Genome-wide detection of CNVs and their association with performance traits in broilers
| Autor: | Luiz Lehmann Coutinho, Vinicius Henrique da Silva, Anna Carolina Fernandes, Maurício Egídio Cantão, Thaís Fernanda Godoy, Carolina Purcell Goes, Mônica Corrêa Ledur, Fernanda Marcondes de Rezende, Gabriel Costa Monteiro Moreira, A. M. G. Ibelli, Jane de Oliveira Peixoto |
|---|---|
| Přispěvatelé: | ANNA CAROLINA FERNANDES, ESALQ, VINICIUS HENRIQUE DA SILVA, ESALQ, CAROLINA PURCELL GOES, ESALQ, GABRIEL COSTA MONTEIRO MOREIRA, University of Liège, THAIS FERNANDA GODOY, ESALQ, ADRIANA MERCIA GUARATINI IBELLI, CNPSA, JANE DE OLIVEIRA PEIXOTO, CNPSA, MAURICIO EGIDIO CANTAO, CNPSA, MONICA CORREA LEDUR, CNPSA, FERNANDA MARCONDES REZENDE, University of Florida, LUIZ LEHMANN COUTINHO, ESALQ. |
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Genome-wide association study
Quantitative trait loci DNA Copy Number Variations Genética Animal Performance Population Gallus gallus Biology QH426-470 Polymorphism Single Nucleotide Genome 03 medical and health sciences Quantitative polymerase chain reaction Gallus Domesticus Genetics Animals Humans GWAS Copy number variations Copy-number variation education Gene 030304 developmental biology CNVs 0303 health sciences education.field_of_study 0402 animal and dairy science 04 agricultural and veterinary sciences QTLs 040201 dairy & animal science Phenotype Genetic architecture QPCR qPCR SEQUENCIAMENTO GENÉTICO Animal genetics DNA microarray Chickens TP248.13-248.65 Research Article Genome-Wide Association Study Desempenho zootécnico Animal performance Biotechnology |
| Zdroj: | BMC Genomics, Vol 22, Iss 1, Pp 1-18 (2021) Repositório Institucional da USP (Biblioteca Digital da Produção Intelectual) Universidade de São Paulo (USP) instacron:USP Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA-Alice) Empresa Brasileira de Pesquisa Agropecuária (Embrapa) instacron:EMBRAPA BMC Genomics |
| ISSN: | 1471-2164 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|