Genome-wide association study for loin muscle area of commercial crossbred pigs

Abstract

Objective: Loin muscle area (LMA) is an important target trait of pig breeding. This study aimed to identify single nucleotide polymorphisms (SNPs) and genes associated with LMA in the Duroc×(Landrace×Yorkshire) crossbred pigs (DLY).Methods: A genome-wide association study was performed using the Illumina 50K chip to map the genetic marker and genes associated with LMA in 511 DLY pigs (255 boars and 256 sows).Results: After quality control, we detected 35,426 SNPs, including six SNPs significantly associated with LMA in pigs, with MARC0094338 and ASGA0072817 being the two key SNPs responsible for 1.77% and 2.48% of the phenotypic variance of LMA, respectively. Based on previous research, we determined two candidate genes (growth hormone receptor [<i>GHR</i>] and 3-oxoacid Co A-transferase 1 [<i>OXCT1</i>]) that are associated with fat deposition and muscle growth and found further additional genes (<i>MYOCD</i>, <i>ARHGAP44</i>, <i>ELAC2</i>, <i>MAP2K4</i>, <i>FBXO4</i>, <i>FBLL1</i>, <i>RARS1</i>, <i>SLIT3</i>, and <i>RANK3</i>) that are presumed to have an effect on LMA.Conclusion: This study contributes to the identification of the mutation that underlies quantitative trait loci associated with LMA and to future pig breeding programs based on marker-assisted selection. Further studies are needed to elucidate the role of the identified candidate genes in the physiological processes involved in LMA regulation.