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斑马鱼TYRP1b基因SNPs筛查及其与体色性状的关联分析

宋兴超 王云艳 王莎莎 方月 巴家文 梅杰 梁正其

宋兴超,王云艳,王莎莎,等. 斑马鱼TYRP1b基因SNPs筛查及其与体色性状的关联分析 [J]. 福建农业学报,2024,39(4):387−397 doi: 10.19303/j.issn.1008-0384.2024.04.003
引用本文: 宋兴超,王云艳,王莎莎,等. 斑马鱼TYRP1b基因SNPs筛查及其与体色性状的关联分析 [J]. 福建农业学报,2024,39(4):387−397 doi: 10.19303/j.issn.1008-0384.2024.04.003
SONG X C, WANG Y Y, WANG S S, et al. SNPs and Correlation of TYRP1b with Color of Zebrafish [J]. Fujian Journal of Agricultural Sciences,2024,39(4):387−397 doi: 10.19303/j.issn.1008-0384.2024.04.003
Citation: SONG X C, WANG Y Y, WANG S S, et al. SNPs and Correlation of TYRP1b with Color of Zebrafish [J]. Fujian Journal of Agricultural Sciences,2024,39(4):387−397 doi: 10.19303/j.issn.1008-0384.2024.04.003

斑马鱼TYRP1b基因SNPs筛查及其与体色性状的关联分析

doi: 10.19303/j.issn.1008-0384.2024.04.003
基金项目: 国家自然科学基金项目(32060274);贵州省科技计划项目(黔科合基础-ZK〔2022〕一般559);贵州省科技支撑项目(黔科合支撑〔2023〕一般081号);贵州省高层次创新型“千”层次人才培养项目(2024-〔2022〕-048);贵州省重点实验室项目(黔科合平台人才〔2020〕2003号)
详细信息
    作者简介:

    宋兴超(1982 —),男,博士,副教授,主要从事水产动物遗传育种研究,E-mail:songxingchao_888@126.com

    通讯作者:

    梁正其(1985 —),男,硕士,教授,主要从事水生动物繁殖与发育生物学研究,E-mail:940429393@qq.com

  • 中图分类号: S917.4

SNPs and Correlation of TYRP1b with Color of Zebrafish

  • 摘要:   目的  探究酪氨酸酶相关蛋白1b(tyrosinase-related protein 1b, TYRP1b)基因变异与斑马鱼体色性状的相关性。  方法  以体色表型存在显著差异的红色、黄色和蓝色斑马鱼共计219个样本的肌肉组织DNA为模板,设计3对引物,采用PCR扩增、Sanger测序技术筛查TYRP1b基因单核苷酸多态性(single nucleotide polymorphisms, SNPs),并将SNPs与斑马鱼体色性状进行关联分析。  结果  获得的斑马鱼TYRP1b基因外显子2、部分内含子3、外显子4、内含子4、外显子5、内含子5、外显子6和外显子7长度分别为134、212、168、135、180、113、150、171 bp。SNPs筛查显示,3种体色斑马鱼群体共筛查到18个SNPs,部分内含子3存在11个SNPs位点:g.2125G>A、g.2150G>A、g.2152G>T、g.2161C>A、g.2175A>T、g.2180G>T、g.2185A>T、g.2192A>C、g.2200A>T、g.2201A>C和g.2213T>C;内含子4检测到4个SNPs位点:g.7C>A、g.65A>G、g.84T>A和g.103C>T;内含子5存在1个SNPs位点:g.61G>T;外显子4、6分别存在1个SNPs位点:g.125G>T和g.80T>A,且均为同义突变;外显子2、5和7均未检测到SNPs。关联分析表明,TYRP1b基因内含子3中g.2152G>T、g.2175A>T、g.2180T>G、g.2192A>C、g.2200A>T、g.2201A>C位点、内含子4中g.65A>G位点及外显子6中g.80T>A位点的基因型均与斑马鱼体色性状极显著相关(P<0.01)。  结论  斑马鱼TYRP1b基因内含子3、4及外显子6存在8个与体色表型存在关联的SNPs,可能影响斑马鱼体色性状或与之紧密连锁。
  • 图  1  斑马鱼TYRP1b基因3对引物PCR产物电泳图谱

    M:DL2000 DNA Marker;A图中1~6:Tb-2引物PCR产物;B图中1~3:Tb-1引物PCR产物,4~6:Tb-3引物PCR产物。

    Figure  1.  Electrophoresis of products of TYRP1b in zebrafish from 3 pairs of primers

    M: DL2000 DNA marker; A1-6: PCR product of Tb-2 primer; B1-3: PCR product of Tb-1 primer; B4-6: PCR product of Tb-3 primer.

