Single nucleotide polymorphisms, haplotypes and combined genotypes of LAP3 gene in bovine and their association with milk production traits

Zheng, Xue Bin; Ju, Zhihua; Wang, Ji; Li, Qiuling; Huang, Jinming; Zhang, Aiwu; Zhong, Jun; Wang, Changfa

doi:10.1007/s11033-010-0524-1

Cited by 59 publications

(64 citation statements)

References 21 publications

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“…Olsen et al (2005) mapped a QTL to a 420-kb region in bovine chromosome 6 containing six milk production candidate genes including the PEPS gene. Zheng et al (2011) studied the five SNPs in the introns 12 and exon 13 of the PEPS gene, and SNP g.25415 T > C was found to be significantly associated with protein percentage. In the current study, two novel SNPs in the promoter region of the bovine PEPS gene were genotyped, and their combined haplotypes were associated with milk quality traits.…”

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Functional Characterization of Genetic Polymorphisms Identified in the Promoter Region of the BovinePEPSGene

Zheng

Huang

et al. 2012

DNA and Cell Biology

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Peptidase S (PEPS) is a metallopeptidase that cleaves N-terminal residues from proteins and peptides. PEPS is used as a cell maintenance enzyme with critical roles in peptide turnover. The promoter region located upstream of the initiation site plays an important role in regulating gene expression. Polymorphism in the promoter region can alter gene expression and lead to biological changes. In the current study, polymorphisms in the promoter region of the PEPS gene were investigated. Polymerase chain reaction (PCR)-restriction fragment length polymorphism and DNA sequencing methods were used to screen sequence variations in the promoter region of DNA samples from 743 Chinese Holstein cattle. Two polymorphisms (g. -534 T > C and g. -2545 G > A) were identified and eight haplotypes were classified by haplotype analysis. The two genetic polymorphisms and haplotypes were associated with fat percentage and somatic cell score in Chinese Holstein cattle. The results of real-time PCR showed that cow kidneys exhibit the highest PEPS expression level. Moreover, bioinformatics analysis predicted that the single-nucleotide polymorphism g. -534 T > C is located in the core promoter region and in the transcription factor binding sites. The promoter activities of the polymorphism of -543 T > C were measured by luciferase assay in the human kidney epithelial cell line 293T. Transcriptional activity is significantly lower in cell lines transfected with the reporter construct containing 2.5 kb upstream fragments with -543 C than in those with wild-type -543 T. The results indicated that genetic variation at locus -543 influences PEPS promoter activity. The genetic variation in the promoter region of PEPS gene may regulate PEPS gene transcription and might have consequences at a regulatory level.

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Functional Characterization of Genetic Polymorphisms Identified in the Promoter Region of the BovinePEPSGene

Zheng

Huang

et al. 2012

DNA and Cell Biology

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“…On BTA6, the LAP3 gene was found associated with PP. Recently this locus was related to milk production by Zheng et al (2011). A significant marker, the BTA-92644-no-rs was located on BTA20 at 38.9 Mb, close to the prolactin receptor (PRLR) gene was found.…”

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Maximum difference analysis: a new empirical method for genome-wide association studies

Cellesi

Dimauro

Sorbolini

et al. 2016

Italian Journal of Animal Science

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The availability of high-density single nucleotide polymorphism (SNPs) panels for humans and, recently, for several livestock species has given a great impulse to genome-wide association studies towards the identification of genes associated with complex traits and diseases. The frequentist and the Bayesian approach are commonly used to investigate marker associations with traits of interest. Briefly, the former is the most widely used method, being intuitive and easily to apply, whereas the latter requires deeper statistical knowledge, but has the advantage to include prior information to obtain a posterior probability of association. Both methods, however, require parameters or distributions to be set a priori by the researcher. In this work, we suggest a new empirical method for genome-wide studies (GWAS), which verifies marker-trait associations using the bootstrap resampling and Chebyshev's inequality. This method, called Maximum Difference Analysis (MDA), was tested on a real dataset of 2093 Italian Holstein bulls with the objective of finding associations between SNPs and milk, fat and protein yield and fat and protein percentage. Results of the MDA method were compared with those obtained to a genome-wide association analysis performed using the R package GenABEL. In addition, we assessed the bovine annotated genes related to the traits under study. The MDA method was able to locate known important loci for milk productive traits, such as the DGAT1, PRLR, GHR and SCD. Moreover, some new putative candidate genes were detected. The python script of MDA procedure is available at www.animalbreeding.uniss.it. ARTICLE HISTORY

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“…As for g.2264T>C SNP in intron 2, the TT genotype had a higher spine BMD, femoral neck hip BMD, and total hip BMD than genotypes TC and CC, almost reaching a significant level (Table 4, P = 0.053, P = 0.061, and P = 0.072, respectively). Although introns are not coding sequences, there is constant evidence to prove that introns play an important role in regulating mRNA splicing, transcription, and gene expression and regulation (Nott et al, 2003;Zheng et al, 2011;Yuan et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

Association between single nucleotide polymorphisms of the osteoprotegerin gene and postmenopausal osteoporosis in Chinese women

Song¹,

Jing²,

Hu³

et al. 2013

Genet. Mol. Res.

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ABSTRACT.Osteoporosis is an important and common complex health problem, particularly in postmenopausal women. It is characterized by a reduction in bone mineral density (BMD) and a deterioration of bone microarchitecture with a consequent increase of fracture risk. The osteoprotegerin (OPG) gene is considered to play an important role in the pathogenesis of osteoporosis. We analyzed SNPs of the OPG gene and associations between these polymorphisms and BMD in 399 Chinese postmenopausal women. BMD was quantified at the lumbar spine (L 2-4 ), femoral neck, and total hip. The g.2264T>C and g.27676A>C SNPs were detected by PCR-RFLP and DNA sequencing methods. A significant association with spine BMD was found for g.27676A>C. The spine BMD value for subjects with genotype AA was significantly higher than those with genotypes GA and AA. No significant association was detected between any of the SNP marker genotypes and the other traits. We conclude that g.27676A>C in the OPG gene affects spine BMD and that the C allele is associated with increased risk for osteoporosis in Chinese postmenopausal women.

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Single nucleotide polymorphisms, haplotypes and combined genotypes of LAP3 gene in bovine and their association with milk production traits

Cited by 59 publications

References 21 publications

Functional Characterization of Genetic Polymorphisms Identified in the Promoter Region of the BovinePEPSGene

Functional Characterization of Genetic Polymorphisms Identified in the Promoter Region of the BovinePEPSGene

Maximum difference analysis: a new empirical method for genome-wide association studies

Association between single nucleotide polymorphisms of the osteoprotegerin gene and postmenopausal osteoporosis in Chinese women

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