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斑点叉尾鮰EGFL9基因变异位点与生长性状的关联分析

张文平 张世勇 刘洪岩 徐思琪 王明华 钟立强 边文冀 朱明 陈校辉

张文平,张世勇,刘洪岩,等. 斑点叉尾鮰EGFL9基因变异位点与生长性状的关联分析 [J]. 福建农业学报,2023,38(3):253−261 doi: 10.19303/j.issn.1008-0384.2023.03.001
引用本文: 张文平,张世勇,刘洪岩,等. 斑点叉尾鮰EGFL9基因变异位点与生长性状的关联分析 [J]. 福建农业学报,2023,38(3):253−261 doi: 10.19303/j.issn.1008-0384.2023.03.001
ZHANG W P, ZHANG S Y, LIU H Y, et al. Variation Sites on EGFL9 Associated with Growth of Channel Catfish [J]. Fujian Journal of Agricultural Sciences,2023,38(3):253−261 doi: 10.19303/j.issn.1008-0384.2023.03.001
Citation: ZHANG W P, ZHANG S Y, LIU H Y, et al. Variation Sites on EGFL9 Associated with Growth of Channel Catfish [J]. Fujian Journal of Agricultural Sciences,2023,38(3):253−261 doi: 10.19303/j.issn.1008-0384.2023.03.001

斑点叉尾鮰EGFL9基因变异位点与生长性状的关联分析

doi: 10.19303/j.issn.1008-0384.2023.03.001
基金项目: 江苏省农业重大新品种创制项目(PZCZ201741);国家现代农业产业技术体系建设专项(CARS-46);江苏省现代农业产业技术体系建设项目[JATS(2022)413]
详细信息
    作者简介:

    张文平(1996−),男,硕士研究生,主要从事鱼类遗传育种研究(E-mail:976261968@qq.com

    通讯作者:

    张世勇(1987−),男,博士,副研究员,主要从事鱼类遗传育种研究(E-mail:shiyongzhang@hotmail.com

    陈校辉(1977−),男,硕士,研究员,主要从事鱼类遗传育种研究(E-mail: cxiaohui416@hotmail.com

  • 中图分类号: S965

Variation Sites on EGFL9 Associated with Growth of Channel Catfish

  • 摘要:   目的  研究斑点叉尾鮰表皮生长因子样结构域蛋白EGFL9(Multiple epidermal growth factor-like domains protein 9)基因与其生长性状的相关性,为斑点叉尾鮰的分子标记辅助育种奠定基础。  方法  采用靶向基因测序技术对EGFL9基因进行测序,与参考基因组比对后筛选变异位点,并将获得的变异位点与生长性状进行关联分析。  结果  在EGFL9上共发现27个多态位点,经过滤,获得22个有效突变位点,其中4个变异位点(g.142、g.573、g.3079、g.7409)对斑点叉尾鮰的生长性状具有显著影响,位点g.142、g.3079、g.7409位于内含子中,位点g.573位于第2外显子上;g.142位点的A/A型个体的平均体长显著高于A/G型个体(P<0.05);g.7409位点A/G型个体的平均体长显著高于G/G型、A/A型个体(P<0.05);g.3079位点C/C型个体的平均体质量和体长均显著高于A/A型个体(P<0.05);位于外显子上的InDel位点g.573使EGFL9基因编码蛋白减少了一个苏氨酸残基,对蛋白质三级结构产生较为明显的影响,该位点TACC/T型个体的平均体质量显著高于TACC/TACC型个体(P<0.05),平均体长显著高于TACC/TACC型与T/T型个体(P<0.05)。  结论  获得的4个斑点叉尾鮰生长相关标记(g.142、g.573、g.3079、g.7409)与其生长性状显著关联,可以应用于后续斑点叉尾鮰育种芯片开发和分子标记辅助育种。
  • 图  1  斑点叉尾鮰EGFL9二级结构预测

    A:EGFL9蛋白质二级结构;B:EGFL9(g.573)蛋白质二级结构。在二级结构中蓝色表示螺旋;红色表示折叠;黄色表示未知结构,在表面残基可溶性中蓝色表示暴露;黄色表示埋藏。

    Figure  1.  Predicted secondary structure of EGFL9 protein in channel catfish

    A: secondary structure of EGFL9 protein; B: secondary structure of EGFL9 (g.573) protein. In secondary structure, blue indicates helix; red, strand; yellow, others. On solvent accessibility, blue indicates exposed; yellow, buried.

