ArticleBMC genomics2022
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.
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 31 citations in OpenAlex.
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- Genes and Gene Functions Associated with Morphological, Productive, Reproductive, and Carcass Quality Traits in Pigs: A Functional Bioinformatics Approach.Current issues in molecular biology · 2026Article
- Comprehensive co-expression analysis reveals candidate regulatory genes associated with carcass and meat quality traits in Neijiang and Large White pigs.Animal bioscience · 2025Article
- Genomic Insights into the Successful Invasion of the Avian Vampire Fly (Philornis downsi ) in the Galápagos Islands.Molecular biology and evolution · 2025Article
- Genome-wide identification of quantitative trait loci and candidate genes for seven carcass traits in a four-way intercross porcine population.BMC genomics · 2024Article
- Identification of molecular markers and candidate regions associated with grain number per spike in Pubing3228 using SLAF-BSA.Frontiers in plant science · 2024Article
- A genome-wide association study identified candidate regions and genes for commercial traits in a Landrace population.Frontiers in genetics · 2024Article
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- Genome-Wide Association Analysis Identifies Genomic Regions and Candidate Genes for Growth and Fatness Traits in Diannan Small-Ear (DSE) Pigs.Animals : an open access journal from MDPI · 2023Article
- Comparison of differentially expressed genes in longissimus dorsi muscle of Diannan small ears, Wujin and landrace pigs using RNA-seq.Frontiers in veterinary science · 2023Article
- Genome-wide association study reveals genetic loci and candidate genes for meat quality traits in a four-way crossbred pig population.Frontiers in genetics · 2023Article
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundCarcass 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.
resultsA 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.
conclusionsA 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.
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