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油料树种千年桐的SSR标记开发、遗传多样性与群体结构分析

赵盼 栗丹阳 马锦林 梁文汇 庞晓明 龙萃 马婧怡 郭惠红

赵盼, 栗丹阳, 马锦林, 梁文汇, 庞晓明, 龙萃, 马婧怡, 郭惠红. 油料树种千年桐的SSR标记开发、遗传多样性与群体结构分析[J]. 北京林业大学学报. doi: 10.12171/j.1000-1522.20210054
引用本文: 赵盼, 栗丹阳, 马锦林, 梁文汇, 庞晓明, 龙萃, 马婧怡, 郭惠红. 油料树种千年桐的SSR标记开发、遗传多样性与群体结构分析[J]. 北京林业大学学报. doi: 10.12171/j.1000-1522.20210054
Zhao Pan, Li Danyang, Ma Jinlin, Liang Wenhui, Pang Xiaoming, Long Cui, Ma Jingyi, Guo Huihong. SSR marker development, genetic diversity and population structure analysis in oil tree species Vernicia montana[J]. Journal of Beijing Forestry University. doi: 10.12171/j.1000-1522.20210054
Citation: Zhao Pan, Li Danyang, Ma Jinlin, Liang Wenhui, Pang Xiaoming, Long Cui, Ma Jingyi, Guo Huihong. SSR marker development, genetic diversity and population structure analysis in oil tree species Vernicia montana[J]. Journal of Beijing Forestry University. doi: 10.12171/j.1000-1522.20210054

油料树种千年桐的SSR标记开发、遗传多样性与群体结构分析

doi: 10.12171/j.1000-1522.20210054
基金项目: 中央高校基本科研业务费专项资金(2017ZY24),国家自然科学基金项目(31870650)
详细信息
    作者简介:

    赵盼。主要研究方向:树木生长发育及调控。Email:zhaopan11250528@163.com 地址:100083 北京市海淀区清华东路35号北京林业大学生物科学与技术学院

    责任作者:

    郭惠红,教授。主要研究方向:树木生长发育及调控。Email:guohh@bjfu.edu.cn 地址:同上

  • 中图分类号: S792.43

SSR marker development, genetic diversity and population structure analysis in oil tree species Vernicia montana

  • 摘要:   目的  千年桐是大戟科油桐属的一种重要的工业油料树种,较同属的油桐具有更强的抗枯萎病能力,近年来受到了广泛关注。然而,因千年桐栽培历史短及种质管理的不足,目前对其分子遗传方面的研究还非常有限。本研究旨在开发千年桐的基因组SSR标记,进而开展其种质的鉴定、遗传多样性与群体结构分析。  方法  采用RAD测序技术获得千年桐简化基因组以开发SSR标记,基于SSR标记利用分子变异分析(AMOVA)、非加权组平均法(UPGMA)聚类、主坐标(PCoA)与群体结构分析等方法对来自3个不同地理分布的共105份千年桐种质资源进行研究。  结果  17个多态性的三核苷酸基因组SSR标记被开发,并能够很好地鉴别所有收集的105份千年桐种质。在其中62份种质中检测到85个私有等位基因,涉及15个SSR位点。AMOVA分析发现,千年桐群体间呈现出中等程度的遗传分化,但群体内的遗传变异远高于群体间的遗传变异。群体结构分析显示,3个来自不同地理分布的千年桐群体中存在4个不同的基因库,群体间既有进化独立性,又有较高程度的遗传混合,这一结果与UPGMA和PCoA分析的结果基本一致。  结论  新开发的17个SSR标记有效鉴定了105份千年桐种质,揭示了其遗传多样性和群体遗传结构,对千年桐种质保存和育种计划具有非常重要的参考价值。

     

  • 图  1  基于17个SSR标记的105份千年桐种质资源遗传关系的进化树

    红色、黄色和蓝色的线段分别代表群体1、2和3。The red, yellow and blue lines represent the population 1, 2, and 3, respectively.

    Figure  1.  A dendrogram of genetic relationship among 105 V. montana germplasm resources based on 17 SSR markers

    图  2  基于17个SSR标记的105份千年桐种质资源的主坐标分析(PCoA)

    红色、黄色和蓝色的点分别代表群体1、2和3。The red, yellow, and blue dots represent population 1, 2 and 3, respectively.