    图  2  斑点叉尾鮰EGFL9三级结构预测

    A:EGFL9蛋白质三级结构;B:EGFL9(g.573)蛋白质三级结构。

    Figure  2.  Predicted tertiary structure of EGFL9 protein in channel catfish

    A: tertiary structure of EGFL9 protein; B: tertiary structure of EGFL9 (g.573) protein.

    表  1  用于EGFL9基因变异位点筛选和分型引物

    Table  1.   Primers used in screening and genotyping variation sites on EGFL9

    位点  
    Locus  
    变异位点位置
    Variation location
    引物序列   
    Primer sequence   
    变异类型  
    Variation type  
    产物大小
    PCR size/bp
    g.137 Intron1 F: GGGGAGCGTTTGTAGTAGACG A/T 193
    R: GTTTCAGTTACTCTTGCTCGCG
    g.142 Intron2 F: GGGGAGCGTTTGTAGTAGACG A/G 193
    R: GTTTCAGTTACTCTTGCTCGCG
    g.339 Exon1 F: TGCATGCAGAATGTTAGTTTTTC A/G 192
    R: GTTTCAGTTACTCTTGCTCGCG
    g.573 Exon2 F: CTGACCTCAGCGCAATTTC TACC/T 195
    R: AACAACAACAACCACCATCACC
    g.716 Intron3 F: GATTTTACCACCACCACCAC C/T 187
    R: TGACAGGTCTATTACTCTTGTACACTTC
    g.913 Intron4 F: CCGCCTGACCTCAAAACCC A/G 191
    R: TCCTATGTATTGAGAACCTCAAGTC
    g.928 Intron5 F: CCGCCTGACCTCAAAACCC A/C 191
    R: TCCTATGTATTGAGAACCTCAAGTC
    g.1877 Intron6 F: CTGTAAGTGTTTGCCCGG C/T 199
    R: CACCTTACAAAGCAGTCGCC
    g.2998 Intron7 F: TAACTGGGTGTGAAATTTCAAC A/AGGATGAT 194
    R: AAAGCAGAATGTTGCGGGAC
    g.3027 Intron8 F: TAACTGGGTGTGAAATTTCAAC G/T 194
    R: AAAGCAGAATGTTGCGGGAC
    g.3029 Intron9 F: TAACTGGGTGTGAAATTTCAAC G/T 194
    R: AAAGCAGAATGTTGCGGGAC
    g.3031 Intron10 F: TAACTGGGTGTGAAATTTCAAC G/T 194
    R: AAAGCAGAATGTTGCGGGAC
    g.3045 Intron11 F: TAACTGGGTGTGAAATTTCAAC A/G 194
    R: AAAGCAGAATGTTGCGGGAC
    g.3079 Intron12 F: TAACTGGGTGTGAAATTTCAAC A/C 194
    R: AAAGCAGAATGTTGCGGGAC
    g.5185 Intron13 F: TGCCATGCGAATGCAATG A/G 203
    R: GCAAGGCCTTCTGAATGCC
    g.5819 Intron14 F: GTGTGTGCCAATCAAACTGGG A/C 192
    R: GCAAGGCCTTCTGAATGCC
    g.6171 Intron15 F: TAACAAAATGCCAAGCTTAAAATG C/T 197
    R: AGCCCCACTGCCAACG
    g.6202 Intron16 F: TAACAAAATGCCAAGCTTAAAATG C/CAT 197
    R: AGCCCCACTGCCAACG
    g.6305 Exon3 F: TAACAAAATGCCAAGCTTAAAATG C/G 197
    R: AGCCCCACTGCCAACG
    g.6477 Exon4 F: CGCTCCTCTCCGGCCTG C/T 199
    R: CAACAGCTATCACGACAGCCTG
    g.7409 Intron17 F: CAGACATGCACTGATGCTTTAG A/G 193
    R: TGGAATAGAAACACATGCAGTTAC
    g.7669 Intron18 F: GGGGCGCTGCCTTATGG A/G 196
    R: AATCGAATTAGTTTTGAATCAGTCC
    下载: 导出CSV

