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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

Variant discovery in the sheep milk transcriptome using RNA sequencing.

Aroa Suárez-Vega¹, Beatriz Gutiérrez-Gil¹, Christophe Klopp²

¹Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain.

|February 17, 2017

Summary

Researchers identified genetic variants in sheep milk transcriptome using RNA-Seq. These variants in milk protein and fat metabolism genes could improve dairy traits through genomic selection.

Keywords:

Dairy Sheep Milk Somatic Cells RNA-Seq Transcriptome Variants

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Area of Science:

Livestock genetics
Transcriptomics
Dairy science

Background:

Identifying genetic variation for desired phenotypes is crucial in livestock research.
High-throughput transcriptome sequencing (RNA-Seq) enables detection of variants in various tissues and species.
This study focused on characterizing genetic variation in the milk transcriptome of dairy sheep breeds.

Purpose of the Study:

To identify genetic variants within coding regions of the milk transcriptome in Churra and Assaf sheep.
To characterize genetic variation in genes related to milk yield, protein, and fat percentages.
To explore the potential of identified variants for genomic selection in dairy sheep.

Main Methods:

RNA-Sequencing (RNA-Seq) of Milk Sheep Somatic Cells (MSCs).
Analysis of genetic variants (SNPs and indels) in coding regions.
Functional enrichment analysis (KEGG pathways) and variant impact prediction.

Main Results:

Detected 216,637 variants in the MSCs transcriptome.
Identified 57,795 variants in Quantitative Trait Loci (QTL) regions for milk production traits, with 21.44% being novel.
Found 561 high-impact and 1,649 moderate-impact variants; "protein processing in endoplasmic reticulum" pathway was highly enriched.
Identified 504 variants in major milk protein genes and 1,063 in lipid metabolism genes, with 20 mutations potentially affecting encoded proteins.

Conclusions:

This is the first transcriptomic study to identify genetic variants in the sheep lactating mammary gland.
Identified variants in QTL regions and candidate genes for milk production traits offer potential for improving dairy sheep.
Identified SNPs can serve as markers for genotyping platforms and genomic selection in the dairy industry.