Gotra is highly regarded while fixing wedding alliance. In the past in order to avoid weddings across the same hereditary channel of blood relationships or sharing similar Gotra, few wedding commandments were established. This indeed had a scientific approach, since it was regulated in a manner so as to avoid hereditary diseases in the offspring, which was on other hand common in western culture. According to the ancient tradition following are the points to be considered:
Weddings are not to be conducted among two individuals sharing common blood relationships that may be among direct descendent from paternal or maternal ancestry. They are commonly called as "direct cousins" like for example Son or Daughter of a blood related Uncle or Aunt (from both paternal as well as maternal side).
Weddings can't be conducted among two individuals sharing same Major Gotra, the one among the eight root originators as specified in the Gotra section.
Weddings can't be conducted among two individuals sharing same Gana which is even termed as their direct Gotra of the Family.
Weddings can't be conducted among two individuals from certain Gotras and their descendent Gana, who have been each other's Rival and so their descendents are said to be traditional foes. Such two sages were Vashistha and Vishwamitra.
Although the perspective behind the above specified rules were to maintain a pool of healthy generation, free from genetic disorders. However during ancient periods there were no precise scientific options for determining direct genetic constitutes (Hollandric & Recessive Genes) that would lead to such genetic disorders. The fact lies in however that whether one follows the commandments or not, the key to a successful and balanced family life is mutual understanding, cooperation, trust and respect for each other.