Genome-Wide Association Studies Associated with Backfat Thickness in Landrace and Yorkshire Pigs

Abstract

Although pork quality traits are important commercially, genome-wide association studies (GWASs) have not well considered Landrace and Yorkshire pigs worldwide. Landrace and Yorkshire pigs are important pork-providing breeds. Although quantitative trait loci of pigs are well-developed, significant genes in GWASs of pigs in Korea must be studied. Through a GWAS using the PLINK program, study of the significant genes in Korean pigs was performed. We conducted a GWAS and surveyed the gene ontology (GO) terms associated with the backfat thickness (BF) trait of these pigs. We included the breed information (Yorkshire and Landrace pigs) as a covariate. The significant genes after false discovery rate (<0.01) correction were AFG1L, SCAI, RIMS1, and SPDEF. The major GO terms for the top 5% of genes were related to neuronal genes, cell morphogenesis and actin cytoskeleton organization. The neuronal genes were previously reported as being associated with backfat thickness. However, the genes in our results were novel, and they included ZNF280D, BAIAP2, LRTM2, GABRA5, PCDH15, HERC1, DTNBP1, SLIT2, TRAPPC9, NGFR, APBB2, RBPJ, and ABL2. These novel genes might have roles in important cellular and physiological functions related to BF accumulation. The genes related to cell morphogenesis were NOX4, MKLN1, ZNF280D, BAIAP2, DNAAF1, LRTM2, PCDH15, NGFR, RBPJ, MYH9, APBB2, DTNBP1, TRIM62, and SLIT2. The genes that belonged to actin cytoskeleton organization were MKLN1, BAIAP2, PCDH15, BCAS3, MYH9, DTNBP1, ABL2, ADD2, and SLIT2.

Selection Signatures Analysis Reveals Genes Associated with High-Altitude Adaptation in Tibetan Goats from Nagqu, Tibet

“…PROP1 (PROP paired-like homeobox 1) ( di value = 15.53), another strongly selected gene, proved to be associated with growth traits of goat and sheep [ 49 , 50 ]. In addition, MKLN1 (muskelin 1) ( di value = 12.37) was associated with backfat thickness in Pigs [ 51 ] and CRH (corticotropin releasing hormone) ( di value = 10.54) proved to be a candidate gene for body conformation traits in cows [ 52 ]. These findings have contributed to understanding the trace of domestication in Tibetan goats.…”

Use of gene expression and whole-genome sequence information to improve the accuracy of genomic prediction for carcass traits in Hanwoo cattle

“…The EPS15L1 gene is an essential component of the endocytic pathway [46]. The SPDEF gene is known to be associated with BFT in pigs [47]. The HEPACAM2 gene was previously identified in a QTL region for mid-test metabolic weight (MMWT) in SimAngus on BTA4 [48].…”

Conservation Genomic Analysis of the Croatian Indigenous Black Slavonian and Turopolje Pig Breeds

“…Most likely polymorphisms in these genes are the consequence of breed adaptation to environmental and human demands. For Black Slavonian pig, we identified important genes associated with steroid receptor activity, such as CYP-40 on porcine chromosome SSC8 (Ratajczak et al, 2015); meat-to-fat ratio in pigs, DEAF1 on SSC2 (Falker-Gieske et al, 2019); growth traits in cattle, KSR2 on SSC14 (Puig-Oliveras et al, 2014); animal organ and system development in pigs, SEZ6L on SSC14 (Kwon et al, 2019); hematological parameters in pigs, RHOBTB1 on SSC 14 (Bovo et al, 2019); female reproduction in mice, CDK1 on SSC 14 (Adhikari et al, 2016); salivary secretion in pigs, KCNMA1 on SSC14 (Li et al, 2013); milk fat percentage in buffaloes, KCTD8 on SSC8 (de Camargo et al, 2015); back fat thickness in pigs, RIMS4 on SSC17 (Lee and Shin, 2018); carcass length in pigs, SPTLC2 on SSC7 (Falker-Gieske et al, 2019); muscle fiber types in pigs, MYO18B on SSC14 (Ropka-Molik et al, 2018); and fatty acid profiles in cattle, RAPGEF2 on SSC8 (Cesar et al, 2014).…”