Figure 7. Whole genome association analyses for average daily gain (ADG).

Part A depicts association analyses performed by the PLINK software for each SNP. The X axis shows SNPs across chromosomes SSC1 to X, unassigned contigs, Y and completely unmapped SNP. The Y axis contains the negative logarithm of the P values adjusted for genomic control. Each spot is a SNP. The green color SNPs are those located in 1 Mb window regions that explain more than 0.2% of genetic variance in part B. Part B illustrates results from the Bayes B model averaging approach used in the Gensel software. Different colors on the X axis indicate genome wide 1MB SNP windows from chromosome 1 to X, unassigned contigs and completely unmapped SNP. The markers from completely unmapped and unassigned contigs were not included in the cumulative genetic variance. The Y axis represents percent genetic variance explained by each 1 Mb window. Part C shows association analyses with the PLINK software based on haplotypes, which were derived for 1 Mb windows that explained a higher than 0.2% of genetic variance in part B. The X axis has haplotypes on specific chromosomes. The Y axis shows the negative logarithm of the P values corrected by genomic control. The arrows in parts A, B and C show the similarities in significant locations of the associated SNPs, SNP windows and their haplotypes. The 1 Mb windows that explained higher than 0.2% percent genetic variance in Gensel analyses and/or were significant in the PLINK analyses were considered to be important putative QTL for ADG. MC4R: melanocortin 4 receptor; TGFBI: transforming growth factor beta induced protein ig-h3; PGM1: phosphoglucomutase 1; GPR81: G-protein coupled receptor 81; U6: spliceosomal RNA.