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Salvian M, Moreira GCM, Silveira RMF, Reis ÂP, Dias D'auria B, Pilonetto F, Gervásio IC, Ledur MC, Coutinho LL, Spangler ML, Mourão GB. Estimation of breeding values using different densities of SNP to inform kinship in broiler chickens. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Ghafouri F, Bahrami A, Sadeghi M, Miraei-Ashtiani SR, Bakherad M, Barkema HW, Larose S. Omics Multi-Layers Networks Provide Novel Mechanistic and Functional Insights Into Fat Storage and Lipid Metabolism in Poultry. Front Genet 2021; 12:646297. [PMID: 34306005 PMCID: PMC8292821 DOI: 10.3389/fgene.2021.646297] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 06/04/2021] [Indexed: 12/25/2022] Open
Abstract
Fatty acid metabolism in poultry has a major impact on production and disease resistance traits. According to the high rate of interactions between lipid metabolism and its regulating properties, a holistic approach is necessary. To study omics multilayers of adipose tissue and identification of genes and miRNAs involved in fat metabolism, storage and endocrine signaling pathways in two groups of broiler chickens with high and low abdominal fat, as well as high-throughput techniques, were used. The gene–miRNA interacting bipartite and metabolic-signaling networks were reconstructed using their interactions. In the analysis of microarray and RNA-Seq data, 1,835 genes were detected by comparing the identified genes with significant expression differences (p.adjust < 0.01, fold change ≥ 2 and ≤ −2). Then, by comparing between different data sets, 34 genes and 19 miRNAs were detected as common and main nodes. A literature mining approach was used, and seven genes were identified and added to the common gene set. Module finding revealed three important and functional modules, which were involved in the peroxisome proliferator-activated receptor (PPAR) signaling pathway, biosynthesis of unsaturated fatty acids, Alzheimer’s disease metabolic pathway, adipocytokine, insulin, PI3K–Akt, mTOR, and AMPK signaling pathway. This approach revealed a new insight to better understand the biological processes associated with adipose tissue.
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Affiliation(s)
- Farzad Ghafouri
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.,Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Mostafa Sadeghi
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Seyed Reza Miraei-Ashtiani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Maryam Bakherad
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Herman W Barkema
- Department of Production Animal Health, University of Calgary, Calgary, AB, Canada
| | - Samantha Larose
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
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Moreira GCM, Poleti MD, Pértille F, Boschiero C, Cesar ASM, Godoy TF, Ledur MC, Reecy JM, Garrick DJ, Coutinho LL. Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach. BMC Genet 2019; 20:83. [PMID: 31694549 PMCID: PMC6836328 DOI: 10.1186/s12863-019-0783-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/11/2019] [Indexed: 12/25/2022] Open
Abstract
Background Feed efficiency and growth rate have been targets for selection to improve chicken production. The incorporation of genomic tools may help to accelerate selection. We genotyped 529 individuals using a high-density SNP chip (600 K, Affymetrix®) to estimate genomic heritability of performance traits and to identify genomic regions and their positional candidate genes associated with performance traits in a Brazilian F2 Chicken Resource population. Regions exhibiting selection signatures and a SNP dataset from resequencing were integrated with the genomic regions identified using the chip to refine the list of positional candidate genes and identify potential causative mutations. Results Feed intake (FI), feed conversion ratio (FC), feed efficiency (FE) and weight gain (WG) exhibited low genomic heritability values (i.e. from 0.0002 to 0.13), while body weight at hatch (BW1), 35 days-of-age (BW35), and 41 days-of-age (BW41) exhibited high genomic heritability values (i.e. from 0.60 to 0.73) in this F2 population. Twenty unique 1-Mb genomic windows were associated with BW1, BW35 or BW41, located on GGA1–4, 6–7, 10, 14, 24, 27 and 28. Thirty-eight positional candidate genes were identified within these windows, and three of them overlapped with selection signature regions. Thirteen predicted deleterious and three high impact sequence SNPs in these QTL regions were annotated in 11 positional candidate genes related to osteogenesis, skeletal muscle development, growth, energy metabolism and lipid metabolism, which may be associated with body weight in chickens. Conclusions The use of a high-density SNP array to identify QTL which were integrated with whole genome sequence signatures of selection allowed the identification of candidate genes and candidate causal variants. One novel QTL was detected providing additional information to understand the genetic architecture of body weight traits. We identified QTL for body weight traits, which were also associated with fatness in the same population. Our findings form a basis for further functional studies to elucidate the role of specific genes in regulating body weight and fat deposition in chickens, generating useful information for poultry breeding programs.
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Affiliation(s)
| | - Mirele Daiana Poleti
- University of São Paulo (USP) / College of Animal Science and Food Engineering (FZEA), Pirassununga, São Paulo, Brazil
| | - Fábio Pértille
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Clarissa Boschiero
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Thaís Fernanda Godoy
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - James M Reecy
- Department of Animal Science, Iowa State University (ISU), Ames, Iowa, USA
| | - Dorian J Garrick
- School of Agriculture, Massey University, Ruakura, Hamilton, New Zealand
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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Moreira GCM, Boschiero C, Cesar ASM, Reecy JM, Godoy TF, Pértille F, Ledur MC, Moura ASAMT, Garrick DJ, Coutinho LL. Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken. Sci Rep 2018; 8:16222. [PMID: 30385857 PMCID: PMC6212401 DOI: 10.1038/s41598-018-34364-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/12/2018] [Indexed: 02/07/2023] Open
Abstract
Excessive fat deposition is a negative factor for poultry production because it reduces feed efficiency, increases the cost of meat production and is a health concern for consumers. We genotyped 497 birds from a Brazilian F2 Chicken Resource Population, using a high-density SNP array (600 K), to estimate the genomic heritability of fat deposition related traits and to identify genomic regions and positional candidate genes (PCGs) associated with these traits. Selection signature regions, haplotype blocks and SNP data from a previous whole genome sequencing study in the founders of this chicken F2 population were used to refine the list of PCGs and to identify potential causative SNPs. We obtained high genomic heritabilities (0.43-0.56) and identified 22 unique QTLs for abdominal fat and carcass fat content traits. These QTLs harbored 26 PCGs involved in biological processes such as fat cell differentiation, insulin and triglyceride levels, and lipid biosynthetic process. Three of these 26 PCGs were located within haplotype blocks there were associated with fat traits, five overlapped with selection signature regions, and 12 contained predicted deleterious variants. The identified QTLs, PCGs and potentially causative SNPs provide new insights into the genetic control of fat deposition and can lead to improved accuracy of selection to reduce excessive fat deposition in chickens.
