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Yang T, Chen S, Qiu L, Guo Q, Wang Z, Jiang Y, Bai H, Bi Y, Chang G. Effect of High Dietary Iron on Fat Deposition and Gut Microbiota in Chickens. Animals (Basel) 2024; 14:2254. [PMID: 39123780 PMCID: PMC11310990 DOI: 10.3390/ani14152254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Revised: 07/30/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024] Open
Abstract
To meet the demand of consumers for chicken products, poultry breeders have made improvements to chickens. However, this has led to a new problem in the modern poultry industry, namely excessive fat deposition. This study aims to understand the effects of dietary iron supplementation on fat deposition and gut microbiota in chickens. In this study, we investigated the effects of iron on the growth performance, fat deposition, and gut microbiota of silky fowl black-bone chickens. A total of 75 7-week-old silky fowl black-bone chickens were randomly divided into three groups (five replicates per group, five chickens per replicate) and fed them for 28 days using a growing diet (control group), a growing diet + 10% tallow (high-fat diet group, HFD group), and a growing diet + 10% tallow + 500 mg/kg iron (HFDFe500 group), respectively. We detected the effects of iron on the growth performance, fat deposition, and gut microbiota of silky fowl black-bone chickens using the growth performance index test, oil red O staining, and HE staining, and found that the high-fat diet significantly increased liver and serum fat deposition and liver injury, while the addition of iron to the diet could reduce the fat deposition caused by the high-fat diet and alleviate liver injury. In addition, 16S rDNA sequencing was used to compare the relative abundance of gut microbiota in the cecal contents in different feeding groups. The results showed that the high-fat diet could induce gut microbiota imbalance in chickens, while the high-iron diet reversed the gut microbiota imbalance. PICRUSt functional prediction analysis showed that dietary iron supplementation affected amino acid metabolism, energy metabolism, cofactors, and vitamin metabolism pathways. In addition, correlation analysis showed that TG was significantly associated with Firmicutes and Actinobacteriota (p < 0.05). Overall, these results revealed high dietary iron (500 mg/kg) could reduce fat deposition and affect the gut microbiota of silky fowl black-bone chickens, suggesting that iron may regulate fat deposition by influencing the gut microbiota of chickens and provides a potential avenue that prevents excessive fat deposition in chickens by adding iron to the diet.
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Affiliation(s)
- Ting Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Shihao Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Lingling Qiu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Qixin Guo
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Zhixiu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Yong Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Hao Bai
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Yulin Bi
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Guobin Chang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
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Davoodi P, Ehsani A, Vaez Torshizi R, Masoudi AA. New insights into genetics underlying of plumage color. Anim Genet 2021; 53:80-93. [PMID: 34855995 DOI: 10.1111/age.13156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 01/12/2023]
Abstract
Plumage color can be considered as a social signal in chickens and a breeding identification tool among breeders. The relationship between plumage color and trait groups of immunity, growth and fertility is still a controversial issue. This research aimed to determine the genome-wide additive and epistatic variants affecting plumage color variation in chickens using the chicken Illumina 60k high-density SNP array. Two scenarios of genome-wide additive association studies using all SNPs and independent SNPs were carried out. To perform epistatic association analysis, the LD pruning approach was used to reduce the complexity of the analysis. We detected seven novel significant loci using all of the SNPs in the model and 14 SNPs using the LD pruning approach associated with plumage color. Moreover, 89 significantly associated SNP-SNP interactions (P-value <10-6 ) distributed in 25 chromosomes were identified, indicating that all of the signals together putatively influence the quantitative variation of plumage color. By annotating genes relevant to top SNPs, we have distinguished 18 potential candidate genes comprising HNF4beta, CKMT1B, TBC1D22A, RPL8, CACNA2D1, FZD4, SGMS1, IRF8, OPTN, LOC420362, TRABD, OvoDA1, DAD1, USP6, RBM12B, MIR1772, MIR1709 and MIR6696 and also 89 putative gene-gene combinations responsible for plumage color variation in chickens. Furthermore, several KEGG pathways including metabolic pathway, cytokine-cytokine receptor interaction, focal adhesion, melanogenesis, glycosaminoglycan biosynthesis-keratan sulfate and sphingolipid metabolism were enriched in the gene-set analysis. The results indicated that plumage color is a highly polygenic trait which, in turn, can be affected by multiple coding genes, regulatory genes and gene-gene epistasis interactions. In addition to genes with additive effects, epistatic genes with tiny individual effect sizes but significant effects in a pair have the potential to control plumage coloration in chickens.
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Affiliation(s)
- P Davoodi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, 14115-336, Tehran, Iran
| | - A Ehsani
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, 14115-336, Tehran, Iran
| | - R Vaez Torshizi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, 14115-336, Tehran, Iran
| | - A A Masoudi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, 14115-336, Tehran, Iran
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Genome-wide association study reveals the genetic determinism of growth traits in a Gushi-Anka F 2 chicken population. Heredity (Edinb) 2020; 126:293-307. [PMID: 32989280 PMCID: PMC8026619 DOI: 10.1038/s41437-020-00365-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 08/18/2020] [Accepted: 08/30/2020] [Indexed: 02/07/2023] Open
Abstract
Chicken growth traits are economically important, but the relevant genetic mechanisms have not yet been elucidated. Herein, we performed a genome-wide association study to identify the variants associated with growth traits. In total, 860 chickens from a Gushi-Anka F2 resource population were phenotyped for 68 growth and carcass traits, and 768 samples were genotyped based on the genotyping-by-sequencing (GBS) method. Finally, 734 chickens and 321,314 SNPs remained after quality control and removal of the sex chromosomes, and these data were used to carry out a GWAS analysis. A total of 470 significant single-nucleotide polymorphisms (SNPs) for 43 of the 68 traits were detected and mapped on chromosomes (Chr) 1-6, -9, -10, -16, -18, -23, and -27. Of these, the significant SNPs in Chr1, -4, and -27 were found to be associated with more than 10 traits. Multiple traits shared significant SNPs, indicating that the same mutation in the region might have a large effect on multiple growth or carcass traits. Haplotype analysis revealed that SNPs within the candidate region of Chr1 presented a mosaic pattern. The significant SNPs and pathway enrichment analysis revealed that the MLNR, MED4, CAB39L, LDB2, and IGF2BP1 genes could be putative candidate genes for growth and carcass traits. The findings of this study improve our understanding of the genetic mechanisms regulating chicken growth and carcass traits and provide a theoretical basis for chicken breeding programs.
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Deng MT, Zhang F, Zhu F, Yang YZ, Yang FX, Hao JP, Hou ZC. Genome-wide association study reveals novel loci associated with fat-deposition and meat-quality traits in Pekin ducks. Anim Genet 2020; 51:953-957. [PMID: 32844456 DOI: 10.1111/age.12995] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2020] [Indexed: 01/23/2023]
Abstract
Meat-quality traits play an essential role in meat poultry production. To determine the genetic mechanisms of meat quality in Pekin ducks, we performed a large-scale GWAS to identify quantitative trait loci affecting meat quality in Pekin ducks. We measured 10 traits in 542 Pekin ducks and genotyped each duck using genotyping-by-sequencing. The genetic parameters (genomic heritability, genetic correlation) for 10 meat-quality related traits were evaluated. Based on the large genotype-phenotype dataset, we performed GWASs for all of these traits. A total of 33 significant QTL (P < 3.03 × 10-5 ) across 13 chromosomes were identified by loci-based analysis. Some newly identified candidate genes were discovered for fat-deposition and meat-quality traits, including PAG1 for body weight and eviscerated weight, INTU and NUP35 for abdominal fat weight and ratio, NUP3 and ARHGDIB for skin fat weight and ratio, GOLGA5 for breast muscle toughness and breast tenderness, and CTDSPL and PKP1 for breast muscle thickness. The current study is the first systematic report regarding duck meat quality.
