基于高密度遗传图谱定位大豆蛋白质含量相关的QTL

doi:10.3724/SP.J.1006.2023.24121

作物学报 ›› 2023, Vol. 49 ›› Issue (6): 1532-1541.doi: 10.3724/SP.J.1006.2023.24121

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

基于高密度遗传图谱定位大豆蛋白质含量相关的QTL

刘亭萱¹^,²^,^**(), 谷勇哲²^,^**(), 张之昊³, 王俊¹^,^*(), 孙君明²^,^*(), 邱丽娟¹^,²^,^*()

¹长江大学, 湖北荆州 434025
²中国农业科学院作物科学研究所/农业农村部北京大豆生物学重点实验室/农业农村部种质资源利用重点实验室, 北京 100081
³东北农业大学农学院, 黑龙江哈尔滨 150030

收稿日期:2022-05-19 接受日期:2022-10-10 出版日期:2023-06-12 网络出版日期:2022-10-20
通讯作者: *邱丽娟, E-mail: qiulijuan@caas.cn;王俊, E-mail: wangjagri@yangtzeu.edu.cn;孙君明, E-mail: qiulijuan@caas.cn
作者简介:刘亭萱, E-mail: 18834408825@163.com;
谷勇哲, E-mail: guyongzhe@caas.cn第一联系人：^**同等贡献
基金资助:
中国和乌拉圭联合实验室合作项目(2018YFE0116900)

Mapping soybean protein QTLs based on high-density genetic map

LIU Ting-Xuan¹^,²^,^**(), GU Yong-Zhe²^,^**(), ZHANG Zhi-Hao³, WANG Jun¹^,^*(), SUN Jun-Ming²^,^*(), QIU Li-Juan¹^,²^,^*()

¹Yangtze University, Jingzhou 434025, Hubei, China
²National Key Facility for Gene Resources and Genetic Improvement of MARA/Beijing Key Laboratory of Soybean Biology of MARA/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
³College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China

Received:2022-05-19 Accepted:2022-10-10 Published:2023-06-12 Published online:2022-10-20
Contact: *E-mail: qiulijuan@caas.cn;E-mail: wangjagri@yangtzeu.edu.cn;E-mail: qiulijuan@caas.cn
About author:First author contact:^**Contributed equally to this work
Supported by:
Sino-Uruguayan Joint Laboratory(2018YFE0116900)

摘要/Abstract

摘要：

大豆是重要的粮食作物和经济作物, 其籽粒蛋白约为40%, 是优质植物蛋白主要来源之一。挖掘控制大豆高蛋白数量性状位点(Quantitative trait loci, QTL)以及分子标记育种对高蛋白大豆培育具有重要的意义。本研究利用蛋白含量存在明显差异的中黄35 (Zhonghuang 35, ZH35)和中黄13 (Zhonghuang 13, ZH13)杂交构建的包含192个株系的重组自交系群体为供试材料, 通过对两亲本及RIL群体重测序, 构建了包含4879个bin标记的高密度遗传图谱, 总遗传距离为3760.71 cM, 相邻标记间的遗传距离为0.77 cM。RIL群体及亲本分别于北京顺义和河南濮阳种植, 2个环境共检测到15个蛋白含量相关QTL位点, 分布于5号、12号、15号、17号、18号、19号和20号染色体, 贡献率为4.36%~11.39%。其中, 北京顺义和河南濮阳检测到qPro-20-1和qPro-20-3, 2个QTL贡献率分别为7.65%和7.58%, 重叠区域包括33个基因。本研究有助于精细定位和图位克隆大豆蛋白含量相关基因, 并为进一步培育高蛋白大豆品种提供基因资源。

关键词: 大豆, 蛋白质含量, 重组自交系, bin图谱, QTL定位

Abstract:

Soybean is an important food crop and economic crop, and its grain protein is about 40%, which is one of the main sources of high-quality vegetable protein. Mining the quantitative trait loci (QTL) that control soybean high protein and molecular marker breeding are of great significance for the breeding of high protein soybean. In this study, a recombinant inbred line population consisting of 192 lines constructed by crossing Zhonghuang 35 (ZH35) and Zhonghuang 13 (ZH13) with significant differences in protein content was used as the experimental materials. A high-density genetic map containing 4879 bin markers was constructed with the total genetic distance of 3760.71 cM and the genetic distance between adjacent markers of 0.77 cM by resequencing the two parents and the RIL population. The RIL population and its parents were grown in Shunyi, Beijing and Puyang, Henan, respectively. A total of 15 protein content-related QTL loci were detected in the two environments, which were distributed on chromosomes 5, 12, 15, 17, 18, 19, and 20, respectively. The contribution rate was 4.36%-11.39%, among which, qPro-20-1 and qPro-20-3 were detected in Shunyi, Beijing and Puyang, Henan, respectively. The contribution rates of the two QTLs were 7.65% and 7.58%, respectively, and the overlapping regions included 33 genes. This study is helpful for fine mapping and map-based cloning of soybean protein content-related genes, and provides genetic resources for further breeding of high-protein soybean varieties.

