REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological Samples
Canis familiaris	Various veterinary referral hospitals	N/A
Chemicals, Peptides, and Recombinant Proteins
Trizol	Life Technologies	15596026
RNAlater	Life Technologies	AM7020M
Critical Commercial Assays
CanineHD Whole-Genome Genotyping SNP BeadChip	Illumina	WG-440-1001
Truseq DNA nano kit	Illumina	FC-121-4001
TruSeq Stranded mRNA Library Prep Kit High Throughput	Illumina	RS-122-2103
Illumina TruSeq Nano DNA library prep HT	SeqLab	20000903
Deposited Data
RNA and DNA sequencing data	This paper	ENA: PRJEB17926, http://www.ebi.ac.uk/ena
Dog reference genome (CanFam3.1, ENSEMBL release-85)	ENSEMBL	http://www.ensembl.org/index.html
Dog genotypes	This paper	http://dx.doi.org/10.5061/dryad.cq612
Dog genetic variants	Dog Biomedical Variant Database Consortium (tosso.leeb@vetsuisse.unibe.ch)	N/A
Experimental Models: Organisms/Strains
Mouse: Smoc2tm1.1(KOMP)Vlcg	The Jackson Laboratory	https://www.jax.org
Mouse embryos	Roslin Institute Biological Research Facility	N/A
Chicken embryos	NARF	http://www.narf.ac.uk
Oligonucleotides
gDNA targeted primer: SMOC2 Forward: GGCAGGGGATGGGGAAGGCT	This paper	N/A
gDNA targeted primer: SMOC2 Reverse (ancestral): ACTGTGTGCTTTGCCCAAACTCA	This paper	N/A
gDNA targeted primer: SMOC2 Reverse (derived): TGCCCATAAAGTTCAGGGTCCACT	This paper	N/A
gDNA targeted primer: IGF1 Forward: CACTGATCCAGAAGAATCCAACT	[27]	N/A
gDNA targeted primer: IGF1 Reverse: CAAAGAACCATGTAAGCCTATTTGT	[27]	N/A
gDNA targeted primer: STC2 Forward: ATACAATCCACCTAGTGTCCCCAACCAT	[27]	N/A
gDNA targeted primer: STC2 Reverse: GGCCACAGCCCCTTTAAT	[27]	N/A
gDNA targeted primer: SMAD2 Forward: GCTTCAAGTCAGTGTGCTCC	This paper	N/A
gDNA targeted primer: SMAD2 Reverse: CGTATTTGTTGCTGCTGGGT	This paper	N/A
gDNA targeted primer: SMAD2 Reverse: AGAGCCCTGACATCATGACC	This paper	N/A
gDNA targeted primer: FGF4 retrogene Forward: CACACAGATGGACCATGAAA	This paper	N/A
gDNA targeted primer: FGF4 retrogene Reverse (ancestral): TTTTAGATTCCGCACATGAG	This paper	N/A
gDNA targeted primer: FGF4 retrogene Reverse (derived): CTCTTTGAACTTGCACTCCTC	This paper	N/A
gDNA targeted primer: BMP3 Forward: GATACAGGAGATTGTGCCAAATGGGTAA	[8]	N/A
gDNA targeted primer: BMP3 Reverse: CTCCTGGTGGAAATCGTCAGTCTATCTG	[8]	N/A
gDNA targeted primer: CFA30 QTL Forward: AGGGATAGTCCAGCTCCAAGGCTGGTAT	This paper	N/A
gDNA targeted primer: CFA30 QTL Reverse: CTCTTTCAGGCTTCCCCAGTTGTACCTA	This paper	N/A
gDNA targeted primer: IGF1R Forward: AGATGACCAACCTCAAGGATATT	[27]	N/A
gDNA targeted primer: IGF1R Reverse: AGTCCTGCCATCCCACAAAG	[27]	N/A
gDNA targeted primer: GHR(1) & GHR(2) Forward: GCTCTCCGTTAAATCAAGCTG	[27]	N/A
gDNA targeted primer: GHR(1) & GHR(2) Reverse: AAGGAGAGAGGTGTTGTTGGT	[27]	N/A
cDNA targeted primer: SMOC2 Exon 2/3 Forward: TGCTTATCGAGGAAATTGCAG	This paper	N/A
cDNA targeted primer: SMOC2 Exon 2/3 Reverse: TGGGATGAACACCTGCTGTA	This paper	N/A
cDNA targeted primer: SMOC2 Exon 10/11 Forward: CGCGCTCTCTACCGACAT	This paper	N/A
cDNA targeted primer: SMOC2 Exon 10/11 Reverse: GGGGTCGGGTTCTGAGAG	This paper	N/A
cDNA targeted primer: MRPS7 Forward: AGTGCAGGGAGAAGAAGCAC	[54]	N/A
cDNA targeted primer: MRPS7 Reverse: CAGCAGCTCGTGTGACAACT	[54]	N/A
Software and Algorithms
Read alignment: bwa v0.7.8	[55]	https://sourceforge.net/projects/bio-bwa/files/
Variant caller: GATK v3.7	[56]	http://gatkforums.broadinstitute.org/gatk
WGS utility: Picard	http://broadinstitute.github.io/picard	https://github.com/broadinstitute/picard/releases
Structural variant caller: Pindel v0.2.3	[57]	http://gmt.genome.wustl.edu/packages/pindel/
Annotation: SNPsift v4.0	[58]	http://snpeff.sourceforge.net/SnpSift.html
Effect prediction: HaploReg v4.1	[59]	N/A
Effect prediction: CADD v3.1	[60]	N/A
Utility: PLINK v1.07	[61]	http://zzz.bwh.harvard.edu/plink/
Utility: PLINK v1.90 beta	[62]	https://www.cog-genomics.org/plink2
Admixture assessments: STRUCTURE v2.3	[63]	http://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/html/structure.html
Linear mixed model: GEMMA v0.94.1	[64]	http://www.xzlab.org/software.html
Phasing: SHAPEIT v2.r837	[65]	https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html
Graphics and data analysis: R v3.3.0	The Comprehensive R Archive Network (CRAN)	https://cran.r-project.org
RNaseq alignment: STAR v2.5.1b	[66]	https://github.com/alexdobin/STAR
RNaseq analysis: DESeq2 v1.12.14	[67]	https://bioconductor.org
RNaseq analysis: RSubread v1.22.3	[68]	https://bioconductor.org
Data visualization: Integrative Genomics Viewer v2.3.59	[69]	http://software.broadinstitute.org/software/igv/
DICOM reconstruction and landmarking: CheckPoint v2016.11.21.0711 WIN x64	Stratovan	https://www.stratovan.com
ImageJ v1.50 g	[70]	https://imagej.nih.gov/ij/
Geometric morphometrics: MorphoJ v1.06c	[71]	http://www.flywings.org.uk/morphoj_page.htm
Other
KOD Xtreme HotStart Polymerase	Merck	71975-3
Saliva sample collection kit	Peformagene	PG-100
Lysing matrix D 2mL tube	MPBio	116913050
RNeasy Minikit	QIAGEN	C-74104
SuperScript III First- Strand Synthesis SuperMix	Life Technologies	11752050