Data from: Multiple QTL underlie milk phenotypes at the CSF2RB locus

Background: Over many years, artificial selection has substantially
improved milk production by cows. However, the genes that underlie milk
production quantitative trait loci (QTL) remain relatively poorly
characterised. Here, we investigate a previously reported QTL located at
the CSF2RB locus on chromosome 5, for several milk production phenotypes,
to better understand its underlying genetic and molecular causes. Results:
Using a population of 29,350 taurine dairy cows, we conducted association
analyses for milk yield and composition traits, and identified highly
significant QTL for milk yield, milk fat concentration, and milk protein
concentration. Strikingly, protein concentration and milk yield appear to
show co-located yet genetically distinct QTL. To attempt to understand the
molecular mechanisms that might be mediating these effects, gene
expression data were used to investigate eQTL for 11 genes in the broader
interval. This analysis highlighted genetic impacts on CSF2RB and NCF4
expression that share similar association signatures to those observed for
lactation QTL, strongly implicating one or both of these genes as
responsible for these effects. Using the same gene expression dataset
representing 357 lactating cows, we also identified 38 novel RNA editing
sites in the 3′ UTR of CSF2RB transcripts. The extent to which two of
these sites were edited also appears to be genetically co-regulated with
lactation QTL, highlighting a further layer of regulatory complexity that
involves the CSF2RB gene. Conclusions: This locus presents a diversity of
molecular and lactation QTL, likely representing multiple overlapping
effects that, at a minimum, highlight the CSF2RB gene as having a causal
role in these processes.