• 主管:福建省海洋与渔业局
  • 主办:福建省水产学会,福建省水产研究所

软鳍新光唇鱼MC4R基因多态性与生长性状关联性分析

唐智慧, 殷艳慧, 潘晓赋, 吴安丽, 张源伟, 王茉, 王晓爱

唐智慧,殷艳慧,潘晓赋,等. 软鳍新光唇鱼MC4R基因多态性与生长性状关联性分析[J]. 渔业研究,2025,47(1) :1 − 10. DOI: 10.14012/j.jfr.2024134
引用本文: 唐智慧,殷艳慧,潘晓赋,等. 软鳍新光唇鱼MC4R基因多态性与生长性状关联性分析[J]. 渔业研究,2025,47(1) :1 − 10. DOI: 10.14012/j.jfr.2024134
Tang Z H,Yin Y H,Pan X F,et al. Polymorphisms of MC4R gene and its association with growth traits in Neolissochilus benasi[J]. Journal of Fisheries Research,2025,47(1) :1 − 10. DOI: 10.14012/j.jfr.2024134
Citation: Tang Z H,Yin Y H,Pan X F,et al. Polymorphisms of MC4R gene and its association with growth traits in Neolissochilus benasi[J]. Journal of Fisheries Research,2025,47(1) :1 − 10. DOI: 10.14012/j.jfr.2024134

软鳍新光唇鱼MC4R基因多态性与生长性状关联性分析

基金项目: 中国科学院战略性先导科技专项(XDA24030505);云南省科技厅重点研发计划(202303AC100011);云南省“兴滇英才支持计划”青年人才专项(XDYC-QNRC-2023-0542、152301198408141020);云南省基础研究专项(202201AT070046)
详细信息
    作者简介:

    唐智慧,女,研究方向为水生生物学。 E-mail: chihTowne@outlook.com

    通讯作者:

    王 茉,女,副教授,博士,研究方向为湿地生物进化与保护。E-mail: wangmo139@live.cn

    王晓爱,女,正高级工程师,博士,研究方向为鱼类保护与利用。E-mail: xueaiw@126.com

  • 中图分类号: S917.4

Polymorphisms of MC4R gene and its association with growth traits in Neolissochilus benasi

  • 摘要:
    背景 

    软鳍新光唇鱼(Neolissochilus benasi)是重要的水产种质资源,但在培育过程中存在个体间生长速度差异较大的问题。

    目的 

    筛选与软鳍新光唇鱼生长性状显著相关的分子标记,推动其生长性状的改良。

    方法 

    本研究对与摄食、能量代谢、生长发育密切相关的黑素皮质素受体-4(MC4R)基因开展研究,通过PCR-Sanger测序技术进行单核苷酸多态性(SNP)检测和分型,并将SNP位点与其生长性状进行关联性分析,挖掘软鳍新光唇鱼生长性状关联的SNP标记。

    结果 

    MC4R基因2个拷贝共存在15个SNP位点,其中第1个拷贝有1个SNP位点,第2个拷贝有14个SNP位点。15个SNP位点中仅G227A为错义突变,氨基酸类型由缬氨酸(V)变为异亮氨酸(I),其余位点均为同义突变;群体遗传分析结果显示,除第1个拷贝SNP位点G669C 遗传参数值较低外,MC4R基因第2个拷贝的SNP位点期望杂合度 (He)和观测杂合度(Ho)分别为0.860±0.027和0.503±0.001,多态信息含量(PIC)为0.373~0.375,属于中度多态性,表明该群体的遗传多样性处于中上水平;关联性分析显示,MC4R基因2个拷贝15个SNP位点中,13个位点对软鳍新光唇鱼的生长性状具有不同程度的影响:位点G227A、A322G、C364T、G403A、T451C、G457A、G472A、T484C、G520A、T583C、G736A、C775G与体长、体质量显著相关(P<0.05),且均以纯合子为优势基因型,分别为AA、GG、TT、AA、CC、AA、AA、CC、AA、CC、AA、GG型;位点C664T仅检测到CC和CT两种基因型,并以杂合子CT型为优势基因型,与体质量显著相关(P<0.05)。

    结论 

    本研究初步筛选了15个与软鳍新光唇鱼生长性状相关联的候选SNP位点,为今后其生长相关机制和分子标记的进一步解析,以及生长性状的改良提供了科学依据。

    Abstract:
    Background 

    Neolissochilus benasi is an important aquatic germplasm resource, but there is a problem of large differences in growth rate among individuals during the breeding process.

    Objective 

    The study aims to identify molecular markers significantly associated with the growth traits in N. benasi and promote the improvement of its growth characteristics.

    Methods 

    The study focused on melanocortin-4 receptor (MC4R) gene, which are deeply related to ingestion, energy metabolism and growth development. Single nucleotide polymorphism (SNP) detection and genotyping were performed using PCR-Sanger sequencing technology, and association analysis was conducted between the SNP loci and growth traits to identify SNP markers related to the growth traits of N. benasi.

