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基于SSR标记和单拷贝核基因的蔷薇属植物系统发生分析

杨晨阳 于超 马玉杰 罗乐 潘会堂 张启翔

杨晨阳, 于超, 马玉杰, 罗乐, 潘会堂, 张启翔. 基于SSR标记和单拷贝核基因的蔷薇属植物系统发生分析[J]. 北京林业大学学报, 2018, 40(12): 85-96. doi: 10.13332/j.1000-1522.20180088
引用本文: 杨晨阳, 于超, 马玉杰, 罗乐, 潘会堂, 张启翔. 基于SSR标记和单拷贝核基因的蔷薇属植物系统发生分析[J]. 北京林业大学学报, 2018, 40(12): 85-96. doi: 10.13332/j.1000-1522.20180088
Yang Chenyang, Yu Chao, Ma Yujie, Luo Le, Pan Huitang, Zhang Qixiang. Phylogenetic relationships of the genus Rosa based on SSR markers and single copy nuclear gene[J]. Journal of Beijing Forestry University, 2018, 40(12): 85-96. doi: 10.13332/j.1000-1522.20180088
Citation: Yang Chenyang, Yu Chao, Ma Yujie, Luo Le, Pan Huitang, Zhang Qixiang. Phylogenetic relationships of the genus Rosa based on SSR markers and single copy nuclear gene[J]. Journal of Beijing Forestry University, 2018, 40(12): 85-96. doi: 10.13332/j.1000-1522.20180088

基于SSR标记和单拷贝核基因的蔷薇属植物系统发生分析

doi: 10.13332/j.1000-1522.20180088
基金项目: 

国家自然科学基金项目 31600565

中央高校基本科研业务费专项 2015ZCQ-YL-03

详细信息
    作者简介:

    杨晨阳。主要研究方向:观赏植物资源与育种。Email: cheny6622@foxmail.com  地址:100083北京市海淀区清华东路35号北京林业大学

    责任作者:

    于超,博士,讲师。主要研究方向:观赏植物资源与育种。Email: yuchao@bjfu.edu.cn  地址:同上

  • 中图分类号: S685.12

Phylogenetic relationships of the genus Rosa based on SSR markers and single copy nuclear gene

  • 摘要: 目的通过深入分析中国产野生蔷薇属植物的遗传背景,为其品种演化、系统分类提供分子学依据,也为种间杂交亲本的选择提供一定的指导,从而为进一步开发我国丰富的野生蔷薇属植物资源提供理论基础。方法本研究以50份蔷薇属植物样本、42个种或品种为研究对象,运用SSR标记及单拷贝核基因GAPDH对其遗传多样性进行分析。利用MAC-PR理论预测不同倍性蔷薇属植物的SSR基因型。结果在29个SSR位点上共计检测出382个等位基因变异,多态性信息含量介于0.413 9至0.934 0之间,平均值为0.798 9。计算Bruvo遗传距离并构建了邻接树,解决了SSR标记在不同倍性样本之间应用困难的问题。同时基于GAPDH基因序列片段构建了50个样本的贝叶斯树。基于SSR标记构建的系统发生树显示,50个样本聚成了6个分类群,月季组、桂味组样本聚类效果较好,而其他种类与现有分类系统差异较大。通过测序及克隆成功获得了所有样本的GAPDH基因序列片段,其中,比对后的序列长度为841 bp,变异位点数164个;基于GAPDH基因的聚类结果与现有的分类系统也有较大的差异。结论蔷薇属植物基于遗传关系的分类体系与现有的植物学分类系统有较大的差别。月季组、合柱组间遗传关系十分紧密;芹叶组、桂味组没有形成单系类群,这两组间可能存在着基因交流事件;小叶组中两个种没有很近的亲缘关系。

     

  • 图  1  四倍体云蒸霞蔚不同位点的基因型

    Figure  1.  Different genotypes on tetraploid sample R. 'Yunzheng Xiawei'