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Affiliation(s)
- M-T Deng
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - F Zhang
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - F Zhu
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Y-Z Yang
- Beijing General Station of Animal Husbandry, Beijing, 100107, China
| | - F-X Yang
- Beijing Jinxing Golden Star Duck Center, Beijing, 100076, China
| | - J-P Hao
- Beijing Jinxing Golden Star Duck Center, Beijing, 100076, China
| | - Z-C Hou
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
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Ishikawa A, Sakaguchi M, Nagano AJ, Suzuki S. Genetic Architecture of Innate Fear Behavior in Chickens. Behav Genet 2020; 50:411-422. [PMID: 32770288 DOI: 10.1007/s10519-020-10012-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/29/2020] [Indexed: 01/12/2023]
Abstract
The genetic architecture of innate fear behavior in chickens is poorly understood. Here, we performed quantitative trait loci (QTL) analysis of innate responses to tonic immobility (TI) and open field (OF) fears in 242 newly hatched chicks of an F2 population between the native Japanese Nagoya breed and the White Leghorn breed using 881 single nucleotide polymorphism markers obtained by restriction site-associated DNA sequencing. At genome-wide 5% significance levels, four QTL for TI traits were revealed on chromosomes 1-3 and 24. Two of these loci had sex-specific effects on the traits. For OF traits, three QTL were revealed on chromosomes 2, 4 and 7. The TI and OF QTL identified showed no overlaps in genomic regions and different modes of inheritance. The three TI QTL and one OF QTL exerted antagonistic effects on the traits. The results demonstrated that context-dependent QTL underlie the variations in innate TI and OF behaviors.
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Affiliation(s)
- Akira Ishikawa
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan.
| | - Marina Sakaguchi
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Sae Suzuki
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
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Cahyadi M, Park HB, Seo DW, Jin S, Choi N, Heo KN, Kang BS, Jo C, Lee JH. Association of the thyroid hormone responsive spot 14 alpha gene with growth-related traits in Korean native chicken. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2020; 33:1755-1762. [PMID: 32106653 PMCID: PMC7649070 DOI: 10.5713/ajas.19.0541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 02/10/2020] [Indexed: 11/28/2022]
Abstract
Objective Thyroid hormone responsive spot 14 alpha (THRSP) has been used to investigate the regulation of de novo lipogenesis because the variation of THRSP mRNA content in the tissue affects directly the ability of that tissue to synthetize lipids. Also, this gene responds to thyroid hormone stimulation and high level of carbohydrate feeding or insulin-injection. This study was carried out to investigate variations within THRSP and their effects on body and carcass weights in Korean native chicken (KNC). Methods A total of 585 chickens which represent the five lines of KNC (Black, Gray-Brown, Red-Brown, White, and Yellow-Brown) were reared and body weight data were recorded every two weeks from hatch until 20 weeks of age. Polymerase chain reaction-restriction fragment length polymorphism, DNA chips for Agilent 2100 Bioanalyzer, and Fluidigm Genotyping Technology, were applied to genotype selected markers. A linear mixed-effect model was used to access association between these single nucleotide polymorphism (SNP) markers and growth-related traits. Results A total of 30 polymorphisms were investigated in THRSP. Of these, nine SNPs for loci were selected to perform association analyses. Significant associations were detected between g.-49G>T SNP with body weight at 20 weeks of age (BW20), g.451T>C SNP with growth at 10 to 12 weeks of age (GR10-12), and g.1432A>C SNP with growth at 14 to 16 weeks trait (GR14-16) and body weight at 18 weeks of age (BW18). Moreover, diplotype of the THRSP gene significantly affected body weight at 12 weeks of age (BW12) and GR10-12 traits. Diplotype of ht1/ht2 was favorable for BW12 and GR10-12 traits. Conclusion These results suggest that THRSP can be regarded as a candidate gene for growth traits in KNC.
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Affiliation(s)
- Muhammad Cahyadi
- Department of Animal Science, Faculty of Agriculture, Universitas Sebelas Maret, Surakarta 57126, Indonesia
| | - Hee-Bok Park
- Department of Animal Resources Science, Kongju National University, Yesan 32439, Korea
| | - Dong Won Seo
- Department of Animal and Dairy Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Shil Jin
- Department of Animal and Dairy Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Korea.,Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang 25340, Korea
| | - Nuri Choi
- Division of Biotechnology, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 54596, Korea
| | - Kang Nyeong Heo
- Poultry Research Institute, National Institute of Animal Science, RDA, Pyeongchang 25340, Korea
| | - Bo Seok Kang
- Poultry Research Institute, National Institute of Animal Science, RDA, Pyeongchang 25340, Korea
| | - Cheorun Jo
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 151921, Korea
| | - Jun Heon Lee
- Department of Animal and Dairy Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Korea
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Zhou Y, Liu H, Wang X, Fu B, Yu X, Tong J. QTL Fine Mapping for Sex Determination Region in Bighead Carp (Hypophthalmichthys nobilis) and Comparison with Silver Carp (Hypophthalmichthys molitrix). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:41-53. [PMID: 31776800 DOI: 10.1007/s10126-019-09929-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
Bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix) are genetically close aquaculture fish in the Cyprinidae, which have been confirmed to hold XX/XY sex determination. However, genomic locations of potential sex-related loci in these two fishes are still unknown. In this study, a high-resolution genetic linkage map was constructed by using 2976 SNP and 924 microsatellite markers in a F1 full-sib family of bighead carp, the length of which spanned 2022.34 cM with an average inter-marker distance of 0.52 cM. Comparative genomics revealed a high level of genomic synteny between bighead carp and zebrafish as well as grass carp. QTL fine mapping for sex trait was performed based on this linkage map of bighead carp and an unpublished linkage map of silver carp. A map distance of 3.863 cM (69.787-73.650 cM) on LG19 of bighead carp and 4.705 cM (79.096-83.801 cM) on LG21 of silver carp was significantly associated with sex phenotypes, and these two LGs are homologous between two fish species. Fourteen markers harboring in these regions were in strong linkage disequilibrium with the sex phenotype variance explained (PVE) varying from 89 to 100%. Two common markers were mapped on the QTL regions of bighead carp and silver carp, suggesting that these two carp species may have similar genetic bases for sex determination. Eleven potentially sex-related genes were identified within or near the sex QTL markers in two species. This study provided insights into elucidating mechanisms and evolution of sex determination in cyprinid fishes.
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Affiliation(s)
- Ying Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Haiyang Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xinhua Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, 450046, China
| | - Beide Fu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
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Ono T, Kouguchi T, Ishikawa A, Nagano AJ, Takenouchi A, Igawa T, Tsudzuki M. Quantitative trait loci mapping for the shear force value in breast muscle of F2 chickens. Poult Sci 2019; 98:1096-1101. [PMID: 30329107 DOI: 10.3382/ps/pey493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 10/10/2018] [Indexed: 12/18/2022] Open
Abstract
The shear force value is one of the major traits that determine meat quality. In the present study, we performed QTL analysis for chicken breast muscle shear force value at 7 wk of age using 545 single nucleotide polymorphism (SNP) markers developed via restriction-site associated DNA sequencing (RAD-seq). An F2 resource family was generated by mating Oh-Shamo, a native Japanese chicken breed, and the White Plymouth Rock chicken breed. A total of 215 F2 birds were produced. Simple interval mapping revealed one significant main-effect QTL between 6.28 and 8.10 Mb SNPs on the chromosome Z with a logarithm of odds score of 5.53 at the genome-wide 5% level. At this QTL, the confidence interval, phenotypic variance explained, and additive effect were 26 cM, 12.24%, and -0.31 in males and -0.34 in females, respectively. No QTL with epistatic interaction effects were detected. To our knowledge, this is the first report on a QTL affecting the shear force value in the chicken breast muscle, using SNP markers derived from RAD-seq.