    Results 

    The results showed that there were 15 SNP loci in the two copies of MC4R gene, with one SNP locus in the first copy and 14 SNP loci in the second copy. Among the 15 SNP loci, only G227A was a missense mutation, with the amino acid type changed from valine (V) to isoleucine (I). The remaining loci were synonymous mutations. Population genetic analysis showed that, except for SNP locus G669C in the first copy with low genetic parameter values, the SNP loci in the second copy of MC4R gene had an expected heterozygosity (He) and observed heterozygosity (Ho) of 0.860 4±0.027 2 and 0.503 2±0.001 4, respectively, and their polymorphic information content (PIC) ranged from 0.3731 to 0.3749, indicating a middle-upper level of genetic diversity in this population. Association analysis revealed that 13 SNP loci in the two copies of MC4R gene had varying degrees of influence on the growth traits of N. benasi: G227A, A322G, C364T, G403A, T451C, G457A, G472A, T484C, G520A, T583C, G736A, and C775G were significantly associated with body length and body mass (P<0.05), with homozygous genotypes AA, GG, TT, AA, CC, AA, AA, CC, AA, CC, AA, and GG being the dominant genotypes, respectively. Meanwhile, C664T was only detected two genotypes (CC and CT), with the heterozygous CT genotype being dominant and strongly associated with body mass (P<0.05).

    Conclusion 

    This study preliminarily screens 15 candidate SNP loci associated with growth traits in N. benasi, providing a scientific basis for further analysis of growth-related mechanisms and molecular markers, as well as for the improvement of growth traits in this species.

  • 软鳍新光唇鱼(Neolissochilus benasi)隶属于鲤形目(Cypriniformes)、鲤科(Cyprinidae)、新光唇鱼属(Neolissochilus),是红河水系特有珍稀鱼类,在中国主要分布于元江、李仙江流域[1]。由于大规模水利建设、鱼类资源利用强度增加、保护意识薄弱等原因,软鳍新光唇鱼野外种群数量急剧下降[2],目前仅在云南江城县和西畴县保留有较大种群[3]。中国科学院昆明动物研究所经过长期努力,突破了软鳍新光唇鱼的精子超低温冷冻保存[4]和人工繁殖技术[5],有效避免了该物种的灭绝,且人工繁殖的成功,为其可持续利用奠定了坚实的基础。在人工繁育的基础上,经过4代群体选育,复杂肌间刺弱化的软鳍新光唇鱼“墨龙1号”于2022年获得农业农村部的新品种认证,为云南乃至中国水产养殖业的发展提供了良好的种质资源。

    然而,养殖过程中个体间生长速度差异大等问题仍然对产业化发展具有较大制约作用[6]。因此,选育生长速度快的稳定品系是推动其产业化发展的重要环节。近年来,分子生物学技术的飞速发展,促使分子辅助育种成为当前选择育种的热门方法[7],而获取高效、可识别性强的分子标记是分子辅助育种的前提。已有研究表明,生长是典型的数量性状,受多种基因的共同调控,并且不同物种生长相关调控机制、主效调控基因和关键调控元件不尽相同[8]。因此,对特定物种开展生长相关分子标记的筛选是推动优良品种选育的前提。

    黑素皮质素受体-4(Melanocortin-4 receptor,MC4R)是下丘脑腹内侧核分泌的一种肽类物质[9],可与垂体分泌的内源性激动剂α-促黑素细胞激素(Alpha melanocyte stimulating hormone,α-MSH)及其拮抗剂agouti相关蛋白(Agouti related protein,AGRP)结合,以调节食欲和摄食行为、控制能量稳态[10-11]。作为重要的食欲调节基因,MC4R在中枢神经系统高度表达,对动物生长发育具有重要调控作用[12-14]。动物MC4R基因多态性研究已发现多个单核苷酸多态性(Single nucleotide polymorphism,SNP)位点,与动物体长、体质量等生长表型显著相关[15-16],但其在软鳍新光唇鱼生长发育中的调控作用研究尚未报道,与其相关的显著分子标记仍有待挖掘。因此,本研究通过PCR-Sanger测序技术对软鳍新光唇鱼MC4R基因进行SNP位点检测,并进行关联性分析,筛选出与软鳍新光唇鱼生长性状显著相关的SNP位点及其优势基因型,旨在为软鳍新光唇鱼的良种培育发掘具有较高应用潜力的SNP位点,同时为鱼类MC4R基因的进一步研究提供基础数据。

    实验所用样本为养殖于中国科学院昆明动物研究所珍稀鱼类繁殖基地,于相同饲养环境和管理方法下长成的同一家系的6月龄软鳍新光唇鱼。通过对该家系所有样本进行体长、全长、体质量的测量,表型数据呈正态分布。选择分布于两端的50尾极端大个体[平均体长为(107.80±4.72)mm,体质量为(25.48±3.37)g],50尾极端小个体[平均体长为(56.84±3.16)mm、体质量为(3.45±0.55)g],剪取鳍条组织浸泡于无水乙醇中,放置在−20 ℃冰箱中保存,用于后续实验。体长、全长采用游标卡尺(精度0.01 mm)测量,体质量采用电子天平(精度0.01 g)测量。

    取出鱼鳍组织样品,使用异丙醇DNA提取法[17-18]提取100个鱼鳍样品的DNA,并于4 ℃溶解过夜后,放置在−20 ℃冰箱中保存。中国科学院昆明动物研究所生命科学伦理委员会批准动物实验,批准编号为SMKX-SQ-2021-111。