    Figure  2.  Principal coordinate analysis (PCoA) of the 105 V. montana germplsm resources based on 17 SSR markers

    图  3  基于17个SSR标记的105份千年桐种质资源的群体结构分析

    a. K = 1 ~ 8时Delta ~ K的变化图;b. 基于每个K值的5个重复,使用Ln P(D)的平均值进行种群估计;c. 105份千年桐种质在K = 2时的种群结构;d. 105份千年桐种质在K = 4时的种群结构。a, plot of Delta − K for K ranging from 1 to 8; b, estimation of population using the mean of Ln P(D) based on five repetitions for each K-value; c, population structure of the 105 V. montana germplasms at K = 2; d, population structure of the 105 V. montana germplasms at K = 4.

    Figure  3.  Population structure of the 105 V. montana germplasm resources based on 17 SSR markers

    表  1  测序数据质量统计总表

    Table  1.   Quality summary of sequencing data

    原始数据
    Raw read/Mbp
    原始Q20
    Raw Q20/Gbp
    原始Q30
    Raw Q30/Gbp
    过滤后数据
    Cleaned read/Mbp
    过滤后Q20
    Cleaned Q20/Gbp
    过滤后Q30
    Cleaned Q30/Gbp
    平均长度
    Average length/bp
    GC含量
    GC content/%
    45.9326.580 (95.5%)6.257 (90.8%)30.996 (67.5%)4.510 (98.3%)4.374 (95.4%)148.040.51
    注:Q20. 质量值 ≥ 30的碱基所占百分比;Q30. 质量值 ≥ 30的碱基所占百分比。Notes: Q20, percentage of bases with the quanlity value ≥ 20; Q30, percentage of bases with the quanlity value ≥ 30.
    下载: 导出CSV

    表  2  具有不同重复基序的SSR位点在千年桐基因组中的分布

    Table  2.   Distribution of SSRs with the different repeat motifs in the genome of Vernicia montana

    SSR重复基序
    SSR repeat motif
    SSR数量
    Number of SSR
    频率
    Frequency/%
    二核苷酸 Dinucleotide 2 174 63.47
    三核苷酸 Trinucleotide 1 023 29.87
    四核苷酸 Tetranucleotide 131 3.83
    五核苷酸 Pentanucleotide 97 2.83
    总计 Total 3 425
    下载: 导出CSV

    表  3  针对105份千年桐种质开发的17个多态性SSR标记的信息

    Table  3.   Information on the 17 polymorphic SSR markers developed for 105 V. montana

    引物编号 Primer No.重复基序 Repeat motif引物序列(5′—3′) Primer sequence (5′−3′)退火温度 Ta/℃预期大小 Expected size/bp
    Vm-BFU01 (TTG)5 AACCACTGCTACTTCACCATTTTC 55 167
    ACCCAATGTTTTCTCCGACC
    Vm-BFU02 (AGA)5 GTGTTGAGCCAGAAACCCATTA 55 165
    CAGAGAAGCCTCGGTCCCTA
    Vm-BFU03 (CAT)6 TCTACTCCCACACTTCCAAAACA 55 161
    TAATCTCCTTCTGTCCTTCACGA
    Vm-BFU04 (CAG)9 GGGAGTGGTGGCAATGGC 55 181
    GCTGGGAGGCATTGTTGAAG
    Vm-BFU05 (AGA)9 GAGCCAAGAGAAGACGAAAAGAG 55 146
    ACCGTTTACAGTGTTTCGCTATG
    Vm-BFU06 (GGA)8 TGTGCCGCTTGTAACTGCC 55 164
    TGCGGCTGTGTCAGGTGTAG
    Vm-BFU07 (TCT)7 AGCCTTTGCCACTGTTGAGC 55 127
    GATGGGTCCGCCAAGTTCA
    Vm-BFU08 (TCT)5 ATTGTGAAGGATTTGCGATGG 55 161
    CGGCGAAAACGAAACAGAG
    Vm-BFU09 (GTT)7 TCGCCTAAGGTGGTCTTGATG 55 178
    GCCCAACGAAATCTAACTCTAATAA
    Vm-BFU10 (TAA)12 TTCCTCCTCTGGTGACGCTT 55 252
    TTCCTTCCATCATCAACTTTTACC
    Vm-BFU11 (TCC)7 GCCGCCGCCTACTACTTACTT 55 131
    TTTCTCAAACCAAACAGGAGTTG
    Vm-BFU12 (CTT)5 TATTTTTCTTGGGAGTAAAGTCACC 55 198
    TATGTGAAATGGAGAGTTCGGAG
    Vm-BFU13 (CAG)6 TTGTCAACAAGCCTTCTCACCT 55 160
    GCTCCAAGTCCCATCATCATTT
    Vm-BFU14 (GGC)5 CCAAAACCATCAATCTCTTCGC 55 204
    TGATTTCGCACAAGTCCCAAG
    Vm-BFU15 (ACC)10 GCGTTCCTGACCCTACCTTT 55 184
    AGAGAAACAAAAAAGCCACCAG
    Vm-BFU16 (TTA)12 TCCCCACAGCCATAAAACAAG 55 199
    TTTCCAAAACTCTCAAACCACAA
    Vm-BFU17 (AAT)10 ACCCCATCTATGACATCCCACT 55 195
    CCCCGTTCTTGCTCTCCC
    注:重复基序括号外的数字为其重复次数。Note: the number of repeats is marked outside the parentheses of repeat motifs.
    下载: 导出CSV

