Scientia Agricultura Sinica ›› 2014, Vol. 47 ›› Issue (18): 3700-3707.doi: 10.3864/j.issn.0578-1752.2014.18.018

• ANIMAL SCIENCE·VETERINARY SCIENCERE·SOURCE INSECT • Previous Articles     Next Articles

Genome-Wide Association Study on Porcine Serum Glucose (GLU) and Glycosylated Serum Proteins (GSP) with High Density SNP Markers

ZENG Zhi-jun, LIU Chen-long, YANG Hui, YANG Bin, YANG Zhu-qing, CHEN Cong-ying   

  1. Candidate of National Key Laboratory for Animal Biotechnology, Jiangxi Agricultural University, Nanchang 330045
  • Received:2013-10-10 Revised:2014-06-23 Online:2014-09-16 Published:2014-09-16

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Abstract: 【Objective】 Serum glucose (GLU) and glycosylated serum protein (GSP) contents in a Sutai population and a large-scale White Duroc×Erhualian F2 intercross at the age of 240 days were measured. A genome-wide association study was carried out to identify the SNPs or chromosomal regions associated with GLU and GSP. The aim of the study is to establish a foundation for identification of causative genes influencing the serum GLU and GSP, and provide the clues for genetic analysis of human hypoglycemia and diabetes.【Method】 The experimental pigs used in this study included 435 Sutai pigs that were bought from Sutai Pig Breeding Center in Suzhou city and 760 F2 individuals from White Duroc × Erhualian intercross that was constructed by Key Laboratory for Animal Biotechnology of Jiangxi Agricultural University. All experimental pigs were fed under the same farm conditions and slaughtered at the age of 240 days at Guohong abattoir. The collected blood samples were kept at room temperature for 5 hours, then centrifuged at 4℃, 3 000 r/min for 20 min. The serum GLU and GSP were determined with commercial kits. Genomic DNA was extracted from ear tissues using a standard phenol/chloroform method, the concentration and quality were determined by NANODROP 1000 analyzer. All DNA samples were diluted to 20ng•μL-1, and then stored at -20℃ until used. All experimental animals were genotyped with Illumina porcine 60K SNP chip. Quality control of genotyping results was carried out using PLINK software. The genome-wide association studies were performed with the mixed linear model with the SNPs passed the quality control by using GenABEL software in the R packages to identify the significant SNPs associated with GLU and GSP at 240 days in the Sutai and White Duroc × Erhualian F2 intercross. The possible candidate genes were chosen for each of significant region according to gene annotations in Ensembl or NCBI websites. 【Result】A total of 5 SNPs that significantly associated with GLU and GSP were identified. In the White Duroc × Erhualian F2 resource population, one SNP (ALGA0057739, P=1.58×10-5) was identified that significantly associated with GSP at chromosome 10: 24.67Mb, which explained 3.72% of phenotypic variance, but any SNPs that significantly associated with GLU in this population were not detected. In the Sutai population, two SNPs (ALGA0108699 and DRGA0017552, P=1.45×10-5) that significantly associated with serum GSP were identified and explained 3.72% of phenotypic variance, but these two SNPs could not be mapped to pig reference genome by using Sus scrofa 10.2 reference genome assembly. Through comparative genome analysis of human and pig, it was found that these two SNPs locate on SSC8 and map to the 180.0-193.0kb downstream of STPG2 gene 3’ end. Any SNPs that significantly associated with GLU in Sutai pigs were not identified. No significantly associated SNPs were identified for GSP in the Meta analysis. But the authors found two SNPs at SSC1: 250.32Mb (DRGA0002016, P=2.48×10-5) and SSC14: 43.97Mb (ASGA0062984, P=1.29×10-5), respectively, that were significantly associated with GLU. The candidate genes around the top SNPs and its functional annotations were searched, and it was found that ASPM, TRPM3 and KCTD10 were the important candidate genes for GLU and GSP. 【Conclusion】A total of 5 SNP regions that significantly associated with serum GLU and GSP were identified. ASPM, TRPM3, STPG2 and KCTD10 are the important candidate genes influencing GLU and GSP.

Key words: pig, serum glucose, glycosylated serum proteins, genome-wide association study

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