Linked genetic loci and genotype-dependent temperature effects shape craniofacial morphology in medaka

Abstract Craniofacial morphology is a fundamental and complex trait, vital for survival and crucial for social interactions such as individual recognition and mate selection. While its overall form is conserved within a species, significant individual diversity exists, controlled by both genetic and environmental factors. To elucidate its genetic basis, we employed quantitative trait locus (QTL) analysis using F2 progeny obtained from 2 medaka inbred strains (HNI-II and HdrR-II1), identifying multiple genetic loci that significantly contribute to variation in craniofacial morphological traits. Further fine-mapping using congenic strains for 2 selected traits demonstrated that each phenotype is influenced by multiple QTLs within a single chromosome. Specifically, a cluster of 3 candidate QTLs on chromosome 6 is found to regulate the head length-to-height ratio (L33), potentially involving interactions to affect the phenotype. High-resolution Hi-C analysis revealed physical chromatin interactions among these clustered QTLs, suggesting that spatial genomic architecture facilitates their functional interactions. Our study also revealed that L33 is sensitive to rearing temperature. We observed a genotype-dependent response, in which low temperature (23 °C) significantly altered phenotypes in HdrR-II1 but not in HNI-II. Our findings suggest that craniofacial diversity is shaped by the complex interplay of multiple QTLs and temperature effects, highlighting medaka as a powerful model for investigating how genetic interactions and environmental plasticity shape morphological diversity.