Genome-wide Characterization Of The Ethiopian And Chinese Indigenous Goat Populations By Whole Genome Re-sequencing And SNP Array

Investigations of genome-wide level provide valuable information on genetic diversity,population structure,and divergence within or among populations.This also can identify the potential genes/genomic regions associated with production,reproduction and adaption traits in various livestock species including goats.The rapid development of high throughput genotyping technology such as whole genome re-sequencing and SNP arrays are among the powerful,cost-effective tools possibly to discover several million SNPs of the individual genome and quantify genome-wide genetic variation in goat populations.However,comprehensive research works using these platforms are still limited and uncovered in Ethiopia as a whole and China to some extent.Therefore,two sets of data were used in this thesis.The first set comprised a total of 193 individuals representing 6Chinese goat breeds such as Nanjing?n=23?,Qinggeda?n=24?,Arbas Cashmere?n=40?,Jining Grey?n=39?,Luoping Yellow?n=24?and Guangfeng?n=24?were genotyped for SNP50K Bead Chips.The second set comprised whole genome sequence with an average effective sequencing depth of 16×for 44 individuals geographically representative of five phenotypically distinct indigenous populations in Ethiopia goats namely;Abergelle?n=11?,Afar?n=5?,Begait?n=11?,Central Highland?n=12?and Meafure?n=5?.In the second chapter,we provided a comprehensive literature review of goat origin,domestication,genetic resources in Asia and Africa,overview and distribution of Ethiopian indigenous goats,techniques and its importance of molecular characterization,and significance of genetic diversity and population structure that make them important targets for research,breeding,and conservation.In the third chapter,our aim was to investigate the genetic diversity and population structure of Chinese goat breeds in order to understand the breed characteristics and then properly maintain,utilize,conservation and it is essential for genetic improvement.We found a high proportion of informative SNPs ranging from 83.9%in Luoping Yellow to93%in Jining Grey goat populations with an average mean of 97.1%.The heterozygosity analysis showed the low to moderate genetic differentiation among populations but high within the population,respectively.The phylogenetic analysis assigned the breeds into four clusters corresponding to their geographic origins.Chapter 3 contributes valuable genetic information about within-breed diversity,which provides a good opportunity for sustainable utilization of and maintenance of genetic resource improvements in the Chinese goat breeds.In the fourth chapter,we determine the genome-wide linkage disequilibrium?LD?and the extent of effective population size?Ne?of the six Chinese goat breeds.Across the 29autosomes chromosomes,minor allele frequency was highest on chromosome 1?0.321?and lowest on chromosome 25?0.309?.The Jining Grey and Qinggeda,the population showed higher Ne estimates after 13 generations ago.While a declining recent Ne was distinguished for the Arbas Cashmere and Guangfeng breeds.In this chapter,results of the LD and Ne predict for further genomic selection analysis on the Arbas Cashmere and Guangfeng Chinese goat breeds.The fifth chapter focuses on genetic diversity and population structure of Ethiopian indigenous goats in order to clearly characterize the populations and a greater understanding of their genetic potentials.Whole-genome re-sequencing of 44 Ethiopian indigenous goats produced over 16 million SNPs and 123,577 of insertions and deletions.Level of genetic diversity was highest for Begait and lowest for Afar.Positive inbreeding coefficient was observed for Begait and Abergelle.Weak phylogenetic relationship and principal component analyses were observed,which indicates the closer relationship among the goat populations and the admixture were revealed among these populations.The distinct genetic background was found between Begait and the remaining populations.This chapter showed the genetic uniqueness of the genetic resource of the Ethiopian indigenous goats.In the sixth chapter,we performed the genome-wide selection signature investigation.The comparison of the Begait genome with other Ethiopian breeds detected 211 common selective windows by combining two different methods(F_ST and pi ratio).Gene ontology?GO?enrichment analysis identified 36 GO terms and 6 KEGG pathways.The candidate genes are involved in body growth,milk and production traits?ZNF385B,GLYCAM1,PDE1B,and PPP1R1A?,reproduction/fertility traits?MCTP1,and STK35?,and thermotolerance.?MAPK13 and MAPK14?and immune response?SCN7A,IL12A,and DEFB119?.Overall,the thesis provided the valuable genome-wide information of diversity,genetic structure and selection signatures,which could be a good opportunity for sustainable utilization and maintenance of the Ethiopian and Chinese indigenous goat populations.