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Affiliation(s)
- Takashi Ono
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | | | - Akira Ishikawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan.,Japanese Avian Bioresource Project Research Center, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga 520-2194, Japan
| | - Atsushi Takenouchi
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Takeshi Igawa
- Japanese Avian Bioresource Project Research Center, Higashi-Hiroshima, Hiroshima 739-8528, Japan.,Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Masaoki Tsudzuki
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan.,Japanese Avian Bioresource Project Research Center, Higashi-Hiroshima, Hiroshima 739-8528, Japan
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Quantitative trait loci for morphometric and mineral composition traits of the tibia bone in a broiler × layer cross. Animal 2019; 13:1563-1569. [PMID: 30614429 DOI: 10.1017/s175173111800335x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Many economic losses occur in the poultry industry due to leg fragility. Knowing the genomic regions that influence traits associated with the growth and composition of the leg's bone can help to improve the selection process leading to increased leg resistance to fracture. The present study aimed to map quantitative trait loci (QTL) for mineral composition and morphometric traits of the tibia in 478 animals from an F2 broiler × layer cross. The measurement of weight, length and width of Tibia was carried out at 42 days of age. Ash, dry matter, levels of calcium (Ca), phosphorus (P), magnesium (Mg), Zinc (Zn) and Calcium:Phosphorus (Ca:P) ratio were also recorded. The population was genotyped for 128 microsatellite markers and one single nucleotide polymorphism, covering 2630 cM of the chicken genome. A likelihood ratio test was performed to find QTLs. Additive and dominance effects of the QTLs were included in the model. In the chromosomes 2 (GGA2), 6 (GGA6), 8 (GGA8), 24 (GGA24) and 26 (GGA26) some suggestive QTLs (P<0.00276) were mapped for tibia weight (GGA2 and GGA26), ash percentage (GGA2 and GGA6), dry matter percentage (GGA2), Ca (GGA8 and GGA24) and Ca:P ratio (GGA8), many of which are close to genes already identified as good candidates for those traits. The suggestive QTL on GGA2 has a pleiotropic effect on ash percentage, dry matter and bone weight, whereas in the GGA8 there seems to be two QTLs, one for Ca and another for Ca:P ratio. Thus, this study identified at least five genomic regions, in different chromosomes, that can be targeted for further research to identify potential mutations influencing the development and composition of leg bones in Gallus gallus.
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Mapping of Quantitative Trait Loci for Growth and Carcass-Related Traits in Chickens Using a Restriction-Site Associated DNA Sequencing Method. J Poult Sci 2019; 56:166-176. [PMID: 32055211 PMCID: PMC7005382 DOI: 10.2141/jpsa.0180066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In the present study, quantitative trait loci (QTLs) analysis was performed to identify the chromosomal positions of growth and carcass-related trait QTLs using 319 F2 chickens obtained from intercrosses of an Oh-Shamo male and four White Plymouth Rock females. Body weight was measured weekly until the birds were 7 weeks old. Carcass-related traits were also measured at this timepoint. A genetic linkage map was constructed using 545 single nucleotide polymorphism (SNP) markers that were developed using a restriction-site associated DNA sequencing method. The linkage map included the 23 autosomes and the Z chromosome. Using simple interval QTL mapping, we were able to identify 10 significant and suggestive main-effect QTLs for growth and carcass-related traits present on chromosomes 1, 2, 3, 5, 8, 19, 24, and Z. These loci explained 5.60–16.52% of the phenotypic variances. The chromosomal positions of the 10 QTLs overlapped with those of previously reported QTLs, whereas the targeted traits varied. Our QTLs will aid future breeding programs in improving growth and meat yield of chickens (e.g., via marker-assisted selection), particularly in the Japanese brand chicken industry.
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Moreira GCM, Boschiero C, Cesar ASM, Reecy JM, Godoy TF, Trevisoli PA, Cantão ME, Ledur MC, Ibelli AMG, Peixoto JDO, Moura ASAMT, Garrick D, Coutinho LL. A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens. BMC Genomics 2018; 19:374. [PMID: 29783939 PMCID: PMC5963092 DOI: 10.1186/s12864-018-4779-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/10/2018] [Indexed: 12/21/2022] Open
Abstract
Background Excess fat content in chickens has a negative impact on poultry production. The discovery of QTL associated with fat deposition in the carcass allows the identification of positional candidate genes (PCGs) that might regulate fat deposition and be useful for selection against excess fat content in chicken’s carcass. This study aimed to estimate genomic heritability coefficients and to identify QTLs and PCGs for abdominal fat (ABF) and skin (SKIN) traits in a broiler chicken population, originated from the White Plymouth Rock and White Cornish breeds. Results ABF and SKIN are moderately heritable traits in our broiler population with estimates ranging from 0.23 to 0.33. Using a high density SNP panel (355,027 informative SNPs), we detected nine unique QTLs that were associated with these fat traits. Among these, four QTL were novel, while five have been previously reported in the literature. Thirteen PCGs were identified that might regulate fat deposition in these QTL regions: JDP2, PLCG1, HNF4A, FITM2, ADIPOR1, PTPN11, MVK, APOA1, APOA4, APOA5, ENSGALG00000000477, ENSGALG00000000483, and ENSGALG00000005043. We used sequence information from founder animals to detect 4843 SNPs in the 13 PCGs. Among those, two were classified as potentially deleterious and two as high impact SNPs. Conclusions This study generated novel results that can contribute to a better understanding of fat deposition in chickens. The use of high density array of SNPs increases genome coverage and improves QTL resolution than would have been achieved with low density. The identified PCGs were involved in many biological processes that regulate lipid storage. The SNPs identified in the PCGs, especially those predicted as potentially deleterious and high impact, may affect fat deposition. Validation should be undertaken before using these SNPs for selection against carcass fat accumulation and to improve feed efficiency in broiler chicken production. Electronic supplementary material The online version of this article (10.1186/s12864-018-4779-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gabriel Costa Monteiro Moreira
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - Clarissa Boschiero
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - Aline Silva Mello Cesar
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - James M Reecy
- Department of Animal Science, Iowa State University (ISU), Ames, Iowa, USA
| | - Thaís Fernanda Godoy
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - Priscila Anchieta Trevisoli
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | | | | | | | | | | | - Dorian Garrick
- School of Agriculture, Massey University, Ruakura, Hamilton, New Zealand
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil.
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12
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Kodama M, Hard JJ, Naish KA. Mapping of quantitative trait loci for temporal growth and age at maturity in coho salmon: Evidence for genotype-by-sex interactions. Mar Genomics 2018; 38:33-44. [DOI: 10.1016/j.margen.2017.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 07/01/2017] [Accepted: 07/22/2017] [Indexed: 11/26/2022]
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13
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Komatsu M, Nishino K, Fujimori Y, Haga Y, Iwama N, Arakawa A, Aihara Y, Takeda H, Takahashi H. Epistatic effects between pairs of the growth hormone secretagogue receptor 1a, growth hormone, growth hormone receptor, non-SMC condensin I complex, subunit G and stearoyl-CoA desaturase genes on carcass, price-related and fatty acid composition traits in Japanese Black cattle. Anim Sci J 2017; 89:273-288. [PMID: 29154485 DOI: 10.1111/asj.12947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/25/2017] [Indexed: 01/11/2023]
Abstract
Growth hormone secretagogue receptor 1a (GHSR1a), growth hormone (GH), growth hormone receptor (GHR), non-SMC condensin I complex, subunit G (NCAPG) and stearoyl-CoA desaturase (SCD), are known to play important roles in growth and lipid metabolisms. Single and epistatic effects of the five genes on carcass, price-related and fatty acid (FA) composition traits were analyzed in a commercial Japanese Black cattle population of Ibaraki Prefecture. A total of 650 steers and 116 heifers for carcass and price-related traits, and 158 steers for FA composition traits were used in this study. Epistatic effects between pairs of the five genes were found in several traits. Alleles showing strain-specific differences in the five genes had significant single and epistatic effects in some traits. The data suggest that a TG-repeat polymorphism of the GHSR1a.5'UTR-(TG)n locus plays a central role in gene-gene epistatic interaction of FA composition traits in the adipose tissue of Japanese Black cattle.
