title: Expression, SNV identification, linkage disequilibrium, and combined genotype association analysis of the muscle-specific gene CSRP3 in Chinese cattle.
abstract: The cysteine and glycine-rich protein 3 (CSRP3) plays an important role in the myofiber differentiation. Here, we identified five SNVs in all exon and intron regions of the CSRP3 gene using DNA sequencing, PCR-RFLP and forced-PCR-RFLP methods in 554 cattle. Four of the five SNVs were significantly associated with growth performance and carcass traits of the cattle. In addition, we evaluated haplotype frequency and linkage disequilibrium coefficient of five sequence variants. The result of haplotype analysis demonstrated 28 haplotypes present in Qinchuan and two haplotypes in Chinese Holstein. Only haplotypes 1 and 8 were being shared by two populations, haplotype 14 had the highest haplotype frequency in Qinchuan (17.4%) and haplotype 8 had the highest haplotype frequency in Chinese Holstein (94.4%). Statistical analyses of combined genotypes indicated that some combined genotypes were significantly or highly significantly associated with growth and carcass traits in the Qinchuan cattle population. qPCR analyses also showed that bovine CSRP3 gene was exclusively expressed in longissimus dorsi muscle and heart tissues. The data support the high potential of the CSRP3 as a marker gene for the improvement of growth performance and carcass traits in selection programs.
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China.
authors.forename: Hua
authors.initials: H
authors.lastname: He
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China.
authors.forename: Hui-Lin
authors.initials: HL
authors.lastname: Zhang
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China.
authors.forename: Zhi-Xiong
authors.initials: ZX
authors.lastname: Li
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Liu
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China. Electronic address: liuxiaolin@nwsuaf.edu.cn.
authors.forename: Xiao-Lin
authors.initials: XL
authors.lastname: Liu
mesh_terms: D000818:Animals; D001483:Base Sequence; D002417:Cattle / Q000235:genetics*; D002681:China; D017931:DNA Primers; D005091:Exons; D005838:Genotype; D006239:Haplotypes; D007438:Introns; D060588:LIM Domain Proteins / Q000235:genetics*; D015810:Linkage Disequilibrium; D009124:Muscle Proteins / Q000235:genetics*; D009132:Muscles / Q000378:metabolism*; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide
chemical_list: D017931:DNA Primers; D060588:LIM Domain Proteins; D009124:Muscle Proteins; C090114:cysteine and glycine-rich protein 3
keywords: Association analysis; CH; CSRP3; CSRP3 gene; Cattle; Chi-squared test; Chinese Holstein; Combined genotypes; GLI3; GLM; Gene expression; HWE; Hardy–Weinberg equilibrium; He; Ho; IGF2; LD; LSD; MRF4; MTDEREML; MyoD; NCBI; NPM1; National Centre for Biotechnology Information; Ne; PCR; PCR-RFLP; PIC; QC; Qinchuan; SNVs; Single nucleotide variants; bHLH; cysteine and glycine-rich protein 3; effective allele numbers; forced polymerase chain reaction-restriction fragment length polymorphism; forced-PCR-RFLP; gene heterozygosity; gene homozygosity; glioma-associated oncogene family zinc finger 3; helix-loop-helix; insulin-like growth factor 2; linkage disequilibrium; muscle regulatory factor 4; nucleophosmin 1; polymerase chain reaction; polymerase chain reaction-restriction fragment length polymorphism; polymorphism information content; qPCR; quantitative real-time PCR; single nucleotide variants; the bHLH transcription factor; the general linear models; the least significant difference; the multiple trait derivative-free restricted maximum likelihood; χ(2)