Comparison of the effects of the Da gene upon the spheno-occipital synchondrosis in rabbits of strain DA and unrelated strain IIIDa has made possible study of the relative effects of Da growth retardation and strain differences of primary and secondary growth gradients and their interaction. When Da is absent and parental border shift dosages (which portray the localization and magnitude of thoracic and lumbar gradients) are most anterior, synchondrosis fusion is minimal in both strains. Presence of Da in either Da/+ or Da/Da genotype significantly increases the penetrance and expression of fusion in both strains. Fusion tends to be additively increased when parental thoracolumbar and lumbosacral borders are shifted anteriorly, and antagonistically decreased when they are replaced by posterior border shifts. The interaction of these two (gene and genome) influences results in patterns of continuous distribution involving from two to five classes. Penetrance of fusion is outstandingly affected by Da whereas expressivity obviously is more specifically associated with vertebral border shifts. This differentiates their associations with primary and secondary gradients respectively. The study shows how such epigenetic variants and specific gene induced localized retardations could be used in genetic analyses of basic growth processes. Studied developmentally in time and relation to function, they could establish firm grounds for prediction and control of abnormal development.