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Affiliation(s)
- Masanori Komatsu
- Institute of Livestock and Grassland Science, National Agriculture and Food, Research Organization (NARO), Tsukuba, Ibaraki, Japan.,Komatsu Laboratory of Computational Biology for Domestic Animals, Ryugasaki, Ibaraki, Japan
| | - Kagetomo Nishino
- Ibaraki Prefecture Livestock Research Centre, Hitachi-Ohmiya, Ibaraki, Japan
| | - Yuki Fujimori
- Ibaraki Prefecture Livestock Research Centre, Hitachi-Ohmiya, Ibaraki, Japan.,Nagano Animal Industry Experiment Station, Shiojiri, Nagano, Japan
| | - Yasutoshi Haga
- Ibaraki Prefecture Livestock Research Centre, Hitachi-Ohmiya, Ibaraki, Japan.,Ibaraki Prefecture Agricultural College, Tsuchiura, Ibaraki, Japan
| | - Nagako Iwama
- Ibaraki Prefecture Livestock Research Centre, Hitachi-Ohmiya, Ibaraki, Japan.,Ibaraki Prefecture Ken-nan Livestock Office of Agriculture and Forestry, Tsuchiura, Ibaraki, Japan
| | - Aisaku Arakawa
- Institute of Livestock and Grassland Science, National Agriculture and Food, Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Yoshito Aihara
- Ibaraki Prefecture Livestock Research Centre, Hitachi-Ohmiya, Ibaraki, Japan
| | - Hisato Takeda
- Institute of Livestock and Grassland Science, National Agriculture and Food, Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Hideaki Takahashi
- Institute of Livestock and Grassland Science, National Agriculture and Food, Research Organization (NARO), Tsukuba, Ibaraki, Japan
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Resnyk CW, Carré W, Wang X, Porter TE, Simon J, Le Bihan-Duval E, Duclos MJ, Aggrey SE, Cogburn LA. Transcriptional analysis of abdominal fat in chickens divergently selected on bodyweight at two ages reveals novel mechanisms controlling adiposity: validating visceral adipose tissue as a dynamic endocrine and metabolic organ. BMC Genomics 2017; 18:626. [PMID: 28814270 PMCID: PMC5559791 DOI: 10.1186/s12864-017-4035-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 08/08/2017] [Indexed: 11/10/2022] Open
Abstract
Background Decades of intensive genetic selection in the domestic chicken (Gallus gallus domesticus) have enabled the remarkable rapid growth of today’s broiler (meat-type) chickens. However, this enhanced growth rate was accompanied by several unfavorable traits (i.e., increased visceral fatness, leg weakness, and disorders of metabolism and reproduction). The present descriptive analysis of the abdominal fat transcriptome aimed to identify functional genes and biological pathways that likely contribute to an extreme difference in visceral fatness of divergently selected broiler chickens. Methods We used the Del-Mar 14 K Chicken Integrated Systems microarray to take time-course snapshots of global gene transcription in abdominal fat of juvenile [1-11 weeks of age (wk)] chickens divergently selected on bodyweight at two ages (8 and 36 wk). Further, a RNA sequencing analysis was completed on the same abdominal fat samples taken from high-growth (HG) and low-growth (LG) cockerels at 7 wk, the age with the greatest divergence in body weight (3.2-fold) and visceral fatness (19.6-fold). Results Time-course microarray analysis revealed 312 differentially expressed genes (FDR ≤ 0.05) as the main effect of genotype (HG versus LG), 718 genes in the interaction of age and genotype, and 2918 genes as the main effect of age. The RNA sequencing analysis identified 2410 differentially expressed genes in abdominal fat of HG versus LG chickens at 7 wk. The HG chickens are fatter and over-express numerous genes that support higher rates of visceral adipogenesis and lipogenesis. In abdominal fat of LG chickens, we found higher expression of many genes involved in hemostasis, energy catabolism and endocrine signaling, which likely contribute to their leaner phenotype and slower growth. Many transcription factors and their direct target genes identified in HG and LG chickens could be involved in their divergence in adiposity and growth rate. Conclusions The present analyses of the visceral fat transcriptome in chickens divergently selected for a large difference in growth rate and abdominal fatness clearly demonstrate that abdominal fat is a very dynamic metabolic and endocrine organ in the chicken. The HG chickens overexpress many transcription factors and their direct target genes, which should enhance in situ lipogenesis and ultimately adiposity. Our observation of enhanced expression of hemostasis and endocrine-signaling genes in diminished abdominal fat of LG cockerels provides insight into genetic mechanisms involved in divergence of abdominal fatness and somatic growth in avian and perhaps mammalian species, including humans. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4035-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- C W Resnyk
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA
| | - W Carré
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA.,Laboratoire de Génétique Moléculaire et Génomique, CHU Pontchaillou, 35033, Rennes, France
| | - X Wang
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA.,Department of Biological Sciences, Tennessee State University, Nashville, TN, 37209, USA
| | - T E Porter
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - J Simon
- UR83 Recherches Avicoles, Institut National de la Recherche Agronomique (INRA), F-37380, Nouzilly, France
| | - E Le Bihan-Duval
- UR83 Recherches Avicoles, Institut National de la Recherche Agronomique (INRA), F-37380, Nouzilly, France
| | - M J Duclos
- UR83 Recherches Avicoles, Institut National de la Recherche Agronomique (INRA), F-37380, Nouzilly, France
| | - S E Aggrey
- Department of Poultry Science, University of Georgia, Athens, GA, 30602, USA
| | - L A Cogburn
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA.
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15
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Zheng X, Kuang Y, Lv W, Cao D, Sun Z, Sun X. Genome-Wide Association Study for Muscle Fat Content and Abdominal Fat Traits in Common Carp (Cyprinus carpio). PLoS One 2016; 11:e0169127. [PMID: 28030623 PMCID: PMC5193488 DOI: 10.1371/journal.pone.0169127] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/12/2016] [Indexed: 12/24/2022] Open
Abstract
Muscle fat content is an important phenotypic trait in fish, as it affects the nutritional, technical and sensory qualities of flesh. To identify loci and candidate genes associated with muscle fat content and abdominal fat traits, we performed a genome-wide association study (GWAS) using the common carp 250 K SNP assay in a common carp F2 resource population. A total of 18 loci surpassing the genome-wide suggestive significance level were detected for 4 traits: fat content in dorsal muscle (MFdo), fat content in abdominal muscle (MFab), abdominal fat weight (AbFW), and AbFW as a percentage of eviscerated weight (AbFP). Among them, one SNP (carp089419) affecting both AbFW and AbFP reached the genome-wide significance level. Ten of those loci were harbored in or near known genes. Furthermore, relative expressions of 5 genes related to MFdo were compared using dorsal muscle samples with high and low phenotypic values. The results showed that 4 genes were differentially expressed between the high and low phenotypic groups. These genes are, therefore, prospective candidate genes for muscle fat content: ankyrin repeat domain 10a (ankrd10a), tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2 (tanc2), and four jointed box 1 (fjx1) and choline kinase alpha (chka). These results offer valuable insights into the complex genetic basis of fat metabolism and deposition.
