基于重测序的南方高蛋白大豆品种福豆234的遗传变异

张玉梅; 萧涵; 蓝新隆; 夏春英; 林国强

doi:10.19303/j.issn.1008-0384.2024.06.004

基于重测序的南方高蛋白大豆品种福豆234的遗传变异

doi: 10.19303/j.issn.1008-0384.2024.06.004

福建省农业科学院作物研究所/福建省特色旱作物品种选育工程技术研究中心/福建省蔬菜遗传育种重点实验室，福建　福州　350013

基金项目: 福建省科技厅区域发展项目（2023N3001）；福建省科技计划公益类专项（2022R1031006）；福建省财政专项（CXTD2021011-2）

详细信息

作者简介:
张玉梅（1980 —），女，博士，副研究员，主要从事大豆育种与栽培研究，E-mail：2407270791@qq.com

通讯作者:
林国强（1965 —），男，研究员，主要从事大豆育种与栽培研究，E-mail：542057656@qq.com

中图分类号: S565.1
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出版历程
- 收稿日期: 2024-05-17
- 录用日期: 2024-07-24
- 修回日期: 2024-06-11
- 网络出版日期: 2024-08-15
- 刊出日期: 2024-06-28

Genetic Variations in Southern High-protein Soybean Fudou 234 by Re-sequencing

Crop Research Institute, Fujian Academy of Agricultural Sciences/Fujian Engineering Research Center for Characteristic Dry Crop Varieties Breeding/Fujian Key Laboratory of Vegetable Genetics and Breeding Fuzhou, Fuzhou, Fujian　350013, China

摘要

摘要: 目的揭示南方高蛋白大豆遗传变异提供理论参考。方法通过高通量测序技术对南方高蛋白大豆品种福豆234进行全基因组重测序。结果共获得64 757 037条Clean reads，测序深度为17×，基因组覆盖度分别达98.08%（1×）和96.25%（5×）。共鉴定出1478393个单核苷酸多态性（Single nucleotide polymorphism, SNP）位点和356739个小片段插入缺失（Small insertion-deletion, Small InDel）位点。其中共鉴定出14323个非同义SNP突变的基因，4186个Small Indel的突变基因位于编码区（Coding sequence, CDS）。通过COG（Clusters of orthologous groups of proteins）分析发现信号传导机制、转录、碳水化合物转输和代谢等和KEGG（Kyoto encyclopedia of genes and genomes）分析发现碳代谢、淀粉和蔗糖代谢、氨基酸生物合成、植物激素信号传导、内质网蛋白质加工等通路与福豆234遗传变异相关。此外，本研究以大豆籽粒蛋白质含量数量性状基因座（Quantitative trait locus, QTL）的两个主要区段内的候选基因进行分析，发现有65个基因发生SNP或Small InDel水平的变异，其中，SNP变异类型达10种，Small InDel变异类型达7种。结论本研究初步揭示南方高蛋白大豆的遗传变异规律，为高蛋白大豆品种选育和分子标记的开发提供数据支持和理论依据。
- 福豆234 /
- 全基因组重测序 /
- 单核苷酸多态性 /
- 小片段插入缺失 /
- 变异
Abstract: Objective Genetic variations in the southern high-protein soybeans were revealed by re-sequencing the whole genome. Method High-throughput sequencing was conducted on the whole genome of the southern high-protein soybean Fudou 234 to detect genetic variations. Result In the 64757037 clean reads, the sequencing depth was 17× with genome coverage of 98.08% (1×) and 96.25% (5×). There were 1478393 single nucleotide polymorphisms (SNPs) and 356739 small insertion-deletions (Small InDels) identified. Among them, 14323 non-synonymous SNP mutations and 4186Small InDel mutated genes were found in the coding sequence (CDS). Analysis by COG (Clusters of orthologous groups of proteins) revealed that signal transduction mechanisms, transcription, carbohydrate translocation and metabolism and KEGG(Kyoto encyclopedia of genes and genomes) analyses revealed that the pathways of carbon metabolism, starch and sucrose metabolism, amino acid biosynthesis, phytohormone signalling, and endoplasmic reticulum protein processing were associated with genetic variation in Fudou 234. In addition, by studying the candidate genes in two major segments of soybean kernel protein quantitative trait locus (QTL), 10 SNP and 7 Small InDel type variations were discovered in 65 genes. Conclusion The genetic variations in the southern high-protein soybeans deviated from the regular varieties were unveiled to provide new venue for breeding and developing molecular markers in studying soybeans.
- Fudou 234 /
- whole genome re-sequencing /
- single nucleotide polymorphism /
- small InDel /
- variation

HTML全文

图 1 福豆234测序数据分析

A：福豆234染色体覆盖深度分布；B：福豆234各类型变异在染色体的分布。

Figure 1. Analysis of sequencing data of Fudou 234

A: distribution of chromosomes coverage depth of Fudou 234; B: the distribution of the variations of Fudou 234 on the chromosomes.

下载: 全尺寸图片幻灯片

图 2 福豆234的SNP注释结果

A：福豆234的SNP变异分布全基因组注释结果；B：福豆234的SNP变异分布CDS注释结果。

Figure 2. SNP annotations of Fudou 234

A: genome-whole annotation statistics of SNP variant distribution of Fudou 234; B: CDS annotation statistics of SNP variant distribution of Fudou 234.

