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浦市黑猪保种群体基于SNP芯片的遗传结构分析

邓缘 崔清明 陈四海 左剑波 刘莹莹 朱吉 任慧波 胡雄贵 李华丽 喻国均 陈晨 彭英林

邓缘,崔清明,陈四海,等. 浦市黑猪保种群体基于SNP芯片的遗传结构分析 [J]. 福建农业学报,2023,38(11):1312−1320 doi: 10.19303/j.issn.1008-0384.2023.11.007
引用本文: 邓缘,崔清明,陈四海,等. 浦市黑猪保种群体基于SNP芯片的遗传结构分析 [J]. 福建农业学报,2023,38(11):1312−1320 doi: 10.19303/j.issn.1008-0384.2023.11.007
DENG Y, CUI Q M, CHEN S H, et al. Genetics of Preserved Pushi Black Pigs Analyzed Using SNP Chip [J]. Fujian Journal of Agricultural Sciences,2023,38(11):1312−1320 doi: 10.19303/j.issn.1008-0384.2023.11.007
Citation: DENG Y, CUI Q M, CHEN S H, et al. Genetics of Preserved Pushi Black Pigs Analyzed Using SNP Chip [J]. Fujian Journal of Agricultural Sciences,2023,38(11):1312−1320 doi: 10.19303/j.issn.1008-0384.2023.11.007

浦市黑猪保种群体基于SNP芯片的遗传结构分析

doi: 10.19303/j.issn.1008-0384.2023.11.007
基金项目: 湖南省自然科学基金项目(2021JJ30386);湖南省创新平台与人才计划项目(2021NK1009);湖南省重点研发计划项目(2020NK2024、2019NK2193);湖南省重点实验室开放研究基金项目(2017TP1030)
详细信息
    作者简介:

    邓缘(1981 —),男,硕士,高级畜牧师,主要从事猪遗传育种方向研究,E-mail:369409457@qq.com

    通讯作者:

    陈晨(1986 —),男,博士,副研究员,主要从事猪遗传育种方向研究,E-mail:2004chch@163.com

    彭英林(1965 —),男,博士,研究员,博士生导师,主要从事猪遗传育种方向研究,E-mail:13907487646@126.com

  • 中图分类号: S828

Genetics of Preserved Pushi Black Pigs Analyzed Using SNP Chip

  • 摘要:   目的  通过SNP芯片技术分析浦市黑猪群体遗传多样性和家系结构,为保护和利用浦市黑猪资源提供支撑。  方法  利用“中芯一号”50K SNP芯片,对79头成年浦市黑猪(10头公猪、69头母猪)进行SNP测定,采用多种分析软件(Plink、Gmatix及Mega X)对群体遗传多样性和亲缘关系开展分析,进而构建群体家系结构。  结果  在79头浦市黑猪中共检出57466个SNPs位点,平均基因型检出率为99.15%。遗传多样性分析提示SNP位点具有多态性,群体存在近交(有效群体含量Ne仅为1.5,且平均观察杂合度<平均期望杂合度)。群体平均状态同源(Idengtical by state,IBS)遗传距离为(0.294 9±0.072 6),公猪为(0.277 1±0.091 8),共检测到长纯合片段(Runs of hemozygosity,ROH)(29.60±16.12)个,其中长度在0~100 Mb的占40.5%,且群体基于ROH的平均近交系数为0.108。IBS距离矩阵、G矩阵结果以及群体ROH值的分析结果均反映出群体内个体之间存在较近的亲缘关系。根据群体进化树结果,将群体划分成2个含公猪的家系,以及1个不含公猪的家系。  结论  浦市黑猪群体家系少,各家系的个体数量差异大,近交程度高。因此,应注重引入或创建新的血统,扩大有效群体含量,降低近交系数。
  • 图  1  基因组DNA电泳图

    M:DNA相对分子质量标准;1−10:基因组DNA。

    Figure  1.  Electrophoresis of genomic DNA

    M: DNA Marker;1−10: Genomic DNA.

    图  2  各染色体质控后SNP数量

    Figure  2.  SNP typing on chromosome after quality control

    图  3  浦市黑猪保种群遗传多样性结果

    Figure  3.  Genetic diversity of preserved population of Pushi black pigs

    图  4  浦市黑猪保种群G矩阵可视化结果

    矩阵中每一个小方格代表两两样本之间的亲缘关系值,两个体亲缘关系越近,对应方格越接近红色。

    Figure  4.  Visualized G matrix on Pushi black pig population

    Small square in matrix shows relationship between pair of samples; redder color indicates closer relationship.

    图  5  浦市黑猪公猪样本聚类分析结果

    图中数字为公猪耳号,被评估为同一家系的样本标注同一种颜色。

    Figure  5.  Clusters of Pushi black boars

    Codes are IDs of individual boars; pigs of same family shown in same color.

    图  6  浦市黑猪群体所有样本聚类分析结果

    图中数字为个体号,标颜色的为公猪样本,一种颜色代表一个家系。

    Figure  6.  Clusters of all Pushi black pigs

    Codes are IDs of individual pigs; boars are colored; same family shown in same color.

    图  7  浦市黑猪ROH长度的样本数分布

    Figure  7.  Distribution of total ROH length of Pushi black pigs

    图  8  基于ROH片段数量的浦市黑猪样本数

    Figure  8.  Sample number of Pushi black pigs based on number of ROH fragments

    图  9  基于ROH的近交系数可视化结果

    P1代表浦市黑猪群体FROH的中位数,P2和P3分别代表浦市黑猪群体FROH的上四分位数和下四分位数。图中越宽的部分表示处于该水平值的群体FROH的样本数越多,反之则越少。

    Figure  9.  Visualized inbreeding coefficient based on ROH

    P1: Median FROH of Pushi black pigs; P2 and P3: upper and lower quartile FROH of Pushi black pigs, respectively; wider portion indicates more samples at median FROH.

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出版历程
  • 收稿日期:  2023-02-03
  • 修回日期:  2023-05-14
  • 网络出版日期:  2023-12-21
  • 刊出日期:  2023-11-28

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