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Affiliation(s)
- Xianhu Zheng
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
| | - Youyi Kuang
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
| | - Weihua Lv
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Dingchen Cao
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
| | - Zhipeng Sun
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
| | - Xiaowen Sun
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
- * E-mail:
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16
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Wang W, Zhang T, Wang J, Zhang G, Wang Y, Zhang Y, Zhang J, Li G, Xue Q, Han K, Zhao X, Zheng H. Genome-wide association study of 8 carcass traits in Jinghai Yellow chickens using specific-locus amplified fragment sequencing technology. Poult Sci 2016; 95:500-6. [PMID: 26614681 PMCID: PMC4957485 DOI: 10.3382/ps/pev266] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Carcass traits are important to the commercial chicken industry, and understanding the genetics of these traits will be useful in the development of commercially viable varieties of chickens. We conducted a genome-wide association study based on 8 carcass trait phenotypes in a population of 400 43-week-old Jinghai Yellow chickens. Specific-locus amplified fragment sequencing technology was used to identify 90,961 single nucleotide polymorphisms (SNP) distributed among 29 chromosomes and the mitochondrial genome. SNP that were significantly associated with phenotypic traits were identified by a simple general linear model. Fifteen SNP attained genome-wide significance (P < 1.87E−6) and were associated with 5 of the 8 carcass traits; only one SNP was significantly associated with 2 traits (foot weight and wing weight). Twelve genes were associated with these 15 SNP. A region of chromosome 4 between 75.5 and 76.1 Mb was associated with carcass weight, foot weight, and wing weight. An 84-kb region on chromosome 3 (51.2 Mb) was associated with eviscerated weight and semi-eviscerated weight.
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Affiliation(s)
- Wenhao Wang
- Department of Animal Science, Yangzhou University, Yangzhou 225009, China
- Department of Life Science, Resources and Environment, Yichun University, Yichun 336000, China
- These authors contributed equally to this study
| | - Tao Zhang
- Department of Animal Science, Yangzhou University, Yangzhou 225009, China
- These authors contributed equally to this study
| | - Jinyu Wang
- Department of Animal Science, Yangzhou University, Yangzhou 225009, China
- Corresponding author:
| | - Genxi Zhang
- Department of Animal Science, Yangzhou University, Yangzhou 225009, China
| | - Yongjuan Wang
- JiangsuJinghai Poultry Industry Group CD, LTD, Nantong 226000, China
| | - Yinwen Zhang
- Biomarker Technologies Corporation, Beijing 100000, China
| | - Jianhui Zhang
- Biomarker Technologies Corporation, Beijing 100000, China
| | - Guohui Li
- Department of Animal Science, Yangzhou University, Yangzhou 225009, China
| | - Qian Xue
- Department of Animal Science, Yangzhou University, Yangzhou 225009, China
| | - Kunpeng Han
- Department of Animal Science, Yangzhou University, Yangzhou 225009, China
| | - Xiuhua Zhao
- Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Hongkun Zheng
- Biomarker Technologies Corporation, Beijing 100000, China
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17
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Genome-Wide Linkage Analysis Identifies Loci for Physical Appearance Traits in Chickens. G3-GENES GENOMES GENETICS 2015; 5:2037-41. [PMID: 26248982 PMCID: PMC4592986 DOI: 10.1534/g3.115.020883] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Physical appearance traits, such as feather-crested head, comb size and type, beard, wattles size, and feathered feet, are used to distinguish between breeds of chicken and also may be associated with economic traits. In this study, a genome-wide linkage analysis was used to identify candidate regions and genes for physical appearance traits and to potentially provide further knowledge of the molecular mechanisms that underlie these traits. The linkage analysis was conducted with an F2 population derived from Beijing-You chickens and a commercial broiler line. Single-nucleotide polymorphisms were analyzed using the Illumina 60K Chicken SNP Beadchip. The data were used to map quantitative trait loci and genes for six physical appearance traits. A 10-cM/0.51-Mb region (0.0−10.0 cM/0.00−0.51 Mb) with 1% genome-wide significant level on LGE22C19W28_E50C23 linkage group (LGE22) for crest trait was identified, which is likely very closely linked to the HOXC8. A QTL with 5% chromosome-wide significant level for comb weight, which partly overlaps with a region identified in a previous study, was identified at 74 cM/25.55 Mb on chicken (Gallus gallus; GG) chromosome 3 (i.e., GGA3). For beard and wattles traits, an identical region 11 cM/2.23 Mb (0.0−11.0 cM/0.00−2.23 Mb) including WNT3 and GH genes on GGA27 was identified. Two QTL with 1% genome-wide significant level for feathered feet trait, one 9-cM/2.80-Mb (48.0-57.0/13.40-16.20 Mb) region on GGA13, and another 12-cM/1.45-Mb (41.0−53.0 cM/11.37−12.82 Mb) region on GGA15 were identified. These candidate regions and genes provide important genetic information for the physical appearance traits in chicken.
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18
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Stainton JJ, Haley CS, Charlesworth B, Kranis A, Watson K, Wiener P. Detecting signatures of selection in nine distinct lines of broiler chickens. Anim Genet 2014; 46:37-49. [PMID: 25515710 DOI: 10.1111/age.12252] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2014] [Indexed: 01/26/2023]
Abstract
Modern commercial chickens have been bred for one of two specific purposes: meat production (broilers) or egg production (layers). This has led to large phenotypic changes, so that the genomic signatures of selection may be detectable using statistical techniques. Genetic differentiation between nine distinct broiler lines was calculated using Weir and Cockerham's pairwise FST estimator for 11 003 genome-wide markers to identify regions showing evidence of differential selection across lines. Differentiation measures were averaged into overlapping sliding windows for each line, and a permutation approach was used to determine the significance of each window. A total of 51 regions were found to show significant differentiation between the lines. Several lines were consistently found to share significant regions, suggesting that the pattern of line divergence is related to selection for broiler traits. The majority of the 51 regions contain QTL relating to broiler traits, but only five of them were found to be significantly enriched for broiler QTL, including a region on chromosome 27 containing 39 broiler QTL and 114 genes. Additionally, a number of these regions have been identified by other selection mapping studies. This study has identified a large number of potential selection signatures, and further tests with higher-density marker data may narrow these regions down to individual genes.
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Affiliation(s)
- John J Stainton
- The Roslin Institute and R(D)SVS, University of Edinburgh, Midlothian, EH25 9RG, UK
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19
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Liu F, Sun F, Xia JH, Li J, Fu GH, Lin G, Tu RJ, Wan ZY, Quek D, Yue GH. A genome scan revealed significant associations of growth traits with a major QTL and GHR2 in tilapia. Sci Rep 2014; 4:7256. [PMID: 25435025 PMCID: PMC4248272 DOI: 10.1038/srep07256] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 11/04/2014] [Indexed: 12/02/2022] Open
Abstract
Growth is an important trait in animal breeding. However, the genetic effects underpinning fish growth variability are still poorly understood. QTL mapping and analysis of candidate genes are effective methods to address this issue. We conducted a genome-wide QTL analysis for growth in tilapia. A total of 10, 7 and 8 significant QTLs were identified for body weight, total length and standard length at 140 dph, respectively. The majority of these QTLs were sex-specific. One major QTL for growth traits was identified in the sex-determining locus in LG1, explaining 71.7%, 67.2% and 64.9% of the phenotypic variation (PV) of body weight, total length and standard length, respectively. In addition, a candidate gene GHR2 in a QTL was significantly associated with body weight, explaining 13.1% of PV. Real-time qPCR revealed that different genotypes at the GHR2 locus influenced the IGF-1 expression level. The markers located in the major QTL for growth traits could be used in marker-assisted selection of tilapia. The associations between GHR2 variants and growth traits suggest that the GHR2 gene should be an important gene that explains the difference in growth among tilapia species.
