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

Anna Carolina Fernandes,Adriana Mércia Guaratini Ibelli,Jane De Oliveira Peixoto,Gabriel Costa Monteiro Moreira,Mônica Corrêa Ledur,Thaís Fernanda Godoy,Luiz Lehmann Coutinho,Maurício Egídio Cantão,Carolina Purcell Goes,Vinicius Henrique Da Silva,Fernanda Marcondes De Rezende

doi:10.1186/s12864-021-07676-1

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® 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.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.

Highlights

Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation of complex traits, in humans, and in livestock animals
We identified overlaps of significant CNV segments associated with body weight at 35, 41, 42 days and body weight gain with four previously mapped quantitative trait loci (QTL) for weight traits and residual feed intake (RFI)
We identified 32 genes annotated within a 1-Mb window of significant CNV segments associated with birth weight, body weight at 35, 41 and 42 days and body weight gain from 35 to 41 days

Summary

Introduction

Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation of complex traits, in humans, and in livestock animals. We identified CNVs along the chicken genome and analyzed their association with performance traits. Variations in the genome, especially single nucleotide polymorphisms (SNPs), are known to be associated with phenotypic variation [5]. Structural variations, such as copy number variations (CNVs) have been increasingly studied and associated with quantitative traits of economic interest in livestock [6,7,8,9]

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