大豆油分相关功能基因分子标记开发与鉴定及优异等位变异聚合分析

doi:10.3864/j.issn.0578-1752.2024.22.002

中国农业科学 ›› 2024, Vol. 57 ›› Issue (22): 4402-4415.doi: 10.3864/j.issn.0578-1752.2024.22.002

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

大豆油分相关功能基因分子标记开发与鉴定及优异等位变异聚合分析

吴传磊¹(), 胡晓渝¹, 王伟¹, 苗龙¹, 白鹏宇¹, 王郭伋¹, 李娜¹, 舒阔¹, 邱丽娟²(), 王晓波¹()

¹ 安徽农业大学农学院，合肥 230036
² 中国农业科学院作物科学研究所/农业农村部作物基因资源与遗传改良重大科学工程/农业农村部作物基因资源与种质创制重点实验室，北京 100081

收稿日期:2024-04-27 接受日期:2024-05-28 出版日期:2024-11-16 发布日期:2024-11-22
通信作者:
王晓波，E-mail：wxbphd@163.com。
邱丽娟，E-mail：qiulijuan@cass.cn
联系方式: 吴传磊，E-mail：83616275@qq.com。
基金资助:
国家重点研发计划(2021YFD1201605)

Development and Identification of Molecular Markers for Oil-Related Functional Genes and Polymerization Analysis of Excellent Alleles in Soybean

WU ChuanLei¹(), HU XiaoYu¹, WANG Wei¹, MIAO Long¹, BAI PengYu¹, WANG GuoJi¹, LI Na¹, SHU Kuo¹, QIU LiJuan²(), WANG XiaoBo¹()

¹ College of Agriculture, Anhui Agricultural University, Heifei 230036
² Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic lmprovement (NFCRl). Mlinistry of Agriculture and Rural Affairs/Key Laboratory of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Beijing 100081

Received:2024-04-27 Accepted:2024-05-28 Published:2024-11-16 Online:2024-11-22

摘要/Abstract

摘要：

【目的】聚合大豆高油基因型旨在育种出更高含油量的品种，以提高经济效益和营养价值。为增加农业产出、降低加工成本、满足全球对植物油增长需求提供依据。【方法】利用生物信息学分析方法对Glyma.18G027100所在的C2基因家族在全基因组水平上进行鉴定，共鉴定出66个大豆C2基因家族成员，根据染色体位置命名为GmC2-01.1—GmC2-20.2。组织模式表达分析，在66个C2家族基因中共发现7个在籽粒中高表达基因（GmC2-03.6、GmC2-02.7、GmC2-07.2、GmC2-18.1、GmC2-18.4、GmC2-19.1和GmC2-20.2），为分析上述基因在大豆油分含量中的效应位点，从SFGB数据库中获得上述基因在编码区的SNP位点，2年油分含量相关分析表明，GmC2-18.1存在极显著影响油分含量的SNP位点。利用12份极端材料对GmC2-18.1编码区遗传多样性进行分析，在Wm82.a2.v1版本编码区2 038 273 bp处存在G/A变异调控种子油分含量，初步推测这个基因在籽粒发育或者营养物质积累中发挥作用。接着，对GmC2-18.1^-G/A基因结合已报道的功能基因GmSWEET39起始密码子上游225 bp的InDel自然等位变异位点、GmST1在编码区8 381 058处存在T/C自然等位变异位点、GmMFT在编码区在41 854 422 bp第三个外显子处存在A/C自然等位变异位点开发SNP/InDel分子标记，并通过2年1 200份来自全国三大生态区的大豆种质资源材料进行标记验证。【结果】方差分析结果表明，GmC2-18.1^-G、GmSWEET39^-Deletion、GmST1^-T和GmMFT^-A显著增加油分含量1.72、1.95、1.58和2.06个百分点（P<0.01）。进一步对上述基因进行聚合分析，结果表明，携带GmC2-18.1^-G、GmSWEET39^-Deletion、GmST1^-T和GmMFT^-A高油等位变异类型（PFAT-1）的大豆种子平均油分含量为22.89%，相较于携有GmC2-18.1^-A、GmSWEET39^-Insertion、GmST1^-C和GmMFT^-C低油等位变异类型（PFAT-14）大豆种子平均油分含量增加约4.5个百分点，对油分含量的贡献率约为21.69%。【结论】基于上述所开发标记，筛选出115份PFAT-1类型高油等位变异材料。

