DOI: 10.5061/dryad.c866t1g3g
title: Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features

description: 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.
description: Details of data collection may be found in the Materials and
 Methods section of the paper.   
description: 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.
 <br> 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.