    图  2  斑马鱼TYRP1b基因SNPs位点测序峰图

    箭头所指表示碱基突变位点。

    Figure  2.  Sequencing profiles of SNPs in zebrafish TYRP1b

    Arrows point at mutated bases.

    图  3  斑马鱼TYRP1b基因SNPs分布

    括号中数字表示SNPs的数量;黑色和白色矩形分别代表外显子和内含子。

    Figure  3.  SNPs distribution of zebrafish TYRP1b

    Number in brackets is quantity of SNPs. Black rectangles represent exons, and white introns.

    表  1  引物信息

    Table  1.   Information on primer

    引物
    Primers
    序列(5′-3′)
    Sequence(5′-3′)
    退火温度
    Annealing temperature/ ℃
    延伸时间
    Extended time/s
    产物长度
    Product length/bp
    扩增区域
    Amplified region
    Tb-1F:CTGTTGTCTGGCCCGAAGAT60.225134外显子2
    Exon 2
    R:AGGAATGTGCTGACGCTGAG
    Tb-2F:CCCACAGCTCTAATGCAAACT59.659956部分内含子3~外显子6
    Partial intron 3–exon 6
    R:GCAATCAGCCGTCACTCACTT
    Tb-3F:GTAGCGTCACACCACTGACT58.428171外显子7
    Exon 7
    R:ATCACGGTAACGGTGGTAGC
    下载: 导出CSV

    表  2  不同体色斑马鱼TYRP1b基因内含子3中11个SNPs的基因型与等位基因频率

    Table  2.   Genotypes and allele frequencies of 11 SNPs in intron 3 of TYRP1b of zebrafish with different body colors

    突变位点
    SNPs
    基因型与等位基因
    Genotype and allele
    基因型与等位基因频率
    Genotype and allele frequencies
    红色 RZ 黄色 YZ 蓝色 BZ
    g.2125G>AGG1.0000(70)0.5625(36)1.0000(85)
    GA0(0)0.3750(24)0(0)
    AA0(0)0.0625(4)0(0)
    G1.00000.75001.0000
    A00.25000
    g.2150G>AGG0.2000(14)1.0000(64)0.7647(65)
    GA0.4000(28)0(0)0.2353(20)
    AA0.4000(28)0(0)0(0)
    G0.40001.00000.8823
    A0.600000.1177
    g.2152G>TGG0.2000(14)0.3125(20)0.4706(40)
    GT0.4000(28)0.3750(24)0.5294(45)
    TT0.4000(28)0.3125(20)0(0)
    G0.40000.50000.7353
    T0.60000.50000.2647
    g.2161C>ACC1.0000(70)0.3125(20)0.7059(60)
    CA0(0)0.3750(24)0.2941(25)
    AA0(0)0.3125(20)0.0000(0)
    C1.00000.50000.8530
    A00.50000.1470
    g.2175A>TAA0.4000(28)0.5000(32)0.4706(40)
    AT0.4000(28)0.5000(32)0.5294(45)
    TT0.2000(14)0(0)0(0)
    A0.60000.75000.7353
    T0.40000.25000.2647
    g.2180T>GTT0.2000(14)0.3125(20)0.4706(40)
    TG0.4000(28)0.3750(24)0.5294(45)
    GG0.4000(28)0.3125(20)0(0)
    T0.40000.50000.7353
    G0.60000.50000.2647
    g.2185A>TAA1.0000(70)0.3125(20)0.7059(60)
    AT0(0)0.3750(24)0.2941(25)
    TT0(0)0.3125(20)0(0)
    A1.00000.50000.8530
    T00.50000.1470
    g.2192A>CAA0.2000(14)0.3125(20)0.4706(40)
    AC0.4571(32)0.3750(24)0.5294(45)
    CC0.3429(24)0.3125(20)0(0)
    A0.42860.50000.7353
    C0.57140.50000.2647
    g.2200A>TAA0.2000(14)0.3125(20)0.4706(40)
    AT0.4571(32)0.3750(24)0.5294(45)
    TT0.3429(24)0.3125(20)0(0)
    A0.42860.50000.7353
    T0.57140.50000.2647
    g.2201A>CAA0.2000(14)0.5000(32)0.4706(40)
    AC0.4571(32)0.5000(32)0.5294(45)
    CC0.3429(24)0(0)0(0)
    A0.42860.75000.7353
    C0.57140.25000.2647
    g.2213T>CTT0.2000(14)1.0000(64)0.7059(60)
    TC0.4571(32)0(0)0.2941(25)
    CC0.3429(24)0(0)0(0)
    T0.42861.00000.8530
    C0.571400.1470
    括号内的数字为SNPs位点基因型数,下表同。
    Data in brackets are number of genotypes. Same for below.
    下载: 导出CSV

