Genome-wide Association Study On Muscle Fiber And Eye Muscle Area Traits In Swine

With the pursuit of a higher quality of life, consumers require higher quality pork. Muscle fiber and eye muscle area as the main factors affecting meat quality attracted more and more attention of researchers. In recent years, SNP chips with high density SNPs were sustained researched by some biotechnology companies and genotyping technique was developed, which make it possible to implement the Genome-wide Association Study （GWAS） for muscle fiber and eye muscle area traits in pigs. This study aimed to look for SNPs and candidate genes associated with muscle fiber and eye muscle area traits by using GWAS.Total of 575 pigs from the Large White x Minzhu F2 generation intercross resource population was used as the experimental animals. The Illumina PorcineSNP60 BeadChip with 62163 SNPs, Regression-Genomic Control （GRAMMAR-GC） and the Genome-wide Rapid Association using the Mixed Model, GenABEL software package under the R statistical environment and DMU software were used to carry out the GWAS analysis on nine traits. The traits included the muscle fiber diameter （MFDI）, muscle fiber density （MFDE）, muscle fiber area （MFA）, percentage of white muscle fiber （PWMF）, percentage of red muscle fiber （PRMF）, percentage of intermediate muscle fiber （PIMF）, eye muscle area at 5-6th rib （EMA5₆th）, eye muscle area at 10-11th rib （EMAs-6th） and eye muscle area at the last rib （EMA5-6last）. The genetic variation related to the muscle fiber and eye muscle area traits were searched. Results indicated that:1. After slaughtering the 75 pigs and cutting the carcasses, nine traits related to muscle fiber and eye muscle area were measured and recorded. The descriptive statistics indicated that the distribution of phenotype values of all traits were in accordance with the characteristic of resource family segregating population. The relationship between muscle fiber traits （P< 0.01） and between muscle fiber traits and eye muscle area traits were significant （P< 0.01）.2. The results of GWAS analysis showed that the number of significant SNPs at chromosome level were 5,8,7,4,1,2,12 and 36, respectively, and that the number of significant SNPs at genome level were 4,6,5,1,0,0,4 and 15, respectively. The SNP related to eye muscle area at 5-6 rib was not detected.3. According to the sequence information of SNPs on chip, the significant SNPs related to muscle fiber and eye muscle area traits were annotated using NCBI database and Sus scrofa Build 10.2 genome database. The results indicated that ALGA0020217 significantly associated with muscle fiber diameter, which was located within SRBD1 gene on SSC3; DRGA0006607 significantly associated with muscle fiber density, which was located within TOX3 gene on SSC6; ALGA0020217 significantly associated with muscle fiber area, which was located within SRBD1 gene on SSC3; ASGA0094812, H3GA0005590, ASGA0008564 significantly associated with eye muscle area at 10-11th rib, which were located within USP43 gene on SSC12, PPP6R3 gene on SSC2 and SSH3 gene on SSC2, respectively; ASGA0094812, H3GA0034538, ALGA0066656, ALGA0104212, ALGA0109059, MARC0108602, H3GA0053692, DIAS0000896, M1GA0016908, H3GA0033824, MARC0087562, CASI0008458, ASGA0035681, H3GA0005590, DIAS0000861 and ASGA0055225 were significantly associated with eye muscle area at the last rib, which were located within USP43, NLK, NLK, NOS2, KIAA0100, AATF, KSR1, NOS2, SLC13A5, MPP2, MY01D, GLP2R, MAP2K4, PPP6R3, MYH3 and MYH13 genes.4. According to the database information from KEGG, NCBI and Ensembl, the function of genes in the vicinity of the significant SNPs were annotated using comparative genomics and bioinformatics. The results showed that the gene functions mainly involved in DNA repair, transcriptional regulation and translational control, cytoskeleton and matrix components, regulating metabolism and balance of nutrients, cell proliferation, regeneration and apoptosis, kinase activity, participating in cellular signal transduction and ion channels constitute, etc. Some genes and gene families among them were confirmed association with meat quality, muscle fiber and eye muscle area.5. The HAPLOVIEW V3.31 program and the Haplo.Stats R package were used to detect and visualize haplotype blocks and to analyze the association of the detected haplotype blocks with eye muscle area at the last rib. The results showed that four haplotype blocks were associated with eye muscle area at the last rib. A linkage analysis revealed that the four haplotype blocks contained 4,4,2, and 4 SNPs, respectively. Annotations from pig reference genome suggested two genes （NOS2, NLK） in block 1 （266 kb）, one gene （TMIGD1） in block 2 （348 kb）, and one gene （MAP2K4） in block 3 （453 kb）.6. In summary, USP43, PPP6R3, NLK, NOS2, SLC13A5, MYOID, MYH3, MYH13 genes or gene families were preliminary identified as the key candidate genes or gene families for muscle fiber and eye muscle area traits in the study.