Key words: soybean, protein content, recombinant inbred lines, bin map, QTL mapping

刘亭萱, 谷勇哲, 张之昊, 王俊, 孙君明, 邱丽娟. 基于高密度遗传图谱定位大豆蛋白质含量相关的QTL[J]. 作物学报, 2023, 49(6): 1532-1541.

LIU Ting-Xuan, GU Yong-Zhe, ZHANG Zhi-Hao, WANG Jun, SUN Jun-Ming, QIU Li-Juan. Mapping soybean protein QTLs based on high-density genetic map[J]. Acta Agronomica Sinica, 2023, 49(6): 1532-1541.

图/表 9

表1

图1

图2

图3

表2

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图4

表4

重叠区间内候选基因的功能注释"

基因名称 Gene name	功能注释 Functional annotation
Glyma.20G237700	α/β-水解酶折叠蛋白 Alpha/beta-Hydrolase fold-containing protein
Glyma.20G237800	植物转化酶/果胶甲酯酶抑制剂 Plant invertase/pectin methylesterase inhibitor
Glyma.20G238000	脂质生物合成过程 Lipid biosynthetic process
Glyma.20G238400	WD40重复蛋白 WD40 repeat-containing protein
Glyma.20G238500	预测PRP38剪接因子 Predicted PRP38-like splicing factor
Glyma.20G238600	线粒体靶向单链DNA结合蛋白 Mitochondrially targeted single-stranded DNA binding protein
Glyma.20G238700	蛋白质去磷酸化; 蛋白质丝氨酸/苏氨酸磷酸酶活性 Protein dephosphorylation; protein serine/threonine phosphatase activity
Glyma.20G238800	锌指(C3HC4型环指)家族蛋白; BRCT结构域蛋白/RING/U-box蛋白 Zinc finger (C3HC4-type RING finger) family protein; BRCT domain-containing protein/RING/U-box protein
Glyma.20G238900	磷酸甘油酸变位酶家族蛋白 Phosphoglycerate mutase family protein
Glyma.20G239000	干旱响应家族蛋白; 干旱诱导的19蛋白(Di19), 锌结合 Drought-responsive family protein; rought induced 19 protein (Di19), zinc-binding
Glyma.20G239100	细胞内蛋白质转运; 囊泡介导的转运 Intracellular protein transport; vesicle-mediated transport
基因名称 Gene name	功能注释 Functional annotation
Glyma.20G239200	蛋白质转运; 导入α亚型 Protein transport; importin alpha isoform
Glyma.20G239300	多核苷酸转移酶, 核糖核酸酶H样超家族蛋白; 3¢-5¢外切酶活性 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; 3¢-5¢ exonuclease activity
Glyma.20G239600	分泌相关的RAS超家族2; 细胞内蛋白质转运 Secretion-associated RAS super family 2; intracellular protein transport
Glyma.20G239700	PsbP样蛋白2; 光系统II氧进化复合物 PsbP-like protein 2; photosystem II oxygen evolving complex
Glyma.20G239800	跨膜转运; ATP酶活性, 与物质的跨膜运动相耦合 Transmembrane transport; ATPase activity, coupled to transmembrane movement of substances
Glyma.20G240000	碳水化合物代谢过程; β-N-乙酰氨基己糖苷酶活性 Carbohydrate metabolic process; beta-N-acetylhexosaminidase activity
Glyma.20G240200	多核苷酸转移酶, 核糖核酸酶H样超家族蛋白 Polynucleotidyl transferase, ribonuclease H-like superfamily protein
Glyma.20G240300	谷胱甘肽代谢过程; 谷胱甘肽转移酶活性 Glutathione metabolic process; glutathione transferase activity
Glyma.20G240400	质体转录活性17; 钴胺素合成蛋白 Plastid transcriptionally active 17; cobalamin synthesis protein
Glyma.20G240500	裂解和多腺苷酸化特异性因子(CPSF) A亚基蛋白; 通过剪接体剪接mRNA Cleavage and polyadenylation specificity factor (CPSF) A subunit protein; mRNA splicing, via spliceosome
Glyma.20G240600	α/β-水解酶超家族蛋白; 脂质代谢过程 Alpha/beta-Hydrolases superfamily protein; lipid metabolic process
Glyma.20G240700	核糖体L29家族蛋白; 核糖体的结构成分 Ribosomal L29 family protein; structural constituent of ribosome
Glyma.20G240800	果胶裂解酶样超家族蛋白; 果胶分解代谢过程 Pectin lyase-like superfamily protein; pectin catabolic process
Glyma.20G240900	脂质生物合成过程 Lipid biosynthetic process