    图  2  基于SSR标记的蔷薇属植物系统发生树

    Figure  2.  Phylogenetic tree based on SSRs

    图  3  基于GAPDH基因的蔷薇属植物系统发生树

    Figure  3.  Phylogenetic tree based on GAPDH

    表  1  50个样本名录

    Table  1.   List of samples

    编号No. 种/品种名Specie/variety 组Section 倍性Ploidy level
    1 月月红R. chinensis ‘Slater’s Crimson China’ 月季组Sect. Chinenses 2[1]
    2 月月粉R. chinensis ‘Old Blush’ 月季组Sect. Chinenses 2[1]
    3 单瓣月季花R. chinensis var. spontanea 月季组Sect. Chinenses 2[1]
    4 ‘云蒸霞蔚’R. ‘Yunzheng Xiawei’ 月季组Sect. Chinenses 4[23]
    5 香水月季R. odorata 月季组Sect. Chinenses 2[24]
    6 粉红香水月季R. odorata var. erubescens 月季组Sect. Chinenses 未知Unkonwn
    7 粉红香水R. odorata var. erubescens 月季组Sect. Chinenses 未知Unkonwn
    8 香水月季R. odorata 月季组Sect. Chinenses 2[24]
    9 ‘软香红’R.‘Ruanxianghong’ 月季组Sect. Chinenses 4[24]
    10 ‘四面镜’R.‘Simianjing’ 月季组Sect. Chinenses 3[24]
    11 桔黄香水月季R. odorata var. pseudindica 月季组Sect. Chinenses 2[24]
    12 大花香水月季R. odorata var. gigantea 月季组Sect. Chinenses 2[24]
    13 香水月季R. odorata 月季组Sect. Chinenses 2[24]
    14 亮叶月季R. lucidissima 月季组Sect. Chinenses 未知Unkonwn
    15 弯刺蔷薇R. beggeriana 桂味组Sect. Cinnamomeae 2[1]
    16 弯刺蔷薇R. beggeriana 桂味组Sect. Cinnamomeae 2[1]
    17 刺蔷薇R. acicularis 桂味组Sect. Cinnamomeae 4, 8[1]
    18 疏花蔷薇R. laxa 桂味组Sect. Cinnamomeae 2[1]
    19 疏花蔷薇R. laxa 桂味组Sect. Cinnamomeae 2[1]
    20 疏花蔷薇R. laxa 桂味组Sect. Cinnamomeae 2[1]
    21 美蔷薇R. bella 桂味组Sect. Cinnamomeae 4[11]
    22 山刺玫R. davurica 桂味组Sect. Cinnamomeae 2, 4, 6[11]
    23 华西蔷薇R. moyesii 桂味组Sect. Cinnamomeae 未知Unkonwn
    24 大叶蔷薇R. macrophylla 桂味组Sect. Cinnamomeae 2[1]
    25 西藏蔷薇R. tibetica 桂味组Sect. Cinnamomeae 未知Unkonwn
    26 密刺蔷薇R. spinosissima 芹叶组Sect. Pimpinellifoliae 4[11]
    27 黄刺玫R. xanthina 芹叶组Sect. Pimpinellifoliae 2[1]
    28 异味蔷薇R. foetida 芹叶组Sect. Pimpinellifoliae 4[11]
    29 绢毛蔷薇R. sericea 芹叶组Sect. Pimpinellifoliae 2[1]
    30 单瓣黄刺玫R. xanthina f. normalis 芹叶组Sect. Pimpinellifoliae 2, 4[1]
    31 报春刺玫R. primula 芹叶组Sect. Pimpinellifoliae 2[24]
    32 密刺蔷薇R. spinosissima 芹叶组Sect. Pimpinellifoliae 4[11]
    33 峨眉蔷薇R. omeiensis 芹叶组Sect. Pimpinellifoliae 2[11]
    34 毛叶蔷薇R. mairei 芹叶组Sect. Pimpinellifoliae 未知Unkonwn
    35 少对峨眉蔷薇R. omeiensis f. paucijuga 芹叶组Sect. Pimpinellifoliae 未知Unkonwn
    36 绢毛蔷薇R. sericea 芹叶组Sect. Pimpinellifoliae 2[1]
    37 川西蔷薇R. sikangensis 芹叶组Sect. Pimpinellifoliae 未知Unkonwn
    38 白玉堂R. multiflora var. albo-plena 合柱组Sect. Synstylae 2, 3[1]
    39 野蔷薇R. multiflora 合柱组Sect. Synstylae 2, 3[1]
    40 长尖叶蔷薇R. longicuspis 合柱组Sect. Synstylae 2[11]
    41 小叶川滇蔷薇R. soulieana var. microphylla 合柱组Sect. Synstylae 2[11]
    42 卵果蔷薇R. helenae 合柱组Sect. Synstylae 2[11]
    43 悬钩子蔷薇R. rubus 合柱组Sect. Synstylae 2, 3[11]
    44 银粉蔷薇R. anemoniflora 合柱组Sect. Synstylae 4[24]
    45 金樱子R. laevigata 金缨子组Sect. Laevigatae 2[11]
    46 木香花R. banksiae 木香组Sect. Banksianae 2, 4[1]
    47 单瓣木香花R. banksiae var. normalis 木香组Sect. Banksianae 2[1]
    48 硕苞蔷薇R. bracteata 硕苞组Sect. Bracteatae 2[24]
    49 缫丝花R. roxburghii 小叶组Sect. Microphyllae 2[11]
    50 中甸刺玫R. praelucens 小叶组Sect. Microphyllae 10[11]
    下载: 导出CSV

