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Sun S, Wei L, Chen Z, Chai Y, Wang S, Sun R. Nondestructive estimation method of live chicken leg weight based on deep learning. Poult Sci 2024; 103:103477. [PMID: 38364605 PMCID: PMC10879787 DOI: 10.1016/j.psj.2024.103477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/12/2024] [Accepted: 01/13/2024] [Indexed: 02/18/2024] Open
Abstract
In the broiler-breeding industry, phenotype determination is critical. Leg weight is a fundamental indicator for breeding, and noninvasive testing technology can reduce damage to animals. This study proposes a broiler leg weight estimation system comprising a weight-estimation model and computed tomography (CT) acquisition equipment. The weight-estimation model can automatically process the scan results of live broiler chickens from the CT acquisition equipment. The weight-estimation model comprises an improved you-only-look-once (YOLOv5) segmentation algorithm and a random forest fitting network. The segmentation head was introduced into the YOLOv5 network, combined with a multiscale attention mechanism and an atrous spatial pyramid pooling architecture, and a new network model, YOLO- measuring chicken leg weight (YOLO-MCLW), was proposed to improve segmentation efficiency and accuracy. Morphological parameters were extracted from the obtained mask image, and a random forest network was used for fitting. The experiments show that the system exhibited an average absolute error of 7.27 g and an average percentage error of 4.82% in tests on 50 individual legs of 25 broiler chickens. The prediction R2 of broiler chicken legs can reaches 88.98%, the segmentation intersection over union result reaches 95.45%, and 37.04 images are processed per second. This system provides technical support for the part determination of broiler chickens in commercial breeding.
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Affiliation(s)
- Shulin Sun
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100083, China
| | - Lei Wei
- College of Biological Sciences, China Agricultural University, Beijing 100083, China
| | - Zeqiu Chen
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100083, China
| | - Yinqian Chai
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100083, China
| | - Shufan Wang
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100083, China
| | - Ruizhi Sun
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100083, China; Scientific Research Base for Integrated Technologies of Precision Agriculture (Animal Husbandry), the Ministry of Agriculture, Beijing 100083, China.
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2
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Volkova NA, Romanov MN, Abdelmanova AS, Larionova PV, German NY, Vetokh AN, Shakhin AV, Volkova LA, Sermyagin AA, Anshakov DV, Fisinin VI, Griffin DK, Sölkner J, Brem G, McEwan JC, Brauning R, Zinovieva NA. Genome-Wide Association Study Revealed Putative SNPs and Candidate Genes Associated with Growth and Meat Traits in Japanese Quail. Genes (Basel) 2024; 15:294. [PMID: 38540354 PMCID: PMC10970133 DOI: 10.3390/genes15030294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/08/2024] [Accepted: 02/23/2024] [Indexed: 06/14/2024] Open
Abstract
The search for SNPs and candidate genes that determine the manifestation of major selected traits is one crucial objective for genomic selection aimed at increasing poultry production efficiency. Here, we report a genome-wide association study (GWAS) for traits characterizing meat performance in the domestic quail. A total of 146 males from an F2 reference population resulting from crossing a fast (Japanese) and a slow (Texas White) growing breed were examined. Using the genotyping-by-sequencing technique, genomic data were obtained for 115,743 SNPs (92,618 SNPs after quality control) that were employed in this GWAS. The results identified significant SNPs associated with the following traits at 8 weeks of age: body weight (nine SNPs), daily body weight gain (eight SNPs), dressed weight (33 SNPs), and weights of breast (18 SNPs), thigh (eight SNPs), and drumstick (three SNPs). Also, 12 SNPs and five candidate genes (GNAL, DNAJC6, LEPR, SPAG9, and SLC27A4) shared associations with three or more traits. These findings are consistent with the understanding of the genetic complexity of body weight-related traits in quail. The identified SNPs and genes can be used in effective quail breeding as molecular genetic markers for growth and meat characteristics for the purpose of genetic improvement.
