Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: IV. Growth performance

Abstract

Reciprocal crosses between the inbred lines New Hampshire (NHI) and White Leghorn (WL77) comprising 579 F2 individuals were used to map QTL for body weight and composition. Here, we examine the growth performance until 20 weeks of age. Linkage analysis provided evidence for highly significant QTL on GGA1, 2, 4, 10 and 27 which had specific effects on early or late growth. The highest QTL effects, accounting for 4.6-25.6% of the phenotypic F2 variance, were found on the distal region of GGA4 between 142 and 170 cM (F ≥ 13.68). The NHI QTL allele increased body mass by 141.86 g at 20 weeks. Using body weight as a covariate in the analysis of body composition traits provided evidence for genes in the GGA4 QTL region affecting fat mass independently of body mass. The QTL effect size differed between sexes and depended on the direction of cross. TBC1D1, CCKAR and PPARGC1A are functional candidate genes in the QTL peak region. Our study confirmed the importance of the distal GGA4 region for chicken growth performance. The strong effect of the GGA4 QTL makes fine mapping and gene discovery feasible.

Fine mapping of a distal chromosome 4 QTL affecting growth and muscle mass in a chicken advanced intercross line

“…However, sex effects on our QTL have been investigated before by Nassar et al . (). Association Analysis between markers and body composition traits not only confirmed the growth QTL region but also replicated previous findings concerning muscle weight and carcass compositions.…”

“…The QTL region between the two flanking markers (rs14488203 and rs14494169) of the peak marker ( UMA4.034 ) from our previous study (Nassar et al . ) was selected as the target region for fine mapping; this was between 69 583 407 and 78 715 886 base pairs on GGA4 (Ensembl 81). Based on genotype data obtained from SNP chips, nine SNPs with alternative alleles between NHI and WL77 chickens and an average marker distance of approximately 1 Mb were selected for fine mapping (Table ).…”

“…In our previous study, the confidence interval was 26.9 Mb between 61.5 and 88.4 Mb (Nassar et al . ), in which reside 292 genes that could potentially be causal for the observed difference in growth performance. To reduce the number of potential candidate genes, the QTL region has to be fine mapped.…”

Genomic approaches and bioinformatics tools to identify genomic regions for economic traits and their applications in chicken breeding programs

“…Body composition measurements included weights of carcass, breast muscle, wings, residual carcass, drumsticks and thighs, as well as visceral and subcutaneous adipose tissue masses and intramuscular fat content at the age of 20 weeks. Genotyping and sequencing: Genome-wide linkage analysis using 123 microsatellite (short sequence repeats; SSR) and single nucleotide polymorphism (SNP) loci were sued to map QTL covering 25 chromosomes (for detail see Goraga et al 2012;Nassar et al 2012Nassar et al , 2015. Chicken 60K and 600K SNP chips as well as whole genome sequencing were used to fine map and characterize the major growth QTL in the distal part of chromosome 4 (for detail see Lyu et al 2017).…”

“…Sex-averaged genetic map (Kosambi) was used for the QTL scans. Interval mapping was performed using multiple regressions (Nassar et al , 2015. Once a single QTL in a linkage group was identified, the presence of a second QTL was investigated by using the two QTL model.…”