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Updated: Jun 6, 2026
09:40
Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood
Published on: November 28, 2018
SNP discovery in the bovine milk transcriptome using RNA-Seq technology.
Angela Cánovas1, Gonzalo Rincon, Alma Islas-Trejo
1IRTA, Genètica i Millora Animal, 191 Alcalde Rovira Roure Av, 25198, Lleida, Spain.
Summary
RNA sequencing (RNA-Seq) efficiently discovers single nucleotide polymorphisms (SNPs) in bovine milk. This study identified over 33,000 coding SNPs in Holstein cattle, valuable for genetic trait association studies.
Area of Science:
- Genomics
- Molecular Biology
- Animal Science
Background:
- High-throughput RNA sequencing (RNA-Seq) is primarily for gene expression analysis.
- RNA-Seq also offers an efficient method for discovering coding single nucleotide polymorphisms (SNPs).
Purpose of the Study:
- To conduct a SNP discovery analysis within the milk transcriptome of Holstein cows using RNA-Seq.
- To evaluate the accuracy and cost-effectiveness of RNA-Seq for identifying SNPs in transcribed regions.
Main Methods:
- Seven Holstein cow milk samples were sequenced using the Illumina Genome Analyzer.
- SNP detection involved analyzing expressed genes and comparing them to the Hereford bovine genome assembly.
- Validation was performed using Sanger sequencing and the KASPar Genotyping System.
Main Results:
- 19,175 genes were detected in milk samples, representing about 70% of analyzed genes.
- 100,734 SNPs were identified in Holstein samples, with 33,045 being polymorphic within the breed.
- RNA-Seq identified 70 out of 86 SNPs previously found by Sanger sequencing, demonstrating high accuracy.
Conclusions:
- RNA-Seq is a cost-effective method for identifying SNPs in transcribed regions of the bovine milk transcriptome.
- The study provides guidelines to enhance SNP discovery accuracy and minimize false positives.
- Over 33,000 coding SNPs in lactation-expressed genes were identified, enabling the development of genotyping platforms for marker-trait association studies in Holstein cattle.
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