Developmental Systems Genomics of morphogenetic timing and facial shape variation

The objective of this proposal is to elucidate the complex genetic, transcriptional, and histological landscape underpinning palate morphogenesis by leveraging a systems genomics approach in genetically diverse mice. Craniofacial morphogenesis involves the outgrowth and fusion of facial prominences, which must be coordinated with skeletal specification and differentiation to generate a functional craniofacial complex. Underscoring the sensitivity of this intricate choreography, orofacial clefts (OFCs) are the most common facial anomaly in humans, affecting 1/700 births worldwide. Mouse models provide a key platform for human disease allele discovery owing to recent developments in gene editing that enable rapid validation of novel variants. However, multiple published examples demonstrate the profound effect that mouse genetic background can have on the penetrance and expressivity of craniofacial phenotypes. Thus, our limited understanding of the effect of natural strain variation on developmental processes presents a major challenge to validation of disease variants and our ability to model human congenital malformations. While individual genes are critically required for normal development, it is the collective function of genes and their interactions, modularly organized into gene regulatory networks (GRNs), that control the transcriptional dynamics and timing of morphogenesis and differentiation. Variation in these dynamics likely accounts for normal variation in facial shape but can also underpin craniofacial birth defects. However, feasibility limits studies of genetic variation in developing embryos to only a few genes at a time and experimental models that accurately relate genomic sequence variation to variation in transcriptional dynamics are critically lacking. These challenges complicate a systematic address of genome-scale mechanisms that drive morphogenesis and the potential for pathological outcomes. The complementary Collaborative Cross (CC) recombinant inbred strains and Diversity Outbred (DO) heterogeneous stock combine the genetic and phenotypic diversity of 8 common inbred founder strains of mice in a design optimized for systems-level genetic dissection of complex traits. It has been demonstrated that QTLs for facial shape in adult DO mice are enriched for genes with established function in craniofacial and skeletal development. However, these studies do not address mechanisms of where, when, or how QTL candidate genes influence facial shape. The proposed aims will apply a developmental systems genomics approach to map the influence of genetic variation within a model of palate morphogenesis. Aim 1 will define the temporal dynamics of morphogenetic networks within the segmentally organized upper jaw and identify QTL/eQTL underlying strain differences in developmental timing and palate morphogenesis. Aim 2 will employ single-cell and spatial genomics to genetically dissect the molecular signatures of QTL/eQTL with cellular and histological resolution. Aim 3 will leverage quantitative phenotyping to relate differences in morphogenetic dynamics and resulting morphology to variation in underlying genotype and thereby derive mechanistic insight into the integration of genomic regulatory systems. Project Number: 1R01DE034778-01A1 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of Dental and Craniofacial Research (NIDCR) | Principal Investigator: Ian Welsh | Institution: JACKSON LABORATORY, BAR HARBOR, ME | Award Amount: $795,730 | Activity Code: R01 | Study Section: Development - 2 Study Section[DEV2] View on NIH RePORTER: https://reporter.nih.gov/project-details/11297588