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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (6): 1532-1541.doi: 10.3724/SP.J.1006.2023.24121

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

Mapping soybean protein QTLs based on high-density genetic map

LIU Ting-Xuan1,2,**(), GU Yong-Zhe2,**(), ZHANG Zhi-Hao3, WANG Jun1,*(), SUN Jun-Ming2,*(), QIU Li-Juan1,2,*()   

  1. 1Yangtze University, Jingzhou 434025, Hubei, China
    2National Key Facility for Gene Resources and Genetic Improvement of MARA/Beijing Key Laboratory of Soybean Biology of MARA/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    3College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
  • Received:2022-05-19 Accepted:2022-10-10 Online:2023-06-12 Published:2022-10-20
  • Contact: *E-mail: qiulijuan@caas.cn;E-mail: wangjagri@yangtzeu.edu.cn;E-mail: qiulijuan@caas.cn
  • About author:First author contact:**Contributed equally to this work
  • Supported by:
    Sino-Uruguayan Joint Laboratory(2018YFE0116900)

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Abstract:

Soybean is an important food crop and economic crop, and its grain protein is about 40%, which is one of the main sources of high-quality vegetable protein. Mining the quantitative trait loci (QTL) that control soybean high protein and molecular marker breeding are of great significance for the breeding of high protein soybean. In this study, a recombinant inbred line population consisting of 192 lines constructed by crossing Zhonghuang 35 (ZH35) and Zhonghuang 13 (ZH13) with significant differences in protein content was used as the experimental materials. A high-density genetic map containing 4879 bin markers was constructed with the total genetic distance of 3760.71 cM and the genetic distance between adjacent markers of 0.77 cM by resequencing the two parents and the RIL population. The RIL population and its parents were grown in Shunyi, Beijing and Puyang, Henan, respectively. A total of 15 protein content-related QTL loci were detected in the two environments, which were distributed on chromosomes 5, 12, 15, 17, 18, 19, and 20, respectively. The contribution rate was 4.36%-11.39%, among which, qPro-20-1 and qPro-20-3 were detected in Shunyi, Beijing and Puyang, Henan, respectively. The contribution rates of the two QTLs were 7.65% and 7.58%, respectively, and the overlapping regions included 33 genes. This study is helpful for fine mapping and map-based cloning of soybean protein content-related genes, and provides genetic resources for further breeding of high-protein soybean varieties.

Key words: soybean, protein content, recombinant inbred lines, bin map, QTL mapping

Table 1

Statistical analysis of protein content in two generations of parents recombinant inbred lines"

环境
Environment		 中黄35
Zhonghuang 35
(mean±SD, %)		 中黄13
Zhonghuang 13 (mean±SD, %)		 RIL群体RIL population
最大值
Max. (%)		 最小值
Min. (%)		 变异系数
CV (%)		 峰度
Kurtosis		 偏度
Skewness
北京顺义
Shunyi, Beijing		 38.24±0.17 44.99±0.25 46.00 37.51 2.48 0.22 -0.07
河南濮阳
Puyang, Henan		 38.20±0.22 44.20±0.32 45.98 37.04 2.98 -0.17 0.02

Fig. 1

F2:6 population protein content phenotype box plots in two environments ***: P < 0.001."

Fig. 2

Distribution of protein content and oil phenotype of ZH35/ZH13 RIL population and parents A: the distribution of protein content of RIL population in Shunyi, Beijing; B: the distribution of protein content of RIL population in Puyang, Henan. ZH35: Zhonghuang 35; ZH13: Zhonghuang 13. RIL: the recombinant inbred lines."

Fig. 3

Linkage group marker distribution map X-axis represents chromosome number; Y-axis represents genetic distance (cM); the blue represents the bin mark."

Table 2

Information of molecular on the RIL linkage map derived from Zhonghuang 35/Zhonghuang 13"

染色体
Chr.		 上图标记数
Total marker		 总图距
Total distance (cM)		 平均图距
Average distance (cM)		 小于5 cM gap数量/gap总数×100%
Gap less than 5 cM/gap total number×100%
Chr.01 247 169.29 0.69 100
Chr.02 264 213.61 0.81 99.62
Chr.03 301 179.80 0.60 100
Chr.04 226 205.36 0.91 99.56
Chr.05 203 177.41 0.87 100
Chr.06 290 291.38 1.00 98.62
Chr.07 235 186.79 0.79 100
Chr.08 289 216.94 0.75 100
Chr.09 245 183.47 0.75 100
Chr.10 227 199.14 0.88 100
Chr.11 214 219.26 1.02 98.13
Chr.12 205 163.48 0.80 99.02
Chr.13 126 96.81 0.77 97.62
Chr.14 204 153.72 0.75 99.51
Chr.15 402 215.29 0.54 99.75
Chr.16 209 158.00 0.76 100
Chr.17 220 192.44 0.87 99.55
Chr.18 266 198.39 0.75 99.25
Chr.19 299 176.74 0.59 100
Chr.20 207 163.40 0.79 99.52
平均Average 243.95 188.03 0.77 99.51

Table 3

QTLs for soybean protein content detected in two environments"

