Genome-wide association study identifying genetic variants associated with carcass backfat thickness, lean percentage and fat percentage in a four-way crossbred pig population using SLAF-seq technology

Abstract Background Carcass backfat thickness (BFT), carcass lean percentage (CLP) and carcass fat percentage (CFP) are important to the commercial pig industry. Identification of the candidate SNPs and genes associated with these traits will be beneficial to pig breeding. We performed a GWAS based on SLAF-seq to analyze seven traits, including five BFTs, CLP, and CFP on 223 four-way intercross pigs. Results A total of 1, 552, 377 SLAFs from the pig reference genome (Sscrofa 11. 1₁02) were predicted using RsaI and HaeIII enzyme combination. With an average sequencing depth of 11. 94-fold, a total of 10, 784, 484 SNPs were obtained. After SNPs’ filtering, 227, 921 SNPs were identified to perform GWAS. Using the mixed linear model (MLM) model, a total of 21 SNP loci significantly related to these traits were identified on ten chromosomes. Interestingly, nine shared traits SNPs were detected. Among these, SSC7: 29503670 for average backfat thickness (ABFT, P=3. 26E-08) and SSC7: 29486003 for ABFT (P=2. 12E-07) exceed 1% and 10% genome-wide significance, respectively. The two loci were located in the intron of COL21A1, which was highlighted as a strong candidate gene for porcine BFT traits. On SSC9, three adjacent significant SNPs were detected within a region of 0. 19Mb (between 87. 44Mb and 87. 63Mb). PGM2L1 was considered a candidate gene for the region. Finally, a total of 13 genes, including ZNF184, ZNF391, COL21A1, OR4P4L, OR4C13L, OR5D14, OR5D13L, OR1J4L, HMGA1, PGM2L1, FAM171A1, PLBD2 and KIAA121 associated with carcass backfat thickness, and/or carcass lean percentage, and/or carcass fat percentage were considered potential candidate genes for further study. Conclusions The results of this GWAS will greatly advance our understanding of the genetic architecture of BFT, CLP, and CFP traits. The identified SNPs and candidate genes were beneficial to pig breeding.