Genetics of murine craniofacial morphology: diallel analysis of the eight founders of the Collaborative Cross

Abstract

Using eight inbred founder strains of the mouse Collaborative Cross (CC) project and their reciprocal F1 hybrids, we quantified variation in craniofacial morphology across mouse strains, explored genetic contributions to craniofacial variation that distinguish the founder strains, and tested whether specific or summary measures of craniofacial shape display stronger additive genetic contributions. This study thus provides critical information about phenotypic diversity among CC founder strains and about the genetic contributions to this phenotypic diversity, which is relevant to understanding the basis of variation in standard laboratory strains and natural populations. Craniofacial shape was quantified as a series of size-adjusted linear dimensions (RDs) and by principal components (PC) analysis of morphological landmarks captured from computed tomography images from 62 of the 64 reciprocal crosses of the CC founder strains. We first identified aspects of skull morphology that vary between these phenotypically 'normal' founder strains and that are defining characteristics of these strains. We estimated the contributions of additive and various non-additive genetic factors to phenotypic variation using diallel analyses of a subset of these strongly differing RDs and the first eight PCs of skull shape variation. We find little difference in the genetic contributions to RD measures and PC scores, suggesting fundamental similarities in the magnitude of genetic contributions to both specific and summary measures of craniofacial phenotypes. Our results indicate that there are stronger additive genetic effects associated with defining phenotypic characteristics of specific founder strains, suggesting these distinguishing measures are good candidates for use in genotype-phenotype association studies of CC mice. Our results add significantly to understanding of genotype-phenotype associations in the skull, which serve as a foundation for modeling the origins of medically and evolutionarily relevant variation.

Keywords: collaborative cross; craniofacial form; diallel; micro-computed tomography; morphometrics; mouse models; normal variation.

Figure 1

Landmark identification on the (A) superior, (B) inferior, (C) superior with calotte removed, and (D) lateral views of an adult mouse skull. Midline landmarks start with M, bilateral landmarks start with L&R.

Figure 2

Linear relationship between centroid size of skull landmarks and a shape summary score derived from Procrustes coordinates in morphoj (Klingenberg, 2011) for each specimen. Founder strains are differentiated by colors and F1 cross‐specimens are black dots.

Figure 3

Subset relative linear dimension (RD) identification on the (A) lateral (anterior to left, superior up) and (B) inferior (anterior to left) views. Subset RDs representing the facial (red), cranial base (blue), and cranial vault (orange) regions of the skull are identified. Landmarks associated with these subset RDs are labeled.

Figure 4

Specimens from founder strains (colored) and F1 strains (black dots) plotted across principal components (PC), with % of variance explained in parentheses, including (A) PC1 vs. PC2, (B) PC3 vs. PC4, (C) PC5 vs. PC6, (D) PC7 vs. PC8. (E) The Euclidean distance of strain mean PC scores and the grand mean across PCs 1–8.

Figure 5

Comparison of founder strain (Table 1) features. Relative linear dimensions (RDs) identified as defining characteristics that are always larger (red) or shorter (blue) and strongly differing LDs that are not always larger or smaller (gray) are plotted from the lateral (left) and inferior (middle) views. μCT surface reconstructions of real specimens that are closest to mean strain shape are displayed for comparison, from the lateral view (right).

Figure 6

Distributions of diallel estimated strain‐specific additive effects (absolute values scaled to SD) for relative linear dimensions (RDs) identified as founder strain‐specific defining characteristics or strongly differing RDs of founder strains, as well as other strain‐specific additive values. Boxplots illustrate median and quartile values. Significant pair‐wise differences are labeled with the P‐values from pairwise t‐tests.

Figure 7

Heritability estimates for strain‐ and cross‐specific additive and non‐additive factors of phenotypic measures. Subset relative linear dimensions are illustrated as lines with widths proportional to estimated additive e (A,C) and non‐additive (B,D) heritability, from the lateral (top) and inferior (bottom) views. (E) Lines with length proportional to heritability estimates for additive and non‐additive factors associated with each of the first eight principal components (PCs).