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In most mammalian species, females have two X sex chromosomes and males have an X and Y. As a result, mutations on the X chromosome in females may be masked by the presence of a normal allele on the second X. In contrast, a mutation on the X chromosome in males more often causes observable biological defects, as there is no normal X to compensate. Trait variations arising from mutations on the X chromosome are called “X-linked”.

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

Irene van den Berg¹, Amanda J Chamberlain^2,3, Iona M MacLeod²

¹Agriculture Victoria, AgriBio, Centre of AgriBioscience, 5 Ring Road, Bundoora, VIC, 3082, Australia. irene.vandenberg@agriculture.vic.gov.au.

Genetics, Selection, Evolution : GSE

|June 6, 2024

Summary

Identifying genetic variants linked to dairy cattle fertility is key for genomic prediction. This study combined expression data and genome-wide association studies to pinpoint genes influencing female fertility, offering new targets for breeding programs.

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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.