Using both the genetic drift and inbreeding approaches, we derive more general equations for effective size (N(e)) of a diploid species under random mating. These equations show explicitly that inbreeding or genetic drift comes from two sources, the variation in the number of offspring from each parent and the variation in contribution between these parents' own paternally and maternally derived genes to their offspring. The first source can be easily and effectively controlled by choosing an equal number of offspring from each family, while the second can be manipulated by using information on genetic markers to reduce the variance due to Mendelian segregation. Marker-assisted selection (MAS) methods to increase N(e) for the whole genome with single or multiple marker loci per chromosome, different numbers of males, and females are developed and implemented in stochastic simulations. The analytical and simulation results show that, although in principle N(e) can be increased indefinitely, the efficiency of MAS is restricted in practice by the amount of marker information, the genome size, and the number of marker-genotyped offspring per family. The assumptions made in developing the theory and methods and the applications of MAS in conservation are discussed.
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