Additional file 2: Figure S1. of Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing

The distributions of novel SNV and known SNP in each chromosome. Figure S2. A statistical enrichment test (Fisher’s exact test) for detecting enriched non-synonymous SNP site on targeted genes. Figure S3. A statistical enrichment test (Fisher’s exact test) for detecting enriched Indel site on targeted genes. Figure S4. The overall reads mapping rate of assembled contigs for each breed and reference genome by aligning the total sequence reads of each Berkshire sample. (DOCX 3433 kb

Additional file 1: of An integrated in silico approach for functional and structural impact of non- synonymous SNPs in the MYH1 gene in Jeju Native Pigs

Figure S1. Graphical views of the GO related to the muscle growth and development of porcine MYH1. (A) The biological process of muscle contraction. (B) The biological process of muscle organ development. Figure S2. The significant pathways terms of MYH1 gene in porcine. Figure S3. The scatter plot of differentially expressed genes and QTLs map in MYH1 region of SSC12. (A) Scatter plots was constructed with log2- for the visual comparison of gene expression levels in muscle tissue samples of JNP and Berkshire. The CNR scores and position of MYH1 gene demonstrated with in the box. (B) The position of most significant QTLs those are associated with meat and carcass quality traits reported in MYH1 region. Figure S4. The 3D homologous model of MYH1. The tertiary structure of native MYH1 is drawn here as a cartoon model. Figure S5. Ramachandran Plot of native MYH1. The red, brown, and yellow regions represent favored, allowed, and “generously allowed” regions as defined by ProCheck. Figure S6. The 3D homologous model of MYLPF is drawn here as a cartoon model. Figure S7. Ramachandran Plot of MYLPF represents the favored, allowed, and “generously allowed” regions as defined by ProCheck for MYLPF. Figure S8. The RMSD values of all backbone atoms of MYH1- MYLPF protein complexes. The RMSD (in nanometer) is at ordinate and Time (in nano-second) at abscissa. The structural simulations for the native MYH1 (green), mutant MYH1 L884T (blue), K972C (black), N981G (pink) and Q1285C (red) complexes with MYLPF. Table S1. Ontology of MYH1 gene of Sus scrofa. Table S2. Pathways of MYH1 gene of Sus scrofa. Table S3. Prediction of the mutational effects. Prediction of the mutational effects on the function on MYH1 protein from JNP and Berkshire using MutPred. Table S4. Predication the functional partners of protein-protein interactions from STRING database. (DOCX 966 kb

Additional file 2: of An integrated in silico approach for functional and structural impact of non- synonymous SNPs in the MYH1 gene in Jeju Native Pigs

The ARRIVE Guidelines Checklist Animal Research: Reporting In Vivo Experiments. (PDF 386 kb