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

Qinghua Zeng; Hu Gao; Shishu Yin; Yinglin Peng; Fang Yang; Yawei Fu; Xiaoxiao Deng; Yue Chen; Xiaohong Hou; Qian Wang; Zhao Jin; Gang Song; Jun He; Yulong Yin; Kang Xu

doi:10.3390/ani13203192

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

Animals (Basel). 2023 Oct 13;13(20):3192. doi: 10.3390/ani13203192.

Authors

Qinghua Zeng¹, Hu Gao^{1

2}, Shishu Yin¹, Yinglin Peng³, Fang Yang¹, Yawei Fu^{1

2}, Xiaoxiao Deng², Yue Chen², Xiaohong Hou², Qian Wang^{1

2}, Zhao Jin^{1

2}, Gang Song^{1

2}, Jun He¹, Yulong Yin^{1

2

4}, Kang Xu^{2

4}

Affiliations

¹ Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China.
² Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.
³ Hunan Institute of Animal & Veterinary Science, Changsha 410131, China.
⁴ Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.

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.

Keywords: GWAS; longissimus dorsi; monounsaturated fatty acids; polyunsaturated fatty acids; saturated fatty acids.

Grants and funding

This research was funded by the Laboratory of Lingnan Modern Agriculture Project (NT2021005), the Strategic Priority Research Program of Chinese Academy of Sciences (Grant No. XDA24030204), the Special Funds for the Construction of Innovative Provinces in Hunan (Grant numbers 2021NK1009 and 2021NK1012); the Natural Science Foundation of Hunan Province Project (2023JJ20043 and 2020JJ5635).