Screening and bioinformatics analysis of SNP in PPARGC1B gene of Sichuan Yak
10.16303/j.cnki.1005-4545.2024.10.14
- VernacularTitle:四川牦牛PPARGC1B基因SNP位点筛选及生物信息学分析
- Author:
Xuanxu CHEN
1
;
Xinyi JIANG
;
Jinghao PENG
;
Jing LI
;
Fengshuai MIAO
;
Zhihui ZHAO
;
Haibin YU
;
Weizhong LAI
;
Ping JIANG
;
Ziwei LIN
Author Information
1. 广东海洋大学滨海农业学院粤西地区畜禽遗传资源与种质创新重点实验室,广东湛江 524088
- Keywords:
Sichuan yak;
PPARGC1B gene;
SNP;
bioinformatics analysis
- From:
Chinese Journal of Veterinary Science
2024;44(10):2179-2189
- CountryChina
- Language:Chinese
-
Abstract:
The peroxisome proliferator-activated receptor gamma(peroxisome proliferator-activated receptor gamma,coactivator 1 beta,PPARGC1B)gene is an intranuclear receptor transcription fac-tor 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 cod-ing region of the PPARGC1B gene was obtained via PCR amplification and sequencing.Bioinforma-tics 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 106 phosphorylation sites,one glycosylation site,and one conserved RRM structure.The secondary structure comprises mainly α-helix and random coils.Although the protein structure of the PPARGC1B gene remained unchanged post-mutation,there were significant differences in mRNA secondary structure.These findings suggest that the polymorphic loci of the PPARGC1B gene in Sichuan yaks could serve as a theoretical basis for enhancing meat quality traits through molecular biological methods,presen-ting practical applications in breeding.
