PMC

Neighbor-joining tree of 27 major haplotypes for a 750-kb critical region of the major QTL on SSC7. Haplotypes with frequencies greater than 0.05 were used to construct a NJ tree using the 750-kb critical region of SSC7. Hap 1 is the Q-bearing haplotype; haplotypes specific to Chinese indigenous breeds are indicated in red blocks; haplotypes present in both Chinese and Western breeds are highlighted in blue blocks; haplotypes prominently occurring in Chinese breeds and Western breeds are marked in red and green triangular blocks, respectively; haplotypes specific to Chinese indigenous breeds and Chinese synthetic breeds are indicated by red inverted triangular blocks.

Manhattan plots for the analyses of growth traits in F ₂ and Sutai pigs. (A): GWAS for birth weight (BW0), body weight at day 46 (BW46) and body weight at day 240 (BW240) in F₂ animals. (B): GWAS for BW0, BW21 and BW240 in Sutai pigs. In the Manhattan plots, negative log₁₀ P-values of the filtered high-quality SNPs SNPs were plotted against their genomic positions; solid and dashed lines indicate the 5% genome-wide and chromosome-wide (i.e., suggestive) Bonferroni-corrected thresholds, respectively.

Manhattan plots for the analyses of fatness traits in F ₂ animals. GWAS results are shown for ABFT (A), LFW (B), VFW (C) and AFW (D) in F₂ animals. In the Manhattan plots, negative log₁₀ P values of the filtered high-quality SNPs were plotted against their genomic positions; SNPs on different chromosomes are denoted by different colors; solid and dashed lines indicate the 5% genome-wide and chromosome-wide (i.e., suggestive) Bonferroni-corrected thresholds, respectively; ABFT: average backfat thickness; LFW: leaf fat weight; VFW: veil fat weight; AFW: abdominal fat weight.

Fine mapping of the major QTL for growth and fatness traits on SSC7 in the F ₂ population. (A) Linkage disequilibrium and linkage analysis for average backfat thickness. In the Manhattan plots, negative log₁₀ P values of the filtered high-quality SNPs SNPs are plotted against their genomic positions on SSC7; SNPs surpassing the 5% genome-wide significance threshold are denoted in red; solid line indicates the 5% genome-wide Bonferroni-corrected threshold; the 95% confidence interval (CI) defined by the LOD-dropoff-2 method is indicated by a gray shaded block. (B) Haplotype analysis for a 3.2-Mb region encompassing the 95% CI of the SSC7 locus in 17 F₀ sows and 2 F₀ boars. The allele with the higher frequency is denoted as 2, and the allele with the lower frequency is denoted as 1; the number of each haplotype in the 19 founder animals is given in the bracket; a total of 30 Q-bearing chromosomes corresponding to 12 haplotypes were derived from Erhualian founder sows, which shared a ~1.7-Mb segment, from ss131343640 to ss478941605; the shared 1.7-Mb segment containing the top SNP (ss107837325) is highlighted in red; six q-bearing chromosomes corresponding to three haplotypes were derived from two White Duroc F₀ boars (individuals 73 and 75, q1 and q2) and two Erhualian F₀ sows (individuals 124 and 126, q3). One haplotype, originating from Erhualian F₀ individuals 142 and 146, is indicated by the symbol “?”; this haplotype is most likely a q-type haplotype; the ~750-kb region of overlap between the 95% CI and the Q-chromosome-containing segment is indicated by two vertical yellow lines. (C) The 22 informative SNPs and eight annotated genes in the 750-kb critical region. The top SNP (ss107837325) is marked in red.