Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing

Abstract

Background: Ascites syndrome is a hypertensive, multifactorial, multigene trait affecting meat-type chickens imposing significant economic losses on the broiler industry. A region containing the CPQ gene has been previously identified as significantly affecting ascites phenotype. The region was discovered through whole genome resequencing focused on chicken chromosome 2. The association was confirmed through further genotyping in multiple broiler populations. Results: The whole genome resequencing analyses have now been extended to the current chicken genome assembly. DNA samples were pooled according to gender and phenotype and the pools subjected to next generation sequencing. Loci were identified as clusters of single nucleotide polymorphisms where frequencies of the polymorphisms differed between resistant and susceptible chickens. The chickens are an unselected line descended from a commercial elite broiler line. Regions identified were specific to one or both genders. The data identify a total of 28 regions as potential quantitative trait loci for ascites. The genes from these regions have been associated with hypertensive-related traits in human association studies. One region on chicken chromosome 28 contains the LRRTM4 gene. Additional genotyping for the LRRTM4 region demonstrates an epistatic interaction with the CPQ region for ascites phenotype. Conclusions: The 28 regions identified were not previously identified in a multi-generational genome wide association study using 60k Single Nucleotide Polymorphism panels. This work demonstrates the utility of whole genome resequencing as a cost effective, direct, and efficient method for identifying specific gene regions affecting complex traits. The approach is applicable to any organism with a genome assembly and requires no a priori assumptions.

SNP-Based Breeding for Broiler Resistance to Ascites and Evaluation of Correlated Production Traits

“…Birds used for breeding were genotyped by collecting 10 µl of blood from the brachial vein which was further processed using a rapid DNA extraction method [47]. These DNAs were then genotyped using exonuclease assays run in triplicate for both CPQ and LRRTM4 genes, as described [45,46]. Selected breeders were then moved into individual breeder cages for insemination and production of MAS offspring.…”

“…A series of genome-wide association studies (GWAS) using SNP panels identi ed a few candidate SNPs as associated with ascites phenotype, but subsequent MAS-based breeding projects were unsuccessful in validating these few loci [41][42][43][44]. More recently, whole genome resequencing (WGR) identi ed 28 genomic regions where SNP clusters (100s to 1000s of SNPs) showed frequency bias with respect to ascites phenotype [45,46]. Two of these regions were validated by further genotyping of additional DNA samples and found to have potential epistatic interaction.…”

SNP-Based Breeding for Broiler Resistance to Ascites and Evaluation of Correlated Production Traits

“…A series of genome-wide association studies (GWAS) using SNP panels identified a few candidate SNPs as associated with ascites phenotype, but subsequent MAS-based breeding projects were unsuccessful in validating these few loci [41][42][43][44]. More recently, whole genome resequencing (WGR) identified 28 genomic regions where SNP clusters (100s to 1000s of SNPs) showed frequency bias with respect to ascites phenotype [45,46]. Two of these regions were validated by further genotyping of additional DNA samples and found to have potential epistatic interaction.…”

SNP-based breeding for broiler resistance to ascites and evaluation of correlated production traits

“…A series of genome-wide association studies (GWAS) using SNP panels identi ed a few candidate SNPs as associated with ascites phenotype, but subsequent MAS-based breeding projects were unsuccessful in validating these few loci [41][42][43][44]. More recently, whole genome resequencing (WGR) identi ed 28 genomic regions where SNP clusters (100s to 1000s of SNPs) showed frequency bias with respect to ascites phenotype [45,46]. Two of these regions were validated by further genotyping of additional DNA samples and found to have potential epistatic interaction.…”

“…Birds used for breeding were genotyped by collecting 10 µl of blood from the brachial vein which was further processed using a rapid DNA extraction method [47]. These DNAs were then genotyped using exonuclease assays run in triplicate for both CPQ and LRRTM4 genes, as described [45,46]. Selected breeders were then moved into individual breeder cages for insemination and production of MAS offspring.…”