Localization of the primary sites of genetic influence

When studying the nervous system of animal lines developed for specific genetically-determined behavioral differences, how does one tell whether a difference between the lines found at one specific location was caused by a direct genetic interaction at that location or by an interaction at some distant site which was then imposed on the tested location? The form of the line difference can help to answer this question. One particular form, called an inverse line difference, is shown to have a higher probability of being close to the location of the direct gentic interaction.