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Asian-Australas J Anim Sci > Accepted Articles
DOI: https://doi.org/10.5713/ajas.18.0483    [Accepted] Published online October 26, 2018.
Genome-wide association study for intramuscular fat content in Chinese Lulai black pigs
Yanping Wang1, Chao Ning2, Cheng Wang1, Jianfeng Guo1, Jiying Wang1,*, Ying Wu1,*
1Institute of Animal Husbandry and Veterinarian of Shandong Agricultural Academy, Jinan, China
2College of Animal Science and Technology, China Agricultural University, Beijing, China
Correspondence:  Jiying Wang, Tel: +86-15510028332, Fax: +86-0531-88618978, Email: jnwangjiying@163.com
Ying Wu,Email: wusaas@163.com
Received: 27 June 2018   • Revised: 16 September 2018   • Accepted: 16 October 2018
Objective: Intramuscular fat (IMF) content plays an important role in meat quality. Identification of SNPs and genes related to pig IMF, especially using pig populations with high IMF content variation, can help to establish novel molecular breeding tools for optimizing IMF in pork and unveil the mechanisms that underlie fat metabolism.


We collected muscle samples of 453 Chinese Lulai black pigs, measured IMF content by Soxhlet petroleum-ether extraction method, and genotyped genome-wide SNPs using GeneSeek Genomic Profiler Porcine HD BeadChip. Then a genome-wide association study was performed using a linear mixed model implemented in the GEMMA software.


A total of 43 SNPs were identified to be significantly associated with IMF content by the cutoff P < 0.001. Among these significant SNPs, the greatest number of SNPs (n=19) were detected on Chr.9, and two LD blocks were formed among them. Additionally, 17 significant SNPs are mapped to previously reported QTLs of IMF and confirmed previous QTLs studies. Forty-two annotated genes centering these significant SNPs were obtained from Ensembl database. Overrepresentation test of pathways and GO terms revealed some enriched reactome pathways and GO terms, which mainly involved regulation of basic material transport, energy metabolic process and signaling pathway.
These findings improve our understanding of the genetic architecture of IMF content in pork and facilitate the follow-up study of fine-mapping genes that influence fat deposition in muscle.
Keywords: Genome-wide Association Study; Intramuscular Fat Content; Single Nucleotide Polymorphisms; Pigs

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