Genetic analysis of an F(2) intercross between two chicken lines divergently selected for body-weight

Abstract

Background: We have performed Quantitative Trait Loci (QTL) analysis of an F(2) intercross between two chicken lines divergently selected for juvenile body-weight. In a previous study 13 identified loci with effects on body-weight, only explained a small proportion of the large variation in the F(2) population. Epistatic interaction analysis however, indicated that a network of interacting loci with large effect contributed to the difference in body-weight of the parental lines. This previous analysis was, however, based on a sparse microsatellite linkage map and the limited coverage could have affected the main conclusions. Here we present a revised QTL analysis based on a high-density linkage map that provided a more complete coverage of the chicken genome. Furthermore, we utilized genotype data from ~13,000 SNPs to search the genome for potential selective sweeps that have occurred in the selected lines.

Results: We constructed a linkage map comprising 434 genetic markers, covering 31 chromosomes but leaving seven microchromosomes uncovered. The analysis showed that seven regions harbor QTL that influence growth. The pair-wise interaction analysis identified 15 unique QTL pairs and notable is that nine of those involved interactions with a locus on chromosome 7, forming a network of interacting loci. The analysis of ~13,000 SNPs showed that a substantial proportion of the genetic variation present in the founder population has been lost in either of the two selected lines since ~60% of the SNPs polymorphic among lines showed fixation in one of the lines. With the current marker coverage and QTL map resolution we did not observe clear signs of selective sweeps within QTL intervals.

Conclusion: The results from the QTL analysis using the new improved linkage map are to a large extent in concordance with our previous analysis of this pedigree. The difference in body-weight between the parental chicken lines is caused by many QTL each with a small individual effect. Although the increased chromosomal marker coverage did not lead to the identification of additional QTL, we were able to refine the localization of QTL. The importance of epistatic interaction as a mechanism contributing significantly to the remarkable selection response was further strengthened because additional pairs of interacting loci were detected with the improved map.

Figure 1

Comparison of QTL results for body-weight at 56 days of age using the old microsatellite map and an improved map including 434 markers. The black line represents F-values plotted for each cM throughout the genome for the new marker map while the red line displays F-values using the previous microsatellite-based map. The x-axis shows the start and end of each linkage group covered in the new map. Horizontal lines in the graph indicate the 5% genome-wide and the suggestive significance threshold. Black and red vertical bars underneath the x-axis indicate marker positions in the new and old map, respectively. Chromosome 29 denotes linkage group 'E22C19W28E50C23' that has not yet been placed on a chromosome.

Figure 2

Pairs of genome-wide significant interacting loci identified in the HWS/LWS intercross. Bold circle line indicates that the locus had a significant (genome-wide or suggestive) marginal effect for at least one body-weight trait. Solid connection lines between loci (--) represent 1% significant interactions whereas dotted connection lines (--) indicate 5% significant interactions between loci.

Figure 3

Genotype-phenotype plots for genome-wide significant epistatic QTL pairs for body-weight at 56 days of age (A-E). The mean values of body-weight (in grams) for each of the nine possible allelic combinations are shown in the plot. The genotype classes for one QTL are listed on the X-axis (i.e. HH, HL and LL) and the curves represent each genotype class of the other QTL. Error bars represent the standard error of mean (s.e.m). HWS alleles are abbreviated as "H" and LWS alleles as "L".

Figure 4

A combined analysis of a four locus epistatic network affecting body-weight at 56 days of age. Phenotypic mean values for body-weight at 56 days of age for alternative Growth9 genetic backgrounds plotted by the degree of HWS line homozygosity at Growth4, Growth6 and Growth12. Horizontal lines give the mean values for Growth9 HH and LL homozygotes. Error bars represent s.e.m. HWS line alleles are abbreviated as "H" and LWS alleles as "L".