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Affiliation(s)
- Natalia A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Michael N. Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK;
| | - Alexandra S. Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Polina V. Larionova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Nadezhda Yu. German
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Anastasia N. Vetokh
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Alexey V. Shakhin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Ludmila A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Alexander A. Sermyagin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Dmitry V. Anshakov
- Breeding and Genetic Center “Zagorsk Experimental Breeding Farm”—Branch of the Federal Research Center “All-Russian Poultry Research and Technological Institute”, Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Vladimir I. Fisinin
- Federal Research Center “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK;
| | - Johann Sölkner
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences Vienna, 1180 Vienna, Austria;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - John C. McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Natalia A. Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
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3
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Guo J, Qu L, Shao D, Wang Q, Li Y, Dou T, Wang X, Hu Y, Tong H. Genetic Architecture of Abdominal Fat Deposition Revealed by a Genome-Wide Association Study in the Laying Chicken. Genes (Basel) 2023; 15:10. [PMID: 38275592 PMCID: PMC10815693 DOI: 10.3390/genes15010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Fat has a high energy density, and excessive fatness has been recognized as a problem for egg production and the welfare of chickens. The identification of a genetic polymorphism controlling fat deposition would be helpful to select against excessive fatness in the laying hen. This study aimed to estimate genomic heritability and identify the genetic architecture of abdominal fat deposition in a population of chickens from a Dongxiang blue-shelled local breed crossbred with the White Leghorn. A genome-wide association study was conducted on abdominal fat percentage, egg production and body weights using a sample of 1534 hens genotyped with a 600 K Chicken Genotyping Array. The analysis yielded a heritability estimate of 0.19 ± 0.04 for abdominal fat percentage; 0.56 ± 0.04 for body weight at 72 weeks; 0.11 ± 0.03 for egg production; and 0.24 ± 0.04 for body weight gain. The genetic correlation of abdominal fat percentage with egg production between 60 and 72 weeks of age was -0.35 ± 0.18. This implies a potential trade-off between these two traits related to the allocation of resources. Strong positive genetic correlations were found between fat deposition and weight traits. A promising locus close to COL12A1 on chromosome 3, associated with abdominal fat percent, was found in the present study. Another region located around HTR2A on chromosome 1, where allele substitution was predicted to be associated with body weight gain, accounted for 2.9% of phenotypic variance. Another region located on chromosome 1, but close to SOX5, was associated with egg production. These results may be used to influence the balanced genetic selection for laying hens.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Haibing Tong
- Jiangsu Institute of Poultry Science, Yangzhou 225125, China; (J.G.)
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4
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Understanding microbial networks of farm animals through genomics, metagenomics and other meta-omic approaches for livestock wellness and sustainability. ANNALS OF ANIMAL SCIENCE 2022. [DOI: 10.2478/aoas-2022-0002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Abstract
The association of microorganisms with livestock as endosymbionts, opportunists, and pathogens has been a matter of debate for a long time. Several livestock-associated bacterial and other microbial species have been identified and characterized through traditional culture-dependent genomic approaches. However, it is imperative to understand the comprehensive microbial network of domestic animals for their wellness, disease management, and disease transmission control. Since it is strenuous to provide a niche replica to any microorganisms while culturing them, thus a substantial number of microbial communities remain obscure. Metagenomics has laid out a powerful lens for gaining insight into the hidden microbial diversity by allowing the direct sequencing of the DNA isolated from any livestock sample like the gastrointestinal tract, udder, or genital system. Through metatranscriptomics and metabolomics, understanding gene expression profiles of the microorganisms and their molecular phenotype has become unchallenging. With large data sets emerging out of the genomic, metagenomic, and other meta-omics methods, several computational tools have also been developed for curation, assembly, gene prediction, and taxonomic profiling of the microorganisms. This review provides a detailed account of the beneficial and pathogenic organisms that dwell within or on farm animals. Besides, it highlights the role of meta-omics and computational tools in a comprehensive analysis of livestock-associated microorganisms.