    根据软鳍新光唇鱼基因组中MC4R基因编码区序列(Coding sequence,CDS)(NCBI序列号:PQ682452,PQ682453),采用Primer Premier 5.0 (Premier Biosoft International)软件设计引物,引物送至昆明擎科生物有限公司合成。通过筛选并选取5个样本进行预实验,以验证引物的特异性,最终确定M1、M2两对引物用于MC4R基因2个拷贝的扩增,扩增目的片段度分别为1 027、1 050 bp。引物序列详情见表1。扩增反应总体系为25 μL,包括基因组DNA模板1 μL,上下游引物各1 μL,power POL 2 PCR mix (爱博泰克生物科技有限公司,武汉)12.5 μL,dH2O(无菌去离子水) 9.5 μL;PCR反应程序:94 ℃预变性3 min,30个扩增循环(94 ℃变性30 s;55 ℃退火30 s;72 ℃延伸1 min),最后72 ℃延伸5 min。

    表  1  软鳍新光唇鱼PCR引物信息
    Table  1.  Primers used in the amplification of N. benasi
    目标基因
    Gene of interest
    引物
    Primers
    序列(5’-3’ )
    Sequence (5’-3’)
    退火温度/℃
    Annealing temperature
    产物长度/bp
    Product length
    MC4R M1 F:AAACCACTGACTACGGATAT
    R:CGTCAAACAGAAACAAGC
    55 1 027
    M2 F:AAACCACTGACTACGGATAT
    R:TTGCTTAGTGTTGTCTTGC
    55 1 050
    下载: 导出CSV 
    | 显示表格

    扩增产物送至昆明擎科生物有限公司进行测序,本研究采用直接测序法。将返回产物序列用DNAStar 7.1软件包中的SeqMan 7.1.0[19]软件进行剪切、拼接,根据测序峰图确定SNP位点并按照单双峰型划分各位点的基因型,并通过Emboss transeq在线工具(https://www.ebi.ac.uk/Tools/st/emboss_transeq/)对MC4R基因2个拷贝的SNP位点进行氨基酸突变分析。

    统计不同基因型的样本数量,并利用Popgene 1.32[20]、Power Marker[21]软件进行群体遗传学分析,包括计算各基因位点的基因型频率、等位基因频率、有效等位基因数(Effective number of alleles,Ne)、期望杂合度(Expected heterozygosity,He)、观测杂合度(Observed heterozygosity,Ho)、多态信息含量(Polymorphism information content,PIC)、固定指数(Fixation index,Fis),以及通过X2分析进行哈代温伯格(Hardy-Weinberg,HWE)平衡检验,X2<5.991为HWE平衡,X2>5.991为偏离HWE平衡。

    运用SPSS 26.0[22]统计软件将各样本基因型与生长性状进行关联分析,对符合Levene’s test和正态分布的位点进行单因素方差分析,事后检验通过Duncan’s test进行;反之,则采取非参数检验,事后多重比较通过Kruskal-Wallis test进行,以分析各基因型相关的表型间的差异显著性。结果均采用平均值±标准差表示。

    对PCR扩增产物测序后,MC4R基因2个拷贝各有82条和69条序列用于多态性检测。结果显示:MC4R第1个拷贝有1个SNP位点,为位于669 bp处的G669C;第2个拷贝有14个SNP位点,分别是位于227、322、403、457、472、520、736 bp处的G/A突变,位于364、451、484、583、664、742 bp处的C/T突变,以及位于775 bp处的C/G突变;各位点测序峰图结果见图1

    图  1  软鳍新光唇鱼MC4R基因两个拷贝15个SNP位点测序峰图
    注:图 a为第1个拷贝SNP位点;图b~图o为第2个拷贝SNP位点。
    Figure  1.  Sequence peak diagram of 15 SNP loci in two copies of MC4R gene of N. benasi
    Notes: Figure a shows SNP loci of 1st copy; figure b−figure o show SNP loci of 2nd copy.

    氨基酸突变分析结果显示:第1个拷贝序列中G669C突变点为同义突变,编码氨基酸为精氨酸(R);第2个拷贝发现的14个SNP位点中,仅位点G227A为错义突变,氨基酸类型由缬氨酸 (V)变为异亮氨酸(I),其余位点均为同义突变,未发生氨基酸改变,具体信息见表2

    表  2  MC4R基因两个拷贝SNP位点的氨基酸突变
    Table  2.  Amino acid mutations at various SNP loci in two copies of the MC4R gene
    位点
    Loci
    突变序列
    Mutant sequences
    突变氨基酸类型
    Types of mutant amino acid
    突变区
    Region
    G669C CGG→CGC R-R 精氨酸 exon
    G227A GTC→ATC V-I 缬氨酸−异亮氨酸 exon
    A322G ACA→ACG T-T 苏氨酸 exon
    C364T CGC→CGT R-R 精氨酸 exon
    G403A TCG→TCA S-S 丝氨酸 exon
    T451C ATT→ATC I-I 异亮氨酸 exon
    G457A GTG→GTA V-V 缬氨酸 exon
    G472A ACG→ACA T-T 苏氨酸 exon
    T484C GCT→GCC A-A 丙氨酸 exon
    G520A GCG→GCA A-A 丙氨酸 exon
    T583C TAT→TAC Y-Y 酪氨酸 exon
    C664T CAC→CAT H-H 组氨酸 exon
    G736A GCG→GCA A-A 丙氨酸 exon
    C742T AAC→AAT N-N 天冬酰胺 exon
    C775G CTC→CTG L-L 亮氨酸 exon
    下载: 导出CSV 
    | 显示表格

