A Genome-Wide Association Study of Seed Size Traits in Soybean Germplasm : GWAS 분석을 통한 콩 유전자원의 종자 크기 관련 유전체 영역 확인

다국어 초록 (Multilingual Abstract)

Seed size is a key determinant of yield and market quality in soybean (Glycine max L. Merr.), yet its underlying genetic regulation remains incompletely understood. To elucidate the genomic basis of seed morphology, a genome-wide association study (GWAS) was conducted on 269 soybean accessions genotyped with 108,221 high-quality SNPs. Four major seed-size traits (seed length, width, thickness, and 100-seed weight) were evaluated under field conditions. Significant associations were identified on several chromosomes, with the strongest and most consistent signals on chromosomes 2 and 11. The lead SNP on Chr 2 (AX-90386436) was associated with seed length and 100-seed weight, whereas the lead SNP on Chr 11 (AX-90470426) influenced seed width and thickness. Linkage disequilibrium (LD) analysis revealed key candidate genes within these regions, including Glyma.02G148800 (ubiquitin-conjugating enzyme), Glyma.02G149100 (glutaredoxin), Glyma.11G162800 (expansin), and Glyma.11G163300 (WRKY transcription factor), which play roles in protein turnover, redox regulation, and cell-wall expansion. Two-locus analysis (Chr 2 × Chr 11) demonstrated a significant epistatic interaction (p < 0.001), where the G–T allelic combination produced the largest seed dimensions and heaviest seed weight, reflecting coordinated genetic control. These findings provide new insights into the polygenic and interactive nature of seed-size regulation in soybean. The identified loci and interacting alleles offer valuable molecular targets for marker-assisted selection (MAS) and genomic breeding strategies aimed at improving seed yield and quality. Keywords: Soybean (Glycine max), GWAS, seed size, 100-seed weight, linkage disequilibrium, allelic interaction, candidate genes, epistasis. * A thesis submitted to the Council of the Graduate School of Kyungpook National University in partial fulfillment of the requirements for the degree of Master of Agriculture in December 2025

목차 (Table of Contents)

• 1.0 Introduction 1
• 1.1 Understanding genome-wide association studies (GWAS) 1
• 1.2 Procedure of GWAS 2
• 1.3 Importance of GWAS and genetic mapping in soybean trait discovery 3
• 1.3.1 Importance of GWAS 3
• 1.3.2 Importance of genetic mapping 4
• 1.3.3 The combination of using GWAS and genetic mapping 5
• 1.4 Understanding the genetic architecture of soybean seed traits 6
• 1.5 Soybean Traits Discovery through the use of GWAS and Genetic Mapping 7
• 1.6 Previous Studies on Soybean Seed Traits Using GWAS 9
• 1.7 Comprehensive Seed Trait Studies 12
• 2. Objectives of the study 13
• 3. Materials and Methods 16
• 3.1 Plant materials 16
• 3.2 Phenotypic assessment and statistical analysis 16
• 3.3 Genotypic data and SNP filtering 17
• 3.4 Population structure and kinship analysis 17
• 3.5 Genome-wide association study (GWAS) 18
• 3.6 Linkage disequilibrium (LD) and haplotype block analysis 18
• 3.7 Candidate gene identification and functional annotation 19
• 3.8 Allelic and two-locus interaction analyses 19
• 4. Results 21
• 4.1 Descriptive statistics and distribution of seed traits 21
• 4.2 Analysis of variance and correlation analysis 25
• 4.2.1 Analysis of variance 25
• 4.2.2 Correlation analysis 28
• 4.3 Population structure and kinship analysis 28
• 4.3.1 Population Structure 28
• 4.4 Genome-Wide Association Study (GWAS) for Seed Size Traits 31
• 4.4.1 Trait-specific associations 31
• Seed Length 31
• 4.5 Linkage disequilibrium analysis 36
• 4.5.1 LD Block on Chromosome 2 (15.07–15.57 Mb) 36
• 4.5.2 LD block on chromosome 11 (14.82–15.82 Mb) 36
• 4.7 Allele class analysis of significant SNPs 46
• 4.7.1 Single-locus allelic effects chromosome 2 (AX-90386436) 46
• Single-locus allelic effects Chromosome 11 (AX-90470426) 47
• 4.7.2 Two-locus allelic effects (chromosome 2 allele × chromosome 11 allele) 47
• Seed length 48
• Seed width 48
• Seed thickness 49
• 100-seed weight 49
• 5. Discussion 55
• 5.1 Phenotypic variation and statistical analysis 55
• 5.2 Population structure and kinship 56
• 5.3 Significant genomic regions from GWAS 56
• 5.3.1 Functional interpretation of chromosome 2 (15.79–15.81 Mb) 57
• 5.3.2 Functional interpretation of chromosome 11 (15.29–15.36 Mb) 57
• 5.4 Possible candidate genes 58
• 5.4.1 Chromosome 2: ubiquitin–redox–epigenetic complex regulating seed length and 100-seed weight 58
• 5.4.2 Chromosome 11: hormonal and structural network influencing seed width and thickness 59
• 5.4.3 Integrative perspective 60
• 5.5 Allele class analysis of significant SNPs discussion 61
• 6. Conclusion 64
• REFERENCES 65