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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (12): 3277-3288.doi: 10.3724/SP.J.1006.2023.34031

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

Genome-wide association study for amino acid content at R6 stage in soybean (Glycine max L.) seed

ZHANG Hong-Mei1(), XIONG Ya-Wen2, XU Wen-Jing3, ZHANG Wei1, WANG Qiong1, LIU Xiao-Qing1, LIU Hui3, CUI Xiao-Yan1, CHEN Xin1, CHEN Hua-Tao1,2,*()   

  1. 1Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
    2College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
    3College of Horticulture, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
  • Received:2023-02-20 Accepted:2023-05-24 Online:2023-12-12 Published:2023-06-09
  • Contact: * E-mail: cht@jaas.ac.cn
  • Supported by:
    Key Research and Development Project of Jiangsu Province(BE2019376);Key Research and Development Project of Jiangsu Province(BE2022328);Jiangsu Agricultural Science and Technology Innovation Fund(CX(22)5002);Jiangsu Agricultural Science and Technology Innovation Fund(CX(21)3117);Open Competition Project of Seed Industry Revitalization of Jiangsu Province(JBGS[2021]060);National Natural Science Foundation of China(32001455)

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Abstract:

In order to analyze the genetic mechanism of amino acid content in soybean seeds at R6 stage, the contents of arginine, alanine, glutamic acid, and aspartic acid related to flavor quality of vegetable soybean were determined using 264 soybean germplasm materials in 2020 and 2021, and genome-wide association analysis (GWAS) was performed. The results showed that a total of 89 SNP loci were significantly associated with the contents of four amino acids at R6 stage in soybean in two years, among which 5 SNPs [S03_40647948 (Chr. 3), S05_2727464 (Chr. 5), S10_4122977 (Chr. 10), S17_34559022 (Chr. 17), and S19_48541685 (Chr. 19)] could be repeatedly detected by two years or two traits, respectively, which explained 11.25%-28.19% of phenotypic variation. The SNP marker S17_34559022 on Chr. 17 was significantly associated with glutamic acid content in different environments, which belonged to a stable genetic locus. A total of 9 candidate genes were excavated, including bHLH (bHLH DNA-binding superfamily protein), auxin-responsive protein family, and aspartyl protease family protein, it may be an important gene that affected amino acid content. In this study, 5 amino acid content dominant SNP sites and 9 candidate genes were excavated, which provided an insight into the genetic basis of amino acid content in soybean seed at R6 stage and laid a foundation for further mechanism exploration and breeding for flavor quality of vegetable soybean.

Key words: soybean [Glycine max (L.) Merr.], R6 stage, seed, amino acid contents, GWAS, candidate gene

Table 1

Phenotypic variation of amino acid content in soybean at R6 stage"

性状
Trait		 年份
Year		 平均值
Mean		 标准差
SD		 变幅
Range		 变异系数
CV (%)
Arg 2020 1.23 1.75 0.00-6.79 24.95
2021 1.22 0.81 0.22-4.83 69.20
Ala 2020 0.44 0.83 0.00-5.03 17.56
2021 1.35 0.86 0.29-4.96 63.38
Glu 2020 0.82 0.96 0.00-4.75 36.73
2021 1.15 0.81 0.05-4.79 83.47
Asp 2020 0.23 0.61 0.00-4.08 24.21
2021 0.67 0.55 0.10-5.62 86.23

Table S1

Analysis of variance (ANOVA) for amino acid of soybean seed at R6 stage in two years"

年份 氨基酸 变异来源 自由度 均方 F值
Year Amino acid Source of variation DF MS F-value
2020 精氨酸Arginine 基因型 Genotype 219 10.07 248.21**
重复 Replication 2 0.22 5.48**
误差 Residual error 438 0.04
丙氨酸Alanine 基因型 Genotype 220 2.09 254.15**
重复 Replication 2 0.05 6.48**
误差 Residual error 440 0.01
谷氨酸Glutamic acid 基因型 Genotype 219 2.79 147.16**
重复 Replication 2 0.18 9.46**
误差 Residual error 438 0.02
天冬氨酸Aspartic acid 基因型 Genotype 219 1.10 239.36**
重复 Replication 2 0.03 6.56**
误差 Residual error 438 0
2021 精氨酸Arginine 基因型 Genotype 239 1.94 96.44**
重复 Replication 2 0.38 19.07**
误差 Residual error 478 0.02
丙氨酸Alanine 基因型 Genotype 247 2.204895 72.78**
重复 Replication 2 0.140069 4.62*
误差 Residual error 494 0.030295
谷氨酸Glutamic acid 基因型 Genotype 243 4.31 132.85**
重复 Replication 2 0.32 9.81**
误差 Residual error 486 0.03
天冬氨酸Aspartic acid 基因型 Genotype 236 0.92 105.30**
重复 Replication 2 0.03 3.03*
误差 Residual error 472 0.01

Fig. 1

Frequency distribution of amino acid content in soybean at R6 stage for two years"

