Abstract
The present PhD dissertation aimed to comprehensively characterise the genomic makeup of Greek sheep breeds, emphasizing on the genomic architecture of climate resilience of milk production and local environmental adaptation. This is the first study to investigate the demographic history of several native sheep breeds along with globally distributed populations, while innovative methodological approaches were developed to dissect livestock resilience to climatic perturbations. A total of 1,625 animals genotyped from Chios, Frizarta, Mytilini, Boutsko and Pelagonia sheep using the Illumina Ovine SNP50K Bead Chip, featuring more than 50,000 SNP markers, and collectively analyzed with 38 world breeds from Sheep HapMap project. A diverse genomic profile of Greek sheep was demonstrated using principal component analysis and model-based ancestry approaches. A central position was depicted for the Greek indigenous populations between European, Asian and African sheep. The admixture patterns, ...
The present PhD dissertation aimed to comprehensively characterise the genomic makeup of Greek sheep breeds, emphasizing on the genomic architecture of climate resilience of milk production and local environmental adaptation. This is the first study to investigate the demographic history of several native sheep breeds along with globally distributed populations, while innovative methodological approaches were developed to dissect livestock resilience to climatic perturbations. A total of 1,625 animals genotyped from Chios, Frizarta, Mytilini, Boutsko and Pelagonia sheep using the Illumina Ovine SNP50K Bead Chip, featuring more than 50,000 SNP markers, and collectively analyzed with 38 world breeds from Sheep HapMap project. A diverse genomic profile of Greek sheep was demonstrated using principal component analysis and model-based ancestry approaches. A central position was depicted for the Greek indigenous populations between European, Asian and African sheep. The admixture patterns, heterozygosity (Ho-observed, He-expected) and genetic differentiation levels (pairwise FST) revealed different within-breed selection practices related to specific production and adaptation purposes. These genetic patterns indicated the contribution of the Greek farmers to sheep evolution and dispersal during domestication and post-domestication times within Europe. Novel animal phenotypes were developed using reaction norm functions to evaluate the effect of seasonality on milk yield changes in response to temperature variation (climate resilience) in Chios dairy sheep. Seasonal adaptation of Chios resilience to daily and weekly cumulative climate variation was showed, especially exemplified by spring lambing animals. Diversified heritable trait variation (h2= 0.03–0.17) obtained for seasonal resilience under cold and hot weather conditions. Both favourable and antagonistic genetic correlations were estimated between resilience and lifetime milk production. Separate customized breeding objectives could be developed according to the calendar season of lambing to apply genetic selection. Genome-wide association study (GWAS) and regional heritability mapping revealed genomic regions on chromosomes 5 and 19 significantly associated with Chios overall resilience to heat stress conditions (25 °C) and lifetime milk production. Neighboring genes encode olfactory receptors that are involved in animal thermal homeostasis through respiratory evaporation. Additionally, highly homozygous and heterozygous hotspots were identified on chromosomes 3, 10, 13 and 19 based on the detection of runs of homozygosity (ROH) and heterozygosity (ROHet). These hotspots represent potential signals of directional selection and include annotated genes previously associated with milk traits, local adaptation to harsh environments, improved animal fitness and potential disease resistance. A genotype-environment association analysis was also performed using seasonal high and low altitude grazing locations of purebred Boutsko transhumant populations. Five annotated regions on chromosomes 6, 15 and 22 were significantly associated with precipitation seasonality. The spatial distribution of the homozygous genotypes partially coincided with the geographical variation of the bioclimatic variable. Several genes spanning these chromosomal regions were enriched in climate-driven biological processes, such as hypoxia and metabolic responses, developmental pathways and body conformation traits. The methodology deployed in this dissertation could be used for the effective management of farm animal genetic resources to apply multi-trait genomic selection and preserve long-term sustainability of livestock. This could enhance global food security and meet the challenges of climate change.
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