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Acta Agronomica Sinica ›› 2024, Vol. 50 ›› Issue (5): 1223-1235.doi: 10.3724/SP.J.1006.2024.34202

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

Genome-wide association study for vitamin E content in soybean (Glycine max L.) seed

ZHANG Hong-Mei1(), ZHANG Wei1, WANG Qiong1, JIA Qian-Ru1, MENG Shan2, XIONG Ya-Wen3, LIU Xiao-Qing1, CHEN Xin1, CHEN Hua-Tao1,3,*()   

  1. 1Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
    2Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
    3College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
  • Received:2023-12-01 Accepted:2024-01-31 Online:2024-05-12 Published:2024-02-09
  • Contact: E-mail: cht@jaas.ac.cn
  • Supported by:
    Jiangsu Agricultural Science and Technology Innovation Fund(CX(22)5002);National Natural Science Foundation of China(32001455);National Natural Science Foundation of China(30771360)

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Abstract:

Vitamin E (Ve) is a natural antioxidant in soybean oil and an important index to evaluate the nutritional value of soybean oil. In this study, α-, γ-, and δ- contents of seed were determined from a natural soybean population containing 264 germplasm resources in 2021 and 2022, and genome-wide association study (GWAS) was conducted. A total of 199 SNPs significantly associated with soybean Ve content were detected in this study, among which 9 SNPs that could be repeatedly detected in two different environments or two traits, which located on chromosomes 3, 7, 11, 12, 13, 15, 17, and 18, respectively. Among them, the significant association signal on chromosome 7 was a major effect site controlling α-tocopherol content, which can be detected in two environments, with the explanation rate of phenotypic variation 9.83%. By screening the candidate genes of this site, Glyma.07G054000 encoding myb transcription factor was obtained, which may be the effect gene of this site. In addition, two genes encoding γ-tocopherol methyltransferase Glyma.12G014200 and Glyma.12G014300 obtained on chromosome 12, may be important genes affecting Ve content. The results of this study are helpful to analyze the genetic basis and regulatory mechanism of Ve content in soybean seed, and lay a foundation for genetic improvement of soybean quality.

Key words: soybean, seed, Ve content, GWAS, candidate gene

Table 1

Phenotypic variation of Ve content in soybean seed"

性状
Trait		 年份
Year		 平均值
Mean		 标准差
SD		 变幅
Range		 变异系数
CV (%)
α-Toc 2021 20.22 6.18 5.62-40.26 30.57
2022 15.00 8.37 1.79-59.72 55.78
γ-Toc 2021 164.37 33.56 56.69-269.85 20.42
2022 188.31 73.68 46.57-426.70 39.13
δ-Toc 2021 19.96 4.63 4.53-35.04 23.19
2022 22.26 8.49 5.26-47.24 38.16
TVe 2021 204.48 40.47 75.69-321.98 19.79
2022 225.57 87.78 54.70-498.38 38.92

Fig. 1

Frequency distribution of Ve content in soybean seed"

Table S1

Analysis of variance (ANOVA) for Ve of soybean seed in two years"

年份
Year		 生育酚
Tocopherol		 变异来源
Source of variation		 自由度
DF		 均方
MS		 F值
F-value
2021 α-生育酚α-Toc 基因型Genotype 253 114.61 37.78**
重复Replication 2 5.45 1.80
误差Residual error 506 3.03
γ-生育酚γ-Toc 基因型Genotype 253 3379.16 28.53**
重复Replication 2 1588.32 13.41**
误差Residual error 506 118.43
δ-生育酚δ-Toc 基因型Genotype 253 64.15 52.03**
重复Replication 2 5.50 4.46*
误差Residual error 506 1.23
总生育酚TVe 基因型Genotype 253 4914.24 16.96**
重复Replication 2 2022.39 6.98**
误差Residual error 506 289.80
2022 α-生育酚α-Toc 基因型Genotype 208 182.18 118.53**
重复Replication 2 0.77 0.50
误差Residual error 416 1.54
γ-生育酚γ-Toc 基因型Genotype 208 16,365.00 90.26**
重复Replication 2 315.28 1.74
误差Residual error 416 181.31
δ-生育酚δ-Toc 基因型Genotype 209 210.00 79.66**
重复Replication 2 4.74 1.80
误差Residual error 416 2.64
总生育酚TVe 基因型Genotype 208 23,217.00 130.40**
重复Replication 2 10,967.00 61.60**
误差Residual error 416 178.04

Table 2

Correlation analysis of Ve content in soybean seed"

性状Trait 年份Year α-Toc γ-Toc δ-Toc
γ-Toc 2021 0.46** 1.00
2022 0.73** 1.00
δ-Toc 2021 0.37** 0.77** 1.00
2022 0.62** 0.92** 1.00
TVe 2021 0.58** 0.99** 0.81**
2022 0.77** 1.00 0.93**

Fig. 2

Manhattan and Q-Q diagrams of Ve content of soybean seed in two years A: Manhattan and Q-Q plots of α-tocopherol content in 2021 and 2022; B: Manhattan and Q-Q plots of δ-tocopherol content in 2021 and 2022; C: Manhattan and Q-Q plots of γ-tocopherol acid content in 2021 and 2022; D: Manhattan and Q-Q plots of total-tocopherol content in 2021 and 2022. When the threshold of SNP -log10(P) ≥ 5.0 (above the red line), it is considered the SNP is significant site."