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Affiliation(s)
- Feng Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Fei Sun
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Jun Hong Xia
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Jian Li
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Gui Hong Fu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Grace Lin
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Rong Jian Tu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Zi Yi Wan
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Delia Quek
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Gen Hua Yue
- 1] Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore [2] Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore 117543
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20
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Roux PF, Boutin M, Désert C, Djari A, Esquerré D, Klopp C, Lagarrigue S, Demeure O. Re-sequencing data for refining candidate genes and polymorphisms in QTL regions affecting adiposity in chicken. PLoS One 2014; 9:e111299. [PMID: 25333370 PMCID: PMC4205046 DOI: 10.1371/journal.pone.0111299] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/22/2014] [Indexed: 12/30/2022] Open
Abstract
In this study, we propose an approach aiming at fine-mapping adiposity QTL in chicken, integrating whole genome re-sequencing data. First, two QTL regions for adiposity were identified by performing a classical linkage analysis on 1362 offspring in 11 sire families obtained by crossing two meat-type chicken lines divergently selected for abdominal fat weight. Those regions, located on chromosome 7 and 19, contained a total of 77 and 84 genes, respectively. Then, SNPs and indels in these regions were identified by re-sequencing sires. Considering issues related to polymorphism annotations for regulatory regions, we focused on the 120 and 104 polymorphisms having an impact on protein sequence, and located in coding regions of 35 and 42 genes situated in the two QTL regions. Subsequently, a filter was applied on SNPs considering their potential impact on the protein function based on conservation criteria. For the two regions, we identified 42 and 34 functional polymorphisms carried by 18 and 24 genes, and likely to deeply impact protein, including 3 coding indels and 4 nonsense SNPs. Finally, using gene functional annotation, a short list of 17 and 4 polymorphisms in 6 and 4 functional genes has been defined. Even if we cannot exclude that the causal polymorphisms may be located in regulatory regions, this strategy gives a complete overview of the candidate polymorphisms in coding regions and prioritize them on conservation- and functional-based arguments.
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Affiliation(s)
- Pierre-François Roux
- INRA, UMR1348 PEGASE, Saint-Gilles, France
- Agrocampus Ouest, UMR1348 PEGASE, Rennes, France
- Université Européenne de Bretagne, Rennes, France
| | - Morgane Boutin
- INRA, UMR1348 PEGASE, Saint-Gilles, France
- Agrocampus Ouest, UMR1348 PEGASE, Rennes, France
- Université Européenne de Bretagne, Rennes, France
| | - Colette Désert
- INRA, UMR1348 PEGASE, Saint-Gilles, France
- Agrocampus Ouest, UMR1348 PEGASE, Rennes, France
- Université Européenne de Bretagne, Rennes, France
| | | | - Diane Esquerré
- INRA, UMR1388 GenPhySE, GeT-PlaGe, Castanet-Tolosan, France
| | | | - Sandrine Lagarrigue
- INRA, UMR1348 PEGASE, Saint-Gilles, France
- Agrocampus Ouest, UMR1348 PEGASE, Rennes, France
- Université Européenne de Bretagne, Rennes, France
| | - Olivier Demeure
- INRA, UMR1348 PEGASE, Saint-Gilles, France
- Agrocampus Ouest, UMR1348 PEGASE, Rennes, France
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21
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Fragomeni BDO, Misztal I, Lourenco DL, Aguilar I, Okimoto R, Muir WM. Changes in variance explained by top SNP windows over generations for three traits in broiler chicken. Front Genet 2014; 5:332. [PMID: 25324857 PMCID: PMC4181244 DOI: 10.3389/fgene.2014.00332] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 09/04/2014] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
| | - Ignacy Misztal
- Department of Animal and Dairy Science, University of Georgia Athens, GA, USA
| | | | - Ignacio Aguilar
- Instituto Nacional de Investigación Agropecuaria Las Brujas, Uruguay
| | | | - William M Muir
- Department of Animal Sciences, Purdue University West Lafaytee, IN, USA
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23
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Xu Z, Nie Q, Zhang X. Overview of Genomic Insights into Chicken Growth Traits Based on Genome-Wide Association Study and microRNA Regulation. Curr Genomics 2013; 14:137-46. [PMID: 24082823 PMCID: PMC3637678 DOI: 10.2174/1389202911314020006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 01/28/2013] [Accepted: 01/29/2013] [Indexed: 01/09/2023] Open
Abstract
Over the two past decades, a significant number of studies have observed animal growth traits to examine animal genetic mechanisms due to their ease of measurement and high heritability. Chicken which has a significant impact on fundamental biology is a major source of protein worldwide, making it an ideal model for examining animal growth trait development. The genetic mechanisms of chicken growth traits have been studied using quantitative trait loci mapping through genome-scan and candidate gene approaches, genome-wide association studies (GWAS), comparative genomic strategies, microRNA (miRNA) regulation of growth development analysis, and epigenomic analysis. This review focuses on chicken GWAS and miRNA regulation of growth traits. Several recently published GWAS reports showed that most genome-wide significant single nucleotide polymorphisms are located on chromosomes 1 and 4 in chickens. Chicken growth, particularly skeletal muscle growth and development, is greatly regulated by miRNA. Using dwarf and normal chickens, let-7b was found to be involved in determining chicken dwarf phenotypes by regulating growth hormone receptor gene expression.
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Affiliation(s)
- Zhenqiang Xu
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, Guang-dong, China
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Demeure O, Duclos MJ, Bacciu N, Le Mignon G, Filangi O, Pitel F, Boland A, Lagarrigue S, Cogburn LA, Simon J, Le Roy P, Le Bihan-Duval E. Genome-wide interval mapping using SNPs identifies new QTL for growth, body composition and several physiological variables in an F2 intercross between fat and lean chicken lines. Genet Sel Evol 2013; 45:36. [PMID: 24079476 PMCID: PMC3851061 DOI: 10.1186/1297-9686-45-36] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 09/10/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND For decades, genetic improvement based on measuring growth and body composition traits has been successfully applied in the production of meat-type chickens. However, this conventional approach is hindered by antagonistic genetic correlations between some traits and the high cost of measuring body composition traits. Marker-assisted selection should overcome these problems by selecting loci that have effects on either one trait only or on more than one trait but with a favorable genetic correlation. In the present study, identification of such loci was done by genotyping an F2 intercross between fat and lean lines divergently selected for abdominal fatness genotyped with a medium-density genetic map (120 microsatellites and 1302 single nucleotide polymorphisms). Genome scan linkage analyses were performed for growth (body weight at 1, 3, 5, and 7 weeks, and shank length and diameter at 9 weeks), body composition at 9 weeks (abdominal fat weight and percentage, breast muscle weight and percentage, and thigh weight and percentage), and for several physiological measurements at 7 weeks in the fasting state, i.e. body temperature and plasma levels of IGF-I, NEFA and glucose. Interval mapping analyses were performed with the QTLMap software, including single-trait analyses with single and multiple QTL on the same chromosome. RESULTS Sixty-seven QTL were detected, most of which had never been described before. Of these 67 QTL, 47 were detected by single-QTL analyses and 20 by multiple-QTL analyses, which underlines the importance of using different statistical models. Close analysis of the genes located in the defined intervals identified several relevant functional candidates, such as ACACA for abdominal fatness, GHSR and GAS1 for breast muscle weight, DCRX and ASPSCR1 for plasma glucose content, and ChEBP for shank diameter. CONCLUSIONS The medium-density genetic map enabled us to genotype new regions of the chicken genome (including micro-chromosomes) that influenced the traits investigated. With this marker density, confidence intervals were sufficiently small (14 cM on average) to search for candidate genes. Altogether, this new information provides a valuable starting point for the identification of causative genes responsible for important QTL controlling growth, body composition and metabolic traits in the broiler chicken.
