Title Page
ABSTRACT
Contents
Abbreviation 8
1. Introduction 9
2. Materials and Methods 11
2.1. Plant materials 11
2.2. Phenotypic data for salt tolerance 11
2.3. Genomic DNA extraction and NGS analysis 13
2.4. Population structure analysis 13
2.5. Genome-wide association study analysis 14
3. Results 15
3.1. Phenotype analysis to screening data for salt stress 15
3.2. Population structure analysis 17
3.3. Genome-wide association study (GWAS) analysis for SALT stress traits 18
3.4. Haplotype Analysis to identify salt stress candidate genes 25
4. Discussion 37
5. Conclusion 38
6. Bibliography 39
Summary in Korean 43
Appendices 45
Appendix 1. List of 25 rice varieties used for population structure, List of 25 3k rice varieties. 45
Appendix 2. List of novel candidate genes. 46
Table 1. NK rice morphological data using SES. 17
Table 2. NK rice morphological data using RDR. 17
Table 3. NK rice morphological data using SDW. 17
Table 4. List of known candidate genes with highly associated signal in GWAS. 23
Table 5. List of novel candidate genes with highly associated signal in GWAS. 24
Figure 1. Criteria for the Standard evaluation scoring system 12
Figure 2. Salt stress screening of NK population. (A-C) Rice plants grown in control condition for (A) 20 days (B) 34 days (C) 50 days after seeding. (D-F) Rice plants treated by 150 mM NaCl. Photo was... 15
Figure 3. Frequency distributions of Salt stress traits range in NK rice population. (A, B, C) Graph of standard evaluation score (SES). (D, E, F) Graph of Reduction rate (RDR). (G, H, I) Graph of shoot dry weight(SDW). 16
Figure 4. population structure analysis of NK rice population. (A) Principal Component Analysis (PCA). orange, blue, red, blue, green represent the TemJ, TroJ, Aro, Aus, Ind rice variety, respectively. (B) NJ-... 18
Figure 5. Manhattan plots and quantile-quantile(Q-Q) plots of GWAS for 2019, 2020 and 2021 SES traits of 190 rice accessions. The horizontal red line indicated thresholds(-log ₁₀(p)=5.934). (A) 2019... 20
Figure 6. Manhattan plots and quantile-quantile(Q-Q) plots of GWAS for 2020 and 2021 RDR (reduction rate=((normal condition-stress condition)/normal condition) x100). traits of 190 rice... 21
Figure 7. Manhattan plots and quantile-quantile(Q-Q) plots of GWAS for 2019, 2020 and 2021 SDW (shoot dry weight) traits of 190 rice accessions. The horizontal red line indicated thresholds (-... 22
Figure 8. Haplotype analysis result of OsMAR1 for salt stress tolerance on chromosome 6. (A) LD plot shows association loci for OsMAR1. (B) Gene structure and haplotype analysis of OsMAR1. A... 28
Figure 9. Haplotype analysis result of OsMAPK4/OsMSRMK3 for salt stress tolerance on chromosome 6. (A) LD plot shows association loci for OsMAPK4/OsMSRMK3. (B) Gene structure and haplotype... 29
Figure 10. Haplotype analysis result of OsAPX2 for salt stress tolerance on chromosome 7. (A) LD plot shows association loci for OsAPX2. (B) Gene structure and haplotype analysis of OsAPX2. A schematic... 30
Figure 11. Haplotype analysis result of OsSOS1 for salt stress tolerance on chromosome 12. (A) LD plot shows association loci for OsSOS1. (B) Gene structure and haplotype analysis of OsSOS1. A schematic... 31
Figure 12. Haplotype analysis result of LOC_Os03g06710 for salt stress tolerance on chromosome 3. (A) LD plot shows association loci for LOC_Os03g06710. (B) Gene structure and haplotype analysis... 32
Figure 13. Haplotype analysis result of LOC_Os06g26234 for salt stress tolerance on chromosome 6. (A) LD plot shows association loci for LOC_Os06g26234. (B) Gene structure and haplotype analysis... 33
Figure 14. Haplotype analysis result of LOC_Os07g10230 for salt stress tolerance on chromosome 7. (A) LD plot shows association loci for LOC_ Os07g10230. (B) Gene structure and haplotype analysis... 34
Figure 15. Haplotype analysis result of LOC_Os07g31884 for salt stress tolerance on chromosome 7. (A) LD plot shows association loci for LOC_Os07g31884. (B) Gene structure and haplotype analysis... 35
Figure 16. Haplotype analysis result of LOC_Os11g17014 for salt stress tolerance on chromosome 11. (A) LD plot shows association loci for LOC_ Os11g17014. (B) Gene structure and haplotype analysis... 36