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Single nucleotide polymorphisms affect miRNA target prediction in bovine.

Marco Antônio Perpétuo de Sousa1, Flavia Regina Florêncio de Athayde1, Mariângela Bueno Cordeiro Maldonado1

  • 1Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil.

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Single nucleotide polymorphisms (SNPs) within bovine microRNAs (miRNAs) can alter gene expression and affect cattle traits. These findings offer potential for genetic improvement in livestock production.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Animal Science

Background:

  • Single nucleotide polymorphisms (SNPs) are key genetic variations influencing phenotypic traits in cattle.
  • MicroRNAs (miRNAs) are crucial post-transcriptional regulators that bind to messenger RNAs (mRNAs).

Purpose of the Study:

  • To investigate the in silico effects of SNPs on bovine miRNA sequences.
  • To analyze SNP impacts on miRNA target binding, maturation, QTL association, and evolutionary conservation.

Main Methods:

  • Scanned approximately 56 million SNPs against 1,064 bovine miRNA sequences.
  • Performed in silico analyses for target binding prediction, Minimum Free Energy (MFE), QTL region association, and evolutionary conservation.
  • Evaluated SNP effects on miRNA seed regions and maturation capacity.

Main Results:

  • 71.6% of predicted miRNA targets were altered by SNPs in mature miRNA seed regions.
  • 48.6% of analyzed sequences exhibited MFE variations sufficient to alter miRNA maturation.
  • Identified 131 SNPs in 46 miRNAs within QTL regions, suggesting functional relevance.
  • SNP loci showed evolutionary conservation, indicating conserved biological functions.

Conclusions:

  • SNPs within bovine miRNAs can significantly impact gene regulation and phenotypic characteristics.
  • These findings highlight the potential of miRNA SNPs for cattle genetic improvement and production studies.