Table 3

Significant SNP associated with Ve in soybean seed"

代表性SNP
Lead SNP		 性状
Trait		 染色体
Chr.		 位置
Position		 -log10(P) 表型变异
R2 (%)
S03_22378753 γ-Toc (2022), δ-Toc (2022) 3 22,378,753 6.46 11.05
S07_4623771 α-Toc (2021, 2022) 7 4,623,771 5.49 9.83
S11_5633216 γ-Toc (2022), TVe (2022) 11 5,633,216 5.81 9.36
S12_980498 γ-Toc (2022), δ-Toc (2022), TVe (2022) 12 980,498 5.75 9.62
S13_26738088 γ-Toc (2022), δ-Toc (2022), TVe (2022) 13 26,738,088 5.77 9.68
S15_15320539 γ-Toc (2022), TVe (2022) 15 15,320,539 5.19 8.20
S17_21854720 γ-Toc (2021), TVe (2021) 17 21,854,720 5.66 8.02
S18_51917901 γ-Toc (2022), TVe (2022) 18 51,917,901 6.34 10.24
S18_55638538 γ-Toc(2022), TVe(2022) 18 55,638,538 5.61 7.94

Fig. 3

Haplotype analysis for SNPs associated with Ve in soybean natural population A: the box plot of γ-tocopherol and δ-tocopherol content of soybean varieties with S03_22378753-G or S03_22378753-T in 2022. B: the box plot of α-tocopherol content of soybean varieties with S07_4623771-C or S07_4623771-A in 2021 and 2022. C: the box plot of γ-tocopherol and TVe content of soybean varieties with S11_5633216-C or S11_5633216-A in 2022. D: the box plot of γ-tocopherol, δ-tocopherol and TVe content of soybean varieties with S12_980498-A or S12_980498-T in 2022. E: the box plot of γ-tocopherol, δ-tocopherol and TVe content of soybean varieties with SNP S13_26738088-G or SNP S13_26738088-A in 2022. F: the box plot of γ-tocopherol and TVe content of soybean varieties with S15_15320539-T or S15_15320539-C in 2022. G: the box plot of γ-tocopherol and TVe content of soybean varieties with S17_21854720-G or S17_21854720-A in 2021. H: the box plot of γ-tocopherol and TVe content of soybean varieties with S18_51917901-A or S18_51917901-C in 2022. I: the box plot of γ-tocopherol and TVe content of soybean varieties with S18_55638538-G or S18_55638538-A in 2022. α-Toc: α-tocopherol; γ-Toc: γ-tocopherol; δ-Toc: δ-tocopherol; TVe: Total Ve. The significance analysis was used t-test. *, **, and *** indicate significance at P < 0.05, P < 0.01, and P < 0.001, respectively."

Table 4

Major candidate genes for Ve content of soybean seed in natural population"

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.03G081900 3 22,433,399-22,436,557 AT2G37630 myb类HTH转录调控家族蛋白
myb-like HTH transcriptional regulator family protein
Glyma.07G054000 7 4,722,086-4,723,755 AT5G49330 myb结构域蛋白111 myb domain protein 111
Glyma.11G074900 11 5,593,155-5,596,693 AT4G38960 B-box型锌指家族蛋白 B-box type zinc finger family protein
Glyma.12G014200 12 1,025,584-1,029,095 AT1G64970 γ-生育酚甲基转移酶 Gamma-tocopherol methyltransferase
Glyma.12G014300 12 1,033,151-1,037,054 AT1G64970 γ-生育酚甲基转移酶 Gamma-tocopherol methyltransferase
Glyma.13G153200 13 26,821,405-26,825,518 AT3G44460 bZIP转录因子家族蛋白
Basic-leucine zipper (bZIP) transcription factor family protein

Fig. 4

Relative expression patterns of six Ve content related candidate genes during soybean seed development"

Table 5

Selected elite accessions of Ve related traits"

性状
Trait		 材料编号
Material No.		 名称
Name		 类型
Type		 来源
Origin		 优异等位变异位点
Excellent allelic variation site		 α-Toc
(μg g-1)		 TVe
(μg g-1)
2021 2022 2022
α-Toc NPS001 9 地方种
Landrace		 河北
Hebei		 S07_4623771-C 37.86 33.60 —
NPS020 NX-NC-39 栽培种
Cultivar		 宁夏
Ningxia		 S07_4623771-C 31.08 33.17 —
NPS023 NX-9484 栽培种
Cultivar		 宁夏
Ningxia		 S07_4623771-C 34.25 35.09 —
NPS027 NX-F5-5 栽培种
Cultivar		 宁夏
Ningxia		 S07_4623771-C 38.72 37.89 —
TVe NPS017 NX-F4-2 栽培种
Cultivar		 宁夏
Ningxia		 S12_980498-T, S13_26738088-G, S15_15320539-T, S18_55638538-A, S18_51917901-C — — 424.20
NPS018 NX-23-25 栽培种
Cultivar		 宁夏
Ningxia		 S13_26738088-G, S15_15320539-T, S18_55638538-A, S18_51917901-C — — 426.32
NPS019 NX-F5-1 栽培种
Cultivar		 宁夏
Ningxia		 S13_26738088-G, S15_15320539-T, S18_55638538-A, S18_51917901-C — — 467.84
NPS020 NX-NC-39 栽培种
Cultivar		 宁夏
Ningxia		 S12_980498-T, S13_26738088-G, S15_15320539-T, S18_55638538-A, S18_51917901-C — — 498.38
NPS023 NX-9484 栽培种
Cultivar		 宁夏
Ningxia		 S13_26738088-G, S15_15320539-T, S18_51917901-C — — 417.22
NPS029 NX-F7-59 栽培种
Cultivar		 宁夏
Ningxia		 S12_980498-T, S13_26738088-G, S15_15320539-T, S18_55638538-A — — 413.86
NPS203 滇豆4号
Diandou 4		 栽培种
Cultivar		 云南
Yunnan		 S12_980498-T, S13_26738088-G, S15_15320539-T, S18_55638538-A — — 409.55
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