Genetic basis of latitudinal variation in vertebral number in the Oryzias latipes species complex

Latitudinal variation plays an important role in driving local adaptation and intraspecific polymorphism across a wide range of organisms. Among teleost fishes, populations from higher latitude tend to have more vertebrae than those from lower latitude, which is known as “Jordan’s rule”. Vertebral number is determined during embryogenesis by the number of somites formed, but the genetic mechanisms underlying this latitudinal variation remain largely unclear. The medaka (Oryzias latipes) species complex, including O. latipes, O. sakaizumii, O. sinensis and an undescribed species from East Korea, is a freshwater teleost species group distributed across a latitudinal range from 25° to 40°N. This wide geographical distribution makes medaka an ideal model system for studying latitudinal variation in morphological trait. In this study, we found a positive correlation between abdominal vertebral number and the latitude of original sampling sites of 90 wild-derived stocks of the O. latipes species complex. To further examine the environmental and genetic contributions to this trait, we reared 10 selected stocks originating from different latitudes at four incubation temperatures (22, 24, 26, 28 °C) until somite stage. Across all temperatures within each phylogenetic subgroup, stocks from higher latitudes consistently developed a greater number of abdominal vertebrae. Finally, we performed a genome-wide association study (GWAS) to identify genomic loci associated with vertebral number variation in these wild-derived stocks. This analysis revealed a single nucleotide polymorphism (SNP) on chromosome 10 that was significantly associated with total vertebral count. Taken together, our findings demonstrate that wild-derived stocks of the O. latipes species complex retain latitudinal variation in vertebral number. This system provides a powerful framework for investigating the evolutionary and genetic bases of geographic trait variation in teleost fishes.