    表  3  不同体色斑马鱼TYRP1b基因内含子4、5和外显子4、6中7个SNPs的基因型与等位基因频率

    Table  3.   Genotypes and allele frequencies of 7 SNPs of TYRP1b in introns 4, 5 and exons 4, 6 in zebrafish of different body colors

    分布区域
    Distribution region
    突变位点
    SNPs
    基因型与等位基因
    Genotype and allele
    基因型与等位基因频率
    Genotype and allele frequencies
    红色 RZ黄色 YZ蓝色 BZ
    内含子4
    Intron 4
    g.7C>ACC1.0000(70)0.5625(36)1.0000(85)
    CA0(0)0.3750(24)0(0)
    AA0(0)0.0625(4)0(0)
    C1.00000.75001.0000
    A00.25000
    g.65A>GAA0.2000(14)0.5625(36)0.7059(60)
    AG0.4571(32)0.3750(24)0.2941(25)
    GG0.3429(24)0.0625(4)0(0)
    A0.42860.75000.8530
    G0.57140.25000.1470
    g.84T>ATT1.0000(70)0.3125(20)0.7059(60)
    TA0(0)0.3750(24)0.2941(25)
    AA0(0)0.3125(20)0(0)
    T1.00000.50000.8530
    A00.50000.1470
    g.103C>TCC0.2000(14)0.7500(64)0.7647(65)
    CT0.4571(32)0.0625(0)0.2353(20)
    TT0.3429(24)0.1875(0)0(0)
    C0.42861.00000.8823
    T0.571400.1177
    内含子5
    Intron 5
    g.61G/TGG1.0000(70)0.5625(36)1.0000(85)
    GT0(0)0.3750(24)0(0)
    TT0(0)0.0625(4)0(0)
    G1.00000.75001.0000
    T00.25000
    外显子4
    Exon 4
    g.125G>TGG1.0000(70)0.5625(36)1.0000(85)
    GT0(0)0.3750(24)0(0)
    TT0(0)0.0625(4)0(0)
    G1.00000.75001.0000
    T00.25000
    外显子6
    Exon 6
    g.80T>ATT0.4571(32)0.5000(32)0(0)
    TA0.3429(24)0.5000(32)0.5294(45)
    AA0.2000(14)0(0)0.4706(40)
    T0.62860.75000.2647
    A0.37140.25000.7353
    下载: 导出CSV

    表  4  TYRP1b基因SNPs位点的各基因型分布及其与体色表型的关联分析

    Table  4.   Distribution and association between TYRP1b SNPs genotypes and body color phenotypes

    分布区域
    Distribution region
    位点
    SNPs
    基因型
    Genotype
    不同体色数量
    Number of different body color
    总计
    Total
    χ2 P
    P value
    红色 RZ 黄色 YZ 蓝色 BZ
    内含子3
    Intron 3
    g.2152G>T GG 14 20 40 74 42.4995 <0.0001
    GT 28 24 45 97
    TT 28 20 0 48
    g.2175A>T AA 28 32 40 100 32.0120 <0.0001
    AT 28 32 45 105
    TT 14 0 0 14
    g.2192A>C AA 14 20 40 74 38.4456 <0.0001
    AC 32 24 45 101
    CC 24 20 0 44
    g.2201A>C AA 14 32 40 86 61.2982 <0.0001
    AC 32 32 45 109
    CC 24 0 0 24
    内含子4
    Intron 4
    g.65A>G AA 14 36 60 110 61.2907 <0.0001
    AG 32 24 25 81
    GG 24 4 0 28
    外显子6
    Exon 6
    g.80T>A TT 32 32 0 64 77.6947 <0.0001
    TA 24 32 45 101
    AA 14 0 40 54
    下载: 导出CSV
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出版历程
  • 收稿日期:  2023-12-26
  • 修回日期:  2024-04-01
  • 网络出版日期:  2024-06-26
  • 刊出日期:  2024-04-28

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