Identification of Flowering Time-Associated SNPs Through Genome-Wide Association Study in Soybean Germplasm : GWAS 분석을 통한 콩 유전자원의 개화기 관련 유전체 영역 확인

다국어 초록 (Multilingual Abstract)

Flowering time is a critical adaptive trait in soybean (Glycine max L.), shaping maturity, yield stability, and regional adaptation. To uncover its genetic basis, genome-wide association studies (GWAS) were conducted using 269 soybean accessions evaluated in replicated field trials, complemented by a larger panel of 1000 accessions. A total of 108,221 high-quality SNPs were analyzed to assess population structure, linkage disequilibrium (LD), and marker–trait associations. A major genomic region influencing flowering time was consistently identified on chromosome 11, where the Nuclear Factor Y subunit B11 (NFYB11; Glyma.11G183100) gene emerged as the most plausible candidate. NFYB11 interacts with CONSTANS-like proteins to activate FT expression, a central component of the photoperiodic flowering pathway. Additional loci on chromosomes 10 and 3 corresponded to previously reported flowering QTLs, including proximity to the maturity gene E2 (Glyma.10G221500). For flower colour, significant SNPs were restricted to chromosome 13, confirming the classical W1 locus encoding flavonoid 3′5′-hydroxylase (F3′5′H), which determines purple versus white pigmentation. Collectively, these findings validate known flowering and pigmentation genes in soybean and highlight NFYB11 as a key regulatory candidate controlling natural variation in flowering time. Keywords: Soybean (Glycine max), Flowering time; NFYB11, Genome-wide association study (GWAS), E2 (GIGANTEA), Flavonoid 3′5′-hydroxylase (F3′5′H). * 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

국문 초록 (Abstract)

개화 시기는 콩(Glycine max L.)에서 성숙도, 수량 안정성, 지역 적응성을 좌우하는 매우 중요한 적응 형질이다. 본 연구에서는 그 유전적 기반을 규명하기 위해, 반복된 포장 실험에서 평가된 269개 콩 재래종과 추가로 1000개 재래종 패널을 이용하여 전장 유전체 연관 분석(GWAS)을 수행하였다. 총 108,221개의 고품질 SNP를 분석하여 집단구조, 연관불평형(LD), 그리고 마커–형질 연관성을 평가하였다. 그 결과, 개화 시기에 영향을 미치는 주요 유전체 영역이 11번 염색체에서 일관되게 확인되었으며, 그 안에서 Nuclear Factor Y 서브유닛 B11(NFYB11; Glyma.11G183100) 유전자가 가장 가능성 높은 후보로 나타났다. NFYB11은 CONSTANS 유사 단백질과 상호작용하여 FT 발현을 활성화하는데, 이는 광주기 개화 경로의 핵심 구성 요소이다. 추가적으로 10번 및 3번 염색체에서 확인된 다른 좌위들은 성숙 유전자 E2(Glyma.10G221500) 주변을 포함하여, 기존에 보고된 개화 QTL과 일치하였다. 꽃 색깔의 경우, 유의한 SNP는 13번 염색체에만 집중되어 있었으며, 이는 자색과 백색의 색소 차이를 결정하는 flavonoid 3′5′-hydroxylase(F3′5′H)를 암호화하는 고전적 W1 유전자 좌위임을 확인해 주었다. 요약하면, 본 연구 결과는 콩에서 알려진 개화 및 색소 형성 관련 유전자를 재확인하는 한편, 자연적인 개화 시기 변이를 조절하는 핵심 조절 후보 유전자로 NFYB11의 중요성을 부각시킨다.

목차 (Table of Contents)

• 1. Introduction 1
• 1.1 Role of maturity and flowering time 3
• 1.2 Photoperiod sensitivity and soybean maturity 4
• 1.3 Genetic control of flowering time in soybean 6
• 1.4 Environmental factors influencing soybean flowering and maturity 7
• 1.5 Maturity group classification and geographic adaptation 9
• 1.6 Genotyping techniques for soybean phenology studies 10
• 1.7 GWAS for dissecting flowering and maturity traits in soybean 11
• 1.8 SNP analysis using GWAS 12
• 2. The objectives of this study 14
• 3. Materials and methods 16
• 3.1 Plant materials 16
• 3.2 Experimental design and field layout 16
• 3.3 Growth conditions and crop management 17
• 3.4 Phenotypic data collection 17
• 3.5 Genome-Wide Association Study 18
• 3.5.1 SNP density analysis 19
• 3.5.2 Population structure and kinship analysis 19
• 3.5.3 Statistical model 20
• 3.5.4 Significance thresholds 20
• 3.6 Linkage disequilibrium (LD) analysis 20
• 3.7 Allele class analysis of lead SNPs 21
• 3.8 Haplotype structure analysis 21
• 3.9 Data analysis 22
• 4. Results 23
• 4.1 Descriptive statistics of phenotypic traits 23
• 4.2 Analysis of variance (ANOVA) 23
• 4.3 Distribution of traits across replications 23
• 4.4 Population structure and kinship 30
• 4.5 SNP density 30
• 4.6 Genome-wide association study 35
• 4.6.1 Flowering time 35
• 4.6.2 Flower color 35
• 4.7 Linkage disequilibrium (LD) analysis (Results) 40
• 4.7.1 Genome-wide LD decay 40
• 4.7.2 Local LD block analysis around AX-90512649 40
• 4.8 Haplotype variation and its association with flowering time 45
• 4.9 Allele class analysis of significant SNPs 47
• 4.9 Candidate gene annotation 49
• 4.9.1 Candidate gene for flowering time 49
• 4.9.2 Candidate genes for flower color 49
• 5. Discussion 52
• 6. Conclusion 57
• 7. References 59
• Abstact In Korean 66