leghorn. The apoVLDL-II polymorphism between broiler and Fayoumi was associated with multiple traits of growth and body composition in the 148 male F2 individuals, including BW, breast muscle weight, drumstick weight, and tibia length. This research suggests that apoVLDL-II or a tightly linked gene has broad effects on growth and development in the chicken.
Poultry Science 06/2005; 84(5):697-703. · 1.73 Impact Factor
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ABSTRACT: Molecular genetic selection on individual genes is a promising method to genetically improve economically important traits in chickens. A resource population was developed to study the genetics of growth, body composition, skeletal integrity, and metabolism traits. Broiler sires were crossed to dams of 2 diverse, highly inbred lines (Leghorn and Fayoumi), and the F1 birds were intermated by dam line to produce broiler-Leghorn and broiler-Fayoumi F2 offspring. Growth, body composition, skeletal integrity, and hormonal and metabolic factors were measured in 713 F2 individuals. Insulin-like growth factor-I (IGF1) was selected for study as a biological and positional candidate gene. A single nucleotide polymorphism (SNP) was identified between the founder lines in the IGF1 promoter region, and a PCR-RFLP assay was developed. A mixed model was used to statistically analyze associations of IGF1-SNP1 with phenotypic traits. The IGF1-SNP1 had significant associations with most recorded traits, except metabolic traits. Strong interactions between the IGF1 gene and genetic background on growth traits in the 2 F2 populations suggest that genetic interaction is an important aspect for consideration before using the IGF1-SNP1 in marker-assisted selection programs. Several beneficial effects (improved growth, increased breast muscle weight, decreased abdominal fat, and enhanced skeletal integrity) associated with 1 allele indicate the presence of 1 or more loci near IGF1-SNP1 controlling biologically diverse and economically important traits in chickens.
Poultry Science 03/2005; 84(2):212-9. · 1.73 Impact Factor
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ABSTRACT: Antibody responses (primary and secondary phases) were measured in an F2 population. The resource population was derived from grandsires of two highly inbred major histocompatibility complex (MHC)-congenic Fayoumi chicken lines (named M5.1 and M15.2) mated with highly inbred Leghorn G-B1 hens. Secondary phase parameters of maximum titres (Ymax) and time required to achieve Ymax (Tmax) were estimated from post-secondary titres by using a non-linear regression model. Associations of single nucleotide polymorphisms (SNP) in transforming growth factor beta2 (TGFB2), 3, and 4 genes with antibody response parameters were evaluated. Multiple immune response parameters were significantly associated with the TGFB2 gene primarily in the lineage of the M5.1 grandsire, suggesting that TGFB2 or linked genes affect antibody response in hens. Significant main effects of the three genes were mostly found in the lineage of the M5.1 grandsire. Significant two-way interactions on antibody response were primarily detected between TGFB3 and TGFB4 genes, and in the lineage of the M15.2 grandsire. Effects preferentially detectable in only one of the MHC-congenic lineages suggest that there was interaction between the MHC and TGFB genes. The characterized TGFB SNPs might be applied in marker-assisted selection to improve antibody production.
Animal Genetics 09/2003; 34(4):275-82. · 2.40 Impact Factor
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ABSTRACT: The chicken B-cell marker (ChB6), caspase-1, inhibitor of apoptosis protein-1 (IAP-1), interleukin-15 receptor alpha-chain (IL-15Ralpha), interleukin-2 receptor gamma-chain (IL-2Rgamma), and immunoglobulin supfamily gene (ZOV3), as physiological candidate genes for chicken immune response, were selected to investigate associations with antibody kinetics to SRBC and killed B. abortus. An F2 population was derived from mating highly inbred (>99%) males of two MHC-congenic Fayoumi lines (named M5.1 and M15.2) with G-B1 Leghorn hens. Antibody response to SRBC and B. abortus after immunization at 19 and 22 wk were measured. Secondary phase parameters of maximum titers (Ymax) and time required to achieve Ymax (Tmax) were estimated from postsecondary titers by using a nonlinear regression model. The DNA polymorphisms of six genes were identified, and associations of single nucleotide polymorphisms (SNP) in the six genes with antibody response parameters were analyzed. Significant main effects of the gene polymorphisms were mostly found in the lineage of the M5.1 grandsire and primarily on antibody response to B. abortus. There was general agreement of allelic effect within antibody parameters among genes. These results suggest that the SNP characterized in the study may serve as markers for genetic enhancement of humoral immune capacity in the chicken.