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Affiliation(s)
| | - Clarissa Boschiero
- Department of Animal Science, University of São Paulo, Piracicaba, SP, Brazil
| | | | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | | | - Fábio Pértille
- Department of Animal Science, University of São Paulo, Piracicaba, SP, Brazil
| | | | | | - Dorian J Garrick
- School of Agriculture, Massey University, Ruakura, Hamilton, New Zealand
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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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Pértille F, Moreira GCM, Zanella R, Nunes JDRDS, Boschiero C, Rovadoscki GA, Mourão GB, Ledur MC, Coutinho LL. Genome-wide association study for performance traits in chickens using genotype by sequencing approach. Sci Rep 2017; 7:41748. [PMID: 28181508 PMCID: PMC5299454 DOI: 10.1038/srep41748] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/23/2016] [Indexed: 12/11/2022] Open
Abstract
Performance traits are economically important and are targets for selection in breeding programs, especially in the poultry industry. To identify regions on the chicken genome associated with performance traits, different genomic approaches have been applied in the last years. The aim of this study was the application of CornellGBS approach (134,528 SNPs generated from a PstI restriction enzyme) on Genome-Wide Association Studies (GWAS) in an outbred F2 chicken population. We have validated 91.7% of these 134,528 SNPs after imputation of missed genotypes. Out of those, 20 SNPs were associated with feed conversion, one was associated with body weight at 35 days of age (P < 7.86E-07) and 93 were suggestively associated with a variety of performance traits (P < 1.57E-05). The majority of these SNPs (86.2%) overlapped with previously mapped QTL for the same performance traits and some of the SNPs also showed novel potential QTL regions. The results obtained in this study suggests future searches for candidate genes and QTL refinements as well as potential use of the SNPs described here in breeding programs.
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Affiliation(s)
- Fábio Pértille
- University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | | | - Ricardo Zanella
- College of Agronomy and Veterinary Medicine, Veterinary School, University of Passo Fundo, Rio Grande do Sul, Brazil
| | | | - Clarissa Boschiero
- University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Gregori Alberto Rovadoscki
- University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Gerson Barreto Mourão
- University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | | | - Luiz Lehmann Coutinho
- University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
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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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Rosario MF, Gazaffi R, Moura ASAMT, Ledur MC, Coutinho LL, Garcia AAF. Composite interval mapping and mixed models reveal QTL associated with performance and carcass traits on chicken chromosomes 1, 3, and 4. J Appl Genet 2013; 55:97-103. [DOI: 10.1007/s13353-013-0185-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 09/23/2013] [Accepted: 11/07/2013] [Indexed: 11/29/2022]
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Sun Y, Zhao G, Liu R, Zheng M, Hu Y, Wu D, Zhang L, Li P, Wen J. The identification of 14 new genes for meat quality traits in chicken using a genome-wide association study. BMC Genomics 2013; 14:458. [PMID: 23834466 PMCID: PMC3707761 DOI: 10.1186/1471-2164-14-458] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 05/28/2013] [Indexed: 12/23/2022] Open
Abstract
Background Meat quality is an important economic trait in chickens. To identify loci and genes associated with meat quality traits, we conducted a genome-wide association study (GWAS) of F2 populations derived from a local Chinese breed (Beijing-You chickens) and a commercial fast-growing broiler line (Cobb-Vantress). Results In the present study, 33 association signals were detected from the compressed mixed linear model (MLM) for 10 meat quality traits: dry matter in breast muscle (DMBr), dry matter in thigh muscle (DMTh), intramuscular fat content in breast muscle (IMFBr), meat color lightness (L*) and yellowness (b*) values, skin color L*, a* (redness) and b* values, abdominal fat weight (AbFW) and AbFW as a percentage of eviscerated weight (AbFP). Relative expressions of candidate genes identified near significant signals were compared using samples of chickens with High and Low phenotypic values. A total of 14 genes associated with IMFBr, meat color L*, AbFW, and AbFP, were differentially expressed between the High and Low phenotypic groups. These genes are, therefore, prospective candidate genes for meat quality traits: protein tyrosine kinase (TYRO3) and microsomal glutathione S-transferase 1 (MGST1) for IMFBr; collagen, type I, alpha 2 (COL1A2) for meat color L*; and RET proto-oncogene (RET), natriuretic peptide B (NPPB) and sterol regulatory element binding transcription factor 1 (SREBF1) for the abdominal fat (AbF) traits. Conclusions Based on the association signals and differential expression of nearby genes, 14 candidate loci and genes for IMFBr, meat L* and b* values, and AbF are identified. The results provide new insight into the molecular mechanisms underlying meat quality traits in chickens.
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Affiliation(s)
- Yanfa Sun
- Chinese Academy of Agricultural Sciences, 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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