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5
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Sahib AM, Al-Khalisy AF, Abdulwahid MT. Association of TGF-β2 Gene Polymorphism with Growth Rate in Local Chickens. THE IRAQI JOURNAL OF VETERINARY MEDICINE 2021. [DOI: 10.30539/ijvm.v45i1.1034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Iraqi native chickens have tasty meat and eggs; however, they are characterized by low production efficiency. In fact, phenotypic traits, such as growth rate, are influenced by genes and environmental factors. During health and disease, a variety of cellular processes such as proliferation, differentiation, motility, adhesion, migration, apoptosis, and immune response regulate the TGF-β genes. The enhancement in body weight can be reached through mass selection, whereas feed conversion ratio (FCR) is relatively more difficult to improve. This means, selecting for body weight has been submitted as an effective way of indirectly improving feed conversion ratio. Therefore, the present study attempts to identify associations between productive traits and polymorphism of TGF-β2 gene in local Iraqi chicken. Seventy-five male birds were used in this study. The restriction enzyme RsaI has been used to detect the target region (284 bp) in the TGF-β2 gene. A single nucleotide polymorphism (SNP) was identified at the position 62 in the exon 1 region of TGF-β2 by using PCR-RFLP and DNA sequencing technique. The genotypic frequencies were 46.7, 40, and 13.3% for CC and TC and TT genotypes, respectively. While the allele frequency of C and T were 0.67 and 0.33%, respectively. Generally, during the last period of rearing the best significant (P<0.05) improve in the body weight, weight gain and FCR were recorded in the TT genotype of the TGF-β2 gene. In conclusion, a functional sequence in the genome could be attributed to the mutation. Therefore, genotype of the TGF-β2 gene could be exploited to select the best individual as a parent to the next generations for improving of growth rate in
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Petry B, Moreira GCM, Copola AGL, de Souza MM, da Veiga FC, Jorge EC, de Oliveira Peixoto J, Ledur MC, Koltes JE, Coutinho LL. SAP30 Gene Is a Probable Regulator of Muscle Hypertrophy in Chickens. Front Genet 2021; 12:709937. [PMID: 34646299 PMCID: PMC8502938 DOI: 10.3389/fgene.2021.709937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/20/2021] [Indexed: 11/13/2022] Open
Abstract
Animals with muscle hypertrophy phenotype are targeted by the broiler industry to increase the meat production and the quality of the final product. Studies characterizing the molecular machinery involved with these processes, such as quantitative trait loci studies, have been carried out identifying several candidate genes related to this trait; however, validation studies of these candidate genes in cell culture is scarce. The aim of this study was to evaluate SAP30 as a candidate gene for muscle development and to validate its function in cell culture in vitro. The SAP30 gene was downregulated in C2C12 muscle cell culture using siRNA technology to evaluate its impact on morphometric traits and gene expression by RNA-seq analysis. Modulation of SAP30 expression increased C2C12 myotube area, indicating a role in muscle hypertrophy. RNA-seq analysis identified several upregulated genes annotated in muscle development in treated cells (SAP30-knockdown), corroborating the role of SAP30 gene in muscle development regulation. Here, we provide experimental evidence of the involvement of SAP30 gene as a regulator of muscle cell hypertrophy.
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Affiliation(s)
- Bruna Petry
- Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
| | | | - Aline Gonçalves Lio Copola
- Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | - Fernanda Cristina da Veiga
- Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
| | - Erika Cristina Jorge
- Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | | | - James E Koltes
- Animal Science Department, Iowa State University, Ames, IA, United States
| | - Luiz Lehmann Coutinho
- Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
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Dadousis C, Somavilla A, Ilska JJ, Johnsson M, Batista L, Mellanby RJ, Headon D, Gottardo P, Whalen A, Wilson D, Dunn IC, Gorjanc G, Kranis A, Hickey JM. A genome-wide association analysis for body weight at 35 days measured on 137,343 broiler chickens. Genet Sel Evol 2021; 53:70. [PMID: 34496773 PMCID: PMC8424881 DOI: 10.1186/s12711-021-00663-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/23/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Body weight (BW) is an economically important trait in the broiler (meat-type chickens) industry. Under the assumption of polygenicity, a "large" number of genes with "small" effects is expected to control BW. To detect such effects, a large sample size is required in genome-wide association studies (GWAS). Our objective was to conduct a GWAS for BW measured at 35 days of age with a large sample size. METHODS The GWAS included 137,343 broilers spanning 15 pedigree generations and 392,295 imputed single nucleotide polymorphisms (SNPs). A false discovery rate of 1% was adopted to account for multiple testing when declaring significant SNPs. A Bayesian ridge regression model was implemented, using AlphaBayes, to estimate the contribution to the total genetic variance of each region harbouring significant SNPs (1 Mb up/downstream) and the combined regions harbouring non-significant SNPs. RESULTS GWAS revealed 25 genomic regions harbouring 96 significant SNPs on 13 Gallus gallus autosomes (GGA1 to 4, 8, 10 to 15, 19 and 27), with the strongest associations on GGA4 at 65.67-66.31 Mb (Galgal4 assembly). The association of these regions points to several strong candidate genes including: (i) growth factors (GGA1, 4, 8, 13 and 14); (ii) leptin receptor overlapping transcript (LEPROT)/leptin receptor (LEPR) locus (GGA8), and the STAT3/STAT5B locus (GGA27), in connection with the JAK/STAT signalling pathway; (iii) T-box gene (TBX3/TBX5) on GGA15 and CHST11 (GGA1), which are both related to heart/skeleton development); and (iv) PLAG1 (GGA2). Combined together, these 25 genomic regions explained ~ 30% of the total genetic variance. The region harbouring significant SNPs that explained the largest portion of the total genetic variance (4.37%) was on GGA4 (~ 65.67-66.31 Mb). CONCLUSIONS To the best of our knowledge, this is the largest GWAS that has been conducted for BW in chicken to date. In spite of the identified regions, which showed a strong association with BW, the high proportion of genetic variance attributed to regions harbouring non-significant SNPs supports the hypothesis that the genetic architecture of BW35 is polygenic and complex. Our results also suggest that a large sample size will be required for future GWAS of BW35.