    MC4R基因筛选出15个SNP位点在软鳍新光唇鱼群体中的遗传参数结果见表3。第1个拷贝SNP位点G669C总体遗传参数值在15个SNP位点中较低,其Ne为1.443,HeHo分别为0.309和0.351,PIC为0.260;第2个拷贝14个SNP位点有效等位基因数为1.981~2.000,各位点有效等位基因数与观测值接近,表明软鳍新光唇鱼种群各等位基因分布均匀[23]HoHe分别为0.860±0.027、0.503±0.001,PIC为0.373~0.375,根据Botstein等[24]的标准,当0.25<PIC<0.50,为中度多态性,因此15个SNP位点均处于中度多态。X2检测结果显示,除第1个拷贝G669C位点外,第2个拷贝所有位点均显著偏离Hardy-Weinberg平衡(P<0.05)。各位点基因型频率结果显示,突变点G669C以纯合子GG占比更高,Fis值为−0.145,剩余位点均以杂合型个体占比更高,Fis值范围为−0.841~−0.625。

    表  3  MC4R基因两个拷贝各SNP位点群体遗传信息
    Table  3.  Population genetic information of each SNP locus of two copies of MC4R gene
    位点
    Loci
    样本数
    Number
    基因型(频率)
    Genotypes (frequency)
    等位基因(频率)
    Aelles (frequency)
    HWE Ne Ho He Fis PIC
    G669C 74 GG(0.635)
    GC(0.351)
    CC(0.014)
    C(0.189)
    G(0.811)
    X2=1.443
    P=0.230)
    1.443 0.351 0.309 −0.145 0.260
    G227A 65 AA(0.064)
    GG(0.095)
    GA(0.841)
    G(0.516)
    A(0.484)
    X2=28.813
    P=0.000)
    1.998 0.841 0.504 −0.684 0.375
    A322G 65 AA(0.077)
    GG(0.062)
    GA(0.861)
    G(0.492)
    A(0.507)
    X2=33.300
    P=0.000)
    2.000 0.862 0.504 −0.724 0.375
    C364T 53 CC(0.113)
    TT(0.076)
    CT(0.811)
    C(0.519)
    T(0.481)
    X2=20.077
    P=0.000)
    1.997 0.811 0.504 −0.625 0.375
    G403A 66 GG(0.106)
    AA(0.061)
    GA(0.833)
    C(0.508)
    A(0.492)
    X2=28.970
    P=0.000)
    1.996 0.833 0.503 −0.670 0.375
    T451C 65 CC(0.062)
    TT(0.077)
    CT(0.861)
    C(0.476)
    A(0.524)
    X2=33.300
    P=0.000)
    2.000 0.862 0.504 −0.724 0.375
    G457A 66 GG(0.076)
    GA(0.864)
    AA(0.060)
    G(0.508)
    A(0.492)
    X2=34.220
    P=0.000)
    2.000 0.864 0.504 −0.728 0.375
    G472A 62 GG(0.081)
    GA(0.855)
    AA(0.064)
    G(0.508)
    A(0.492)
    X2=30.555
    P=0.000)
    2.000 0.855 0.504 −0.841 0.373
    T484C 64 CC(0.062)
    TT(0.078)
    CT(0.860)
    C(0.492)
    T(0.508)
    X2=32.383
    P=0.000)
    2.000 0.859 0.504 −0.719 0.375
    G520A 63 GG(0.063)
    AA(0.080)
    GA(0.857)
    G(0.508)
    A(0.492)
    X2=31.468
    P=0.000)
    2.000 0.857 0.504 −0.715 0.375
    T583C 59 CC(0.068)
    TT(0.085)
    CT(0.847)
    C(0.492)
    T(0.508)
    X2=27.837
    P=0.000)
    1.999 0.848 0.504 −0.695 0.375
    C664T 62 CC(0.097)
    CT(0.903)
    C(0.548)
    T(0.452)
    X2=41.238
    P=0.000)
    1.981 0.903 0.499 −0.824 0.373
    G736A 66 GG(0.076)
    AA(0.061)
    GA(0.863)
    G(0.492)
    A(0.508)
    X2=34.220
    P=0.000)
    2.000 0.864 0.504 −0.728 0.375
    C742T 66 CC(0.076)
    CT(0.924)
    C(0.540)
    T(0.460)
    X2=47.867
    P=0.000)
    1.989 0.924 0.501 −0.826 0.374
    C775G 66 CC(0.076)
    GG(0.061)
    GC(0.863)
    C(0.508)
    G(0.492)
    X2=34.220
    P=0.000)
    2.000 0.864 0.504 −0.728 0.375
      注:HWE为哈代温伯格平衡;He为期望杂合度;Ho为观测杂合度;Ne为有效等位基因数;PIC为多态信息含量;Fis为固定指数。
      Notes: HWE indicates Hardy-Weinberg equilibrium; He indicates expected heterozygosity; Ho indicates observed heterozygosity; Ne indicates eff-ective number of alleles; PIC indicates polymorphism information content; Fis indicates fixation index.
    下载: 导出CSV 
    | 显示表格