关键词: 大豆, 生物信息学分析, 分子标记, 油分含量, 基因聚合

Abstract:

【Objective】Polymerizing soybean high oil genotypes aims at breeding varieties with higher oil content to improve economic efficiency and nutritional value. It is of great significance to increase agricultural output, reduce processing costs and meet global demand for vegetable oil growth.【Method】Glyma.18G027100 C2 gene family was identified by bioinformatic analysis method at the whole genome level. A total of 66 soybean C2 gene family members were identified, named GmC2-01.1-GmC2-20.2 according to chromosome position. Tissue pattern analysis revealed that 7 genes were highly expressed in grains among 66 C2 family genes (GmC2-03.6, GmC2-02.7, GmC2-07.2, GmC2-18.1, GmC2-18.4, GmC2-19.1 and GmC2-20.2). In order to analyze the effect sites of these genes on soybean oil content, SNP sites in the coding regions of these genes were obtained from SFGB database. Correlation analysis of oil content in two years showed that GmC2-18.1 has SNP loci that significantly affect oil content. The genetic diversity of GmC2-18.1 coding region was analyzed by 12 extreme materials. There was a G/A mutation at 2 038 273 bp in coding region of Wm82.a2.v1 version, which regulated seed oil content. It was preliminarily speculated that this gene played a role in seed development or nutrient accumulation. Then, SNP/InDel molecular markers were developed for GmC2-18.1^-G/A gene combined with InDel natural allelic variation site 225 bp upstream of the start codon of GmSWEET39, T/C natural allelic variation site at 8 381 058 bp in coding region of GmST1, A/C natural allelic variation site at the third exon of 41 854 422 bp in coding region of GmMFT. 1 200 soybean germplasm resources from three ecological regions in China were identified by markers in 2 years.【Result】Analysis of variance showed that GmC2-18.1^-G, GmSWEET39^-Deletion, GmST1^-T and GmMFT^-A significantly increased oil content by 1.72, 1.95, 1.58 and 2.06 percentage points (P<0.01). The results showed that the average oil content of soybean seeds carrying GmC2-18.1^-G, GmSWEET39^-Deletion, GmST1^-T and GmMFT^-A high-oil allele type (PFAT-1) was 22.89%, which increased by about 4.5% compared with that carrying GmC2-18.1^-A, GmSWEET39^-Insertion, GmST1^-C and GmMFT^-C low-oil allele type (PFAT-14). 5 percentage points, the contribution rate to oil content is about 21.69%. 【Conclusion】Based on the markers developed above, 115 PFAT-1 high oil alleles were screened.

Key words: soybeans, bioinformatic analysis, molecular markers, oil content, gene aggregation

吴传磊, 胡晓渝, 王伟, 苗龙, 白鹏宇, 王郭伋, 李娜, 舒阔, 邱丽娟, 王晓波. 大豆油分相关功能基因分子标记开发与鉴定及优异等位变异聚合分析[J]. 中国农业科学, 2024, 57(22): 4402-4415.

WU ChuanLei, HU XiaoYu, WANG Wei, MIAO Long, BAI PengYu, WANG GuoJi, LI Na, SHU Kuo, QIU LiJuan, WANG XiaoBo. Development and Identification of Molecular Markers for Oil-Related Functional Genes and Polymerization Analysis of Excellent Alleles in Soybean[J]. Scientia Agricultura Sinica, 2024, 57(22): 4402-4415.