Table 2

Correlation analysis of amino acid content in soybean natural population at R6 stage"

性状Trait 年份Year Arg Ala Glu
Ala 2020 0.337** 1
2021 0.512** 1
Glu 2020 0.008 0.012 1
2021 0.403** 0.545** 1
Asp 2020 -0.097 0.066 0.176**
2021 0.344** 0.550** 0.244**

Fig. 2

Manhattan and Q-Q diagrams of amino acid content of soybean seed at R6 stage for two years A: Manhattan and Q-Q plots of arginine content in 2020 and 2021; B: Manhattan and Q-Q plots of alanine content in 2020 and 2021; C: Manhattan and Q-Q plots of glutamic acid content in 2020 and 2021; D: Manhattan and Q-Q plots of aspartic acid content in 2020 and 2021."

Table 3

Significant GWAS loci of amino acids with MLM in soybean seed at R6 stage"

代表性SNP
Leading SNP		 性状
Trait		 染色体
Chr.		 显著性位点
Pos a		 -log10 P 表型变异
R2 (%)		 已报道QTL
Reported QTL
S03_40647948 2020 (Arg), 2021 (Glu) Gm3 40,647,948 11.82 25.96 —
S05_2727464 2020 (Ala, Glu) Gm5 2,727,464 6.44 12.10 —
S10_4122977 2020 (Ala, Glu) Gm10 4,122,977 6.76 12.82 —
S17_34559022 2020 (Glu), 2021 (Glu) Gm17 34,559,022 6.56 11.25 Seed protein 36-14[33]
S19_48541685 2020 (Ala, Glu) Gm19 48,541,685 13.29 28.19 Seed protein 16-2[34]

Fig. 3

Haplotype for SNPs associated with amino acids in soybean natural population (A): box plot of arginine and glutamate acid content of soybean varieties with S03_40647948-A or S03_40647948-C. (B): box plot of alanine and glutamic acid content of soybean varieties with S05_2727464-A or S05_2727464-T. (C): box plot of alanine and glutamic acid content of soybean varieties with S10_4122977-A or S10_4122977-C. (D): box plot of alanine and glutamic acid content of soybean varieties with S19_48541685-A or S19_48541685-G. (E): box plot of glutamic acid content of soybean varieties with S17_34559022-C or S17_34559022-G. ***: P < 0.001."

Table 4

Candidate genes for amino acid composition in soybean natural population at R6 stage"

基因ID
Gene ID		 染色体
Chr.		 物理位置
Physical position		 拟南芥同源基因
Homologs in A. thaliana		 功能注释
Functional annotation
Glyma.03G195700 3 40,576,339-40,579,198 AT3G52730 泛醇-细胞色素C还原酶
Ubiquinol-cytochrome C reductase
Glyma.03G196600 3 40,625,298-40,629,202 AT1G57790 F-box家族蛋白
G-F-box family protein
Glyma.03G197600 3 40,690,880-40,692,074 AT3G52590 泛素延伸蛋白
Ubiquitin extension protein
Glyma.03G197900 3 40,721,164-40,723,468 AT5G22380 含有蛋白质的NAC结构域
NAC domain containing protein
Glyma.05G031100 5 2,705,628-2,711,940 AT5G62640 富含脯氨酸的家族蛋白
Proline-rich family protein
Glyma.05G032000 5 2,790,581-2,794,268 AT3G08720 丝氨酸/苏氨酸蛋白激酶
Serine/threonine protein kinase
Glyma.05G045600 5 4,055,163-4,057,843 AT1G24400 赖氨酸组氨酸转运体
Lysine histidine transporter
Glyma.10G045200 10 4,034,799-4,035,293 AT2G37430 C2H2和C2HC锌指超家族蛋白
C2H2 and C2HC zinc fingers superfamily protein
Glyma.10G045300 10 4,036,736-4,037,634 AT3G53600 C2H2型锌指家族蛋白
C2H2-type zinc finger family protein
Glyma.10G045400 10 4,040,116-4,040,940 AT3G53600 C2H2型锌指家族蛋白
C2H2-type zinc finger family protein
Glyma.17G046000 17 3,450,099-3,451,186 AT1G72430 生长素反应蛋白家族
Auxin-responsive protein family
Glyma.19G234800 19 48,458,962-48,463,730 AT1G55040 锌指家族蛋白
Zinc finger family protein
Glyma.19G236100 19 48,530,095-48,531,946 AT1G54860 糖蛋白膜前体
Glycoprotein membrane precursor
Glyma.19G236600 19 48,558,165-48,559,649 AT1G03220 天冬氨酸蛋白酶家族蛋白
Aspartyl protease family protein
Glyma.19G236900 19 48,600,159-48,602,744 AT1G72210 bHLH DNA结合超家族蛋白
bHLH DNA-binding superfamily protein

Fig. 4

Relative expression pattern of nine candidate genes during soybean seed development period"

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