Genome-wide detection of CNVs and their association with performance traits in broilers
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 associati...
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| Format: | Article |
| Language: | English |
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BMC
2021-05-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-021-07676-1 |
| _version_ | 1819081967238381568 |
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| author | Anna Carolina Fernandes Vinicius Henrique da Silva Carolina Purcell Goes Gabriel Costa Monteiro Moreira Thaís Fernanda Godoy Adriana Mércia Guaratini Ibelli Jane de Oliveira Peixoto Maurício Egídio Cantão Mônica Corrêa Ledur Fernanda Marcondes de Rezende Luiz Lehmann Coutinho |
| author_facet | Anna Carolina Fernandes Vinicius Henrique da Silva Carolina Purcell Goes Gabriel Costa Monteiro Moreira Thaís Fernanda Godoy Adriana Mércia Guaratini Ibelli Jane de Oliveira Peixoto Maurício Egídio Cantão Mônica Corrêa Ledur Fernanda Marcondes de Rezende Luiz Lehmann Coutinho |
| author_sort | Anna Carolina Fernandes |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-21T20:09:11Z |
| format | Article |
| id | doaj.art-cc2d857f14dd48fb9f66f73c4ae7fd13 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T20:09:11Z |
| publishDate | 2021-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-cc2d857f14dd48fb9f66f73c4ae7fd132022-12-21T18:51:46ZengBMCBMC Genomics1471-21642021-05-0122111810.1186/s12864-021-07676-1Genome-wide detection of CNVs and their association with performance traits in broilersAnna Carolina Fernandes0Vinicius Henrique da Silva1Carolina Purcell Goes2Gabriel Costa Monteiro Moreira3Thaís Fernanda Godoy4Adriana Mércia Guaratini Ibelli5Jane de Oliveira Peixoto6Maurício Egídio Cantão7Mônica Corrêa Ledur8Fernanda Marcondes de Rezende9Luiz Lehmann Coutinho10Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ)Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ)Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ)Unit of Animal Genomics, GIGA-R, University of LiègeDepartment of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ)Embrapa Suínos e Aves: Empresa Brasileira de Pesquisa Agropecuária Suínos e AvesEmbrapa Suínos e Aves: Empresa Brasileira de Pesquisa Agropecuária Suínos e AvesEmbrapa Suínos e Aves: Empresa Brasileira de Pesquisa Agropecuária Suínos e AvesEmbrapa Suínos e Aves: Empresa Brasileira de Pesquisa Agropecuária Suínos e AvesAnimal Sciences Department, University of FloridaDepartment of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ)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.https://doi.org/10.1186/s12864-021-07676-1GWASPerformanceCNVsQTLsqPCR |
| spellingShingle | Anna Carolina Fernandes Vinicius Henrique da Silva Carolina Purcell Goes Gabriel Costa Monteiro Moreira Thaís Fernanda Godoy Adriana Mércia Guaratini Ibelli Jane de Oliveira Peixoto Maurício Egídio Cantão Mônica Corrêa Ledur Fernanda Marcondes de Rezende Luiz Lehmann Coutinho Genome-wide detection of CNVs and their association with performance traits in broilers BMC Genomics GWAS Performance CNVs QTLs qPCR |
| title | Genome-wide detection of CNVs and their association with performance traits in broilers |
| title_full | Genome-wide detection of CNVs and their association with performance traits in broilers |
| title_fullStr | Genome-wide detection of CNVs and their association with performance traits in broilers |
| title_full_unstemmed | Genome-wide detection of CNVs and their association with performance traits in broilers |
| title_short | Genome-wide detection of CNVs and their association with performance traits in broilers |
| title_sort | genome wide detection of cnvs and their association with performance traits in broilers |
| topic | GWAS Performance CNVs QTLs qPCR |
| url | https://doi.org/10.1186/s12864-021-07676-1 |
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