    表  2  斑点叉尾鮰EGFL9基因变异位点遗传多样性参数

    Table  2.   Diversity indices of variation sites on EGFL9 of channel catfish

    位点
    Locus
    变异位点位置    
    Variation location    
    有效等位基因数
    Ne
    期望杂合度
    He
    观测杂合度
    Ho
    多态性信息容量
    PIC
    哈迪-温伯格平衡
    HWE
    g.137 A:0.815 1.4294 0.301 0.358 0.255 NS
    T:0.184
    g.142 A:0.616 1.8963 0.474 0.637 0.361 ***
    G:0.383
    g.339 A:0.077 1.1677 0.144 0.156 0.133 ***
    G:0.922
    g.573 T:0.261 1.6285 0.387 0.204 0.311 ***
    TACC:0.738
    g.716 C:0.86 1.3154 0.240 0.179 0.211 ***
    T:0.139
    g.913 A:0.567 1.9646 0.492 0.527 0.370 NS
    G:0.432
    g.928 A:0.159 1.3656 0.268 0.259 0.232 NS
    C:0.84
    g.1877 C:0.606 1.9136 0.479 0.269 0.363 ***
    T:0.393
    g.2998 A:0.38 1.8914 0.473 0.365 0.360 NS
    AGGATGAT:0.619
    g.3027 G:0.38 1.8914 0.473 0.365 0.360 NS
    T:0.619
    g.3029 G:0.377 1.8869 0.471 0.370 0.360 NS
    T:0.622
    g.3031 G:0.38 1.8914 0.473 0.365 0.360 NS
    T:0.619
    g.3045 A:0.768 1.5526 0.357 0.326 0.293 NS
    G:0.231
    g.3079 A:0.315 1.7607 0.433 0.581 0.339 ***
    C:0.684
    g.5185 A:0.915 1.1832 0.155 0.169 0.143 ***
    G:0.084
    g.5819 A:0.484 1.9982 0.501 0.556 0.375 NS
    C:0.515
    g.6171 C:0.636 1.8607 0.464 0.468 0.356 NS
    T:0.363
    g.6202 C:0.378 1.8878 0.471 0.249 0.360 ***
    CAT:0.621
    g.6305 C:0.803 1.4616 0.317 0.353 0.266 NS
    G:0.196
    g.6477 C:0.937 1.1327 0.117 0.105 0.110 ***
    T:0.062
    g.7409 A:0.44 1.9716 0.494 0.470 0.371 NS
    G:0.56
    g.7669 A:0.206 1.4862 0.328 0.342 0.274 NS
    G:0.793
    哈迪温伯格平衡检验,NS代表不显著,***代表极显著偏离。
    Hardy-Weinberg equilibrium, NS: not significant; ***: significant at 0.001 level.
    下载: 导出CSV

    表  3  斑点叉尾鮰EGFL9基因变异位点与生长性状的关联分析

    Table  3.   Correlation between variation sits on EGFL9 and growth traits of channel catfish

    位点
    Locus
    基因型    
    Genotype    
    频率
    Frequency
    体质量
    Body mass/g
    体长
    Body length/cm
    g.142 A/A(60) 0.298 955.165±273.451 a 46.200±3.602 a
    A/G(128) 0.636 944.849±284.504 a 45.055±3.756 b
    G/G(13) 0.064 988.585±189.377 a 46.154±2.882 ab
    g.573 TACC/TACC(128) 0.636 921.955±281.729 b 45.211±3.588 b
    TACC/T(41) 0.203 1025.578±261.659 a 46.524±3.521 a
    T/T(32) 0.159 970.100±252.701 ab 45.145±4.141 b
    g.3079 A/A(5) 0.025 722.880±285.012 b 42.200±4.086 b
    A/C(115) 0.580 939.037±267.002 ab 45.300±3.655 ab
    C/C(78) 0.393 983.433±283.021 a 45.799±3.636 a
    g.7409 A/A(41) 0.205 955.485±328.208 a 45.456±4.376 b
    A/G(94) 0.470 985.556±268.803 a 46.034±3.518 a
    G/G(65) 0.325 904.335±239.218 a 44.755±3.319 b
    同列数据后不同小写字母表示同一位点不同基因型之间差异显著(P<0.05)。
    Datas with different lowercase letters on the same column indicate significant difference of different genotypes of one same SNP site at P<0.05 level, respectively.
    下载: 导出CSV
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出版历程
  • 收稿日期:  2022-11-07
  • 录用日期:  2022-11-07
  • 修回日期:  2023-03-08
  • 网络出版日期:  2023-04-14
  • 刊出日期:  2023-03-28

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