Genome-wide detection of CNVs and their association with performance traits in broilers

Author(s):Show less -

Fernandes, Anna Carolina ^[1] ; da Silva, Vinicius Henrique ^[1] ; Goes, Carolina Purcell ^[1] ; Monteiro Moreira, Gabriel Costa ^[2] ; Godoy, Thais Fernanda ^[1] ; Guaratini Ibelli, Adriana Mercia ^[3] ; Peixoto, Jane de Oliveira ^[3] ; Cantao, Mauricio Egidio ^[3] ; Ledur, Monica Correa ^[3] ; de Rezende, Fernanda Marcondes ^[4] ; Coutinho, Luiz Lehmann ^[1]

Affiliation

^[1] Univ Sao Paulo, Luiz de Queiroz Coll Agr ESALQ, Dept Anim Sci, BR-13418900 Piracicaba, SP - Brazil

^[2] Univ Liege, Unit Anim Genom, GIGA R, Liege - Belgium

^[3] Embrapa Suinos & Aves Empresa Brasileira Pesquisa, Concordia, SC - Brazil

^[4] Univ Florida, Dept Anim Sci, Gainesville, FL 32608 - USA

• Document type: Journal article
• Source: BMC Genomics; v. 22, n. 1 MAY 17 2021.
• Web of Science Citations: 1

Abstract

BackgroundCopy 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 (R) 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 42days, feed intake from 35 to 41days, feed conversion ratio from 35 to 41days and, body weight gain from 35 to 41days of age.ResultsWe 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.ConclusionsOverall, 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. (AU)

• FAPESP's process: 14/08704-0 - Identification of loci of interest for poultry production
• Grantee: Luiz Lehmann Coutinho
• Support type: Research Projects - Thematic Grants