Leveraging genetically simple traits to identify small-effect variants for complex phenotypes

Kemper, K. E., Littlejohn, M. D., Lopdell, T., Hayes, B. J., Bennett, L. E., Williams, R. P., Xu, X. Q., Visscher, P. M., Carrick, M. J. and Goddard, M. E. (2016) Leveraging genetically simple traits to identify small-effect variants for complex phenotypes. BMC Genomics, 17 1: 858-858. doi:10.1186/s12864-016-3175-3


Author Kemper, K. E.
Littlejohn, M. D.
Lopdell, T.
Hayes, B. J.
Bennett, L. E.
Williams, R. P.
Xu, X. Q.
Visscher, P. M.
Carrick, M. J.
Goddard, M. E.
Title Leveraging genetically simple traits to identify small-effect variants for complex phenotypes
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2016-11-03
Year available 2016
Sub-type Article (original research)
DOI 10.1186/s12864-016-3175-3
Open Access Status DOI
Volume 17
Issue 1
Start page 858
End page 858
Total pages 9
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Abstract Polymorphisms underlying complex traits often explain a small part (less than 1 %) of the phenotypic variance (σ(2)P). This makes identification of mutations underling complex traits difficult and usually only a subset of large-effect loci are identified. One approach to identify more loci is to increase sample size of experiments but here we propose an alternative. The aim of this paper is to use secondary phenotypes for genetically simple traits during the QTL discovery phase for complex traits. We demonstrate this approach in a dairy cattle data set where the complex traits were milk production phenotypes (fat, milk and protein yield; fat and protein percentage in milk) measured on thousands of individuals while secondary (potentially genetically simpler) traits are detailed milk composition traits (measurements of individual protein abundance, mineral and sugar concentrations; and gene expression).
Formatted abstract
Background: Polymorphisms underlying complex traits often explain a small part (less than 1 %) of the phenotypic variance (σ2P). This makes identification of mutations underling complex traits difficult and usually only a subset of large-effect loci are identified. One approach to identify more loci is to increase sample size of experiments but here we propose an alternative. The aim of this paper is to use secondary phenotypes for genetically simple traits during the QTL discovery phase for complex traits. We demonstrate this approach in a dairy cattle data set where the complex traits were milk production phenotypes (fat, milk and protein yield; fat and protein percentage in milk) measured on thousands of individuals while secondary (potentially genetically simpler) traits are detailed milk composition traits (measurements of individual protein abundance, mineral and sugar concentrations; and gene expression).

Results: Quantitative trait loci (QTL) were identified using 11,527 Holstein cattle with milk production records and up to 444 cows with milk composition traits. There were eight regions that contained QTL for both milk production and a composition trait, including four novel regions. One region on BTAU1 affected both milk yield and phosphorous concentration in milk. The QTL interval included the gene SLC37A1, a phosphorous antiporter. The most significant imputed sequence variants in this region explained 0.001 σ2P for milk yield, and 0.11 σ2P for phosphorus concentration. Since the polymorphisms were non-coding, association mapping for SLC37A1 gene expression was performed using high depth mammary RNAseq data from a separate group of 371 lactating cows. This confirmed a strong eQTL for SLC37A1, with peak association at the same imputed sequence variants that were most significant for phosphorus concentration. Fitting any of these variants as covariables in the association analysis removed the QTL signal for milk production traits. Plausible causative mutations in the casein complex region were also identified using a similar strategy.

Conclusions: Milk production traits in dairy cows are typical complex traits where polymorphisms explain only a small portion of the phenotypic variance. However, here we show that these mutations can have larger effects on secondary traits, such as concentrations of minerals, proteins and sugars in the milk, and expression levels of genes in mammary tissue. These larger effects were used to successfully map variants for milk production traits. Genetically simple traits also provide a direct biological link between possible causal mutations and the effect of these mutations on milk production.
Keyword Complex traits
Gene expression
Pleiotropy
QTL mapping
Q-Index Code C1
Q-Index Status Provisional Code
Grant ID DP1093502
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
Queensland Brain Institute Publications
 
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