Mapping Expression Quantitative Trait Loci Targeting Candidate Genes for Pregnancy in Beef Cows

Area of Science:

• Animal Genomics
• Reproductive Biology
• Gene Expression Regulation

Background:

• Understanding the genetic basis of reproductive traits is crucial for improving cattle fertility.
• Previous studies have not identified specific causative genes or mutations for complex reproductive traits.

Purpose of the Study:

• To identify regulatory genetic variants influencing gene expression in beef cow uterine luminal epithelial cells.
• To explore the genetic factors governing fertility by integrating genomics and transcriptomics data.

Main Methods:

• Utilized RNA-Seq data to identify expression quantitative trait loci (eQTLs) in beef cows.
• Analyzed cis and trans eQTLs affecting gene expression, focusing on transcription factors and differentially expressed genes.
• Performed functional over-representation analysis and enrichment analysis with CattleQTLdb.

Main Results:

• Identified 4676 cis and 7682 trans eQTLs impacting 1120 and 2503 genes, respectively.
• Found eQTLs associated with transcription factor genes and genes previously linked to pregnancy status.
• Highlighted pathways in metabolism, immune response, and hormone signaling (estrogen, GnRH) regulated by eQTLs.
• Observed enrichment of eQTLs in quantitative trait loci (QTL) regions for 13 reproductive traits.

Conclusions:

• This study reveals novel insights into the genetic architecture of reproductive processes in cattle.
• Identified regulatory variants and pathways provide a foundation for further investigation into the causal mechanisms of uterine gene expression and fertility.