    表  4  17个千年桐SSR位点的遗传多样性参数

    Table  4.   Genetic diversity parameters for 17 SSR loci in V. montana

    LocusNaNeHoHeIFNullPICFSTNmHWENPA
    Vm-BFU012.0001.6180.1900.3840.5700.3350.3090.1471.446***0
    Vm-BFU026.0001.4910.0860.3310.7040.5900.3100.01220.486***1
    Vm-BFU0310.0002.4000.3650.5861.2230.2180.5390.0554.286***9
    Vm-BFU0411.0003.2620.4760.6971.6200.1780.6700.0643.629***3
    Vm-BFU054.0002.1870.2860.5460.9230.3060.4660.01813.956***1
    Vm-BFU065.0002.5950.4170.6181.0750.1790.5470.01813.645***1
    Vm-BFU076.0003.1350.4190.6841.3570.2320.6380.0356.850***2
    Vm-BFU088.0002.1910.5830.5461.1600.0540.5100.0347.124***2
    Vm-BFU094.0002.2370.3900.5560.9080.1620.4530.0723.214***6
    Vm-BFU109.0002.0780.2000.5211.1490.4500.4910.0633.695***12
    Vm-BFU1113.0006.2890.2350.8452.1010.5590.8240.0574.163***3
    Vm-BFU122.0001.8730.3200.4690.6590.1860.3580.0504.742**0
    Vm-BFU1314.0003.1570.4100.6871.6170.2520.6570.0932.439***10
    Vm-BFU1410.0001.8860.2480.4721.1440.3040.4570.0972.338***15
    Vm-BFU1511.0003.1550.3520.6861.5440.3330.6480.0623.808***10
    Vm-BFU169.0005.2530.5480.8141.7870.1930.7820.0564.256***2
    Vm-BFU1714.0003.9130.5380.7481.8520.1580.7250.0317.705***8
    总数 Total138.00048.72885
    平均值 Mean8.1172.8660.3570.5991.2580.2760.5520.0564.2515
    注:Na. 观测到的等位基因数;Ne. 有效等位基因数;Ho. 观测到的杂合度;He. 预期杂合度;I. 香农信息指数;Nm. 基因流;FNull. 无效等位基因频率;PIC. 多态信息含量;FST. 遗传分化指数;HWE. 哈迪−温伯格平衡;*. P < 0.05;**. P < 0.01; ***. P < 0.001;NPA. 私有等位基因的数量。下同。Notes: Na, observed number of alleles; Ne, effective number of alleles; Ho, observed heterozygosity; He, expected heterozygosity; I, Shannon’s information index; Nm, gene flow; FNull, null allele frequency; PIC, polymorphism information content; FST, genetic differentiation coefficient; HWE, Hardy-Weinberg equilibrium; * means P < 0.05; ** means P < 0.01; *** means P < 0.001; NPA, number of private allele. The same below.
    下载: 导出CSV

