Whereas previous selective sweep studies in chicken focused on the characterization of the genome-wide effects of divergent selection on a specific phenotype (Johansson et al. 2010; Zhang et al. 2012), here we integrate QTL mapping and whole-genome-based selective sweep detection for the same phenotype, and also SNPs and expression analyses.
Combining two independent methods increases the power of sweep detection [ 63].
Both methods of selective sweep detection based on the SFS and LD identify a narrow selected region as the CLRmax and ωmax are distant from each other by only ~1 kb.
Due to the interference of the FNR on sweep detection, the sweep analysis should be considered preliminary.
Here, we enhance the H12 and H2/H1 haplotype homozygosity statistics for selective sweep detection by deriving the upper bound on H2/H1 as a function of H12, thereby generating a statistic that normalizes H2/H1 to lie between 0 and 1.
As shown in Figure 1, which summarizes the strategy used in our study, selective sweep detection using DNA resequencing enabled us to markedly reduce the size of some QTL for adiposity (from 12 Mb to 100 kb, on average).
The decreasing cost of sequencing will allow large scale GWAS experiments and selective sweep detection at the genome level in a very close future.
With the availability of genome-wide variations of Silkie and L2, we tried to identify candidate genes for important traits in chicken domestication using multiple approaches including SIFT analysis, functional enrichment, and selective sweep detection.
The definition of α > 0 is also important to this discussion since in the detection of sweeps we must allow for old sweeps in which de novo mutations may have begun to accumulate on the fixed haplotype, genotyping errors which are locus specific but average about 0.5% for this assay, and the incorrect ordering of loci by the UMD3.1 sequence assembly.
This further supports our conjecture that the design of the BovineSNP50 assay to include common variation makes it primarily suitable for the detection of sweeps that have occurred following breed formation.
