Exploration Of Candidate Genes And Variations Affecting Backfat Quality Of Beijing Black Pigs Based On Omics Technology

Fat quality is closely related to meat nutrition,shelf-life,safety and sensory characteristics.It is a significant factor affecting pork quality and pork products quality.However,compared to other meat quality traits(such as intramuscular fat,p H value,water holding capacityand color),Fat quality traits(such as fat color and firmness)have received less attention in the past research.In this study,candidate genes affecting fat quality attributes(such as fat color and firmness)were explored from the genome level and transcriptome level.Direct sequencing was used to screen out important variations in important candidate genes.The main results are as follows:1.A genome-wide association study was performed for the backfat color and firmness of 578 Beijing black pigs using a mixed linear model by GEMMA software.A total of 14 SNPs were identified to be significantly correlated with the backfat color,and 17 SNPs were significantly correlated with the backfat firmness.Gene annotation was performed on the region 1Mb upstream and downstream of significant SNPs.The results showed that 85 annotation genes were obtained from near SNPs related to backfat color and 147 annotation genes were obtained from near SNPs related to backfat firmness.Combined with pathway analysis and literature literature search,four genes KCNJ13,FAXDC2,MYC and ROR2 were regarded as candidate genes associated with the backfat color of Beijing black pigs,and 10 genes MYO9 A,TLE3,FNDC4,PPP1 CB,GCKR,EPHX4,TGFBR3,DPYD,UACA and RPL5 were regarded as candidate genes associated with the backfat firmness of Beijing black pigs.2.RNA-seq sequencing technology was used to compare and analyze the m RNA and lncRNA identified in backfat from high fat quality group(BH)and low fat quality group(BL)of Beijing black pigs.The results showed that 610 differentially expressed m RNA(DEGs)and 290 differentially expressed lncRNA(DELs)were identified after comparing the BH group and BL groups.The target genes of DELs were predicted.The results showed that 1088 genes were considered as cis target genes(cis G)of DELs,and 297 DEGs were trans target genes(tran G)of DELs.The functional enrichment analysis of the target genes predicted by DELs and DEGs showed that they were mainly enriched in the process of pigment deposition and fatty acid metabolism.3.By constructing lncRNA-m RNA interaction network,combined with enrichment analysis results and biological function search,it was considered that lncRNA TCONS＿00214071、TCONS＿00138546、TCONS＿00261208 and TCONS＿00070483 may regulate HACD4,SCD,ELOVL5 and EHHADH genes to affect the backfat firmness of Beijing black pigs through fatty acid metabolism;lncRNA TCONS＿00282681 by regulating DGAT2 gene,lncRNA TCONS＿00296593,TCONS＿00093273 and TCONS＿00111522 by regulating SLC24A5 gene and TCONS＿00304616 and TCONS＿00281166 by regulating TYRP1 gene affected the backfat color of Beijing black pigs by the process of pigment deposition.4.Integrating GWAS and transcriptome results,ELOVL5,EPHX4 and TGFBR3 were regarded as important candidate genes to affecting backfat firmness of Beijing black pigs,and TYRP1 was regarded as important candidate genes to affecting backfat color of Beijing black pigs.The variants g.46858660 C > T,g.125260054 T > C and g.124961177 G > A of ELOVL5,EPHX4 and TGFBR3 genes were screened by direct sequencing and considered as important candidate variants affecting backfat firmness of Beijing black pigs.The variants g.209745701 C > T of TYRP1 gene was an important candidate mutation affecting backfat color of Beijing black pigs.In conclusion,this study obtainded important candidate genes and variants affecting backfat firmness and backfat color of Beijing black pigs through GWAS and transcriptome resuts,which provides a reference for studying the molecular mechanism of pig backfat quality.