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基于SLAF-Seq技术的橄榄种质资源SNP标记开发与遗传关系鉴定

沈朝贵 赖瑞联 陈瑾 冯新 陈义挺 韦晓霞 吴如健

沈朝贵,赖瑞联,陈瑾,等. 基于SLAF-Seq技术的橄榄种质资源SNP标记开发与遗传关系鉴定 [J]. 福建农业学报,2024,39(5):1−6
引用本文: 沈朝贵,赖瑞联,陈瑾,等. 基于SLAF-Seq技术的橄榄种质资源SNP标记开发与遗传关系鉴定 [J]. 福建农业学报,2024,39(5):1−6
SHEN C G, LAI R L, CHEN J, et al. SNP Markers Development and Genetic Relationship Identification of Germplasm Resources of Canarium album Based on SLAF-Seq Technology [J]. Fujian Journal of Agricultural Sciences,2024,39(5):1−6
Citation: SHEN C G, LAI R L, CHEN J, et al. SNP Markers Development and Genetic Relationship Identification of Germplasm Resources of Canarium album Based on SLAF-Seq Technology [J]. Fujian Journal of Agricultural Sciences,2024,39(5):1−6

基于SLAF-Seq技术的橄榄种质资源SNP标记开发与遗传关系鉴定

基金项目: 福建省科技计划公益类专项(2022R1028005、2022R1028003);农业农村部物种品种资源保护项目(18230171)
详细信息
    作者简介:

    沈朝贵(1971 — ),男,助理研究员,主要从事果树种质资源与保鲜加工研究,E-mail:shenchaogui@163.com

    通讯作者:

    吴如健(1965 — ),男,研究员,主要从事果树种质资源与栽培育种研究,E-mail: wurujian@126.com

  • 中图分类号: S667.5

SNP Markers Development and Genetic Relationship Identification of Germplasm Resources of Canarium album Based on SLAF-Seq Technology

  • 摘要:   目的  开发橄榄SNP标记并分析其种质资源遗传多样性,为橄榄种质资源保护和利用提供依据。  方法  基于SLAF-Seq技术进行橄榄SNP标记开发,同时采用系统进化分析、群体聚类分析和主成分分析等研究了橄榄种质资源遗传结构和遗传多样性。  结果  基于SLAF-Seq技术共挖掘到506 701个SLAF标签,其中多态性SLAF标签27 108个,开发获得361 386个群体SNP标记;基于SNP标记,利用系统进化树和群体聚类分析可分别将橄榄种质资源分为3和6个类群,整体Nei多样性指数和Shanon-Wiener指数分别为0.321和0.472。两种分类方法分析结果均发现,不同地区之间的橄榄种质资源并未严格按照地域分布归类。  结论  橄榄种质资源遗传多样性相对丰富,且不同地域间存在种质资源交流,而采用SNP标记可有效鉴定橄榄种质资源。
  • 图  1  基于邻接法的系统发育树

    Figure  1.  Phylogenetic tree based on neighbor-joining method

    图  2  不同K值对应遗传结构聚类图(A)、交叉验证错误率(B)以及主成分分析(C)

    Figure  2.  Genetic structure cluster (A), admixture validation error rate (B) of different K values and PCA analysis (C)

    表  1  供试橄榄种质资源

    Table  1.   Germplasm resources of C. album used in this experiment

    编号
    Number
    名称
    Germplasm
    name
    来源地
    Source
    经纬度
    Longitude and
    latitude
    简写名
    Abbreviated
    name
    1 葡萄 福建福安 119°38′E 27°08′N PT
    2 大目埕橄榄王 福建闽侯 118°59′E 26°12′N DMC
    3 七粒尺 福建闽侯 119°00′E 26°10′N QLC
    4 灵峰 福建闽侯 118°97′E 26°21′N LF
    5 福榄1号 福建闽侯 118°97′E 26°21′N FL1
    6 清榄1号 福建闽清 118°54′E 26°13′N QL1
    7 闽清2号 福建闽清 118°89′E 26°24′N MQ2
    8 牛榄2号 广西浦北 109°33′E 22°19′N NL2
    9 合江三白圆 四川合江 105°53′E 28°46′N HJSBY
    10 平阳3号 浙江平阳 120°30′E 27°37′N PY3
    11 瑞安2号 浙江瑞安 120°35′E 27°53′N RA2
    12 瑞安3号 浙江瑞安 120°35′E 27°53′N RA3
    13 棱尖 广东饶平 116°83′E 23°99′N LJ
    14 乌榄 广东广州 113°22′E 23°09′N WL
    下载: 导出CSV

    表  2  测序数据统计

    Table  2.   Summary of sequencing data

    样本名称
    Sample ID
    全部片段
    Total reads
    GC含量百分比
    GC percentage /%
    Q30百分比
    Q30 percentage/%
    DMC 749 838 40.43 93.28
    FL1 894 002 41.03 93.43
    HJSBY 7 541 767 37.41 93.43
    LF 559 479 39.21 93.54
    LJ 1 012 589 38.36 93.61
    MQ2 1 139 514 40.38 93.51
    NL2 1 071 660 38.80 93.62
    PT 876 458 41.65 93.48
    PY3 964 858 39.20 93.32
    QL1 1 996 699 40.74 93.44
    QLC 813 057 41.57 93.61
    RA2 1 128 676 39.18 93.76
    RA3 873 826 42.05 93.67
    WL 901 408 37.88 93.29
    下载: 导出CSV

    表  3  不同样本中SNP位点数量

    Table  3.   Number of SNP loci in different samples

    样本名称
    Sample ID
    SNP数量
    SNP number
    完整度
    Hetloci ratio/%
    杂合度
    Integrity ratio/%
    DMC 227 472 13.96 62.94
    FL1 239 971 14.73 66.40
    HJSBY 297 219 21.86 82.24
    LF 209 271 12.95 57.90
    LJ 255 598 17.94 70.72
    MQ2 249 658 14.61 69.08
    NL2 256 355 17.77 70.93
    PT 231 235 14.92 63.98
    PY3 239 403 15.00 66.24
    QL1 290 076 30.22 80.26
    QLC 233 083 13.59 64.49
    RA2 254 930 16.64 70.54
    RA3 236 723 15.11 65.50
    WL 165 152 11.72 45.69
    下载: 导出CSV
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  • 收稿日期:  2022-05-09
  • 修回日期:  2023-05-31
  • 网络出版日期:  2024-07-10

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