Two Mutations in the Caprine MTHFR 3'UTR Regulated by MicroRNAs Are Associated with Milk Production Traits

Abstract

Background5,10-Methylenetetrahydrofolate reductase (MTHFR) plays a central role in folate metabolism by irreversibly converting 5,10-methylenetetrahydrofolate to 5-methylenetetrahydrofolate, a predominant circulating form of folate. Folate is reportedly important for milk protein synthesis, and MTHFR may be a key regulatory point of folate metabolism for milk protein synthesis in mammary epithelial cells. Prior to this study, polymorphisms of the MTHFR gene were not associated with milk production traits from a breeding perspective. Single nucleotide polymorphisms (SNPs) at microRNA (miRNA) binding sites (miR-SNPs) can affect gene expression. This study aimed to identify the effects of miR-SNPs (g.2244A>G and g.2264A>G) in the caprine MTHFR 3' UTR on the milk production traits of dairy goats.ResultsGuanzhong dairy (GD, n = 325) goats were used to detect SNPs in the caprine MTHFR 3' UTR by DNA sequencing. Two novel SNPs (g.2244A>G and g.2264A>G) were identified in the said region. The homozygous haplotype A-G of the SNPs g.2244A>G and g.2264A>G was significantly associated with milk yield and milk protein levels in GD goats (P < 0.05). Functional assays indicated that the MTHFR 2244 A → G substitution could increase the binding activity of hsa-miR-1266 with the MTHFR 3' UTR. The MTHFR 2264 A → G substitution could decrease the binding activity of hsa-miR-616 with the MTHFR 3' UTR. In addition, we observed a significant increase in the MTHFR mRNA levels of homozygous haplotype A-G carriers relative to those of homozygous haplotype G-A carriers. These results indicated that both SNPs altered the MTHFR mRNA levels. These altered levels of MTHFR mRNA may account for the association of SNPs with milk production traits.ConclusionsThis study is the first to report that the g.2244A>G and g.2264A>G polymorphisms were associated with milk production traits in GD goats. Further investigations should explore the underlying miRNA-mediated mechanisms that are modified by the g.2244A>G and g.2264A>G SNPs. The current study evaluated these SNPs as potential genetic markers in goats, with potential applications in breeding programs.

Application of mathematical expectation (ME) strategy for detecting low frequency mutations: An example for evaluating 14-bp insertion/deletion (indel) within the bovine PRNP gene

“…When the 14-bp indel in the 3 0 UTR of PRNP was inserted or deleted, the structure and function of genes related to the growth traits would be affected by bonding with miRNA. 31 In summary, an economic ME method was presented to quickly and accurately detect low frequency mutation, such as the 14-bp indel in the 3 0 UTR of the PRNP gene, which would save time and reduce expenses. Besides, the detected 14-bp indel significantly affect growth traits, which might be a potential useful DNA marker for MAS in cattle.…”

Detection of a 4 bp Mutation in the 3′UTR Region of Goat Sox9 Gene and Its Effect on the Growth Traits

“…Several previous studies have shown that 3 UTR variants can affect gene transcription [49,50], and structural changes in the 3 UTR region are closely related to livestock and poultry production performance [51][52][53]. The 3 UTR is generally thought to regulate gene expression by affecting the stability of mRNA.…”

Genetic effects of PRNP gene insertion/deletion (indel) on phenotypic traits in sheep

“…Previous studies have indicated that mutations of basic sequences may alter mRNA stability, processing, and maturation, thereby affecting the allelic expression and co-translational folding pathway [46]. Predicting that the binding sites of transcription factors might exist in the PRNP indel loci, the expression of other growth-related genes would be influenced by bonding with miRNA [47]. For another, indel polymorphism in the 3 0 UTR could modulate traits or disease susceptibility via a microRNA- mediated post-transcriptional mechanism or elements of DNA functions [48].…”