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Acta Agronomica Sinica ›› 2025, Vol. 51 ›› Issue (7): 1747-1756.doi: 10.3724/SP.J.1006.2025.44221

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

QTL mapping and candidate gene screening for branch number in soybean

HU Meng(), SHA Dan, ZHANG Sheng-Rui, GU Yong-Zhe, ZHANG Shi-Bi, LI Jing, SUN Jun-Ming(), QIU Li-Juan(), LI Bin()   

  1. The State Key Laboratory of Crop Gene Resources and Breeding / National Engineering Research Center for Crop Molecular Breeding / Key Laboratory of Soybean Biology (Beijing), Ministry of Agriculture and Rural Affairs / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2024-12-31 Accepted:2025-04-27 Online:2025-07-12 Published:2025-05-09
  • Contact: *E-mail: libin02@caas.cn; E-mail: sunjunming@caas.cn; E-mail: qiulijuan@ caas.cn
  • Supported by:
    Biological Breeding-National Science and Technology Major Project(2023ZD0403701);Agricultural Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences

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Abstract:

Soybean (Glycine max L.) is a vital crop widely used in both the food and feed industries. Branch number is a key agronomic trait that significantly influences soybean yield. In this study, we employed a recombinant inbred line (RIL) F2:7-8 population derived from a cross between the low-branching cultivar Zhonghuang 35 and the high-branching cultivar Zhonghuang 13. A high-density genetic linkage map constructed from resequencing-based genotypic data was used to identify quantitative trait loci (QTL) associated with branch number across five different planting environments, using the inclusive composite interval mapping (ICIM) method implemented in QTL IciMapping software. A total of six QTLs related to branch number were detected on chromosomes 2, 6, 18, and 19. Among them, qVBN02-1, located on chromosome 2, was consistently identified in two environments and accounted for an average of 16.07% of the phenotypic variance, indicating that it is a novel, stable, and major QTL for branch number. This QTL spans a genetic interval of 0.3 cM, corresponding to a physical distance of 261.37 kb and encompassing 29 annotated genes. By analyzing missense single nucleotide polymorphisms (SNPs) between the two parental lines within this region, we identified 22 potential candidate genes. Gene Ontology (GO) annotation revealed that these genes are involved in various biological processes critical to plant growth and development. This study not only provides valuable molecular markers for improving soybean plant architecture but also lays a foundation for the fine mapping and functional characterization of genes regulating branch number in soybean.

Key words: soybean (Glycine max L.), branch number, recombinant inbred line (RIL), QTL mapping, candidate gene

Fig. 1

Phenotypic characteristics of the parental lines of the soybean RIL population"

Table 1

Descriptive statistics, ANOVA and broad-sense heritability of branch number in 192 RILs soybean across five environments"

环境
Environ-
ment		 数量
Number		 亲本
Parent		 最小值Min. 最大值Max. 平均值Mean 标准差
SD		 变异系数
CV (%)		 方差分析P值
ANOVA P-value		 广义
遗传力
H2
中黄35
ZH35		 中黄13
ZH13		 显著性
Sig.		 环境
E		 基因型
G
2020SY 192.00 0.80 5.00 0.00* 0.20 7.00 2.88 1.29 44.70 <0.01 <0.05 0.54
2021CP 184.00 0.00 2.25 0.02* 0.00 11.40 4.04 2.14 52.94
2020NK 150.00 2.00 2.80 0.74 0.00 8.67 2.63 1.61 61.24
2022BPC 180.00 5.40 8.33 0.02* 0.00 16.60 4.68 3.46 73.86
2023CP 177.00 0.51 1.15 0.07 0.00 8.20 1.95 1.43 73.32

Fig. 2

Frequency distribution of branch number in the soybean RIL population across five environments Abbreviations are the same as those given in Table 1. ZH35 indicates the maternal Zhonghuang 35; ZH13 indicates the paternal Zhonghuang 13; black arrows indicate the branch number of two parents."

Table 2

QTL mapping results for branch number in soybean"

QTL名称
QTL name		 环境
Environment		 染色体
Chromosome		 位置
Position		 左标记
Left marker		 右标记
Right marker		 LOD值
LOD score		 贡献率
PVE (%)		 加性效应
Add
qVBN02-1 2020SY 2 172.30 bin296 bin295 32.90 16.10 1.13
2021CP 2 172.40 bin296 bin295 20.93 16.04 1.44
qVBN02-2 2021CP 2 183.50 bin283 bin284 11.68 8.19 -1.03
qVBN06-1 2020SY 6 123.50 bin1433 bin1432 7.95 2.81 -0.47
qVBN06-2 2021CP 6 136.10 bin1411 bin1410 7.00 4.52 -0.76
qVBN18 2020SY 18 186.90 bin4543 bin4544 7.12 2.48 -0.44
qVBN19 2022BPC 19 138.30 bin4814 bin4815 4.23 10.39 -1.12

Fig. 3

QTL for branch number in soybean genetic linkage map"

