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Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features

Citation

Roseman, Charles et al. (2020), Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features, Dryad, Dataset, https://doi.org/10.5061/dryad.c866t1g3g

Abstract

Variation in pelvic morphology has a complex genetic basis and its patterning and specification is governed by conserved developmental pathways. Whether the mechanisms underlying the differentiation and specification of the pelvis also produce the morphological covariation on which natural selection may act is still an open question in evolutionary developmental biology. We use high-resolution Quantitative Trait Locus (QTL) mapping in the F34 generation of an advanced intercross experiment (LG,SM-G34) to characterize the genetic architecture of the mouse pelvis. We test the prediction that genomic features linked to developmental patterning and differentiation of the hind limb and pelvis and the regulation of chondrogenesis are overrepresented in QTL. We find 31 single QTL-trait associations at the genome- or chromosome-wise significance level coalescing to 27 pleiotropic loci. We recover further QTL at a more relaxed significance threshold replicating locations found in a previous experiment in an earlier generation of the same population. QTL were more likely than chance to harbor Pitx1 and Sox9 Class II ChIP-seq features active during development of skeletal features. There was weak or no support for the enrichment of seven more categories of developmental features drawn from the literature. Our results suggest genotypic variation is channeled through a subset of developmental processes involved in the generation of phenotypic variation in the pelvis. This finding indicates the evolvability of complex traits may be subject to biases not evident from patterns of covariance among morphological features or developmental patterning when either is considered in isolation.

Methods

Details of data collection may be found in the Materials and Methods section of the paper. 

 

Usage Notes

Phenotypes and Covariates. (CCRetal_F34HipData.txt)

This file includes all of the data and covariates used in the quantitative genetic and gene mapping components of the paper. Missing values are indicated with a “NA”. Tab delimited.


animal: Animal identification number corresponding to those in the pedigree and genotype files

SIRE: Sire’s identification number corresponding to those in the pedigree file.

DAM: Dam’s identification number corresponding to those in the pedigree file.

SEX: Sex of animal. “F” For female, “M” for male.

DIET: Diet of animal. “H” for high fat, “L” for low fat.

AGE: Age at sacrifice in days.

LITTER_SIZE: Number of pups in the litter from which an animal was drawn.

CODED_LITTER_SIZE: A variable expressing whether (“1”) or not (“0”) the size of the litter from which an animal was drawn exceeded the number of nipples on a dam.

IliumWidth: The width of the ilium as described in the text.

IliumLength: The length of the ilium as described in the text.

PubisMean: The length of the pubis as described in the text.

IschiumMean: The length of the ischium as described in the text.

IschiumPubisMean: The length from the caudal ilium to the pubic symphysis as described in the text.

PubisIliumMean: The length from the pubic symphysis to the ventral ilium as described in the text.

IschiumIliumMean: The length from the caudal ischium to the dorsal ilium as described in the text.

AcetabularBreadkth: The breadth of the acetabulum as described in the text.

Genotypes. (F34GenoCh1toCh19Dryad.txt)

Each column in the genotype file represents genotypic scores at a single locus, the identity of which is indicated in the header. Each row represents an individual, the IDs of which correspond to those in the phenotype file. “1” indicates a homozygote for the large allele, “2” a heterozygote, and “3” a homozygote for the small allele. Missing values are denoted by “NA”. Tab delimited.

Genetic Map. (F34_MapPositions.txt)

A genetic map on mouse genome mm9 used to locate genetic effects in the paper. Tab delimited.

Chrom: Chromosome

Marker: Marker identification number. Those containing a “_” followed by the number are imputed locations.

MapPos: The position, in megabases, of the marker or the

MarkerID: The ID of the SNP used in the mapping corresponding to the headers in the genotypes file.

 

Pedigree. (F34GXShip.ped)

A four generation deep pedigree of the F_34 population of the advanced intercross used in the quantitative genetic and gene mapping parts of the paper to represent relatedness among individuals. “NA” represents a missing value. Tab delimited.

animal: The identification number of the animal corresponding to that in the phenotypes and genotypes files.

sire: The identification number of the sire.

dam: The identification number of the dam.

sex: The sex of an individual “1” for female “2” for male.

Funding

National Science Foundation, Award: BCS 0962903

National Institutes of Health, Award: R01 DE019638