    MC4R基因2个拷贝检测出的15个SNP位点与软鳍新光唇鱼生长性状的关联性分析结果见表4。第1个拷贝G669C位点有3种基因型,CC型个体的质量、体长和全长均高于GC型与GG型个体,但未达到显著性水平(P>0.05)。第2个拷贝C664T、C742T位点仅具有CC、CT两种基因型,关联性分析结果显示,CT杂合型的体长、体质量、全长均优于CC纯合型,C664T处不同基因型个体的体质量呈显著差异(P<0.05),而体长与全长差异不显著;位点C742T不同基因型个体之间性状差异均不显著。第2个拷贝中G227A、C364T、G403A、G472A、T484C、T583C位点均有3种基因型,不同基因型个体体长、全长、体质量间存在显著差异(P<0.05),分别以纯合子AA、TT、AA、AA、CC、CC为优势基因型;位点A322G、T451C、G457A、G520A、G736A、C775G也存在三种基因型,并以纯合型的性状指标高于杂合型,但未在全长上表现出显著差异(P>0.05)。

    表  4  MC4R基因两个拷贝SNP位点各基因型与生长性状关联性分析
    Table  4.  Association analysis between different genotypes of loci of two copies of SNP MC4R gene and growth traits
    位点
    Loci
    基因型(样本量)
    Genotype(n)
    体质量/g
    Body mass
    体长/mm
    Body length
    全长/mm
    Total length
    G669CGC(26)
    GG(47)
    CC(1)
    8.55±9.55a
    14.25±10.97a
    27.84±0.00a
    68.78±22.35a
    82.89±26.30a
    106.90±0.00a
    85.66±26.87a
    101.69±30.29a
    132.73±0.00a
    G227AGG(6)
    AA(4)
    GA(53)
    3.59±0.46b
    26.13±2.13a
    13.77±10.93b
    58.73±2.02b
    109.92±5.41a
    81.06±25.56b
    74.12±2.89b
    134.23±5.46a
    100.71±30.81b
    A322GAA(5)
    GG(4)
    GA(56)
    3.57±0.51b
    26.13±2.13a
    13.67±10.96b
    59.02±2.12b
    109.92±5.41a
    80.81±25.52b
    74.38±3.15a
    134.23±5.46a
    100.44±30.72a
    C364TCC(6)
    CT(43)
    TT(4)
    3.58±0.46b
    14.82±10.96b
    26.13±2.13a
    59.00±1.90b
    83.70±25.32b
    109.92±5.41a
    74.42±2.82b
    103.80±30.42b
    134.23±5.46a
    G403AGG(7)
    GA(55)
    AA(4)
    3.66±0.45b
    13.85±10.98b
    26.13±2.13a
    59.29±1.81b
    81.19±25.60b
    109.92±5.41a
    74.60±2.64b
    100.88±30.82b
    134.23±5.46a
    T451CTT(5)
    CT(56)
    CC(4)
    3.57±0.51b
    13.31±10.94b
    26.13±2.13a
    59.02±2.12b
    79.98±25.44b
    109.92±5.41a
    74.38±3.15a
    99.43±30.63a
    134.23±5.46a
    G457AGG(5)
    GA(57)
    AA(4)
    3.57±0.51b
    13.50±10.94b
    26.13±2.13a
    59.02±2.12b
    80.44±25.45b
    109.92±5.41a
    74.38±3.15a
    99.98±30.64a
    134.23±5.46a
    G472AGG(5)
    GA(53)
    AA(4)
    3.57±0.51b
    13.73±10.88b
    26.13±2.13a
    59.02±2.12b
    80.89±25.49b
    109.92±5.41a
    74.38±3.15b
    100.49±30.67b
    134.23±5.46a
    T484CCC(4)
    TT(5)
    CT(55)
    26.13±2.13a
    3.57±0.51b
    12.86±10.59b
    109.92±5.41a
    59.02±2.12b
    79.19±25.01b
    134.23±5.46a
    74.38±3.15b
    98.44±30.07b
    G520AGG(5)
    AA(4)
    GA(54)
    3.57±0.51b
    26.13±2.13a
    12.86±10.81b
    59.02±2.12b
    109.92±5.41a
    79.06±25.40b
    74.38±3.15a
    134.23±5.46a
    98.27±30.54a
    T583CCC(4)
    TT(5)
    CT(50)
    26.13±2.13a
    3.57±0.51b
    12.70±10.83b
    109.92±5.41a
    59.02±2.12b
    78.51±25.34b
    134.23±5.46a
    74.38±3.15b
    97.60±30.47b
    C664TCC(6)
    CT(56)
    3.41±0.60b
    14.64±11.14a
    58.21±2.75a
    83.01±25.96a
    73.50±3.55a
    102.90±31.09a
    G736AGG(5)
    AA(4)
    GA(57)
    3.57±0.51b
    26.13±2.13a
    13.50±10.94b
    59.02±2.12b
    109.92±5.41a
    80.44±25.45b
    74.38±3.15a
    134.23±5.46a
    99.98±30.64a
    C742TCC(5)
    CT(61)
    3.57±0.51a
    14.33±11.04a
    59.02±2.12a
    82.37±25.69a
    74.38±3.15a
    102.22±30.83a
    C775GCC(5)
    GG(4)
    GC(57)
    3.57±0.51b
    26.13±2.13a
    13.50±10.94b
    59.02±2.12b
    109.92±5.41a
    80.44±25.45b
    74.38±3.15a
    134.23±5.46a
    99.98±30.64a
      注:同一位点同一指标不同上标小写字母表示组内差异显著(P<0.05),相同上标字母表示组内差异不显著(P>0.05)。
      Note: Different superscript lowercase letters in the same column of locus indicate significant difference within the group (P<0.05), and the same superscript lowercase letters indicate no significant differences within the group (P>0.05).
    下载: 导出CSV 
    | 显示表格