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Affiliation(s)
- Olivier Demeure
- INRA, UMR1348 PEGASE, 35042 Rennes, France
- Agrocampus Ouest, UMR1348 PEGASE, 35042 Rennes, France
| | | | - Nicola Bacciu
- INRA, UMR1348 PEGASE, 35042 Rennes, France
- Agrocampus Ouest, UMR1348 PEGASE, 35042 Rennes, France
| | - Guillaume Le Mignon
- INRA, UMR1348 PEGASE, 35042 Rennes, France
- Agrocampus Ouest, UMR1348 PEGASE, 35042 Rennes, France
| | - Olivier Filangi
- INRA, UMR1348 PEGASE, 35042 Rennes, France
- Agrocampus Ouest, UMR1348 PEGASE, 35042 Rennes, France
| | - Frédérique Pitel
- INRA, UMR444 Génétique Cellulaire, 31326 Castanet-Tolosan, France
| | - Anne Boland
- CEA, IG, Centre National de Génotypage, 2 rue Gaston-Crémieux, CP 5721, 91057 Evry, France
| | - Sandrine Lagarrigue
- INRA, UMR1348 PEGASE, 35042 Rennes, France
- Agrocampus Ouest, UMR1348 PEGASE, 35042 Rennes, France
| | - Larry A Cogburn
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19717, USA
| | - Jean Simon
- INRA, UR83 Recherches Avicoles, 37380 Nouzilly, France
| | - Pascale Le Roy
- INRA, UMR1348 PEGASE, 35042 Rennes, France
- Agrocampus Ouest, UMR1348 PEGASE, 35042 Rennes, France
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Podisi BK, Knott SA, Burt DW, Hocking PM. Comparative analysis of quantitative trait loci for body weight, growth rate and growth curve parameters from 3 to 72 weeks of age in female chickens of a broiler-layer cross. BMC Genet 2013; 14:22. [PMID: 23496818 PMCID: PMC3606837 DOI: 10.1186/1471-2156-14-22] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 03/05/2013] [Indexed: 11/29/2022] Open
Abstract
Background Comparisons of quantitative trait loci (QTL) for growth and parameters of growth curves assist in understanding the genetics and ultimately the physiology of growth. Records of body weight at 3, 6, 12, 24, 48 and 72 weeks of age and growth rate between successive age intervals of about 500 F2 female chickens of the Roslin broiler-layer cross were available for analysis. These data were analysed to detect and compare QTL for body weight, growth rate and parameters of the Gompertz growth function. Results Over 50 QTL were identified for body weight at specific ages and most were also detected in the nearest preceding and/or subsequent growth stage. The sum of the significant and suggestive additive effects for bodyweight at specific ages accounted for 23-43% of the phenotypic variation. A single QTL for body weight on chromosome 4 at 48 weeks of age had the largest additive effect (550.4 ± 68.0 g, 11.5% of the phenotypic variation) and a QTL at a similar position accounted 14.5% of the phenotypic variation at 12 weeks of age. Age specific QTL for growth rate were detected suggesting that there are specific genes that affect developmental processes during the different stages of growth. Relatively few QTL influencing Gompertz growth curve parameters were detected and overlapped with loci affecting growth rate. Dominance effects were generally not significant but from 12 weeks of age they exceeded the additive effect in a few cases. No evidence for epistatic QTL pairs was found. Conclusions The results confirm the location for body weight and body weight gain during growth that were identified in previous studies and were consistent with QTL for the parameters of the Gompertz growth function. Chromosome 4 explained a relatively large proportion of the observed growth variation across the different ages, and also harboured most of the detected QTL for Gompertz parameters, confirming its importance in controlling growth. Very few QTL were detected for body weight or gain at 48 and 72 weeks of age, probably reflecting the effect of differences in reproduction and random environmental effects.
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Affiliation(s)
- Baitsi K Podisi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easer Bush, Midlothian, Scotland, EH25 9RG, UK
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Sheng Z, Pettersson ME, Hu X, Luo C, Qu H, Shu D, Shen X, Carlborg O, Li N. Genetic dissection of growth traits in a Chinese indigenous × commercial broiler chicken cross. BMC Genomics 2013; 14:151. [PMID: 23497136 PMCID: PMC3679733 DOI: 10.1186/1471-2164-14-151] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 02/28/2013] [Indexed: 11/18/2022] Open
Abstract
Background In China, consumers often prefer indigenous broiler chickens over commercial breeds, as they have characteristic meat qualities requested within traditional culinary customs. However, the growth-rate of these indigenous breeds is slower than that of the commercial broilers, which means they have not yet reached their full economic value. Therefore, combining the valuable meat quality of the native chickens with the efficiency of the commercial broilers is of interest. In this study, we generated an F2 intercross between the slow growing native broiler breed, Huiyang Beard chicken, and the fast growing commercial broiler breed, High Quality chicken Line A, and used it to map loci explaining the difference in growth rate between these breeds. Results A genome scan to identify main-effect loci affecting 24 growth-related traits revealed nine distinct QTL on six chromosomes. Many QTL were pleiotropic and conformed to the correlation patterns observed between phenotypes. Most of the mapped QTL were found in locations where growth QTL have been reported in other populations, although the effects were greater in this population. A genome scan for pairs of interacting loci identified a number of additional QTL in 10 other genomic regions. The epistatic pairs explained 6–8% of the residual phenotypic variance. Seven of the 10 epistatic QTL mapped in regions containing candidate genes in the ubiquitin mediated proteolysis pathway, suggesting the importance of this pathway in the regulation of growth in this chicken population. Conclusions The main-effect QTL detected using a standard one-dimensional genome scan accounted for a significant fraction of the observed phenotypic variance in this population. Furthermore, genes in known pathways present interesting candidates for further exploration. This study has thus located several QTL regions as promising candidates for further study, which will increase our understanding of the genetic mechanisms underlying growth-related traits in chickens.
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Affiliation(s)
- Zheya Sheng
- State Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing, People's Republic of China
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Felício AM, Boschiero C, Balieiro JCC, Ledur MC, Ferraz JBS, Moura ASAMT, Coutinho LL. Polymorphisms in FGFBP1 and FGFBP2 genes associated with carcass and meat quality traits in chickens. GENETICS AND MOLECULAR RESEARCH 2013; 12:208-22. [PMID: 23408407 DOI: 10.4238/2013.january.24.13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In the past, the focus of broiler breeding programs on yield and carcass traits improvement led to problems related to meat quality. Awareness of public concern for quality resulted in inclusion of meat quality traits in the evaluation process. Nevertheless, few genes associated with meat quality attributes are known. Previous studies mapped quantitative trait loci for weight at 35 and 42 days in a region of GGA4 flanked by the microsatellite markers, MCW0240 and LEI0063. In this region, there are 2 fibroblast growth factor binding protein (FGFBP) genes that play an important role in embryogenesis, cellular differentiation, and proliferation in chickens. The objective of this study was to identify and associate single nucleotide polymorphisms (SNPs) in FGFBP1 and FGFBP2 with performance, carcass, and meat quality in experimental and commercial chicken populations. In the commercial population, SNP g.2014G>A in FGFBP1 was associated with decreased carcass weight (P < 0.05), and SNP g.651G>A in FGFBP2 was associated with thawing loss and meat redness content (P < 0.05). Four haplotypes were constructed based on 2 SNPs and were associated with breast weight, thawing loss, and meat redness content. The diplotypes were associated with thawing loss, lightness, and redness content. The SNPs evaluated in the present study may be used as markers in poultry breeding programs to aid in improving growth and meat quality traits.