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Affiliation(s)
| | | | - Joanna J. Ilska
- The Roslin Institute, University of Edinburgh, Midlothian, UK
| | - Martin Johnsson
- The Roslin Institute, University of Edinburgh, Midlothian, UK
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lorena Batista
- The Roslin Institute, University of Edinburgh, Midlothian, UK
| | | | - Denis Headon
- The Roslin Institute, University of Edinburgh, Midlothian, UK
| | - Paolo Gottardo
- Italian Brown Breeders Association, Loc. Ferlina 204, 37012 Bussolengo, Italy
| | - Andrew Whalen
- The Roslin Institute, University of Edinburgh, Midlothian, UK
| | - David Wilson
- The Roslin Institute, University of Edinburgh, Midlothian, UK
| | - Ian C. Dunn
- The Roslin Institute, University of Edinburgh, Midlothian, UK
| | - Gregor Gorjanc
- The Roslin Institute, University of Edinburgh, Midlothian, UK
| | - Andreas Kranis
- The Roslin Institute, University of Edinburgh, Midlothian, UK
- Aviagen Ltd, Midlothian, UK
| | - John M. Hickey
- The Roslin Institute, University of Edinburgh, Midlothian, UK
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Fernandes AC, da Silva VH, Goes CP, Moreira GCM, Godoy TF, Ibelli AMG, Peixoto JDO, Cantão ME, Ledur MC, de Rezende FM, Coutinho LL. Genome-wide detection of CNVs and their association with performance traits in broilers. BMC Genomics 2021; 22:354. [PMID: 34001004 PMCID: PMC8130382 DOI: 10.1186/s12864-021-07676-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 05/05/2021] [Indexed: 12/12/2022] Open
Abstract
Background Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation of complex traits, not only in humans, but also in livestock animals. We identified CNVs along the chicken genome and analyzed their association with performance traits. Genome-wide CNVs were inferred from Affymetrix® high density SNP-chip data for a broiler population. CNVs were concatenated into segments and association analyses were performed with linear mixed models considering a genomic relationship matrix, for birth weight, body weight at 21, 35, 41 and 42 days, feed intake from 35 to 41 days, feed conversion ratio from 35 to 41 days and, body weight gain from 35 to 41 days of age. Results We identified 23,214 autosomal CNVs, merged into 5042 distinct CNV regions (CNVRs), covering 12.84% of the chicken autosomal genome. One significant CNV segment was associated with BWG on GGA3 (q-value = 0.00443); one significant CNV segment was associated with BW35 (q-value = 0.00571), BW41 (q-value = 0.00180) and BW42 (q-value = 0.00130) on GGA3, and one significant CNV segment was associated with BW on GGA5 (q-value = 0.00432). All significant CNV segments were verified by qPCR, and a validation rate of 92.59% was observed. These CNV segments are located nearby genes, such as KCNJ11, MyoD1 and SOX6, known to underlie growth and development. Moreover, gene-set analyses revealed terms linked with muscle physiology, cellular processes regulation and potassium channels. Conclusions Overall, this CNV-based GWAS study unravels potential candidate genes that may regulate performance traits in chickens. Our findings provide a foundation for future functional studies on the role of specific genes in regulating performance in chickens. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07676-1.