    NeHeHo和PIC等参数是衡量群体遗传变异程度、遗传信息大小,指示遗传多态性的重要指标,各数值越高,则群体遗传多样性越高,对环境的适应力越强,在生长、繁殖性能上也更具培育优势[25-27]。群体遗传分析结果显示,本研究在MC4R基因检测出的15个SNP位点中,除G669C外,其余14个SNP位点的Ne、PIC和Ho均处于较高水平,属中度多态性,群体中等位基因分布均匀。

    Fis是以观测杂合频率与期望杂合频率的差异性反映群体间的近交程度,也被称为HWE平衡偏离系数。Fis值越趋近于0,群体越趋于HWE平衡,当Fis的值小于0时,Ho>He,群体内杂合子较多;反之,则群体纯合子更多[28]。本研究对15个SNP位点进行Hardy-Weinberg平衡检验,结果显示除位点G669C外,其余14个位点P值均小于0.01,Fis值接近于−1,处于Hardy-Weinberg极不平衡状态,种群中杂合子过剩。杂合子过剩是养殖群体较为常见的现象,人工选择压力、非随机交配、亲本数量限制、种群大小和结构变化等因素是造成养殖群体杂合子过剩而偏离Hardy-Weinberg平衡的主要原因[29],如团头鲂(Megalobrama amblycephala)等养殖群体也存在杂合子过剩现象[30-32]。此外,本研究杂合子过剩也可能与样本量相对较少,且样本体长、体质量等表型存在较大差异有关。本研究中软鳍新光唇鱼群体杂合子过剩,表明其正经历人工选育过程,与实际养殖、选育情况相符,一定程度上证明了本研究筛选生长相关SNP位点的可靠性与真实性较高。

    本研究对MC4R基因扩增后产物采取直接测序法进行SNP位点的筛选,MC4R基因筛选出15个SNP位点。MC4R基因一级结构预测分析发现,15个SNP位点中,仅G227A位点出现错义突变,所在序列由GTC变为ATC,导致氨基酸种类由缬氨酸(V)变为异亮氨酸(I),其余位点同属同义突变,虽然同义突变不能通过氨基酸突变直接改变蛋白质的结构和功能,但仍可以改变mRNA二级结构、翻译效率而影响生物体表型[33-34],此结论也在后续软鳍新光唇鱼生长表型的关联性分析中得到印证。

    MC4R基因的15个SNP位点与软鳍新光唇鱼主要生长性状关联分析结果显示13个SNP位点与个体体长、体质量具有不同程度的相关性。其中,G227A、A322G、C364T、G403A、T451C、G457A 、G472A、T484C、G520A、T583C、G736A、C775G等12个SNP位点与体长、体质量显著相关,且均以纯合子为优势基因型,分别为AA、GG、TT、AA、CC、AA、AA、CC、AA、CC、AA、GG型;位点C664T检测到CC、CT两种基因型,虽以杂合子CT型为优势基因型,但仅与体质量显著相关。MC4R基因的多态性与性状关联研究在畜牧中开展较早且更广泛,虽然在尼罗罗非鱼 (Oreochromis niloticus[35]、红鳍东方鲀(Takifugu rubripes[36]、光倒刺鲃(Spinibarbus hollandi[37]中筛选出多个SNP位点,但较少与鱼类的生长性状显著相关,研究更多集中在基因克隆、组织表达[38-41]。不同群体以杂合子或以纯合子为优势基因型,在许多研究中也有报道,如黄李勇等[42]在对巴什拜羊(Ovis ariesMC4R基因与生长性状关联分析中检测出GC和GG两种基因型,并以GC型为群体的优势基因型;周艳等[43]在5个地方鸡种MC4R基因的研究中检测出g.54 C>G、g.315 G>T两处SNP位点,且两位点在各群体中均主要以纯合子为优势基因型。因此,本研究结果支持MC4R基因存在丰富的SNP位点,且对软鳍新光唇鱼的生长性状具有显著影响,可以将其作为鱼类分子育种研究的候选基因进一步挖掘。

    本研究通过直接测序法在软鳍新光唇鱼MC4R基因2个拷贝中检测出15个SNP位点,遗传多样性分析表明该养殖群体具有较高的遗传丰富度,能够作为良种选育的候备种群,同时利用关联性分析筛选出13个SNP位点与生长性状显著相关,为今后软鳍新光唇鱼生长相关机制和分子标记的进一步解析,以及生长性状的改良提供了科学依据。

  • 图  1   软鳍新光唇鱼MC4R基因两个拷贝15个SNP位点测序峰图

    注:图 a为第1个拷贝SNP位点;图b~图o为第2个拷贝SNP位点。

    Figure  1.   Sequence peak diagram of 15 SNP loci in two copies of MC4R gene of N. benasi

    Notes: Figure a shows SNP loci of 1st copy; figure b−figure o show SNP loci of 2nd copy.

