Conservation of wild and livestock/aquaculture species aims at maximizing genetic diversity on the long-term, while selection programs focus mainly on genetic improvement in the next generation. Both genetic drift and selection can lead to high rates at which inbreeding increases if a small number of individuals contribute largely to subsequent generations. Increases in the rate of inbreeding would have negative consequences such as reductions of genetic variability and increased risk of inbreeding depression that may affect specific genomic regions and that can compromise the success of both conservation and selection programs. Traditionally, the control of inbreeding has been tracked by managing the relationships between individuals using pedigree records. With the advent of new genotyping and high-throughput sequencing technologies, obtaining more precise information about the relationships between individuals is now possible. While single nucleotide polymorphisms (SNP) chips or genotyping-by-sequencing data contain only a subset of the polymorphic variants available in a species, whole genome sequencing data provide access to complete information on all the variants of an individual. As a consequence, the estimation of coefficients to measure genetic variability may be affected by the type of data used for their estimation.

During the post-genomics era, a variety of methods to characterize the levels of genetic diversity from genomic information within and between populations have been developed. These are related to the estimation of the selection signature and population structure or coefficients to determine the increase in inbreeding such as effective population size. However, under this new genomic perspective, methods and concepts need to be revised. In parallel to the development of genomic tools, traditional and new strategies to control inbreeding to simultaneously target conservation of genetic diversity and genetic improvement need to be developed or accommodated to the new context. The availability of genomic information opens up possibilities to include genome wide marker information in prediction of total breeding values and to obtain higher genetic gains through genomic selection but controlling the increase of the rate of inbreeding is also necessary to ensure the viability of the programs.

This Research Topic aims to publish basic, applied and methodological studies towards a better understanding and management of genetic diversity in conservation and selection programs in livestock and aquaculture species under the new genomic context. Specifically, we welcome papers that address the development, evaluation and/or application of methods to estimate genetic diversity, the signature of natural and artificial selection and innovative strategies to control the rate of inbreeding both for conservation and selection purposes.

Keywords: Inbreeding, Conservation, Genetic diversity, Effective population size, Selection signature

Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.