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Related Experiment Video

Updated: Mar 7, 2026

Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood

Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood

Published on: November 28, 2018

Single nucleotide polymorphism discovery in bovine liver using RNA-seq technology.

Chandra Shekhar Pareek¹, Paweł Błaszczyk^1,2, Piotr Dziuba¹

¹Division of Functional Genomics in Biological and Biomedical Research, Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland.

|February 25, 2017

Summary

This study used RNA-sequencing to identify millions of breed-specific single nucleotide polymorphisms (SNPs) in Polish Red, Polish Holstein-Friesian, and Hereford cattle liver. These findings reveal genomic variations that may influence cattle production traits.

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Last Updated: Mar 7, 2026

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Published on: November 28, 2018

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Published on: May 19, 2019

Area of Science:

Genomics
Transcriptomics
Animal Breeding

Background:

RNA-sequencing (RNA-seq) is a powerful next-generation sequencing (NGS) technology for understanding mammalian transcriptome.
Breed-specific genomic variation in cattle may correlate with differences in production traits.

Purpose of the Study:

To detect single nucleotide polymorphisms (SNPs) in the liver tissue of three cattle breeds using RNA-seq.
To understand genomic variations that may influence production traits.

Main Methods:

RNA-sequencing of bovine liver tissue from Polish Red, Polish Holstein-Friesian, and Hereford breeds.
Identification and filtering of SNPs and insertion/deletion (indel) mutations.
Construction of breed-specific SNP databases (SNP-dbs).
Validation of identified SNPs using kompetitive allele-specific PCR (KASPTM) assay.

Main Results:

Over 107 million raw paired-end reads were generated, with high mapping rates across breeds.
Millions of SNPs and indel positions were identified in bovine liver tissue.
Three breed-specific SNP-databases were constructed, containing tens of thousands of SNP records.
Validation confirmed the accuracy of RNA-seq derived SNPs, with some loci showing high polymorphism among breeds.

Conclusions:

Breed-specific SNPs with high SNP ratios and mapping coverage were identified in cattle liver.
A comprehensive SNP-db for bovine liver was constructed, yielding millions of SNPs.
The KASPTM assay proved to be a reliable and cost-effective method for validating breed-specific SNPs.