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Affiliation(s)
- Anna Carolina Fernandes
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - Vinicius Henrique da Silva
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - Carolina Purcell Goes
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | | | - 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
| | | | - Jane de Oliveira Peixoto
- Embrapa Suínos e Aves: Empresa Brasileira de Pesquisa Agropecuária Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | - Maurício Egídio Cantão
- Embrapa Suínos e Aves: Empresa Brasileira de Pesquisa Agropecuária Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | - Mônica Corrêa Ledur
- Embrapa Suínos e Aves: Empresa Brasileira de Pesquisa Agropecuária Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | | | - 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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9
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Tarsani E, Kranis A, Maniatis G, Hager-Theodorides AL, Kominakis A. Detection of loci exhibiting pleiotropic effects on body weight and egg number in female broilers. Sci Rep 2021; 11:7441. [PMID: 33811218 PMCID: PMC8018976 DOI: 10.1038/s41598-021-86817-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/16/2021] [Indexed: 12/14/2022] Open
Abstract
The objective of the present study was to discover the genetic variants, functional candidate genes, biological processes and molecular functions underlying the negative genetic correlation observed between body weight (BW) and egg number (EN) traits in female broilers. To this end, first a bivariate genome-wide association and second stepwise conditional-joint analyses were performed using 2586 female broilers and 240 k autosomal SNPs. The aforementioned analyses resulted in a total number of 49 independent cross-phenotype (CP) significant SNPs with 35 independent markers showing antagonistic action i.e., positive effects on one trait and negative effects on the other trait. A number of 33 independent CP SNPs were located within 26 and 14 protein coding and long non-coding RNA genes, respectively. Furthermore, 26 independent markers were situated within 44 reported QTLs, most of them related to growth traits. Investigation of the functional role of protein coding genes via pathway and gene ontology analyses highlighted four candidates (CPEB3, ACVR1, MAST2 and CACNA1H) as most plausible pleiotropic genes for the traits under study. Three candidates (CPEB3, MAST2 and CACNA1H) were associated with antagonistic pleiotropy, while ACVR1 with synergistic pleiotropic action. Current results provide a novel insight into the biological mechanism of the genetic trade-off between growth and reproduction, in broilers.
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Affiliation(s)
- Eirini Tarsani
- Department of Animal Science and Aquaculture, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece.
| | - Andreas Kranis
- Aviagen, Newbridge, EH28 8SZ, Midlothian, UK
- The Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, UK
| | | | - Ariadne L Hager-Theodorides
- Department of Animal Science and Aquaculture, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Antonios Kominakis
- Department of Animal Science and Aquaculture, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
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10
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Marchesi JAP, Ono RK, Cantão ME, Ibelli AMG, Peixoto JDO, Moreira GCM, Godoy TF, Coutinho LL, Munari DP, Ledur MC. Exploring the genetic architecture of feed efficiency traits in chickens. Sci Rep 2021; 11:4622. [PMID: 33633287 PMCID: PMC7907133 DOI: 10.1038/s41598-021-84125-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 02/12/2021] [Indexed: 11/09/2022] Open
Abstract
Chicken feed efficiency (FE) traits are the most important economic traits in broiler production. Several studies evaluating genetic factors affecting food consumption in chickens are available. However, most of these studies identified genomic regions containing putative quantitative trait loci for each trait separately. It is still a challenge to find common gene networks related to these traits. Therefore, here, a genome-wide association study (GWAS) was conducted to explore candidate genomic regions responsible for Feed Intake (FI), Body Weight Gain (BWG) and Feed Conversion Ratio (FCR) traits and their gene networks. A total of 1430 broilers from an experimental population was genotyped with the high density Affymetrix 600K SNP array. A total of 119 associated SNPs located in 20 chromosomes were identified, where some of them were common in more than one FE trait. In addition, novel genomic regions were prospected considering the SNPs dominance effects and sex interaction, identifying putative candidate genes only when these effects were fit in the model. Relevant candidate genes such as ATRNL1, PIK3C2A, PTPRN2, SORCS3 and gga-mir-1759 were highlighted in this study helping to elucidate the genomic architecture of feed efficiency traits. These results provide new insights on the mechanisms underlying the consumption and utilization of food in chickens.
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Affiliation(s)
- Jorge Augusto Petroli Marchesi
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, 14884-900, Brazil.,Departamento de Genética, Universidade de São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Rafael Keith Ono
- Embrapa Suínos e Aves, Concórdia, SC, 89715-899, Brazil.,Pamplona Alimentos S/A, Rio do Sul, SC, 89164-900, Brazil
| | | | | | | | - Gabriel Costa Monteiro Moreira
- Departamento de Zootecnia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, Piracicaba, SP, 13419-900, Brazil
| | - Thaís Fernanda Godoy
- Departamento de Zootecnia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, Piracicaba, SP, 13419-900, Brazil
| | - Luiz Lehmann Coutinho
- Departamento de Zootecnia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, Piracicaba, SP, 13419-900, Brazil
| | - Danísio Prado Munari
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, 14884-900, Brazil
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