    表  2  SSR引物信息

    Table  2.   Information of SSR primers

    SSR编号SSR No. 基序Motif 连锁群[23] Linkage group 退火温度Annealing temperature/℃ 目标片段大小Expected size/bp 上游引物Forward primer (5′-3′) 下游引物Reverse primer (5′-3′)
    CL2996 (CCG)17 2 55.0 183 GCCACCATAGCCAGAGACAT AGAAGAAGTTGACGACAGGGAC
    H22E04 (AAG)7 6 55.0 241 GACATCACCACCACCACAAG AACCAAGGTTTCCAGTTCCA
    H23017 (CT)11 1 55.0 218 ACACCAAGCAAACCAAAACC AGCACGAAAACCGAGAGAGA
    Rw22A3 (TTC)6 6 52.9 150 AGAGAATTGAAAAGGGCAAG GAGCAAGCAAGACACTGTAA
    327 (CTT)6 59.8 277, 232, 202 ACTCCTCCAAAGCTTCACCA CCTCATCGACAGAGTCGTCA
    336 (TC)9 4 59.9 171, 185, 213 CAAACGAAACCCTCTGCTTC GACGATGCATTTGGTGTGAC
    353 (TC)7 5 59.7 212, 107, 223 CGCCCTAGTCTCCTCTCTCTC CTCAAGCTGAAGCTCGGAGT
    373 (CT)10 6 58.9 100, 106, 233 ACAAACTTCGCGATTCCTCT AGTTCCAGACGTTGGAGTGC
    387 (CT)9 2 58.7 202, 229, 223 GCACTCTTGACGTTGTCCAT GTCAATGTAGTCCGGTTCGG
    397 (CT)14 4 59.9 222, 221, 252 GGCCTAGCAAAGCAACAAAC AGTGGAGGGCAGTCTCTGAA
    405 (ATG)5 7 59.9 265, 183, 237 CAGCGAAAAGAACAAGGACC CAGAAGCTAATAAATTAACAATCACCA
    464 (TCGGA)3 59.5 134, 250, 149 TCTTTCGGTTCAGAAAGTTCG CTCGCTGATCTTGTCCATCA
    467 (CGA)5 2 60.0 173, 174, 161 GTACGCTCTCTGGTCTTCGG CCCATGTCTCTGGCTATGGT
    490 (TCT)6 60.0 128, 125, 272 ACAACCAACCCAAGAACTCG TCCCAGCTTCAGTCTCACCT
    509 (CAC)5 7 60.0 208, 252, 261 CAACTGGGTTGGGTCAGTCT TCAAATGTACCTTGCGCTTG
    510 (AAG)5 2 60.1 190, 157, 156 AGAGGTTTAGGGCAGCCATT GCGAATGATGGTGGAGAGTT
    521 (GA)8 6 60.5 225, 224, 229 GTTCCAGCAGCACTCCAAGT AGAGGGGATTAGCTGCACTG
    541 (AG)7 6 59.7 241, 243, 242 CTACTCCAATGTCCGCTTCC GTTGGAGAAGAAGCCGTGAG
    593 (GA)7 60.1 136, 134, 119 TAACCAGGTCCTCACGAAGG AACAAATCCCCCAGGATAGG
    596 (AGG)5 5 60.6 211, 212, 222 CGAGGAAAAACCCAAAATCC TGGAAGCAAGAAAAGGCAGT
    625 (TC)8 7 59.0 143, 213, 142 CGCGTCTCTCACATCTCAAA AAGATCTTCTCTCCGGCCTT
    629 (CTT)7 6 59.7 270, 273, 223 CACGAGCTCTCTCTCCCCTA TTGGTCTGTGAAGTGGTGGA
    632 (GCCACC)3 60.1 153, 152, 154 AACTCATGGGTTCGTTGAGC GGTTGCGGAGAGAGAACAAG
    637 (TTGATT)3 7 60.1 280, 279, 280 GCCGTAATTCGTGGAAAGAA ATGCCACCAGAACCTTGAAC
    648 (CT)8 6 60.5 167, 169, 217 CCTAAAGCTTAAGCCCCCAA GCAATAGACTTGGCAGCCTC
    651 (CAG)5 6 60.2 166, 167, 165 TCTGAGCACGACTCAACAGG AGGCATGTAATGCTGTGGGT
    682 (TC)10 3 59.7 205, 131, 207 TTCTTGAGCTAAAAGTGCATCG CAGATCCAAACCGAACCCTA
    686 (GAA)8 6 59.9 139, 150, 190 CACGAGTGTCACTGTTGCCT AGAATTGGCTTAGCTTGGCA
    695 (TA)8 3 59.8 248, 244, 264 AGAAAAGCGAAAGCACAAGC CTTAAATGCGCCACCAATTT
    下载: 导出CSV

