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Using expression data to fine map QTL associated with fertility in dairy cattle
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Using expression data to fine map QTL associated with fertility in dairy cattle
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Journal Article
Using expression data to fine map QTL associated with fertility in dairy cattle
2024
Overview
Background
Female fertility is an important trait in dairy cattle. Identifying putative causal variants associated with fertility may help to improve the accuracy of genomic prediction of fertility. Combining expression data (eQTL) of genes, exons, gene splicing and allele specific expression is a promising approach to fine map QTL to get closer to the causal mutations. Another approach is to identify genomic differences between cows selected for high and low fertility and a selection experiment in New Zealand has created exactly this resource. Our objective was to combine multiple types of expression data, fertility traits and allele frequency in high- (POS) and low-fertility (NEG) cows with a genome-wide association study (GWAS) on calving interval in Australian cows to fine-map QTL associated with fertility in both Australia and New Zealand dairy cattle populations.
Results
Variants that were significantly associated with calving interval (CI) were strongly enriched for variants associated with gene, exon, gene splicing and allele-specific expression, indicating that there is substantial overlap between QTL associated with CI and eQTL. We identified 671 genes with significant differential expression between POS and NEG cows, with the largest fold change detected for the
CCDC196
gene on chromosome 10. Our results provide numerous candidate genes associated with female fertility in dairy cattle, including
GYS2
and
TIGAR
on chromosome 5 and
SYT3
and
HSD17B14
on chromosome 18. Multiple QTL regions were located in regions with large numbers of copy number variants (CNV). To identify the causal mutations for these variants, long read sequencing may be useful.
Conclusions
Variants that were significantly associated with CI were highly enriched for eQTL. We detected 671 genes that were differentially expressed between POS and NEG cows. Several QTL detected for CI overlapped with eQTL, providing candidate genes for fertility in dairy cattle.
Publisher
BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
Subject
/ Alleles
/ Animal Genetics and Genomics
/ Animals
/ Biomedical and Life Sciences
/ Cattle
/ Exons
/ Female
/ Females
/ Genes
/ Genome-wide association studies
/ genome-wide association study
/ Genome-Wide Association Study - veterinary
/ Genomes
/ Genomics
/ Mutation
/ Polymorphism, Single Nucleotide
/ Puberty
/ Software
