Genome-Wide Association Study and Identification of Candidate Genes for Intramuscular Fat Fatty Acid Composition in Ningxiang Pigs

SIMPLE SUMMARY: In this study, we conducted a comprehensive investigation of the fatty acid composition in Ningxiang pigs using a genome-wide association study. Our findings revealed a combination of previously reported and novel candidate genes associated with saturated fatty acids (SFAs), monounsaturated fatty acids (MUFAs), and polyunsaturated fatty acids (PUFAs). Notably, we identified significant single-nucleotide polymorphisms (SNPs) that are closely linked to specific fatty acids, and some of these genes explained substantial phenotypic variance. These noteworthy discoveries have the potential to significantly improve meat quality and fat deposition in Ningxiang pigs through targeted breeding approaches. Our research provides valuable insights into the intricate composition of fatty acids, thus offering practical implications for elevating meat quality and ultimately benefiting both the pig industry and consumers. The significance of this study is underscored by its potential to drive positive changes in society by promoting healthier and superior-quality pork products. ABSTRACT: Ningxiang pigs exhibit a diverse array of fatty acids, making them an intriguing model for exploring the genetic underpinnings of fatty acid metabolism. We conducted a genome-wide association study using a dataset comprising 50,697 single-nucleotide polymorphisms (SNPs) and samples from over 600 Ningxiang pigs. Our investigation yielded novel candidate genes linked to five saturated fatty acids (SFAs), four monounsaturated fatty acids (MUFAs), and five polyunsaturated fatty acids (PUFAs). Significant associations with SFAs, MUFAs, and PUFAs were found for 37, 21, and 16 SNPs, respectively. Notably, some SNPs have significant PVE, such as ALGA0047587, which can explain 89.85% variation in Arachidic acid (C20:0); H3GA0046208 and DRGA0016063 can explain a total of 76.76% variation in Elaidic Acid (C18:1n-9(t)), and the significant SNP ALGA0031262 of Arachidonic acid (C20:4n-6) can explain 31.76% of the variation. Several significant SNPs were positioned proximally to previously reported genes. In total, we identified 11 candidate genes (hnRNPU, CEPT1, ATP1B1, DPT, DKK1, PRKG1, EXT2, MEF2C, IL17RA, ITGA1 and ALOX5), six candidate genes (ALOX5AP, MEDAG, ISL1, RXRB, CRY1, and CDKAL1), and five candidate genes (NDUFA4L2, SLC16A7, OTUB1, EIF4E and ROBO2) associated with SFAs, MUFAs, and PUFAs, respectively. These findings hold great promise for advancing breeding strategies aimed at optimizing meat quality and enhancing lipid metabolism within the intramuscular fat (IMF) of Ningxiang pigs.