Genomic descriptors of biodiversity – A review

Abstract

Summary The characterization of livestock genetic diversity has experienced extensive changes with the availability of dense nucleotide markers. Among the various forms of markers, the single nucleotide polymorphisms (SNP) have arguably the largest influence. A wide range of indicators for the assessment of genetic diversity was developed, or the existing methods were improved, enabling us to make informed decisions on the management of livestock populations. This review discusses the selected aspects of diversity assessment, with special attention to the SNP based methods. One of the core concepts in genomics of diversity is the linkage disequilibrium (LD), as it was shaped by demographic events during the development of breeds and species. These events, either natural or artificial, left detectable signals within the livestock genomes. Further changes were induced by human activity when mating related animals, leading to fixing or improving the desired traits in the breed, but reducing their genetic variability. The assessment of relatedness is also pivotal to construct meaningful mating plans and to avoid the negative consequences of inbreeding depression that might be detrimental especially in small, endangered populations. Both LD and relatedness are of interest on their own, as well as in their follow-up applications deriving overall measures of effective population size.

Genome-Wide Linkage Disequilibrium and the Extent of Effective Population Sizes in Six Chinese Goat Populations Using a 50K Single Nucleotide Polymorphism Panel

“…Similar results were previously reported in different cattle breeds [39,40]. The lowest r 2 observed between breeds and chromosomes might be due to differences in genetic drift, recombination rates, and less intensive selection which resulted in a lower LD across the genome [41]. Generally, a declining pattern of average r 2 values was observed when moving from 10 to 200 kb.…”

Genomic Tools for Effective Conservation of Livestock Breed Diversity

“…Additionally, the LD patterns have shown clear differences among species. In sheep and goats, the LD levels are lower than in cattle, pig and dogs [59], probably due to comparably lower selection intensities. However, it is important to consider that LD patterns and scale within and between populations/breeds are influenced by several factors such as marker allele frequencies, selection history, population structure and effective size, marker type and density, as well as which LD measure is used.…”