下载: 全尺寸图片幻灯片

图 3 福豆234的CDS区和全基因组Small Indel长度分布

Figure 3. CDS region and distribution of Small Indel lengths in whole genome of Fudou 234

下载: 全尺寸图片幻灯片

图 4 福豆234的Small InDel注释结果

A：福豆234的Small InDel变异分布全基因组注释结果；B：福豆234的Small InDel变异分布CDS注释结果。

Figure 4. Small InDel annotations of Fudou 234

A: genome-whole annotation statistics of Small InDel variant distribution of Fudou 234; B: CDS annotation statistics of Small InDel variant distribution of Fudou 234.

下载: 全尺寸图片幻灯片

图 5 福豆234的遗传变异基因COG富集

Figure 5. COG enrichment of genetic variants in Fudou 234

下载: 全尺寸图片幻灯片

图 6 福豆234的遗传变异基因KEGG富集

Figure 6. KEGG enrichment of genetic variants in Fudou 234

下载: 全尺寸图片幻灯片

表 1 福豆234中与大豆蛋白质含量主要QTL区段候选基因SNP和Small Indel变异

Table 1. SNP and Small InDel variations of candidate genes in main QTL segments related to soybean protein content in Fudou 234

基因名称 Gene ID	变异类型 Variation type		基因名称 Gene ID	变异类型 Variation type		基因名称 Gene ID	变异类型 Variation type
基因名称 Gene ID	SNP	Small InDel	基因名称 Gene ID	SNP	Small InDel	基因名称 Gene ID	SNP	Small InDel
Glyma.20G082300	2	1	Glyma.20G086900	/	2	Glyma.10G133900	1	1
Glyma.20G082700	/	1	Glyma.20G087000	6	/	Glyma.10G134100	1,7,2	7
Glyma.20G082800	7	/	Glyma.20G087200	1	/	Glyma.10G134400	1	1,7
Glyma.20G082900	2	/	Glyma.15G048600	2	2	Glyma.10G134500	1,7	1
Glyma.20G083100	1,7,5,8,6,2	1	Glyma.15G048700	1, 7	2	Glyma.10G136100	1	/
Glyma.20G083200	1,2	1,2	Glyma.15G048800	1, 7, 5,3, 2	1,11,7,3,2	Glyma.10G136300	2,1	2
Glyma.20G083300	1,7, 5,3,2	1,2	Glyma.15G048900	1, 4, 6,2	1,7,2	Glyma.10G136400	2	2
Glyma.20G083500	1,7,4,2	1,7,2	Glyma.15G049000	1,10,6,7,3,2	1,4,11,3,7	Glyma.10G136600	7	/
Glyma.20G083600	1,10,5,6,3,4,2	4,2	Glyma.15G049500	3,5	/	Glyma.10G136800	1,7,2	1,2,3
Glyma.20G083800	4,1	1	Glyma.15G049600	3,7,6,1	1,2,7	Glyma.08G182200	/	1
Glyma.20G084000	1,4,8,7,2	1,2	Glyma.15G049700	2,3,6,10,4,1	2,1	Glyma.08G182300	/	1,7
Glyma.20G084100	1,10,5,3,4,2	1,2,4	Glyma.15G049800	2,5,8,7,1	2,7,1	Glyma.08G182400	/	2
Glyma.20G084200	1,5	1	Glyma.15G049900	2,6,7,9,1	1,11,7,3,4	Glyma.08G182500	/	7
Glyma.20G084500	1,5,2	/	Glyma.15G050100	2,7	2	Glyma.08G182700	/	1,2,7,9
Glyma.20G084900	1	/	Glyma.15G050200	5,1	2,1	Glyma.08G182900	/	1,7
Glyma.20G085000	1	2	Glyma.15G050300	3	1	Glyma.08G183000	/	1,7,3,2
Glyma.20G085100	/	2	Glyma.15G050500	1,2,7	1,7	Glyma.08G183400	/	1
Glyma.20G085300	/	1	Glyma.15G050600	1,2,7	1	Glyma.08G183500	/	7,3,2
Glyma.20G085700	2	2	Glyma.10G132200	1,7,5,6,2	1,2	Glyma.08G183600	/	2
Glyma.20G085900	1	2	Glyma.10G132700	2,6	2,7	Glyma.08G183900	/	7,1
Glyma.20G086100	/	1	Glyma.10G132800	3,1	/	Glyma.08G184100	/	2,7,1
Glyma.20G086800	2	2	Glyma.10G133700	2	/
11种变异类型中，1～11分别代表变异位点发生在基因上游区域、基因下游区域、基因的3’UTR内、基因的5’UTR内、编码区内同义突变、编码区内非同义突变、内含子、剪切位点区域、剪切受体突变、非编码区内起始密码子获得、密码子插入以及移码突变。 1～11 indicate mutation sites in 11 variation types occurred upstream, downstream, UTR 3 prime, UTR 5 prime, synonymous coding, non-synonymous coding, intron, splice site region, splice site donor, start gained, codon insertion, and frame shift, respectively.

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