Abstract
In the present thesis population structure of Greek breeds of small ruminants using novel genomic technologies was studied, which is essential so as to preserve rare breeds and improve livestock performances. Four different Greek sheep breeds were analyzed (Chios, Boutsko, Karagouniko, Frizarta), as well as the two Greek goat breeds (Eghoria and Skopelos). To accomplish the genetic characterization, two approaches were used. First, genotyping microarrays were used to identify ~50Κ SNPs (Single Nucleotide Polymorphisms) spread throughout the genome, whereas the second approach involved transcriptome sequencing of the mammary gland. Genetic characterization for sheep breeds was performed using OvineSNP50K microarray beadchip. Results showed that Greek sheep breeds maintain high levels of genetic heterogeneity with modest genetic distances among them, based on the indices used. Genomic associations of SNPs and breeds revealed 3.802 SNPs that can be used in targeted genetic improvement sch ...
In the present thesis population structure of Greek breeds of small ruminants using novel genomic technologies was studied, which is essential so as to preserve rare breeds and improve livestock performances. Four different Greek sheep breeds were analyzed (Chios, Boutsko, Karagouniko, Frizarta), as well as the two Greek goat breeds (Eghoria and Skopelos). To accomplish the genetic characterization, two approaches were used. First, genotyping microarrays were used to identify ~50Κ SNPs (Single Nucleotide Polymorphisms) spread throughout the genome, whereas the second approach involved transcriptome sequencing of the mammary gland. Genetic characterization for sheep breeds was performed using OvineSNP50K microarray beadchip. Results showed that Greek sheep breeds maintain high levels of genetic heterogeneity with modest genetic distances among them, based on the indices used. Genomic associations of SNPs and breeds revealed 3.802 SNPs that can be used in targeted genetic improvement schemes, conservation programs or traceability purposes, so as to identify two-breed crosses and purebreds. The respective analyses for goats using CaprineSNP50K microarray beadchip, showed that both breeds exhibit high levels of genetic diversity. Genetic relatedness of the two breeds was high and moreover, a geographical clustering pattern was observed, associated with sampling locations. A panel of 288 markers was selected that can be used to distinguish the breeds. Transcriptional profiling of mammary gland in sheep, was performed in the two most highly productive Greek breeds (Chios and Frizarta), as well as in Lacaune breed, in order to catalogue differences in expression patterns. Next generation sequencing revealed that 12.405, 11.763 and 13.480 unigenes are expressed in the mammary gland during lactation, for Chios, Frizarta and Lacaune breeds, respectively. Chios and Lacaune breeds expressed similar transcriptional activity of the mammary gland, from the aspect of genes as well as their levels of expression. The highly expressed genes for the latter breeds encoded caseins and whey proteins. On the contrary, Frizarta breed expressed a different transcriptome profile, due to the fact that other factors were traced that changed the transcriptional profiling of the mammary gland, affecting their productivity. Moreover, genes that are responsible for differences in milk yield were traced and can be used in the design of breeding schemes. The respective analysis for goats showed that 9.264 and 11.896 unigenes are active in the mammary gland during lactation for the Eghoria and Skopelos breeds, respectively. Differences in the highly expressed genes between two breeds were observed; caseins and whey proteins were highly expressed in the Eghoria breed, whereas in Skopelos breed, highly expressed genes seem to induce the expression of caseins and are also involved in the protection of the mammary gland as well as its differentiation during involution. Furthermore, genes were traced that are involved in fatty acid synthesis and are connected with fat content in milk that can be used as biomarkers. This thesis presents the first genome-based analysis on the genetic characterization of Greek indigenous breeds. Genetic markers were identified that can be exploited in breeding programs, targeted genetic improvement schemes and conservation strategies to accelerate genomic selection.
show more
