Multiple QTL underlie milk phenotypes at the CSF2RB locus
Abstract 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 lo...
Main Authors: | , , , , , , , , , |
---|---|
Format: | Article |
Language: | deu |
Published: |
BMC
2019-01-01
|
Series: | Genetics Selection Evolution |
Online Access: | http://link.springer.com/article/10.1186/s12711-019-0446-x |
_version_ | 1819060267322966016 |
---|---|
author | Thomas J. Lopdell Kathryn Tiplady Christine Couldrey Thomas J. J. Johnson Michael Keehan Stephen R. Davis Bevin L. Harris Richard J. Spelman Russell G. Snell Mathew D. Littlejohn |
author_facet | Thomas J. Lopdell Kathryn Tiplady Christine Couldrey Thomas J. J. Johnson Michael Keehan Stephen R. Davis Bevin L. Harris Richard J. Spelman Russell G. Snell Mathew D. Littlejohn |
author_sort | Thomas J. Lopdell |
collection | DOAJ |
description | Abstract 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. |
first_indexed | 2024-12-21T14:24:16Z |
format | Article |
id | doaj.art-9e66835c202f45f5869a32d75de44650 |
institution | Directory Open Access Journal |
issn | 1297-9686 |
language | deu |
last_indexed | 2024-12-21T14:24:16Z |
publishDate | 2019-01-01 |
publisher | BMC |
record_format | Article |
series | Genetics Selection Evolution |
spelling | doaj.art-9e66835c202f45f5869a32d75de446502022-12-21T19:00:41ZdeuBMCGenetics Selection Evolution1297-96862019-01-0151111610.1186/s12711-019-0446-xMultiple QTL underlie milk phenotypes at the CSF2RB locusThomas J. Lopdell0Kathryn Tiplady1Christine Couldrey2Thomas J. J. Johnson3Michael Keehan4Stephen R. Davis5Bevin L. Harris6Richard J. Spelman7Russell G. Snell8Mathew D. Littlejohn9Research and Development, Livestock Improvement CorporationResearch and Development, Livestock Improvement CorporationResearch and Development, Livestock Improvement CorporationResearch and Development, Livestock Improvement CorporationResearch and Development, Livestock Improvement CorporationResearch and Development, Livestock Improvement CorporationResearch and Development, Livestock Improvement CorporationResearch and Development, Livestock Improvement CorporationSchool of Biological Sciences, University of AucklandResearch and Development, Livestock Improvement CorporationAbstract 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.http://link.springer.com/article/10.1186/s12711-019-0446-x |
spellingShingle | Thomas J. Lopdell Kathryn Tiplady Christine Couldrey Thomas J. J. Johnson Michael Keehan Stephen R. Davis Bevin L. Harris Richard J. Spelman Russell G. Snell Mathew D. Littlejohn Multiple QTL underlie milk phenotypes at the CSF2RB locus Genetics Selection Evolution |
title | Multiple QTL underlie milk phenotypes at the CSF2RB locus |
title_full | Multiple QTL underlie milk phenotypes at the CSF2RB locus |
title_fullStr | Multiple QTL underlie milk phenotypes at the CSF2RB locus |
title_full_unstemmed | Multiple QTL underlie milk phenotypes at the CSF2RB locus |
title_short | Multiple QTL underlie milk phenotypes at the CSF2RB locus |
title_sort | multiple qtl underlie milk phenotypes at the csf2rb locus |
url | http://link.springer.com/article/10.1186/s12711-019-0446-x |
work_keys_str_mv | AT thomasjlopdell multipleqtlunderliemilkphenotypesatthecsf2rblocus AT kathryntiplady multipleqtlunderliemilkphenotypesatthecsf2rblocus AT christinecouldrey multipleqtlunderliemilkphenotypesatthecsf2rblocus AT thomasjjjohnson multipleqtlunderliemilkphenotypesatthecsf2rblocus AT michaelkeehan multipleqtlunderliemilkphenotypesatthecsf2rblocus AT stephenrdavis multipleqtlunderliemilkphenotypesatthecsf2rblocus AT bevinlharris multipleqtlunderliemilkphenotypesatthecsf2rblocus AT richardjspelman multipleqtlunderliemilkphenotypesatthecsf2rblocus AT russellgsnell multipleqtlunderliemilkphenotypesatthecsf2rblocus AT mathewdlittlejohn multipleqtlunderliemilkphenotypesatthecsf2rblocus |