Selective genotyping for determination of a major gene associated with cranial cruciate ligament disease in the newfoundland dog

Cranial cruciate ligament disease (CCLD) is the leading cause of lameness in the dog. The objective of this study was to determine the most informative subset of animals on which to carry out selective genotyping for the identification of any major gene affecting CCLD. Two groups of animals were chosen for genotyping from candidate groups of animals having high probabilities (calculated from segregation analysis) for carrying zero and two copies, respectively, of the putative causative allele. A stochastic search algorithm was employed to search the solution space for the ‘best’ two groups of individuals for genotyping based on two alternating fitness functions. The first fitness function was designed to minimize the genetic relationship amongst dogs within groups for each group individually. The second fitness function was designed to maximize the genetic relationship amongst dogs between groups. This approach, and the ramifications of its use, are discussed.