Genomic and pedigree based methods for analysis and improvement of breeding schemes

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Artificial selection in livestock has significantly improved economically important traits and altered conformation traits, primarily through the use of a limited number of genetically superior individuals. This practice has led to decreased effective population sizes and increased inbreeding coefficients. While many livestock populations experienced a decline in genetic diversity following the introduction of artificial insemination, dog breeds and companion animals have faced small effective population sizes for a longer duration due to their high fertility and small total populations. This situation makes them valuable for studying the effects of small historical effective population sizes and for applying new methods to recover from inbreeding depression. Understanding population structure, historical bottlenecks, and breeding schemes is essential for future management. The initial chapters analyze two dog breeds through pedigree-based methods, including monitoring effective population size and assessing popular kennel effects. Small effective population sizes raise the likelihood of homozygosity for recessive deleterious alleles, a key factor in inbreeding depression. A contemporary solution involves predicting the effects of numerous genetic markers from a limited number of genotyped and phenotyped individuals, facilitating early selection of breeding candidates through genomic selection. While current methods mainly con