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Affiliation(s)
- A M Felício
- Departamento de Zootecnia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brasil
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Sun Y, Liu R, Lu X, Hu Y, Zhao G, Zheng M, Chen J, Wang H, Wen J. Associations of Polymorphisms in Four Candidate Genes with Carcass and/or Meat-Quality Traits in Two Meat-Type Chicken Lines. Anim Biotechnol 2013; 24:53-65. [DOI: 10.1080/10495398.2012.742909] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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A genome-wide scan of selective sweeps in two broiler chicken lines divergently selected for abdominal fat content. BMC Genomics 2012; 13:704. [PMID: 23241142 PMCID: PMC3557156 DOI: 10.1186/1471-2164-13-704] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 12/10/2012] [Indexed: 01/04/2023] Open
Abstract
Background Genomic regions controlling abdominal fatness (AF) were studied in the Northeast Agricultural University broiler line divergently selected for AF. In this study, the chicken 60KSNP chip and extended haplotype homozygosity (EHH) test were used to detect genome-wide signatures of AF. Results A total of 5357 and 5593 core regions were detected in the lean and fat lines, and 51 and 57 reached a significant level (P<0.01), respectively. A number of genes in the significant core regions, including RB1, BBS7, MAOA, MAOB, EHBP1, LRP2BP, LRP1B, MYO7A, MYO9A and PRPSAP1, were detected. These genes may be important for AF deposition in chickens. Conclusions We provide a genome-wide map of selection signatures in the chicken genome, and make a contribution to the better understanding the mechanisms of selection for AF content in chickens. The selection for low AF in commercial breeding using this information will accelerate the breeding progress.
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Nassar MK, Goraga ZS, Brockmann GA. Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: III. Fat deposition and intramuscular fat content. Anim Genet 2012; 44:62-8. [PMID: 22607452 DOI: 10.1111/j.1365-2052.2012.02365.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2012] [Indexed: 11/29/2022]
Abstract
In this study, a genome scan was performed to detect genomic loci that affect fat deposition in white adipose tissues and muscles in 278 F (2) males of reciprocal crosses between the genetically and phenotypically extreme inbred chicken lines New Hampshire (NHI) and White Leghorn (WL77). Genome-wide highly significant quantitative trait loci (QTL) influencing fat deposition in white adipose tissues were found on GGA2 and 4. The peak QTL positions for different visceral and subcutaneous white adipose tissues were located between 41.4 and 112.4 Mb on GGA2 and between 76.2 and 78.7 Mb on GGA4, which explained 4.2-10.4% and 4.3-11.6% respectively of the phenotypic F (2) variances. Contrary to our expectations, the QTL allele descending from the lean line WL77 on GGA4 led to increased fat deposition. We suggest a transgressive action of the obesity allele only if it is not in the genetic background of the line WL77. Additional highly significant loci for subcutaneous adipose tissue mass were identified on GGA12 and 15. For intramuscular fat content, a suggestive QTL was located on GGA14. The analysed crosses provide a valuable resource for further fine mapping of fatness genes and subsequent gene discovery.
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Affiliation(s)
- M K Nassar
- Breeding Biology and Molecular Genetics, Department of Crop and Animal Sciences, Humboldt-Universität zu Berlin, Invalidenstraße 42, D-10115, Berlin, Germany
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Nassar MK, Goraga ZS, Brockmann GA. Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: II. Muscle weight and carcass composition. Anim Genet 2012; 43:739-45. [DOI: 10.1111/j.1365-2052.2012.02344.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2011] [Indexed: 11/28/2022]
Affiliation(s)
- M. K. Nassar
- Breeding Biology and Molecular Genetics; Department of Crop and Animal Sciences; Humboldt-Universität zu Berlin; Invalidenstraβe 42; D-10115; Berlin; Germany
| | - Z. S. Goraga
- Breeding Biology and Molecular Genetics; Department of Crop and Animal Sciences; Humboldt-Universität zu Berlin; Invalidenstraβe 42; D-10115; Berlin; Germany
| | - G. A. Brockmann
- Breeding Biology and Molecular Genetics; Department of Crop and Animal Sciences; Humboldt-Universität zu Berlin; Invalidenstraβe 42; D-10115; Berlin; Germany
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Aslam ML, Bastiaansen JWM, Crooijmans RPMA, Vereijken A, Groenen MAM. Whole genome QTL mapping for growth, meat quality and breast meat yield traits in turkey. BMC Genet 2011; 12:61. [PMID: 21745371 PMCID: PMC3142527 DOI: 10.1186/1471-2156-12-61] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 07/11/2011] [Indexed: 12/02/2022] Open
Abstract
Background The turkey (Meleagris gallopavo) is an important agricultural species and is the second largest contributor to the world's poultry meat production. Demand of turkey meat is increasing very rapidly. Genetic markers linked to genes affecting quantitative traits can increase the selection response of animal breeding programs. The use of these molecular markers for the identification of quantitative trait loci, and subsequently fine-mapping of quantitative trait loci regions, allows for pinpointing of genes that underlie such economically important traits. Results The quantitative trait loci analyses of the growth curve, body weight, breast yield and the meat quality traits showed putative quantitative trait loci on 21 of the 27 turkey chromosomes covered by the linkage map. Forty-five quantitative trait loci were detected across all traits and these were found in 29 different regions on 21 chromosomes. Out of the 45 quantitative trait loci, twelve showed significant (p < 0.01) evidence of linkage while the remaining 33 showed suggestive evidence (p < 0.05) of linkage with different growth, growth curve, meat quality and breast yield traits. Conclusion A large number of quantitative trait loci were detected across the turkey genome, which affected growth, breast yield and meat quality traits. Pleiotropic effects or close linkages between quantitative trait loci were suggested for several of the chromosomal regions. The comparative analysis regarding the location of quantitative trait loci on different turkey, and on the syntenic chicken chromosomes, along with their phenotypic associations, revealed signs of functional conservation between these species.
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Affiliation(s)
- Muhammad L Aslam
- Animal Breeding and Genomics Centre, Wageningen University, 6709PG, Wageningen, The Netherlands.
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Goto T, Ishikawa A, Onitsuka S, Goto N, Fujikawa Y, Umino T, Nishibori M, Tsudzuki M. Mapping quantitative trait loci for egg production traits in an F2 intercross of Oh-Shamo and White Leghorn chickens. Anim Genet 2011; 42:634-41. [PMID: 22035005 DOI: 10.1111/j.1365-2052.2011.02190.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We performed quantitative trait locus (QTL) analyses for egg production traits, including age at first egg (AFE) and egg production rates (EPR) measured every 4 weeks from 22 to 62 weeks of hen age, in a population of 421 F(2) hens derived from an intercross between the Oh-Shamo (Japanese Large Game) and White Leghorn breeds of chickens. Simple interval mapping revealed a main-effect QTL for AFE on chromosome 1 and four main-effect QTL for EPR on chromosomes 1 and 11 (three on chromosome 1 and one on chromosome 11) at the genome-wide 5% levels. Among the three EPR QTL on chromosome 1, two were identified at the early stage of egg laying (26-34 weeks of hen age) and the remaining one was discovered at the late stage (54-58 weeks). The alleles at the two EPR QTL derived from the Oh-Shamo breed unexpectedly increased the trait values, irrespective of the Oh-Shamo being inferior to the White Leghorn in the trait. This suggests that the Oh-Shamo, one of the indigenous Japanese breeds, is an untapped resource that is important for further improvement of current elite commercial laying chickens. In addition, six epistatic QTL were identified on chromosomes 2, 4, 7, 8, 17 and 19, where none of the above main-effect QTL were located. This is the first example of detection of epistatic QTL affecting egg production traits. The main and epistatic QTL identified accounted for 4-8% of the phenotypic variance. The total contribution of all QTL detected for each trait to the phenotypic and genetic variances ranged from 4.1% to 16.9% and from 11.5% to 58.5%, respectively.
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Affiliation(s)
- T Goto
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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