大豆R6期籽粒氨基酸含量的全基因组关联分析

doi:10.3724/SP.J.1006.2023.34031

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^,^*()

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)

摘要/Abstract

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

张红梅, 熊雅文, 许文静, 张威, 王琼, 刘晓庆, 刘慧, 崔晓艳, 陈新, 陈华涛. 大豆R6期籽粒氨基酸含量的全基因组关联分析[J]. 作物学报, 2023, 49(12): 3277-3288.

ZHANG Hong-Mei, XIONG Ya-Wen, XU Wen-Jing, ZHANG Wei, WANG Qiong, LIU Xiao-Qing, LIU Hui, CUI Xiao-Yan, CHEN Xin, CHEN Hua-Tao. Genome-wide association study for amino acid content at R6 stage in soybean (Glycine max L.) seed[J]. Acta Agronomica Sinica, 2023, 49(12): 3277-3288.

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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
Arg	2021	1.22	0.81	0.22-4.83	69.20
Ala	2020	0.44	0.83	0.00-5.03	17.56
Ala	2021	1.35	0.86	0.29-4.96	63.38
Glu	2020	0.82	0.96	0.00-4.75	36.73
Glu	2021	1.15	0.81	0.05-4.79	83.47
Asp	2020	0.23	0.61	0.00-4.08	24.21
Asp	2021	0.67	0.55	0.10-5.62	86.23

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

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^**

代表性SNP Leading SNP	性状 Trait	染色体 Chr.	显著性位点 Pos ^a	-log₁₀P	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]

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

大豆R6期籽粒氨基酸含量的全基因组关联分析

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

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