Title Page
Contents
Abstract 12
Introduction 14
Bovine genome and sequencing 14
Resequencing bovine genomes 15
Hanwoo-a Korean indigenous cattle breed 16
Breeding strategies 19
Materials and Methods 23
Overview of NGS process 23
Whole-genome sequencing library preparation 23
Library sequencing and analyses 29
Annotation of variants 32
Results 33
Data production and mapping to reference genome 33
Identification of single nucleotide polymorphisms 38
Comparison of sequencing and array results 47
Identification of insertions, deletions, and inversions 50
Regions of homozygosity 54
Trait-associated genes 63
Variants in the TAGs in ROHs of Hanwoo 63
Discussion 88
Region of homozygosity 88
TAGs in ROHs 91
References 93
한글 요약문 115
Table 1. Summary of data production and mapping. 34
Table 2. Summarized results of previously reported cattle resequencing. 40
Table 3. Statistics of SNPs in Hanwoo. 42
Table 4. The number of total, novel, and homozygous SNPs in each annotation classes. 43
Table 5. Summarized results of previously reported personal whole-genome sequencings. 46
Table 6. Concordant calls with Illumina Bovine SNP50 chip. 49
Table 7. Statistics of insertions, deletions, and inversions in Hanwoo. 51
Table 8. List of bovine trait-associated genes. 65
Table 9. Trait-associated genes in each ROHs of three breeds. 82
Figure 1. Improvement of economic traits of Hanwoo. Rearranged... 18
Figure 2. A proven Hanwoo bull, 27223. 24
Figure 3. Overview of the processes of SOLiD system, ligase-based massively-parallel sequencing. 25
Figure 4. Agarose gel-electrophoresis results for DNA size... 28
Figure 5. Sequencing data analysis flow. 31
Figure 6. Size of the sequenced regions. The size of... 37
Figure 7. Distribution of read depth from the sequencing data used for SNP callings. 39
Figure 8. Transition of the ratio in novel and homozygous...[내용없음] 9
Figure 9. A Venn diagram of the number of genes holding...[내용없음] 9
Figure 10. Size distribution of small indels in Hanwoo. (A) Whole... 52
Figure 11. Size distribution of large indels in Hanwoo. (A) large... 53
Figure 12. Size distribution of inversions in Hanwoo. 55
Figure 13. ROH detection results from chip- and NGS-derived SNP data of Hanwoo. I compared ROH... 57
Figure 14. Comparison between ROH detection results from chip- and NGS-derived SNP data... 58
Figure 15. Distribution of homozygous SNPs and ROHs in three breeds. Grey and red vertical... 59
Figure 16. The size of ROHs in three cattle. Hanwoo showed a distinguished ROH length in... 62
Figure 17. Distribution of bovine trait-associated genes. Trait-associated genes identified... 64
Figure 18. Identified variants in TTN region of Hanwoo. 86
Figure 19. Validation of indels in TTN of Hanwoo. (A) Validation... 87