Using expression data to fine map QTL associated with fertility in dairy cattle

Area of Science:

• Animal Genetics
• Reproductive Biology
• Genomic Selection

Background:

• Female fertility is a crucial trait in dairy cattle breeding.
• Genomic prediction accuracy for fertility can be enhanced by identifying causal variants.
• Expression quantitative trait loci (eQTL) and allele frequencies offer insights into genetic regulation of fertility.

Purpose of the Study:

• To fine-map quantitative trait loci (QTL) associated with fertility in dairy cattle.
• To integrate multiple types of expression data with fertility traits and allele frequencies.
• To identify genomic differences between high (POS) and low (NEG) fertility cows.

Main Methods:

• Genome-wide association study (GWAS) on calving interval (CI) in Australian dairy cattle.
• Analysis of gene, exon, gene splicing, and allele-specific expression (eQTL).
• Comparison of allele frequencies and gene expression between high and low fertility (POS vs. NEG) cows.

Main Results:

• Significant overlap found between variants associated with CI and eQTL.
• 671 genes showed significant differential expression between POS and NEG cows, with CCDC196 showing the largest fold change.
• Candidate genes for fertility identified include GYS2, TIGAR, SYT3, and HSD17B14; several QTL regions contained copy number variants (CNV).

Conclusions:

• Variants associated with calving interval are enriched for eQTL.
• Differential gene expression analysis revealed 671 candidate genes related to fertility.
• Overlapping QTL and eQTL regions provide valuable candidate genes for improving dairy cattle fertility.