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

Abstract

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

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

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

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