Table 3

Mapping result of epstatic QTL for branch number in soybean"

环境
Environment		 染色体1
Chr.1		 位置1
Pos.1		 染色体2
Chr.2		 位置2
Pos.2		 LOD值
LOD score		 贡献率
PVE (%)		 加性效应1
Add 1		 加性效应2
Add 2		 加性互作
Add by Add
2022BPC 6 115.00 6 120.00 5.90 2.68 1.74 -2.00 -2.90
2022BPC 18 100.00 18 110.00 5.35 2.54 2.54 -2.65 -1.94

Table 4

Genes with missense variations between the two parents within the genomic region of the major locus qVBN02-1 for branch number in soybean"

基因ID
Gene ID		 亲本间变异
Inter-parental variation		 变异类型
Type of mutation		 功能注释
Functional description
Glyma.02G059500 SNP 非同义单核苷酸变异
Nonsynonymous SNV		 PQ环重复序列家族蛋白
PQ ring repeat sequence family protein
Glyma.02G059700 SNP 非同义单核苷酸变异/提前终止
Nonsynonymous SNV/stopgain		 受体样激酶
Receptor-like kinase
Glyma.02G059900 InDel 非移码缺失
Nonframeshift deletion		 泛素结合蛋白家族
Ubiquitin-binding protein family
Glyma.02G060000 SNP/InDel 非同义单核苷酸变异/移码插入
Nonsynonymous SNV/frameshift insertion		 BEL家族蛋白BLH4
BEL family protein BLH4
Glyma.02G060200 SNP/InDel 同义单核苷酸变异/移码插入
Synonymous SNV/frameshift insertion		 BTB/POZ结构域的蛋白质
Protein with BTB/POZ structural domain
Glyma.02G060500 SNP/InDel 同义单核苷酸变异/非同义单核苷酸变异/移码缺失
Synonymous SNV/nonsynonymous SNV/frameshift deletion		 SET结构域蛋白SUVR5
SET structural domain protein SUVR5
Glyma.02G060700 SNP/InDel 同义单核苷酸变异/非同义单核苷酸变异/移码插入
Synonymous SNV/nonsynonymous SNV/frameshift insertion		 电子转运蛋白
Electron transport protein
Glyma.02G060800 SNP 同义单核苷酸变异/非同义单核苷酸变异
Synonymous SNV/nonsynonymous SNV		 CAP超家族蛋白
CAP superfamily protein
Glyma.02G060900 SNP 同义单核苷酸变异/非同义单核苷酸变异Synonymous SNV/nonsynonymous SNV 未知蛋白
Unknown protein
Glyma.02G061000 SNP 同义单核苷酸变异/非同义单核苷酸变异Synonymous SNV/nonsynonymous SNV 未知蛋白
Unknown protein
Glyma.02G061500 SNP 非同义单核苷酸变异
Nonsynonymous SNV		 未知蛋白
Unknown protein
Glyma.02G061700 SNP/InDel 非同义单核苷酸变异/移码缺失
Nonsynonymous SNV/frameshift deletion		 蛋白激酶超家族蛋白
Protein kinase superfamily protein
Glyma.02G061800 SNP/InDel 非同义单核苷酸变异/提前终止
Nonsynonymous SNV/stopgain		 未知蛋白
Unknown protein
Glyma.02G061900 SNP 同义单核苷酸变异/非同义单核苷酸变异Synonymous SNV/nonsynonymous SNV 液泡蛋白分选相关蛋白
Vesicle protein sorting related protein
Glyma.02G062000 SNP 非同义单核苷酸变异
Nonsynonymous SNV		 未知蛋白
Unknown protein
Glyma.02G062100 SNP 同义单核苷酸变异
Synonymous SNV		 未知蛋白
Unknown protein
Glyma.02G062200 SNP 非同义单核苷酸变异
Nonsynonymous SNV		 磷酸吡哆醇依赖性转移酶超家族蛋白
Pyridoxal phosphate-dependent transferase superfamily protein
Glyma.02G062300 SNP 同义单核苷酸变异/非同义单核苷酸变异
Synonymous SNV/nonsynonymous SNV		 G-α蛋白
G-α protein
Glyma.02G062400 SNP 非同义单核苷酸变异
Nonsynonymous SNV		 脯氨酰寡肽酶家族蛋白
Prolyl oligopeptidase family protein
Glyma.02G062500 SNP 同义单核苷酸变异/非同义单核苷酸变异
Synonymous SNV/nonsynonymous SNV		 磷酸吡哆醇依赖性转移酶超家族蛋白
Pyridoxal phosphate-dependent transferase superfamily protein
Glyma.02G062700 SNP 同义单核苷酸变异/非同义单核苷酸变异
Synonymous SNV/nonsynonymous SNV		 锌指结构的OBP1|OBF结合蛋白
Zinc finger structure of OBP1|OBF binding protein
Glyma.02G063800 InDel 非移码插入
Nonframeshift insertion		 MLO家族蛋白
MLO family protein
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