Poultry Science 07/2003; 82(7):1118-26. · 1.73 Impact Factor
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ABSTRACT: A linkage disequilibrium approach with microsatellites was employed to investigate QTL affecting immune response. Highly inbred males of two MHC-congenic Fayoumi chicken lines were mated with highly inbred G-B1 Leghorn hens. Adult F2 hens (n = 158) were injected twice with SRBC and fixed Brucella abortus (BA). Agglutinating antibody titers were measured. Secondary phase parameters of maximum titers (Ymax) and time (Tmax) needed to achieve Ymax were estimated from postsecondary titers by using a nonlinear regression model. A three-step genotype strategy (DNA pooling, selective genotyping, and whole population genotyping) was used to identify microsatellite markers that are associated with immune response to SRBC and BA. The linkage distances between adjacent markers in the F2 population were estimated by Crimap. The QTL affecting immune response to SRBC and BA were detected based on F statistic by interval mapping. A total of five significant QTL, as determined by a permutation test, were detected at the 5% chromosome-wise level on Chromosomes 3, 5, 6, and Z. Two (Chromosome 3 and 6) of five QTL were significant at the 1% chromosome-wise level. The variance explained by the QTL ranged from 6.46 to 7.50%. The results suggest that regions on Chromosomes 3, 5, 6, and Z contain QTL that affect antibody kinetics in the hen.
Poultry Science 06/2003; 82(5):699-708. · 1.73 Impact Factor
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ABSTRACT: Transforming growth factor-beta (TGF-beta) belongs to a large family of multifunctional growth factors that regulate a broad spectrum of biological activities involved in morphogenesis, development, and differentiation. The current study was designed to investigate the effects of TGF-beta genes on chicken growth and body composition traits. The Iowa Growth and Composition Resource Population was established by crossing broiler sires with dams from two unrelated highly inbred lines (Leghorn and Fayoumi). The F1 birds were intercrossed, within dam line, to produce two related F2 populations. Body weight and body composition traits were measured in the F2 population. Primers for TGF-beta2, TGF-beta3, and TGF-beta4 were designed from database chicken sequence. Polymorphisms between parental lines were detected by DNA sequencing, and PCR-RFLP methods were then developed to screen the F2 population. The TGF-beta2 polymorphisms between broiler and Leghorn and the TGF-beta4 polymorphism between broiler and Fayoumi were associated with traits of skeletal integrity, such as tibia length, bone mineral content, bone mineral density, and the percentage of each measure to BW. The TGF-beta3 polymorphism between broilers and Leghorns was associated with traits of growth and body composition, such as BW, average daily gain, weight of breast muscle, abdominal fat pad and spleen, as well as the percentage of these organ weights to BW, and the percentage of shank weight and length to BW. The current research supports the broad effects of TGF-beta genes on growth and development of chickens.
Poultry Science 04/2003; 82(3):347-56. · 1.73 Impact Factor
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ABSTRACT: An F2 population was produced from mating G0 highly inbred (>99%) males of two MHC-congenic Fayoumi lines with G-B1 Leghorn hens. The F2 population was essentially a full-sibship with the F1 sire line reflecting MHC effect. Adult F2 hens (n = 158) were injected twice with SRBC and whole fixed Brucella abortus (BA). Agglutinating antibody titer at 7 d after primary immunization and mean titer of the final three samples (Days 18, 32, and 63 after the second immunization) were used as parameters for primary and equilibrium phases, respectively. Secondary phase parameters of minimum (Ymin), maximum titers (Ymax) and time needed to achieve minimum (Tmin) and maximum (Tmax) titers were estimated from seven postsecondary titers with a nonlinear regression model. Three candidate genes, interferon-gamma (IFN-gamma), interleukin-2 (IL-2), and immunoglobulin G light chain (IgL) were studied. Primers for the promoter regions were designed from EMBL chicken genomic sequences. Polymorphisms between parental lines were detected by direct sequencing. Polymerase chain reaction-restriction fragment length polymorphism methods were then developed to directly detect the polymorphism. There were significant main effects (P < 0.05, general linear model analysis) of IFN-gamma polymorphism on Ymax of BA antibody and interaction of IFN-gamma by IgL on primary antibody response to SRBC and BA, and on Tmin and Ymin of antibody response to SRBC in F2 offspring of M5.1 grandsires. There were significant main effects of IFN-gamma polymorphism on Tmax of BA and interaction of IFN-gamma by IL-2 on Ymin to SRBC in F2 offspring of M15.2 grandsires. The results suggest that IFN-gamma genes play an important role in chicken primary and secondary antibody response to SRBC and BA antigens, and there exists interaction among genes for antibody production.
Poultry Science 12/2001; 80(12):1679-89. · 1.73 Impact Factor
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ABSTRACT: Thirteen gene-specific primer sets provided by the U.S. Poultry Genome Coordinators were used to investigate DNA polymorphisms between two highly inbred chicken lines of Leghorn and Fayoumi origin. Nucleotide and predicted amino acid sequences were then compared among these chicken lines and the Genbank sequences of chicken, mouse, and human. The following genes were selected as candidates for immune response or transcription activation: B2M, DAD1, IAP1, IL2, IREB1, LAP18, MAFL, POU1F1, RREB1, TAD, TBP1, TCRG, and ZOV3. Total cDNA was obtained from the spleens of Leghorn and Fayoumi lines by reverse transcriptase-polymerase chain reaction (PCR) and was used as a template to PCR-amplify gene-specific products. All primers except POU1F1 and TCRG generated single PCR products of the predicted 325- to 667-bp size, confirming the efficacy of these gene-specific primers in the chicken. Three and seven of the 11 amplified gene fragments yielded line-specific nucleotide polymorphisms between the Leghorn and Fayoumi sequences and between the Leghorn and Genbank chicken sequences respectively. Similarities between inbred Leghorn and mammalian species were 36 to 86% for nucleotides and 25 to 96% for predicted amino acid sequence. The polymorphisms of some gene fragments between the Leghorn and Fayoumi lines will allow for investigation of associations of these genes with immune response and other biological traits.
