利用高密度SNP对猪血糖和糖基化血清蛋白性状的全基因组关联分析

doi:10.3864/j.issn.0578-1752.2014.18.018

摘要/Abstract

摘要： 【目的】测定苏太猪和白色杜洛克×二花脸F₂资源家系240 d血糖（glucose，GLU）和糖基化血清蛋白（glycosylated serum proteins，GSP）浓度，采用全基因组关联分析定位影响GLU和GSP的染色体位点，为最终鉴别影响该性状的因果基因奠定基础，同时为人类低血糖症和糖尿病的遗传学研究提供参考。【方法】分别将435头苏太猪和760头白色杜洛克×二花脸F2资源家系F₂个体在相同条件下饲养至240日龄进行统一屠宰，收集血液后分离血清，利用全自动生化分析仪测定GLU和GSP浓度。采集猪只耳组织提取DNA并测定DNA浓度。将质检合格的DNA样品利用Illumina porcine 60K SNP芯片判定基因型。运用PLINK软件对SNP判型结果进行质控，将合格的SNP标记用于后续的关联性分析，利用广义混合线性模型及R语言GenABEL软件包进行全基因组关联分析，定位影响苏太猪和白色杜洛克×二花脸F₂资源家系240 d血清GLU和GSP含量的染色体位点。根据全基因组关联分析结果从Ensembl或NCBI网站上分析可能的位置候选基因。【结果】全基因组关联分析共检测到5个与血清GLU和GSP达染色体显著水平相关的SNP位点。其中白色杜洛克×二花脸F₂资源群体在10号染色体（SSC10）24.67Mb处定位到与血清GSP含量显著相关的SNP（ALGA0057739，P=1.58×10^-5），解释表型变异为3.72%。苏太猪群体共检测到2个与血清GSP显著相关的SNP（ALGA0108699和DRGA0017552，P=1.45×10^-5），解释表型变异均为3.72%。使用猪参考基因组序列（10.2版本），无法定位到具体的染色体位置。通过人、猪比较基因组分析，这两个SNP都位于SSC8，距STPG2基因3’端约180.0—193.0 kb。将两个群体进行Meta分析，未发现新的与GSP显著相关的SNP；在1号染色体250.32Mb处（DRGA0002016，P=2.48×10^-5）和14号染色体43.97Mb处（ASGA0062984，P=1.29×10^-5），定位到与血清GLU显著相关的SNP。通过搜寻显著相关SNP所在染色体区域内的注释基因，发现ASPM、TRPM3和KCTD10 等基因是影响血清GSP和GLU的重要候选基因。【结论】检测到5个显著影响猪血清GLU和GSP的SNP位点。这些SNP位点所处染色体区域内的ASPM、TRPM3、STPG2和KCTD10基因是影响血清GSP和GLU的重要候选基因。

关键词: 猪, 血糖, 糖基化血清蛋白, 全基因组关联分析

Abstract: 【Objective】 Serum glucose (GLU) and glycosylated serum protein (GSP) contents in a Sutai population and a large-scale White Duroc×Erhualian F₂intercross 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

曾治君，刘晨龙，杨慧，杨斌，杨竹青，陈从英. 利用高密度SNP对猪血糖和糖基化血清蛋白性状的全基因组关联分析[J]. 中国农业科学, 2014, 47(18): 3700-3707.

ZENG Zhi-jun, LIU Chen-long, YANG Hui, YANG Bin, YANG Zhu-qing, CHEN Cong-ying. Genome-Wide Association Study on Porcine Serum Glucose (GLU) and Glycosylated Serum Proteins (GSP) with High Density SNP Markers[J]. Scientia Agricultura Sinica, 2014, 47(18): 3700-3707.

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