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. Nevertheless, the genetic architecture of BFT, CLP and CFP is still elusive. Here, we performed a genome-wide association study (GWAS) based on specific-locus amplified fragment sequencing (SLAF-seq) to analyze seven fatness-related traits, including five BFTs, CLP, and CFP on 223 four-way crossbred pigs. Results A total of 227, 921 highly consistent single nucleotide polymorphisms (SNPs) evenly distributed throughout the genome were used to perform GWAS. Using the mixed linear model (MLM), a total of 20 SNP loci significantly related to these traits were identified on ten Sus scrofa chromosomes (SSC), of which 10 SNPs were located in previously reported quantitative trait loci (QTL) regions. On SSC7, two SNPs (SSC7:29,503,670 and rs1112937671) for average backfat thickness (ABFT) exceeded 1% and 10% Bonferroni genome-wide significance levels, respectively. These two SNP loci were located within an intron region of the COL21A1 gene, which was a protein-coding gene that played an important role in the porcine backfat deposition by affecting extracellular matrix (ECM) remodeling. In addition, based on the other three significant SNPs on SSC7, five candidate genes, ZNF184, ZNF391, HMGA1, GRM4 and NUDT3 were proposed to influence BFT. On SSC9, two SNPs for backfat thickness at 6–7 ribs (67RBFT) and one SNP for CLP were in the same locus region (19 kb interval). These three SNPs were located in the PGM2L1 gene, which encoded a protein that played an indispensable role in glycogen metabolism, glycolysis and gluconeogenesis as a key enzyme. Finally, one significant SNP on SSC14 for CLP was located within the PLBD2 gene, which participated in the lipid catabolic process. Conclusions A total of two regions on SSC7 and SSC9 and eight potential candidate genes were found for fatness-related traits in pigs. The results of this GWAS based on SLAF-seq will greatly advance our understanding of the genetic architecture of BFT, CLP, and CFP traits. These identified SNP loci and candidate genes might serve as a biological basis for improving the important fatness-related traits of pigs.

Identification of New Genes and Genetic Variant Loci Associated with Breast Muscle Development in the Mini-Cobb F2 Chicken Population Using a Genome-Wide Association Study

“…The Pearson’s correlation coefficient is able to assess the linearity of the relationship between continuous variables, while the Spearman’s correlation coefficient evaluates their monotonic relationship [ 32 ]. In most studies, the Pearson’s correlation coefficient is usually used to describe the correlation between traits [ 28 , 33 ], but in this study, the relationship between these traits, such as breast muscle weight and breast depth ( Figure 1 ), did not show complete linearity. Although they showed the same trend, they did not have a stable rate of change, which is more consistent with monotony.…”

“…Genes located within 100 kb upstream and downstream of the significant SNPs were selected as candidates based on the methods in reference [ 28 ]. GO annotation of candidate genes was then performed using the Gene Ontology Consortium ( , updated on 28 October 2022).…”

Genome-Wide Association Study of Growth Traits in a Four-Way Crossbred Pig Population

“…Abundant novel mutation sites were also effectively detected using SLAF-seq for pig genotyping [ 32 , 33 ]. Furthermore, we also found two regions on SSC7 and SSC9 and eight potential candidate genes related to porcine fatness-related traits using GWAS based on SLAF-seq in our previous research [ 34 ].…”

“…A four-way crossbred pig population was established as described previously [ 34 ]. In short, 7 hybrid boars (Duroc × Saba, DS) and 37 hybrid sows (Yorkshire × (Landrace × Saba), YLS) mated to produce a total of 223 four-way crossbred individuals.…”

“…Molecular markers throughout the entire genome were generated as described previously [ 34 ]. In short, a total of 223 intercross pigs were sequenced using SLAF-seq technology [ 18 ].…”