基于全基因组重测序的藏猪脂质沉积相关基因鉴定

Identification of lipid deposition related genes in Tibetan pigs based on whole genome re-sequencing

  • 摘要: 【目的】从全基因组水平解析藏猪与大白猪间的遗传差异,并鉴定出与藏猪脂质沉积相关的基因,为藏猪优质肉质特征的利用及新品种培育提供理论参考。【方法】选用5份自测云南迪庆藏猪的全基因组重测序数据,以及NCBI数据库中来自西藏、四川、甘肃地区34份藏猪和具有低脂肪沉积特征的14份大白猪全基因组重测序数据,获得全基因组SNP后以VCFtools进行选择信号检测,采用VCFtools分别计算候选SNP在藏猪和大白猪中的等位基因频率,再利用自编Python脚本及所有SNP注释文件进行注释以确定候选基因,最后运用DAVID对候选基因进行GO功能注释和KEGG信号通路富集分析,进一步鉴定与脂质沉积相关的功能基因。【结果】经全基因组重测序及与参考基因组比对、过滤后得到19374832个高质量的SNPs,根据受选择区域条件筛选出370778个候选SNPs,其中符合在藏猪中等位基因频率>0.5而在大白猪中等位基因频率<0.5条件的SNPs有152877个,共注释到1486个候选基因。GO功能注释分析结果显示,1486个候选基因注释到17个GO功能簇(Cluster1~Cluster17),其中Cluster11和Cluster12与脂肪生成相关,涉及与脂滴转运、结合过程相关的基因NME4、C4BPA、AP2M1、CD36、FABP5、PMP2、PDZD8、OSBPL6、APODOSBPL1A,与脂肪酸合成、延伸和代谢过程相关的基因TECR、ELOVL7、HACD2,以及与脂肪形成相关的细胞外基质基因(CCN3、EGFL6、KAZALD1、ASPN、ADAMTS18、ECM2、COL18A1、COL3A1COL4A5);通过文献分析还发现8个基因(APOOL、PLAG1、PLAUR、SUCLG2、CPE、AKR1B1、SLC4A4CHPT1)在藏猪与大白猪皮下脂肪或肌肉组织呈差异表达,且与脂肪形成相关。【结论】藏猪与大白猪间的脂肪沉积差异涉及脂肪形成的多个过程和多个基因,细胞外基质基因也可能与藏猪脂肪形成相关,且这些基因在藏猪中均具有较高的等位基因频率。

     

    Abstract: 【Objective】Exploring the genetic differences between Tibetan pigs(TIB)and Large white pigs(LW)at the whole-genome level,and identifying genes related to lipid deposition in TIB,to provide informative insights into the genetic utilization of its high meat quality traits.【Method】Whole genome re-sequencing data of 5 Yunnan Diqing TIB and whole-genome re-sequencing data of 34 TIB from Tibet,Sichuan and Gansu,and 14 LW with low fat characteristics in NCBI database were selected,which were totally 53 whole genome re-sequencing data for followed analysis.Whole genome SNPs were obtained and selection sweep analysis was performed using VCFtools. Allele frequencies for candidate SNPs in TIB and LW populations were calculated using VCFtools,and candidate SNPs were annotated using in house Pythonscript and all annotation files. Then,DAVID was used for GO functional annotation and KEGG pathway enrichment analysis to further identify genes related to lipid deposition.【Result】 By mapping whole genome sequence to reference genome,19374832 high quality SNPs were obtained. The selection region contained 370778 candidate SNPs,among which 152877 SNPs met the condition of allele frequency>0.5 in TIB and <0.5 in LW and were annotated into 1486 genes. The GO analysis showed that 1486 candidate genes were enriched into 17 GO functional clusters(Cluster 1-Cluster 17), among which Cluster 11 and Cluster 12 were related to lipid synthesis. The two clusters included genes involved in lipid droplet transport,binding processes(NME4,C4BPA,AP2M1,CD36,FABP5,PMP2,PDZD8,OSBPL6, APOD and OSBPL1A),fatty acid synthesis,elongation,and metabolism(TECR,ELOVL7,and HACD2),as well as extracellular matrix genes (CCN3,EGFL6,KAZALD1,ASPN,ADAMTS18,ECM2,COL18A1,COL3A1 and COL4A5). In addition, by surveying literature,eight genes(APOOL,PLAG1,PLAUR,SUCLG2,CPE,AKR1B1, SLC4A4 and CHPT1)were found to have differential expression in subcutaneous adipose tissue or muscle tissue between TIB and LW,and related to lipid formation.【Conclusion】This study reveals that the difference in lipid deposition between TIB and LW involves multiple processes and genes related to lipid formation,extracellular matrix genes might also involved in fat depostition of TIB, and these genes have a relatively high allele frequencies in TIB.

     

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