Table 1.
Summary of sequence read alignments to reference genome in liver samples.
Figure 1.
Heatmap showing differentially expressed genes in liver samples.
The red blocks represent over expressed genes, and the green blocks represent under expressed genes. Legend: LS1–LS3 boars liver with low skatole in backfat and HS1–HS3 boars liver with high skatole in backfat.
Table 2.
Top 30 up and down regulated genes in liver tissues collected from boars with high and low skatole levels in backfat.
Figure 2.
Functional grouping of DEGs in liver from boars with high and low skatole using Ingenuity Pathways Analysis (IPA) software.
The most significant functional groups (p<0.05) are presented graphically. The bars represent the p-value on a logarithmic scale for each functional group.
Figure 3.
Canonical pathways of DEGs in liver from boars with high and low skatole using Ingenuity Pathways Analysis software.
The most significant functional groups (p < 0.05) are presented graphically. The bars represent the p-value on a logarithmic scale for each functional group.
Table 3.
Functional categories and corresponding genes those were over expressed in liver from high skatole boars.
Table 4.
The canonical pathways from the IPA knowledge base that involve transcripts over expressed in liver from higher skatole boars.
Figure 4.
qRT-PCR validations for ten DEGs in liver from boars with divergent skatole levels.
The validation was performed using the same RNA samples as used in the RNA deep sequencing (A); new group of boars with divergent skatole levels were created from the remaining 94 boars for the validation of the same DEGs using qRT-PCR (B). Fold change determined via division of high skatole group gene expression value by low skatole group gene expression value.
Figure 5.
Distribution of the number of alternate splicing.
The distribution of the number of alternate splicing the DEGs (A); number of alternate splicing in the selected genes (B).
Figure 6.
The schematic diagram of differential exon expression in selected genes.
Differential exon expression in ATP5B (A). KRT8 (B) and PGM1(C). (Top panel) Fitted values according to the linear model; (middle panel) normalized counts for each sample; (bottom panel) flattened gene model. (Red) Data for high skatole samples; (green) low skatole.
Table 5.
Differential exon expression in selected DEGs in liver samples from boars with divergent skatole levels in backfat.
Figure 7.
Distribution of the number of SNPs detected in the DEGs.
The distribution of the number of SNPs occurred in each gene (A); numbers of SNPs in the genes selected for the association validation (B). *indicate the genes selected for the SNPs validation.
Table 6.
Polymorphisms detected in highly polymorphic DEGs.
Table 7.
Genotypes and association analysis of selected candidate genes in boars.
Table 8.
Details of primers used for qRT-PCR analysis and genotyping.