环境
Environment		 位点名称
QTL name		 染色体
Chr.		 定位区间
Mapping interval (bp)		 QTL位置
Position (cM)		 阈值
LOD		 加性效应
Additive
effect		 贡献率
R2 (%)		 报道位点
Reported locus
北京顺义
Shunyi, Beijing		 qPro-15-1 15 bin3524-bin3532 71.51 3.05 0.33 5.13 [40][41]
qPro-17-1 17 bin4087-bin4090 19.41 2.71 -0.31 4.63 New
qPro-17-2 17 bin4095-bin4110 28.11 3.67 -0.36 6.21 New
qPro-18-1 18 bin4523-bin4526 170.21 2.57 -0.31 4.44 New
qPro-18-2 18 bin4525-bin4529 175.91 4.14 -0.39 7.26 New
qPro-19-1 19 bin4807-bin4811 130.71 2.57 -0.31 4.38 [42]
qPro-19-2 19 bin4816-bin4821 140.61 3.41 -0.36 5.77 [42]
qPro-19-3 19 bin4824-bin4829 147.41 2.85 -0.33 4.88 New
qPro-20-1 20 bin5059-bin5063 161.01 4.48 -0.40 7.65 New
河南濮阳
Puyang, Henan		 qPro-5-1 5 bin1167-bin1170 84.81 2.67 -0.38 4.83 [39]
qPro-5-2 5 bin1161-bin1164 91.41 4.82 -0.50 8.51 [36] [37] [38]
qPro-5-3 5 bin1154 100.71 3.50 -0.43 6.29 [36] [36] [38]
qPro-12-1 12 bin2906-bin2911 95.01 3.42 0.42 5.94 New
qPro-20-2 20 bin5046-bin5049 150.61 4.14 -0.46 7.28 New
qPro-20-3 20 bin5057-bin5060 159.11 4.33 -0.47 7.58 New

Fig. 4

Correlation analysis between genotype and phenotypic by bin5059 and bin5060 markers in overlapping regions (A): the correlation analysis between genotype and phenotype of bin5059; (B): the correlation analysis between genotype and phenotype of bin5060. The abscissa is the genotype, low protein is denoted as a and A, high protein content is denoted as band B, and the vertical ordinate is the number of protein content. **: P < 0.01."

Table 4

Functional annotation of candidate genes within overlapping interval"

基因名称
Gene name		 功能注释
Functional annotation
Glyma.20G237700 α/β-水解酶折叠蛋白 Alpha/beta-Hydrolase fold-containing protein
Glyma.20G237800 植物转化酶/果胶甲酯酶抑制剂 Plant invertase/pectin methylesterase inhibitor
Glyma.20G238000 脂质生物合成过程 Lipid biosynthetic process
Glyma.20G238400 WD40重复蛋白 WD40 repeat-containing protein
Glyma.20G238500 预测PRP38剪接因子 Predicted PRP38-like splicing factor
Glyma.20G238600 线粒体靶向单链DNA结合蛋白 Mitochondrially targeted single-stranded DNA binding protein
Glyma.20G238700 蛋白质去磷酸化; 蛋白质丝氨酸/苏氨酸磷酸酶活性
Protein dephosphorylation; protein serine/threonine phosphatase activity
Glyma.20G238800 锌指(C3HC4型环指)家族蛋白; BRCT结构域蛋白/RING/U-box蛋白
Zinc finger (C3HC4-type RING finger) family protein; BRCT domain-containing protein/RING/U-box protein
Glyma.20G238900 磷酸甘油酸变位酶家族蛋白 Phosphoglycerate mutase family protein
Glyma.20G239000 干旱响应家族蛋白; 干旱诱导的19蛋白(Di19), 锌结合
Drought-responsive family protein; rought induced 19 protein (Di19), zinc-binding
Glyma.20G239100 细胞内蛋白质转运; 囊泡介导的转运 Intracellular protein transport; vesicle-mediated transport
基因名称
Gene name		 功能注释
Functional annotation
Glyma.20G239200 蛋白质转运; 导入α亚型 Protein transport; importin alpha isoform
Glyma.20G239300 多核苷酸转移酶, 核糖核酸酶H样超家族蛋白; 3¢-5¢外切酶活性
Polynucleotidyl transferase, ribonuclease H-like superfamily protein; 3¢-5¢ exonuclease activity
Glyma.20G239600 分泌相关的RAS超家族2; 细胞内蛋白质转运
Secretion-associated RAS super family 2; intracellular protein transport
Glyma.20G239700 PsbP样蛋白2; 光系统II氧进化复合物 PsbP-like protein 2; photosystem II oxygen evolving complex
Glyma.20G239800 跨膜转运; ATP酶活性, 与物质的跨膜运动相耦合
Transmembrane transport; ATPase activity, coupled to transmembrane movement of substances
Glyma.20G240000 碳水化合物代谢过程; β-N-乙酰氨基己糖苷酶活性
Carbohydrate metabolic process; beta-N-acetylhexosaminidase activity
Glyma.20G240200 多核苷酸转移酶, 核糖核酸酶H样超家族蛋白
Polynucleotidyl transferase, ribonuclease H-like superfamily protein
Glyma.20G240300 谷胱甘肽代谢过程; 谷胱甘肽转移酶活性 Glutathione metabolic process; glutathione transferase activity
Glyma.20G240400 质体转录活性17; 钴胺素合成蛋白 Plastid transcriptionally active 17; cobalamin synthesis protein
Glyma.20G240500 裂解和多腺苷酸化特异性因子(CPSF) A亚基蛋白; 通过剪接体剪接mRNA
Cleavage and polyadenylation specificity factor (CPSF) A subunit protein; mRNA splicing, via spliceosome
Glyma.20G240600 α/β-水解酶超家族蛋白; 脂质代谢过程 Alpha/beta-Hydrolases superfamily protein; lipid metabolic process
Glyma.20G240700 核糖体L29家族蛋白; 核糖体的结构成分 Ribosomal L29 family protein; structural constituent of ribosome
Glyma.20G240800 果胶裂解酶样超家族蛋白; 果胶分解代谢过程 Pectin lyase-like superfamily protein; pectin catabolic process
Glyma.20G240900 脂质生物合成过程 Lipid biosynthetic process

Fig. 5

Relative expression levels of seeds at the different developmental stages in the candidate interval of SoyBase website"

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