The use and integration of molecular DNA information in conservation breeding programmes: a review

Abstract

Conservation breeding programmes often rely on intensive genetic management of the captive population. However, the relatedness between individuals and individual mean kinship are often estimated based on pedigree records, which are frequently incomplete or unreliable. Depending on the quality of a studbook (e.g. expressed as percentage of pedigree known), molecular information can substantially improve knowledge of a population, and therefore contribute to improving the retention of genetic diversity in each generation. As the use of molecular data has been largely under-utilised, this review aims to provide information on the various types of genetic markers that can be used, the estimation of (DNA based) relatedness and pedigrees, their integration in studbooks, the use of molecular information in breeding pair selection, hybridisation issues and population management in general. We discuss recent developments in methodology (e.g. next generation sequencing), theoretical considerations, and software that can aid conservation breeders in each phase of the programme from the founding phase to the (potential) reintroduction, each clarified by various examples from recent literature. Special attention is given to group-managed populations, for which it is difficult to control mating and reconstruct pedigrees as individuals cannot be isolated for management.