    表  3  部分样本的倍性预测

    Table  3.   Ploidy levels of the unknown samples

    编号No. 种/品种名Specie/variety 倍性Ploidy level
    7 粉红香水月季R. odorata var. erubescens 4
    14 亮叶月季R. lucidissima 2
    23 华西蔷薇R. moyesii 4
    25 西藏蔷薇R. tibetica 6
    34 毛叶蔷薇R. mairei 4
    35 少对峨眉蔷薇R. omeiensis f. paucijuga 4
    37 川西蔷薇R. sikangensis 4
    下载: 导出CSV

    表  4  SSR位点变异

    Table  4.   Variation of the 29 SSR lici in 97 rose samples

    位点名称Locus name 等位基因数量Number of alleles 有效等位基因数[30] Effective number of alleles 多态信息含量Polymorphism information content
    RW22A3 14 6.50 0.846 2
    H23017 22 11.40 0.912 4
    H22E04 8 4.78 0.790 9
    CL2996 9 5.32 0.812 1
    695 19 7.85 0.872 7
    686 10 6.60 0.848 5
    682 17 8.53 0.882 9
    651 9 2.71 0.630 9
    648 13 7.57 0.868 1
    637 6 2.19 0.542 7
    632 4 2.38 0.580 0
    629 13 5.77 0.826 7
    625 21 13.68 0.927 0
    596 7 3.78 0.735 8
    593 20 14.69 0.932 0
    541 16 9.40 0.893 7
    521 16 9.71 0.897 2
    510 6 1.71 0.413 9
    509 8 3.81 0.737 5
    490 12 7.07 0.858 7
    467 4 2.38 0.579 2
    464 5 2.10 0.524 5
    405 17 9.81 0.898 2
    397 22 14.28 0.930 1
    387 16 8.94 0.888 2
    373 16 10.02 0.900 3
    353 17 6.86 0.854 4
    336 23 15.13 0.934 0
    327 12 6.62 0.849 1
    总计Total 382
    平均Mean 13.20 7.30 0.798 9
    下载: 导出CSV

    表  5  不同组的SSR位点信息

    Table  5.   Variation of the SSR loci in 6 sections

    组Section 样本容量Sample size 等位基因数量Number of alleles 有效等位基因数Effective number of alleles 多态信息含量Polymorphism information content
    月季组Sect. Chinenses 14 5.97 3.96 0.677 2
    芹叶组Sect. Pimpinellifoliae 12 8.38 5.82 0.740 3
    桂味组Sect. Cinnamomeae 11 7.17 5.79 0.691 6
    合柱组Sect. Synstylae 7 6.48 6.09 0.753 2
    金缨子组Sect. Laevigatae 1 1.38 1.07 0.344 8
    硕苞组Sect. Bracteatae 1 1.28 1.07 0.241 4
    小叶组Sect. Microphyllae 2 3.45 3.8 0.685 2
    木季组Sect. Banksianae 2 2.41 2.61 0.540 0
    平均Mean 6 4.57 3.78 0.584 2
    下载: 导出CSV
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  • 收稿日期:  2018-03-08
  • 修回日期:  2018-08-25
  • 刊出日期:  2018-12-01

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