    表  1   软鳍新光唇鱼PCR引物信息

    Table  1   Primers used in the amplification of N. benasi

    目标基因
    Gene of interest
    引物
    Primers
    序列(5’-3’ )
    Sequence (5’-3’)
    退火温度/℃
    Annealing temperature
    产物长度/bp
    Product length
    MC4R M1 F:AAACCACTGACTACGGATAT
    R:CGTCAAACAGAAACAAGC
    55 1 027
    M2 F:AAACCACTGACTACGGATAT
    R:TTGCTTAGTGTTGTCTTGC
    55 1 050
    下载: 导出CSV

    表  2   MC4R基因两个拷贝SNP位点的氨基酸突变

    Table  2   Amino acid mutations at various SNP loci in two copies of the MC4R gene

    位点
    Loci
    突变序列
    Mutant sequences
    突变氨基酸类型
    Types of mutant amino acid
    突变区
    Region
    G669C CGG→CGC R-R 精氨酸 exon
    G227A GTC→ATC V-I 缬氨酸−异亮氨酸 exon
    A322G ACA→ACG T-T 苏氨酸 exon
    C364T CGC→CGT R-R 精氨酸 exon
    G403A TCG→TCA S-S 丝氨酸 exon
    T451C ATT→ATC I-I 异亮氨酸 exon
    G457A GTG→GTA V-V 缬氨酸 exon
    G472A ACG→ACA T-T 苏氨酸 exon
    T484C GCT→GCC A-A 丙氨酸 exon
    G520A GCG→GCA A-A 丙氨酸 exon
    T583C TAT→TAC Y-Y 酪氨酸 exon
    C664T CAC→CAT H-H 组氨酸 exon
    G736A GCG→GCA A-A 丙氨酸 exon
    C742T AAC→AAT N-N 天冬酰胺 exon
    C775G CTC→CTG L-L 亮氨酸 exon
    下载: 导出CSV

    表  3   MC4R基因两个拷贝各SNP位点群体遗传信息

    Table  3   Population genetic information of each SNP locus of two copies of MC4R gene

    位点
    Loci
    样本数
    Number
    基因型(频率)
    Genotypes (frequency)
    等位基因(频率)
    Aelles (frequency)
    HWE Ne Ho He Fis PIC
    G669C 74 GG(0.635)
    GC(0.351)
    CC(0.014)
    C(0.189)
    G(0.811)
    X2=1.443
    P=0.230)
    1.443 0.351 0.309 −0.145 0.260
    G227A 65 AA(0.064)
    GG(0.095)
    GA(0.841)
    G(0.516)
    A(0.484)
    X2=28.813
    P=0.000)
    1.998 0.841 0.504 −0.684 0.375
    A322G 65 AA(0.077)
    GG(0.062)
    GA(0.861)
    G(0.492)
    A(0.507)
    X2=33.300
    P=0.000)
    2.000 0.862 0.504 −0.724 0.375
    C364T 53 CC(0.113)
    TT(0.076)
    CT(0.811)
    C(0.519)
    T(0.481)
    X2=20.077
    P=0.000)
    1.997 0.811 0.504 −0.625 0.375
    G403A 66 GG(0.106)
    AA(0.061)
    GA(0.833)
    C(0.508)
    A(0.492)
    X2=28.970
    P=0.000)
    1.996 0.833 0.503 −0.670 0.375
    T451C 65 CC(0.062)
    TT(0.077)
    CT(0.861)
    C(0.476)
    A(0.524)
    X2=33.300
    P=0.000)
    2.000 0.862 0.504 −0.724 0.375
    G457A 66 GG(0.076)
    GA(0.864)
    AA(0.060)
    G(0.508)
    A(0.492)
    X2=34.220
    P=0.000)
    2.000 0.864 0.504 −0.728 0.375
    G472A 62 GG(0.081)
    GA(0.855)
    AA(0.064)
    G(0.508)
    A(0.492)
    X2=30.555
    P=0.000)
    2.000 0.855 0.504 −0.841 0.373
    T484C 64 CC(0.062)
    TT(0.078)
    CT(0.860)
    C(0.492)
    T(0.508)
    X2=32.383
    P=0.000)
    2.000 0.859 0.504 −0.719 0.375
    G520A 63 GG(0.063)
    AA(0.080)
    GA(0.857)
    G(0.508)
    A(0.492)
    X2=31.468
    P=0.000)
    2.000 0.857 0.504 −0.715 0.375
    T583C 59 CC(0.068)
    TT(0.085)
    CT(0.847)
    C(0.492)
    T(0.508)
    X2=27.837
    P=0.000)
    1.999 0.848 0.504 −0.695 0.375
    C664T 62 CC(0.097)
    CT(0.903)
    C(0.548)
    T(0.452)
    X2=41.238
    P=0.000)
    1.981 0.903 0.499 −0.824 0.373
    G736A 66 GG(0.076)
    AA(0.061)
    GA(0.863)
    G(0.492)
    A(0.508)
    X2=34.220
    P=0.000)
    2.000 0.864 0.504 −0.728 0.375
    C742T 66 CC(0.076)
    CT(0.924)
    C(0.540)
    T(0.460)
    X2=47.867
    P=0.000)
    1.989 0.924 0.501 −0.826 0.374
    C775G 66 CC(0.076)
    GG(0.061)
    GC(0.863)
    C(0.508)
    G(0.492)
    X2=34.220
    P=0.000)
    2.000 0.864 0.504 −0.728 0.375
      注:HWE为哈代温伯格平衡;He为期望杂合度;Ho为观测杂合度;Ne为有效等位基因数;PIC为多态信息含量;Fis为固定指数。
      Notes: HWE indicates Hardy-Weinberg equilibrium; He indicates expected heterozygosity; Ho indicates observed heterozygosity; Ne indicates eff-ective number of alleles; PIC indicates polymorphism information content; Fis indicates fixation index.
    下载: 导出CSV