Poultry Science 04/2001; 80(3):284-8. · 1.73 Impact Factor
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ABSTRACT: Forty-two microsatellite loci were analysed in 23 highly inbred chicken lines derived from Leghorn, Jungle Fowl, Fayoumi and Spanish breeds. Line-specific alleles among breeds and lines were detected. The band-sharing (BS) values were calculated and the proportion of shared alleles distances (Dps) were estimated. The BS values and Dps between sets of MHC-congenic lines ranged from 0.74 to 0.96, and 0.05-0.35, respectively. The BS values between each pair of noncongenic Leghorn lines were 0.32-0.97, and between Leghorn and exotic (Jungle Fowl, Fayoumi and Spanish) breeds were 0.03-0.55. The Dps between Fayoumi lines and other lines were much larger (0.66-1.34) than within Leghorns, and the Jungle Fowl breed had the largest distances with other lines (1.12-5.38). The phylogenetic consensus tree that was constructed grouped these 23 inbred chicken lines into four different clusters. These results are in accordance with the origin and breeding history of these inbred lines, which indicates that the use of microsatellites for the study of genetic biodiversity is accurate and reliable. In addition, the significance and value of inbred chicken lines in molecular genetic research is discussed.
Animal Genetics 09/1999; 30(4):256-64. · 2.40 Impact Factor
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ABSTRACT: Although previous studies have demonstrated an association between interferon-gamma (IFN-gamma) promoter genotype and antibody response kinetics in chickens, the protein levels that may mediate such a gene-trait association have not been determined. The objective of this study, therefore, was to determine the correlation of circulating IFN-gamma levels with both the IFN-gammaIFN-gamma promoter polymorphisms and antibody response in order to evaluate the potential role of IFN-gamma protein in mediating genetic control of antibody response in chickens. Antibody response after Salmonella enteritidis (SE) vaccination at day 10, antibody response to sheep red blood cells (SRBCs) and killed Brucella abortus after immunizations at 19 wk and 22 wk, and serum IFN-gamma protein level were measured in an F2 population derived from inbred lines. A single nucleotide polymorphism in the IFN-gamma promoter region was associated with IFN-gamma protein expression as measured by an enzyme-linked immunosorbent assay after both primary and secondary immunizations. Higher IFN-gamma protein level was correlated with higher antibody level to SE and with increased maximum level and decreased time to reach the maximum secondary antibody response to SRBCs. These results suggest that one of the mechanisms by which promoter polymorphism of IFN-gamma affects antibody production in chickens may involve the circulating level of IFN-gamma protein.
Avian Diseases 46(4):869-76. · 1.46 Impact Factor
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ABSTRACT: An F2 population was produced from mating G0 highly inbred (>99€males of two MHC-congenic Fayoumi lines with G-B1 Leghorn hens. The F2 population was essentially a full-sibship with the F1 sire line reflecting MHC effect. Adult F2 hens (n = 158) were injected twice with SRBC and whole fixed Brucella abortus (BA). Agglutinating antibody titer at 7 d after primary immunization and mean titer of the final three samples (Days 18, 32, and 63 after the second immunization) were used as parameters for primary and equilibrium phases, respectively. Secondary phase parameters of minimum (Ymin), maximum titers (Ymax) and time needed to achieve minimum (Tmin) and maximum (Tmax) titers were estimated from seven postsecondary titers with a nonlinear regression model. Three candidate genes, interferon-γ (IFN-γ), interleukin-2 (IL-2), and immunoglobulin G light chain (IgL) were studied. Primers for the promoter regions were designed from EMBL chicken genomic sequences. Polymorphisms between parental lines were detected by direct sequencing. Polymerase chain reaction-restriction fragment length polymorphism methods were then developed to directly detect the polymorphism. There were significant main effects (P < 0.05, general linear model analysis) of IFN-γ polymorphism on Ymax of BA antibody and interaction of IFN-γ by IgL on primary antibody response to SRBC and BA, and on Tmin and Ymin of antibody response to SRBC in F2 offspring of M5.1 grandsires. There were significant main effects of IFN-γ polymorphism on Tmax of BA and interaction of IFN-γ by IL-2 on Ymin to SRBC in F2 offspring of M15.2 grandsires. The results suggest that IFN-γ genes play an important role in chicken primary and secondary antibody response to SRBC and BA antigens, and there exists interaction among genes for antibody production.
Poultry Science 80 (2001).
