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作物学报 ›› 2023, Vol. 49 ›› Issue (12): 3277-3288.doi: 10.3724/SP.J.1006.2023.34031

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

大豆R6期籽粒氨基酸含量的全基因组关联分析

张红梅1(), 熊雅文2, 许文静3, 张威1, 王琼1, 刘晓庆1, 刘慧3, 崔晓艳1, 陈新1, 陈华涛1,2,*()   

  1. 1江苏省农业科学院经济作物研究所, 江苏南京 210014
    2南京农业大学生命科学学院, 江苏南京 210095
    3南京农业大学园艺学院, 江苏南京 210095
  • 收稿日期:2023-02-20 接受日期:2023-05-24 出版日期:2023-12-12 网络出版日期:2023-06-09
  • 通讯作者: * 陈华涛, E-mail: cht@jaas.ac.cn
  • 作者简介:E-mail: zhm@jaas.ac.cn
  • 基金资助:
    江苏省重点研发计划项目(BE2019376);江苏省重点研发计划项目(BE2022328);江苏省农业科技自主创新项目(CX(22)5002);江苏省农业科技自主创新项目(CX(21)3117);江苏种业振兴揭榜挂帅项目(JBGS[2021]060);国家自然科学基金项目(32001455)

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 Published:2023-12-12 Published online: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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摘要：

为解析大豆R6期籽粒氨基酸含量的遗传机制, 本研究利用264份大豆种质资源材料在2020年和2021年测定了与菜用大豆食味品质相关的精氨酸、丙氨酸、谷氨酸和天冬氨酸含量, 并进行全基因组关联分析(GWAS)。结果表明, 2年共检测到89个与大豆R6期籽粒4种氨基酸含量显著关联的SNP位点, 其中有5个标记能同时被2年或2个性状重复检测到, 分别为S03_40647948 (Chr.3)、S05_2727464 (Chr.5)、S10_4122977 (Chr.10)、S17_34559022 (Chr.17)和S19_48541685 (Chr.19), 单个位点可以解释11.25%~28.19%的表型变异解, 其中Chr.17上的标记S17_34559022在2020年和2021年被共同检测到与谷氨酸含量显著关联, 属稳定遗传的位点。共挖掘出9个候选基因, 其中ZIP蛋白(zinc finger family protein)、转录因子bHLH (bHLH DNA-binding superfamily protein)、生长素反应蛋白家族(auxin-responsive protein family)和天冬氨酸蛋白酶家族蛋白(aspartyl protease family protein), 可能是影响菜用大豆氨基酸代谢的重要基因。本研究挖掘到的5个氨基酸含量主效SNP位点和9个候选基因, 有助于解析大豆R6期籽粒氨基酸含量的遗传基础及其调控机制, 为菜用大豆食味品质遗传改良奠定了基础。

关键词: 大豆, R6期, 籽粒, 氨基酸含量, 全基因组关联分析, 候选基因

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

表1

大豆R6期籽粒氨基酸含量表型变异"

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

附表1

不同年份大豆R6期籽粒氨基酸含量的方差分析"

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

图1

不同年份大豆R6期籽粒氨基酸含量的频率分布图"

表2

大豆自然群体R6期籽粒氨基酸含量的相关性分析"

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**

图2

不同年份大豆R6期氨基酸含量的曼哈顿图和Q-Q图 A: 2020年和2021年精氨酸含量关联分析Manhattan 图和Q-Q plot图; B: 2020年和2021年丙氨酸含量关联分析Manhattan图和Q-Q plot图; C: 2020年和2021年谷氨酸含量关联分析Manhattan图和Q-Q plot图; D: 2020年和2021年天冬氨酸含量关联分析Manhattan图和Q-Q plot图。"

表3

MLM大豆R6期籽粒氨基酸显著关联位点"

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]

图3

大豆自然群体氨基酸显著关联SNP单倍型分析 (A) 携有SNP S03_40647948-A/C的大豆种质的精氨酸(Arg)和谷氨酸(Glu)含量箱线图; (B) 携有SNP S05_2727464-A/T的大豆种质的丙氨酸(Ala)和谷氨酸(Glu)含量箱线图; (C) 携有S10_4122977-A/C的大豆种质的丙氨酸(Ala)和谷氨酸(Glu)含量箱线图; (D) 携有SNP S19_48541685-A/G的大豆种质的丙氨酸(Ala)和谷氨酸(Glu)含量箱线图; (E) 携有SNP S17_34559022-C/G的大豆种质的谷氨酸(Glu)含量箱线图。"

表4

大豆自然群体R6期籽粒氨基酸候选基因"

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

图4

大豆籽粒发育过程中9个候选基因的表达模式"

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