表4

图5

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环境 Environment	中黄35 Zhonghuang 35 (mean±SD, %)	中黄13 Zhonghuang 13 (mean±SD, %)	RIL群体RIL population
环境 Environment	中黄35 Zhonghuang 35 (mean±SD, %)	中黄13 Zhonghuang 13 (mean±SD, %)	最大值 Max. (%)	最小值 Min. (%)	变异系数 CV (%)	峰度 Kurtosis	偏度 Skewness
北京顺义 Shunyi, Beijing	38.24±0.17	44.99±0.25	46.00	37.51	2.48	0.22	-0.07
河南濮阳 Puyang, Henan	38.20±0.22	44.20±0.32	45.98	37.04	2.98	-0.17	0.02

染色体 Chr.	上图标记数 Total marker	总图距 Total distance (cM)	平均图距 Average distance (cM)	小于5 cM gap数量/gap总数×100% Gap less than 5 cM/gap total number×100%
Chr.01	247	169.29	0.69	100
Chr.02	264	213.61	0.81	99.62
Chr.03	301	179.80	0.60	100
Chr.04	226	205.36	0.91	99.56
Chr.05	203	177.41	0.87	100
Chr.06	290	291.38	1.00	98.62
Chr.07	235	186.79	0.79	100
Chr.08	289	216.94	0.75	100
Chr.09	245	183.47	0.75	100
Chr.10	227	199.14	0.88	100
Chr.11	214	219.26	1.02	98.13
Chr.12	205	163.48	0.80	99.02
Chr.13	126	96.81	0.77	97.62
Chr.14	204	153.72	0.75	99.51
Chr.15	402	215.29	0.54	99.75
Chr.16	209	158.00	0.76	100
Chr.17	220	192.44	0.87	99.55
Chr.18	266	198.39	0.75	99.25
Chr.19	299	176.74	0.59	100
Chr.20	207	163.40	0.79	99.52
平均Average	243.95	188.03	0.77	99.51

环境 Environment	位点名称 QTL name	染色体 Chr.	定位区间 Mapping interval (bp)	QTL位置 Position (cM)	阈值 LOD	加性效应 Additive effect	贡献率 R² (%)	报道位点 Reported locus
北京顺义 Shunyi, Beijing	qPro-15-1	15	bin3524-bin3532	71.51	3.05	0.33	5.13	[40][41]
	qPro-17-1	17	bin4087-bin4090	19.41	2.71	-0.31	4.63	New
	qPro-17-2	17	bin4095-bin4110	28.11	3.67	-0.36	6.21	New
	qPro-18-1	18	bin4523-bin4526	170.21	2.57	-0.31	4.44	New
	qPro-18-2	18	bin4525-bin4529	175.91	4.14	-0.39	7.26	New
	qPro-19-1	19	bin4807-bin4811	130.71	2.57	-0.31	4.38	[42]
	qPro-19-2	19	bin4816-bin4821	140.61	3.41	-0.36	5.77	[42]
	qPro-19-3	19	bin4824-bin4829	147.41	2.85	-0.33	4.88	New
	qPro-20-1	20	bin5059-bin5063	161.01	4.48	-0.40	7.65	New
河南濮阳 Puyang, Henan	qPro-5-1	5	bin1167-bin1170	84.81	2.67	-0.38	4.83	[39]
	qPro-5-2	5	bin1161-bin1164	91.41	4.82	-0.50	8.51	[36] [37] [38]
	qPro-5-3	5	bin1154	100.71	3.50	-0.43	6.29	[36] [36] [38]
	qPro-12-1	12	bin2906-bin2911	95.01	3.42	0.42	5.94	New
	qPro-20-2	20	bin5046-bin5049	150.61	4.14	-0.46	7.28	New
	qPro-20-3	20	bin5057-bin5060	159.11	4.33	-0.47	7.58	New

基于高密度遗传图谱定位大豆蛋白质含量相关的QTL

Mapping soybean protein QTLs based on high-density genetic map

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