Figures & data
Table 1. The average WGs and DWGs, FIs and RFIs of the local and commercial chickens.
Table 2. The number of RNA-Seq reads and mapping rates of the two breeds.
Figure 1. The volcano plot for the differentially expressed genes. Right upper dots denotes the up-regulated genes in the native breed; left upper dots denotes the up-regulated genes in the commercial breed; lower dots denotes the genes with no significant changes.
![Figure 1. The volcano plot for the differentially expressed genes. Right upper dots denotes the up-regulated genes in the native breed; left upper dots denotes the up-regulated genes in the commercial breed; lower dots denotes the genes with no significant changes.](/cms/asset/d7182616-5083-4fc4-9dee-2be1606706e5/tjas_a_1507625_f0001_c.jpg)
Table 3. Top 10 known up- and down-regulated genes in the local breed.
Figure 2. A circus plot showing the chromosomal distribution of the known and novel differentially expressed genes. Each circle from the periphery to the centre represents the following specifications: chromosomal location, the positions of the known genes in the genome, log2-fold change of the commercial to the native breed for the known genes, log2-fold change of the commercial to the native breed for the novel genes and their positions in the genome.
![Figure 2. A circus plot showing the chromosomal distribution of the known and novel differentially expressed genes. Each circle from the periphery to the centre represents the following specifications: chromosomal location, the positions of the known genes in the genome, log2-fold change of the commercial to the native breed for the known genes, log2-fold change of the commercial to the native breed for the novel genes and their positions in the genome.](/cms/asset/df10d1e1-b287-4623-82f6-c9490bcc0ed0/tjas_a_1507625_f0002_c.jpg)
Figure 3. Validation of the differentially expressed genes in the liver tissues of the native and commercial chickens. qRT-PCR: Quantitative Real time Polymerase chain reaction; RNA-Seq: RNA Sequencing.
![Figure 3. Validation of the differentially expressed genes in the liver tissues of the native and commercial chickens. qRT-PCR: Quantitative Real time Polymerase chain reaction; RNA-Seq: RNA Sequencing.](/cms/asset/118b1447-1a44-4dc9-90ba-e330722495a4/tjas_a_1507625_f0003_c.jpg)
Table 4. Significantly enriched GO terms for the down-regulated genes in the local breed.
Table 5. List of the down-regulated genes in the local breed, which were localised in more than one QTL based on feed efficiency.