四川牦牛PPARGC1B基因SNP位点筛选及生物信息学分析

Screening and bioinformatics analysis of SNP in PPARGC1B gene of Sichuan Yak

采用PCR产物直接测序法检测四川牦牛过氧化物酶增殖激活受体γ辅激活因子-1β(peroxisome proliferator-activated receptor gamma,coactivator 1 beta,PPARGC1B)基因SNP位点,同时通过PCR扩增和测序获得四川牦牛PPARGC1B基因编码区,并对编码蛋白和mRNA二级结构进行了生物信息学预测分析。结果显示,本试验通过四川牦牛PPARGC1B基因的单核苷酸多态性检测结果,筛选出E9-189 A→C、E9-387 G→A、E9-542 C→T和E9-554 T→C共4个外显子SNP突变位点,其中E9-387 G→A和E9-554 T→C位点与四川牦牛肉品质性状中的剪切力和背膘厚具有显著相关性;对4个突变位点的生物信息学分析结果显示,PPARGC1B蛋白属于酸性、不稳定、非跨膜和非分泌型亲水蛋白,有卷曲螺旋结构,不存在信号肽和跨膜区域,主要在细胞核中发挥生物学作用,有106个磷酸化位点和1个糖基化位点,1个保守结构RRM结构,二级结构主要α-螺旋和无规则卷曲为主;PPARGC1B基因突变前后蛋白结构未发生变化,mRNA二级结构出现了显著差异。结果表明,PPARGC1B基因SNP位点可作为影响四川牦牛肉品质性状的分子标记,并应用于肉牛的标记辅助选择,同时对PPARGC1B基因相关SNP位点的生物信息学分析也为深入探讨该基因的生物学功能奠定基础。

The peroxisome proliferator-activated receptor gamma(peroxisome proliferator-activated receptor gamma,coactivator 1 beta,PPARGC1B)gene is an intranuclear receptor transcription factor responsible for regulating the expression of target genes.To comprehend the characteristics and mutations of the PPARGC1B gene within the Sichuan yak population,the SNP loci of the PPARGC1B gene were identified through direct sequencing of PCR products.Additionally,the coding region of the PPARGC1B gene was obtained via PCR amplification and sequencing.Bioinformatics analyses were conducted to predict protein-coding and mRNA secondary structure.This study identified four exon SNP mutation sites(E9-189A→C,E9-387G→A,E9-542C→T,and E9-554T→C)based on the single nucleotide polymorphism analysis of the PPARGC1B gene in Sichuan yaks.Notably,the E9-387G→A and E9-554T→C loci exhibited significant correlations with shear force and backfat thickness in Sichuan yaks.Subsequently,bioinformatics analysis of the four mutation sites revealed that the PPARGC1B protein is an acidic,unstable,non-transmembrane,and non-secretory hydrophilic protein with a coiled helix structure.It lacks a signal peptide and transmembrane region,predominantly functions in the nucleus,and features 106phosphorylation sites,one glycosylation site,and one conserved RRM structure.The secondary structure comprises mainlyα-helix and random coils.Although the protein structure of the PPARGC1Bgene remained unchanged post-mutation,there were significant differences in mRNA secondary structure.These findings suggest that the polymorphic loci of the PPARGC1Bgene in Sichuan yaks could serve as a theoretical basis for enhancing meat quality traits through molecular biological methods,presenting practical applications in breeding.