大豆籽粒Ve含量的全基因组关联分析

doi:10.3724/SP.J.1006.2024.34202

作物学报 ›› 2024, Vol. 50 ›› Issue (5): 1223-1235.doi: 10.3724/SP.J.1006.2024.34202

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

大豆籽粒Ve含量的全基因组关联分析

张红梅¹(), 张威¹, 王琼¹, 贾倩茹¹, 孟珊², 熊雅文³, 刘晓庆¹, 陈新¹, 陈华涛¹^,³^,^*()

¹江苏省农业科学院经济作物研究所, 江苏南京 210014
²江苏省农业科学院种质资源与生物技术研究所, 江苏南京 210014
³南京农业大学生命科学学院, 江苏南京 210095

收稿日期:2023-12-01 接受日期:2024-01-31 出版日期:2024-05-12 网络出版日期:2024-02-09
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:
江苏省农业自主创新基金项目(CX(22)5002);国家自然科学基金项目(32001455);国家自然科学基金项目(30771360)

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^,^*()

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 Published:2024-05-12 Published online: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)

摘要/Abstract

摘要：

维生素E (Ve)是大豆油中一种天然抗氧化剂, 是评价大豆油营养价值的重要指标。本研究利用含有264份的大豆自然群体在2021年和2022年测定了籽粒中α-、γ-和δ-生育酚含量, 并进行全基因组关联分析(Genome-wide association study, GWAS)。本研究共检测到199个与大豆Ve含量显著关联的SNP位点, 其中9个可在2个环境或者2个性状被重复检测到, 分别位于3号、7号、11号、12号、13号、15号、17号和18号染色体上。其中位于7号染色体上的显著关联信号是控制α-生育酚含量的主效位点, 可在2年环境中被检测到, 表型变异解释率为9.83%。对该位点候选基因进行筛选, 获得一个编码myb转录因子的基因Glyma.07G054000, 可能是这个位点的效应基因。另外, 在12号染色体上得到2个编码γ-生育酚甲基转移酶的基因Glyma.12G014200和Glyma.12G014300, 有可能是影响Ve含量的重要基因。本研究结果有助于解析大豆籽粒Ve含量的遗传基础及其调控机制, 为大豆品质遗传改良奠定了基础。

关键词: 大豆, 籽粒, Ve含量, 全基因组关联分析, 候选基因

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

张红梅, 张威, 王琼, 贾倩茹, 孟珊, 熊雅文, 刘晓庆, 陈新, 陈华涛. 大豆籽粒Ve含量的全基因组关联分析[J]. 作物学报, 2024, 50(5): 1223-1235.

ZHANG Hong-Mei, ZHANG Wei, WANG Qiong, JIA Qian-Ru, MENG Shan, XIONG Ya-Wen, LIU Xiao-Qing, CHEN Xin, CHEN Hua-Tao. Genome-wide association study for vitamin E content in soybean (Glycine max L.) seed[J]. Acta Agronomica Sinica, 2024, 50(5): 1223-1235.

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参考文献 36

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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 (%)
α-Toc	2021	20.22	6.18	5.62-40.26	30.57
α-Toc	2022	15.00	8.37	1.79-59.72	55.78
γ-Toc	2021	164.37	33.56	56.69-269.85	20.42
γ-Toc	2022	188.31	73.68	46.57-426.70	39.13
δ-Toc	2021	19.96	4.63	4.53-35.04	23.19
δ-Toc	2022	22.26	8.49	5.26-47.24	38.16
TVe	2021	204.48	40.47	75.69-321.98	19.79
TVe	2022	225.57	87.78	54.70-498.38	38.92

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

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^**

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

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

大豆籽粒Ve含量的全基因组关联分析

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

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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)
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	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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