The Construction Of De Novo Assembly Pan-genome And Primary Exploration Of Trait-associated Genetic Variations Among Various Domesticated Bovines

In human society,domestic cattle provides not only meat,milk,and leather globally,but also draught force and transportation in some mountainous areas,which makes it occupy a crucial position in the development of agricultural society.During the domestication process,hundreds of breeds have been created to satisfy different demands,with a variety of distinctive phenotypes.These dramatic variations are mostly determined by the breed-specific genetic background,which remains largely unknown due to the ascertainment of the single reference genome of Hereford cattle.Therefore,a comprehensive landscape of bovine variations is highly required to improve our strategies of breeding,utilization,and management of the species,which is of great significance for the social and economic development.In this thesis,we sequenced 8 geographically and phenotypically representative bovine individuals worldwide using Nanopore sequencing and finished de novo genome assembly and genome annotation for each individual.Subsequently,we constructed the domestic cattle pangenome based on the de novo assemblies of 8 bovine breeds and the current domestic cattle reference genome(ARS UCD1.2).We identified 183.93 Mb non-redundant novel sequence that are missing in the bovine linear reference genome.both GC content(46.57%)and repeat ratio(51.32%)of these non-redundant novel sequences were higher than those of the reference.Reference-genome-based alignment analysis identified 21 Mb SNPs and 3.8 Mb Indels,while the pan-genome-based alignment analysis identified 30.4Mb SNPs and 4.1Mb Indels,suggesting a more comprehensive variation representativeness of this pan-genomes.We analyzed population structure based on SNPs.Phylogenetic relationship,principal component analysis,and ancestral component analysis consistently proved a strong representativeness and reliability of this pan-genome,including.The bovine pan-genome contained 24,459 gene families,of which 14,028 gene families were shared by all individuals.Unique genes shared by Angus and Simmental were significantly enriched in actin filament;those of African cattle were significantly enriched in immune response;those of Yanbian yellow cattle were significantly enriched in lipid metabolism,which may account for cold tolerance.Taking together,unique genes were mainly overrepresented in the functions that have potential associations with important economic traits and environmental adaptation.Furthermore,we retrieved the structural variations that may have potential associations with important economic traits and endemic traits,through 336 genomic re-sequencing data of individuals from various bovine breeds.We found that highly differentiated genes were enriched in basic metabolic functions between taurus and zebu,in immune and neurological development between African cattle and non-African cattle,and in Golgi and O-linked glycosylation with presumed influence on membrane vesicle transport between cow and the other cattle,respectively..Additionally,we identified two strongly linked loci between cows and the other cattle.One belonged to repetitive sequence,the other was LOC512867,a locus with potential effect on Th cell differentiation.This project can not only help assessing the genetic resources of bovine species complex,developing molecular markers for verification,providing evidence for the conservation and breed improvement,but also give deeper insights into the mechanisms underpinning genome evolution in population scale.