Regulatory variation at glypican-3 underlies a major growth QTL in mice

Abstract

The genetic basis of variation in complex traits remains poorly understood, and few genes underlying variation have been identified. Previous work identified a quantitative trait locus (QTL) responsible for much of the response to selection on growth in mice, effecting a change in body mass of approximately 20%. By fine-mapping, we have resolved the location of this QTL to a 660-kb region containing only two genes of known function, Gpc3 and Gpc4, and two other putative genes of unknown function. There are no non-synonymous polymorphisms in any of these genes, indicating that the QTL affects gene regulation. Mice carrying the high-growth QTL allele have approximately 15% lower Gpc3 mRNA expression in kidney and liver, whereas expression differences at Gpc4 are non-significant. Expression profiles of the two other genes within the region are inconsistent with a factor responsible for a general effect on growth. Polymorphisms in the 3' untranslated region of Gpc3 are strong candidates for the causal sequence variation. Gpc3 loss-of-function mutations in humans and mice cause overgrowth and developmental abnormalities. However, no deleterious side-effects were detected in our mice, indicating that genes involved in Mendelian diseases also contribute to complex trait variation. Furthermore, these findings show that small changes in gene expression can have substantial phenotypic effects.

Figure 1. QTL Region

At the top is shown the extent of Chr X segregating in three recombinant families. The horizontal grey bars indicate the regions known to segregate, while the error bars show the uncertainty in the location of recombination. Black bars indicate genes within the QTL region according to the Ensembl database [20]. Below is a LOD score plot for body mass at 6 wk in entire progeny test population (n = 1,909). Triangles indicate the locations of markers. At the bottom, recombination rates are shown for the intervals delimited by diamonds (the Chr X average is 0.40 cM/Mb [40]).

Figure 2. Transcript Levels of Gpc3 and Gpc4 (Divided By β-actin)

Expression was measured in newborn liver and kidney in homozygous low-allele females and hemizygous low-allele males (black bars) and in heterozygous females and hemizygous high-allele males (grey bars). Data are from 23 low-allele mice and 24 high-allele males/heterozygous females, and values are least squares means (± 2× standard error); *, p < 0.05.

Figure 3. Polymorphisms between High- and Low-Line-Derived Chr X

(A) 80 bp from the stop codon of Gpc3 in the 3′ UTR. (B) 332 bp from the stop codon of Gpc3 in the 3′ UTR. (C) 1,455 bp downstream of Gpc3. Sequence in common with reference mouse sequence [20] is denoted by dots.