基于卵形鲳鲹基因组重测序的InDel标记挖掘与耐低氧性状关联分析

伞利择; 刘宝锁; 张楠; 郭梁; 郭华阳; 朱克诚; 张殿昌

doi:10.12131/20210347

基于卵形鲳鲹基因组重测序的InDel标记挖掘与耐低氧性状关联分析

doi: 10.12131/20210347

伞利择^{1, 2,},
刘宝锁^{2, 3},
张楠^{2, 3},
郭梁^{2, 3},
郭华阳^{2, 3},
朱克诚^{2, 3},
张殿昌^{2, 3, ,}

1.
河北农业大学海洋学院，河北秦皇岛 066003
2.
中国水产科学研究院南海水产研究所/农业农村部南海渔业资源开发利用重点实验室，广东广州 510300
3.
广东省海洋生物种业工程技术研究中心，广东广州 510300

基金项目: 国家自然科学基金项目 (U20A2064)；财政部和农业农村部: 国家海水鱼产业技术体系资助 (CARS-47)；国家重点研发计划项目 (2018YFD0900301)；中国水产科学研究院中央级公益性科研院所基本科研业务费专项资金资助 (2020TD29)

详细信息

作者简介:
伞利择 (1996—)，男，硕士研究生，研究方向为水产动物遗传育种。E-mail: cdsanlz@163.com

通讯作者:
张殿昌 (1977—)，男，研究员，博士，从事水产种质资源与遗传育种研究。E-mail: zhangdch@scsfri.ac.cn

中图分类号: S 917.4
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- 文章访问数: 520
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- 被引次数: 0
出版历程
- 收稿日期: 2021-11-24
- 修回日期: 2022-02-06
- 录用日期: 2022-02-18
- 网络出版日期: 2022-03-03
- 刊出日期: 2022-10-05

Mining of InDel marker and association analysis of hypoxia tolerance traits in Trachinotus ovatus based on resequencing

SAN Lize^{1, 2
,},
LIU Baosuo^{2, 3},
ZHANG Nan^{2, 3},
GUO Liang^{2, 3},
GUO Huayang^{2, 3},
ZHU Kecheng^{2, 3},
ZHANG Dianchang^{2, 3
, ,}

1.
Ocean College, Hebei Agricultural University, Qinhuangdao 066003, China
2.
South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Areas, Guangzhou 510300, China
3.
Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China

摘要

摘要: 卵形鲳鲹 (Trachinotus ovatus) 是高耗氧率的鱼类，低氧极易导致其死亡。筛选其耐低氧性状InDel分子标记并挖掘影响耐低氧性状的功能基因，可为选育具有较强耐低氧能力的卵形鲳鲹提供有益指导。利用全基因组重测序技术分析了卵形鲳鲹基因InDel差异，挖掘卵形鲳鲹与耐低氧性状显著关联的InDel位点，并探讨了与耐低氧性状相关的候选基因。结果表明，测序共获得693.48 Gb数据，其中Q30的平均值为90.8%，注释分析发现了共2 574 178个InDel位点。敏感组50尾卵形鲳鲹所特有的InDel共249 395个，其中2 209个位于外显子上，在核苷酸切除修复信号通路和细胞黏着分子中存在变异基因。将InDel位点与耐低氧性状关联分析发现，3个InDel位点 (InDel 22883061、InDel 24919481和InDel 14451779) 接近显著性阈值，注释分析获得了9个候选基因。筛选到的InDel位点对后期分子标记选择育种的选择和鉴定有重要价值，注释到的候选基因为卵形鲳鲹耐低氧的机理研究提供了基础和依据。
- 卵形鲳鲹 /
- InDel /
- 重测序 /
- 耐低氧性状
Abstract: Trachinotus ovatus is a fish with high oxygen consumption rate, and hypoxia can easily lead to its death. Screening for InDel molecular markers for hypoxia tolerance traits in T. ovatus and discovering functional genes affecting hypoxia tolerance traits can provide guidances for selecting and breeding T. ovatus with strong hypoxia tolerance. In this study, we applied the whole genome resequencing technology to analyze the InDel differences of T. ovatus gene, excavated the InDel sites that were significantly associated with hypoxia tolerance traits in T. ovatus, and explored the candidate genes related to hypoxia tolerance traits. Altogether 693.48 Gb was obtained by sequencing, and the average value of Q30 was 90.8%. A total of 2 574 178 InDel markers were found by annotation analysis. A total of 249 395 InDel markers were found in the 50 individuals in the tolerance group, of which 2 209 were located in exons. It is found that there were mutated genes in the nucleotide excise repair signaling pathway and cell adhesion molecules. Three InDel markers (InDel 22883061, InDel 24919481 and InDel 14451779) were found to be close to the significance threshold by association analysis between InDel markers and hypoxia tolerance trait. Nine candidate genes were obtained by annotation analysis. The selected InDel markers were of great value for selecting and identifying molecular marker selection breeding. The annotated candidate genes provide a basis and references for the study of the hypoxia tolerance mechanism of T. ovatus.
- Trachinotus ovatus /
- InDel /
- Resequencing /
- Hypoxia tolerance trait

HTML全文

图 1 卵形鲳鲹基因组 GC含量和测序质量分布图

Figure 1. GC content and sequence quality in T.ovatus

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图 2 InDel在基因组上的分布位置

Figure 2. Region of InDel on genome

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图 3 InDel在基因组上的分布密度

Figure 3. Distribution density of InDel on genome

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图 4 KEGG富集分析

Figure 4. KEGG enrichment scatter plot

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图 5 100尾卵形鲳鲹亲缘关系热图 (a)、主成分分析 (b)、耐低氧性状全基因组关联分析的QQ图 (c) 和曼哈顿图 (d)

Figure 5. Heat map of genetic relationship (a), principal component analysis (b), Q-Q plot (c) and Manhattan plot (d) of genome-wide association analysis for low oxygen tolerance of 100 individuals of T. ovatus

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表 1 鉴定到的不同长度InDel的数量

Table 1. Number of InDels of different sizes identified

InDel类型 InDel Type	InDel大小 InDel Size/bp	数量 Number	百分比 Percentage/%	InDel类型 InDel Type	InDel大小 InDel Size/bp	数量 Number	百分比 Percentage/%
插入 Insertion	1	496002	44.94	缺失 Deletion	1	532256	37.7
	2	189179	17.14		2	292212	20.7
	3	58625	5.31		3	107471	7.6
	4	69620	6.31		4	106766	7.6
	5	23055	2.09		5	43919	3.1
	6	43192	3.91		6	62130	4.4
	7	13832	1.25		7	27167	1.9
	8	28729	2.60		8	39844	2.8
	9	11719	1.06		9	20564	1.5
	10	20236	1.83		10	27837	2.0
	≥11	149421	13.54		≥11	152545	10.8
总计 Total　　　　1103610				总计 Total　　　　1412711

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表 2 变异基因GO功能分类注释

Table 2. GO classification of mutated genes

类别 Classification	条目 Term	变异基因数量 Number of variant genes
细胞组分 Cellular component	染色体	7
	顶体泡	6
	线粒体外膜	4
	电压门控钾离子通道复合物	3
	肌间盘	3
分子功能 Molecular function	核酸结合	11
	GTP结合	8
	电压门控离子通道活性	5
	镁离子结合	5
	转录辅抑制活性	5
生物过程 Biological process	细胞对DNA损伤刺激的反应	7
	Wnt信号通路	6
	细胞器组织	6
	骨骼肌组织发育	5
	DNA整合	5

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