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基因 Gene	引物名称 Primer name	引物序列 Primer sequence (5′-3′)	目的基因片段大小 Fragment size (bp)	参考文献 References
GmSWEET39	SWEET39InDel-F	CTTAAAGTTCTCAAACTTATCCTCC	158	[8]
GmSWEET39	SWEET39InDel-R	GACCAGAAATCAAAAAGAAACAAGG	158	[8]
GmST1	ST1dCAPS-F	GCCGTGATGTCGCATGATATCTCATGTTGTTCTTGTTCCTAACAAGC	132	[9]
GmST1	ST1dCAPS-R	AGGAGTTTGAAGCTGTTGAGTCT	132	[9]
GmMFT	MFTdCAPS-F	CAGCGAAGCAACACTGTTTCCACTTATTTTCCAGAAGC	211	[10]
GmMFT	MFTdCAPS-R	AACATGATGTTTTAGCCCGAAG	211	[10]
GmC2-18.1	C2-18.1CAPS-F	CTCCATGTCATAAGGTCTACATC	1151	[4]
GmC2-18.1	C2-18.1CAPS-R	CAGCAGTGTGTTTACATACC	1151	[4]

编号 Numbers	品种名称 Variety name	来源 Source	油分均值 Average oil content (%)
1	Sprite87	国外Abroad	25.61
2	Hobbit87	国外Abroad	25.12
3	吉密豆2号Jimidou 2	中国东北Northeast China	24.95
4	吉密豆3号Jimidou 3	中国东北Northeast China	24.85
5	辽08012 Liao 08012	中国东北Northeast China	23.14
6	吉林20号Jilin 20	中国东北Northeast China	24.98
7	大黄豆Dahuangdou	中国黄淮Huanghuai, China	18.23
8	大青豆Daqingdou	中国黄淮Huanghuai, China	18.37
9	平顶黄Pingdinghuang	中国黄淮Huanghuai, China	18.82
10	泰州白花乌甲2 Taizhoubaihuawujia 2	中国南方Southern China	18.96
11	早黄豆-1 Zaohuangdou	中国南方Southern China	18.87
12	七月黄-1 Qiyuehuang-1	中国南方Southern China	18.09

GmSWEET39	GmST1	GmMFT	GmC2-18.1	数量 Number	聚合优异等位基因类型 PFAT	范围 Range	油分 Oil content (%)	标准偏差 SD	标准误差 MD	P值 P value
缺失Deletion	T	A	G	115	PFAT-1	8.88	22.89	1.72	0.16	-
缺失Deletion	T	C	G	6	PFAT-2	2.68	21.04	1.00	0.41	0.274
缺失Deletion	T	A	A	409	PFAT-3	8.69	21.67	1.61	0.08	<0.01
缺失Deletion	T	C	A	194	PFAT-4	8.66	20.32	1.19	0.09	<0.01
缺失Deletion	C	A	A	61	PFAT-5	5.77	21.59	1.46	0.19	<0.01
缺失Deletion	C	A	G	12	PFAT-6	7.67	21.53	2.58	0.74	0.252
缺失Deletion	C	C	A	61	PFAT-7	6.91	19.03	1.71	0.22	<0.01
缺失Deletion	C	C	G	5	PFAT-8	4.96	19.84	2.34	1.05	<0.01
插入Insertion	T	A	G	6	PFAT-9	3.59	20.64	1.40	0.57	0.056
插入Insertion	T	A	A	30	PFAT-10	5.83	20.90	1.62	0.30	<0.01
插入Insertion	T	C	A	32	PFAT-11	4.95	19.53	1.24	0.22	<0.01
插入Insertion	T	C	G	9	PFAT-12	5.59	19.28	1.78	0.59	<0.01
插入Insertion	C	C	G	8	PFAT-13	4.67	19.43	1.77	0.63	<0.01
插入Insertion	C	C	A	61	PFAT-14	6.69	18.37	1.89	0.24	<0.01
插入Insertion	C	A	A	9	PFAT-15	4.89	20.70	1.54	0.51	<0.01
插入Insertion	C	A	G	2	PFAT-16	3.78	19.17	2.67	1.89	0.075

大豆油分相关功能基因分子标记开发与鉴定及优异等位变异聚合分析

Development and Identification of Molecular Markers for Oil-Related Functional Genes and Polymerization Analysis of Excellent Alleles in Soybean

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