Genome-wide Association Study for Carcass Primal Cut Yields Using Single-step Bayesian Approach in Hanwoo Cattle

Abstract

The importance of meat and carcass quality is growing in beef cattle production to meet both producer and consumer demands. Primal cut yields, which reflect the body compositions of carcass, could determine the carcass grade and, consequently, command premium prices. Despite its importance, there have been few genome-wide association studies on these traits. This study aimed to identify genomic regions and putative candidate genes related to 10 primal cut traits, including tenderloin, sirloin, striploin, chuck, brisket, top round, bottom round, shank, flank, and rib in Hanwoo cattle using a single-step Bayesian regression (ssBR) approach. After genomic data quality control, 43,987 SNPs from 3,745 genotyped animals were available, of which 3,467 had phenotypic records for the analyzed traits. A total of 16 significant genomic regions (1-Mb window) were identified, of which five large-effect quantitative trait loci (QTLs) located on chromosomes 6 at 38–39 Mb, 11 at 21–22 Mb, 14 at 6–7 Mb and 26–27 Mb, and 19 at 26–27 Mb were associated with more than one trait, while the remaining 11 QTLs were trait-specific. These significant regions were harbored by 154 genes, among which TOX, FAM184B, SPP1, IBSP, PKD2, SDCBP, PIGY, LCORL, NCAPG, and ABCG2 were noteworthy. Enrichment analysis revealed biological processes and functional terms involved in growth and lipid metabolism, such as growth (GO:0040007), muscle structure development (GO:0061061), skeletal system development (GO:0001501), animal organ development (GO:0048513), lipid metabolic process (GO:0006629), response to lipid (GO:0033993), metabolic pathways (bta01100), focal adhesion (bta04510), ECM–receptor interaction (bta04512), fat digestion and absorption (bta04975), and Rap1 signaling pathway (bta04015) being the most significant for the carcass primal cut traits. Thus, identification of quantitative trait loci regions and plausible candidate genes will aid in a better understanding of the genetic and biological mechanisms regulating carcass primal cut yields.

Genetic architectures and selection signatures of body height in Chinese indigenous donkeys revealed by next‐generation sequencing

“…In a study of the functions of the homologous genes of the FAM family (KIAA1409, KIAA1440, KIAA1447, KIAA1768, and KIAA1276), it was found that the phenotype and developmental defects in gene-targeted mice were caused by functional deletion of three of these five genes (Nakayama et al, 2006). FAM184B (KIAA1276) is located downstream of LCORL/NCAPG, which was found to be with bovine organ weight (An et al, 2018), bovine carcass body weight (Naserkheil et al, 2021), and chicken growth traits (Jin et al, 2015) in previous studies. IHH is a member of the hedgehog family and is mainly related to the development of bones, especially cartilage, and regulates the differentiation of cartilage in the growth of long bones (Lanske et al, 1996).…”

Identification of Selection Signatures and Genetic Diversity in the Sheep

“…SNPs identified in this region include FAM110B, UBXN2B, LOC101116841, SDCBP, and NSMAF. It has been reported that these SNPs are associated with meat and carcass traits such as adiposity, sensory and anatomical characteristics (Lee et al 2013;Li & Kim 2015;Li et al 2017;Hay & Roberts 2018;de las Heras-Saldana et al 2020;Naserkheil et al 2020;Srikanth et al 2020;Srivastava et al 2020;Takeda et al 2020;Naserkheil et al 2021;Xu et al 2021;Fonseca et al 2022); health traits such as resistance to temperature stress, mastitis, and diseases (Kommadath et al 2014;Chen et al 2015;Minuti et al 2015;Smith et al 2019;Deng et al 2020;Li et al 2020;Naserkheil et al 2020;Brunes et al 2021;Londoño-Gil et al 2021;Ruan et al 2021;Haire et al 2022); production traits such as growth, feed intake, and feed conversion (Weng et al 2016;Seabury et al 2017); reproductive traits such as female fertility and age at calving (Fortes et al 2012;Gaddis et al 2017;Mota et al 2017;Silva et al 2020;Oliveira et al 2021;Fonseca et al 2022) and appearance traits such as coat color (Senczuk et al 2020;Chhotaray et al 2021). Genomic regions and genes identified as under selection using iHS and ROH approaches have been associated with various ecological and economic traits in studies conducted on livestock.…”

Identification of candidate genes for feed efficiency and growth traits in Wenchang chickens

“…Studies have shown that the NCAPG gene is an important candidate gene for mammalian body size growth traits in growth trait association analysis of horses, sheep and domestic donkeys and is involved in chromosome condensation and methylation [57][58][59][60]. The FAM184B gene has been found in previous studies to be associated with cattle carcass weight [61]. For the chicken growth traits in the study of Jinghai yellow chickens in China, the NCAPG, KCNIP4, LDB2 and FAM184B genes located in the 71.5-78.9 Mb region of GGA4 and near this region had important effects on the growth traits, which was consistent with this study.…”