    表  4   MC4R基因两个拷贝SNP位点各基因型与生长性状关联性分析

    Table  4   Association analysis between different genotypes of loci of two copies of SNP MC4R gene and growth traits

    位点
    Loci
    基因型(样本量)
    Genotype(n)
    体质量/g
    Body mass
    体长/mm
    Body length
    全长/mm
    Total length
    G669CGC(26)
    GG(47)
    CC(1)
    8.55±9.55a
    14.25±10.97a
    27.84±0.00a
    68.78±22.35a
    82.89±26.30a
    106.90±0.00a
    85.66±26.87a
    101.69±30.29a
    132.73±0.00a
    G227AGG(6)
    AA(4)
    GA(53)
    3.59±0.46b
    26.13±2.13a
    13.77±10.93b
    58.73±2.02b
    109.92±5.41a
    81.06±25.56b
    74.12±2.89b
    134.23±5.46a
    100.71±30.81b
    A322GAA(5)
    GG(4)
    GA(56)
    3.57±0.51b
    26.13±2.13a
    13.67±10.96b
    59.02±2.12b
    109.92±5.41a
    80.81±25.52b
    74.38±3.15a
    134.23±5.46a
    100.44±30.72a
    C364TCC(6)
    CT(43)
    TT(4)
    3.58±0.46b
    14.82±10.96b
    26.13±2.13a
    59.00±1.90b
    83.70±25.32b
    109.92±5.41a
    74.42±2.82b
    103.80±30.42b
    134.23±5.46a
    G403AGG(7)
    GA(55)
    AA(4)
    3.66±0.45b
    13.85±10.98b
    26.13±2.13a
    59.29±1.81b
    81.19±25.60b
    109.92±5.41a
    74.60±2.64b
    100.88±30.82b
    134.23±5.46a
    T451CTT(5)
    CT(56)
    CC(4)
    3.57±0.51b
    13.31±10.94b
    26.13±2.13a
    59.02±2.12b
    79.98±25.44b
    109.92±5.41a
    74.38±3.15a
    99.43±30.63a
    134.23±5.46a
    G457AGG(5)
    GA(57)
    AA(4)
    3.57±0.51b
    13.50±10.94b
    26.13±2.13a
    59.02±2.12b
    80.44±25.45b
    109.92±5.41a
    74.38±3.15a
    99.98±30.64a
    134.23±5.46a
    G472AGG(5)
    GA(53)
    AA(4)
    3.57±0.51b
    13.73±10.88b
    26.13±2.13a
    59.02±2.12b
    80.89±25.49b
    109.92±5.41a
    74.38±3.15b
    100.49±30.67b
    134.23±5.46a
    T484CCC(4)
    TT(5)
    CT(55)
    26.13±2.13a
    3.57±0.51b
    12.86±10.59b
    109.92±5.41a
    59.02±2.12b
    79.19±25.01b
    134.23±5.46a
    74.38±3.15b
    98.44±30.07b
    G520AGG(5)
    AA(4)
    GA(54)
    3.57±0.51b
    26.13±2.13a
    12.86±10.81b
    59.02±2.12b
    109.92±5.41a
    79.06±25.40b
    74.38±3.15a
    134.23±5.46a
    98.27±30.54a
    T583CCC(4)
    TT(5)
    CT(50)
    26.13±2.13a
    3.57±0.51b
    12.70±10.83b
    109.92±5.41a
    59.02±2.12b
    78.51±25.34b
    134.23±5.46a
    74.38±3.15b
    97.60±30.47b
    C664TCC(6)
    CT(56)
    3.41±0.60b
    14.64±11.14a
    58.21±2.75a
    83.01±25.96a
    73.50±3.55a
    102.90±31.09a
    G736AGG(5)
    AA(4)
    GA(57)
    3.57±0.51b
    26.13±2.13a
    13.50±10.94b
    59.02±2.12b
    109.92±5.41a
    80.44±25.45b
    74.38±3.15a
    134.23±5.46a
    99.98±30.64a
    C742TCC(5)
    CT(61)
    3.57±0.51a
    14.33±11.04a
    59.02±2.12a
    82.37±25.69a
    74.38±3.15a
    102.22±30.83a
    C775GCC(5)
    GG(4)
    GC(57)
    3.57±0.51b
    26.13±2.13a
    13.50±10.94b
    59.02±2.12b
    109.92±5.41a
    80.44±25.45b
    74.38±3.15a
    134.23±5.46a
    99.98±30.64a
      注:同一位点同一指标不同上标小写字母表示组内差异显著(P<0.05),相同上标字母表示组内差异不显著(P>0.05)。
      Note: Different superscript lowercase letters in the same column of locus indicate significant difference within the group (P<0.05), and the same superscript lowercase letters indicate no significant differences within the group (P>0.05).
    下载: 导出CSV
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出版历程
  • 收稿日期:  2024-10-31
  • 修回日期:  2024-12-04
  • 网络出版日期:  2025-01-06
  • 刊出日期:  2025-02-24

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