Phylogenetic relationships of the genus Rosa based on SSR markers and single copy nuclear gene
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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。 Abstract:ObjectiveThis research provides some information for the controversy over some taxonomy and phylogenetic problems on Rosa species, and provides basis for the selection of parents of interspecific hybrids. This will provide a theoretical basis for further development of abundant wild rose resources in China. MethodIn this study, 50 samples with 42 species and varieties of genus Rosa were used to analyze genetic relationships and construct phylogenetic trees based on SSR markers and single copy nuclear gene (GAPDH). In order to predict the genotype of polyploidies, MAC-PR method was used. ResultA total of 382 alleles were detected at 29 loci. The polymorphism information content ranged from 0.413 9 to 0.934 0 with an average value of 0.798 9. Then we calculated the Bruvo distance and constructed NJ tree (Neighbour-joining tree). The problem to apply SSR markers in polyploidies was solved in the above-mentioned territory. The phylogenetic tree based on GAPDH fragment was also constructed by Bayesian inference. The phylogenetic tree showed that 50 accessions could be clustered into 6 taxa. The traditional classification system of Chinenses and Synstylae is mostly supported by molecular data while others not. GAPDH sequence fragments from all accessions were successfully obtained after cloning and sequencing. The sequence length was 841 bp with 164 variable loci. The phylogenetic relationship based on GAPDH did not correspond to traditional classification system. ConclusionThe result showed that the genus Rosa in its traditional infrageneric circumscription is not supported by molecular data. Sect. Chinenses and Sect. Synstylae are closed in genetic relationship. Sect. Pimpinellifoliae and Sect. Cinnamomeae are not monophyletic and a predicted gene flow exists between these sections. Two species in Sect. Microphyllae are not related based on molecular data. -
Key words:
- Rosa /
- SSR markers /
- single copy nuclear gene /
- genetic diversity
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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'
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] 
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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
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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
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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
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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
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