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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

伞利择, 刘宝锁, 张楠, 郭梁, 郭华阳, 朱克诚, 张殿昌. 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[J]. 南方水产科学. doi: 10.12131/20210347
引用本文: 伞利择, 刘宝锁, 张楠, 郭梁, 郭华阳, 朱克诚, 张殿昌. 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[J]. 南方水产科学. doi: 10.12131/20210347
SAN Lize, LIU Baosuo, ZHANG Nan, GUO Liang, GUO Huayang, ZHU Kecheng, ZHANG Dianchang. Mining of InDel marker and association analysis of hypoxia tolerance traits in Trachinotus ovatus based on resequencing[J]. South China Fisheries Science. doi: 10.12131/20210347
Citation: SAN Lize, LIU Baosuo, ZHANG Nan, GUO Liang, GUO Huayang, ZHU Kecheng, ZHANG Dianchang. Mining of InDel marker and association analysis of hypoxia tolerance traits in Trachinotus ovatus based on resequencing[J]. South China Fisheries Science. 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
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

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

  • 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。
  • 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

    图  2  InDel在基因组上的分布位置

    Figure  2.  Region of InDel on genome

    图  3  InDel在基因组上的分布密度

    Figure  3.  Distribution density of InDel on genome

    图  4  KEGG富集分析

    Figure  4.  KEGG enrichment scatter plot

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

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

    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
    下载: 导出CSV

    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
    下载: 导出CSV
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  • 收稿日期:  2021-11-24
  • 修回日期:  2022-02-06
  • 录用日期:  2022-02-18
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