    表  5  具有一至多个私有等位基因的千年桐种质

    Table  5.   V. montana germplasms with one or more private alleles

    种质
    Germplasm
    群体
    Population
    NPA私有等位基因位点
    Locus with private allele
    种质
    Germplasm
    群体
    Population
    NPA私有等位基因位点
    Locus with private allele
    1-3 1 1 Vm-BFU11 3-3 3 2 Vm-BFU03, Vm-BFU17
    1-4 1 2 Vm-BFU03, Vm-BFU07 3-4 3 3 Vm-BFU03, Vm-BFU14, Vm-BFU16
    1-7 1 2 Vm-BFU03, Vm-BFU07 3-5 3 1 Vm-BFU14
    1-15 1 1 Vm-BFU06 3-6 3 1 Vm-BFU13
    1-18 1 1 Vm-BFU11 3-9 3 3 Vm-BFU03, Vm-BFU11, Vm-BFU13
    1-23 1 1 Vm-BFU13 3-10 3 1 Vm-BFU15
    1-27 1 2 Vm-BFU10, Vm-BFU17 3-12 3 1 Vm-BFU14
    2-2 2 1 Vm-BFU10 3-13 3 1 Vm-BFU15
    2-3 2 1 Vm-BFU09 3-14 3 2 Vm-BFU14, Vm-BFU17
    2-4 2 1 Vm-BFU10 3-15 3 1 Vm-BFU13
    2-5 2 3 Vm-BFU09, Vm-BFU10, Vm-BFU13 3-16 3 1 Vm-BFU14
    2-6 2 2 Vm-BFU03, Vm-BFU13 3-17 3 1 Vm-BFU14
    2-11 2 1 Vm-BFU10 3-22 3 1 Vm-BFU03
    2-13 2 1 Vm-BFU15 3-23 3 2 Vm-BFU04, Vm-BFU14
    2-14 2 2 Vm-BFU10, Vm-BFU15 3-24 3 1 Vm-BFU15
    2-15 2 1 Vm-BFU09 3-25 3 3 Vm-BFU04, Vm-BFU14, Vm-BFU15
    2-16 2 1 Vm-BFU09 3-26 3 1 Vm-BFU14
    2-17 2 1 Vm-BFU09 3-27 3 2 Vm-BFU15, Vm-BFU17
    2-19 2 1 Vm-BFU15 3-28 3 2 Vm-BFU08, Vm-BFU17
    2-20 2 1 Vm-BFU10 3-29 3 1 Vm-BFU14
    2-23 2 1 Vm-BFU10 3-30 3 1 Vm-BFU14
    2-24 2 1 Vm-BFU09 3-31 3 1 Vm-BFU14
    2-26 2 1 Vm-BFU02 3-32 3 2 Vm-BFU03, Vm-BFU05
    2-27 2 2 Vm-BFU10, Vm-BFU15 3-33 3 1 Vm-BFU16
    2-28 2 1 Vm-BFU13 3-35 3 1 Vm-BFU14
    2-29 2 1 Vm-BFU13 10-7 3 1 Vm-BFU17
    2-30 2 2 Vm-BFU10, Vm-BFU13 10-13 3 2 Vm-BFU03, Vm-BFU15
    2-31 2 1 Vm-BFU13 10-16 3 1 Vm-BFU14
    2-33 2 1 Vm-BFU10 10-18 3 1 Vm-BFU10
    3-1 3 1 Vm-BFU17 Guizhou-2 3 2 Vm-BFU08, Vm-BFU17
    3-2 3 1 Vm-BFU14 Guizhou-27 3 1 Vm-BFU04
    总计 Total 85
    下载: 导出CSV

    表  6  千年桐群体间与群体内的AMOVA分子变异分析

    Table  6.   Analysis of molecular variance among and within V. montana populations

    变异来源
    Source of variation
    自由度
    Degree of freedom
    方差和
    Sum of squares
    变异组分
    Variance component
    占总变异的比例
    Percentage of variation/%
    FST
    群体间 Among populations 2 110.841 1.209 8 0.080 (P < 0.001)
    群体内 Within population 102 1 423.025 13.951 92
    总计 Total 104 1 533.867 15.160 100
    下载: 导出CSV
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  • 收稿日期:  2021-02-19
  • 修回日期:  2021-03-26
  • 网络出版日期:  2021-10-16

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