|
|
Botanical Research 2023
基于叶绿体基因组的单核苷酸多态位点的落叶松属(Larix Mill.)植物的分子鉴定新方法——以8个种/变种的分析为例
|
Abstract:
高通量测序技术可低成本获得叶绿体全基因组序列，为落叶松属植物的精确鉴定提供了可能。我们利用叶绿体全基因组中的527个单核苷酸多态位点，作为分子性状，首次精准鉴定落叶松属8个种/变种，研制了分子分类检索表。单核苷酸多态位点存在种间差异。喜马拉雅红杉(Larix himalaica W. C. Cheng & L. K. Fu)、新疆落叶松(L. sibirica Ledeb.)和欧洲落叶松(L. deciduas Mill.)的物种特有单核苷酸多态位点数量均较多，遗传分化较大。落叶松(原变种) (L. gmelinii (Rupr.) Kuzen. var. gmelinii)、黄花落叶松(L. gmelinii var. olgensis (A. Henry) Ostenf. & Syrach)、千岛落叶松(L. gmelinii var. japonica (Maxim. ex Regel) Pilg.)以及凯杨德落叶松(L. cajanderi Mayr)之间遗传差异较小。结果显示叶绿体基因组的单核苷酸多态位点信息，可用于落叶松属植物不同基因型的分子鉴定。本研究对于落叶松属植物种质资源的分类鉴定、保护和利用具有重要价值。
The low experimental cost of high-throughput sequencing technology for yielding sequence data of complete chloroplast genomes has made it possible to challenge the accurate identification of Larix plants. In this study, five hundred and twenty-seven single nucleotide polymorphic charac-ters from the complete chloroplast genomes were used for the first time as molecular traits to identify Larix plants and compile a molecular classification key. There are differences in aspects of single nucleotide polymorphic characters between species and varieties. Among the eight spe-cies/varieties, L. himalaica W. C. Cheng & L. K. Fu, L. sibirica Ledeb .and L. deciduas Mill. has larger number of diverged single nucleotide characters. Genetic variation levels among the four genotypes as named L. gmelinii (Rupr.) Kuzen. var. gmelinii, L. gmelinii var. olgensis (A. Henry) Ostenf. & Syrach, L. gmelinii var. japonica (Maxim. ex Regel) Pilg. and L. cajanderi Mayr are comparatively low. Our results indicated that single nucleotide polymorphic characters from the chloroplast genomes could be used for discrimination of different genotypes in Larix. This study is valuable for identification, conservation and utilization of plant germplasm resources of Larix.
| [1] | 中国科学院中国植物志编辑委员会. 中国植物志第7卷: 落叶松属(松科) [M]. 北京: 科学出版社, 1978.
http://www.cn-flora.ac.cn/ |
| [2] | Wu, Z.Y., Hong, D.Y. and Raven, P.H. (1999) Flora of China, Volume 4, Larix (Pinaceae). Science Press, Beijing and Missouri Botanical Garden Press, St. Louis, 33-37. http://www.iplant.cn/foc |
| [3] | 李林初. 落叶松属的核型及系统位置的研究[J]. 植物分类学报, 1993, 31(5): 405-412.
http://www.plantsystematics.com/CN/Y1993/V31/I5/405 |
| [4] | 王玲, 卓丽环, 杨传平, 张捷. 兴安落叶松等位酶水平的遗传多样性[J]. 林业科学, 2009, 45(8): 170-174.
http://www.cqvip.com/QK/71135X/201107/31398678.html |
| [5] | 张学科, 毛子军, 宋红, 孟斌. 五种落叶松遗传关系的等位酶分析[J]. 植物研究, 2022, 22(2): 224-230.
http://bbr.nefu.edu.cn/CN/Y2002/V22/I2/224 |
| [6] | Guo, Q., Li, H., Qian, Z., Lu, J. and Zheng, W. (2021) Comparative Study on the Chloroplast Genomes of Five Larix Species from the Qinghai-Tibet Plateau and the Screening of Candidate DNA Markers. Journal of Forestry Research, 32, 2219-2226. https://doi.org/10.1007/s11676-020-01279-4 |
| [7] | Suo, Z.L., Zhang, C.H., Zheng, Y.Q., et al. (2012) Revealing Genetic Diversity of Tree Peonies at Micro-Evolution Level with Hyper-Variable Chloroplast Markers and Floral Traits. Plant Cell Reports, 31, 2199-2213.
https://doi.org/10.1007/s00299-012-1330-0 |
| [8] | Suo, Z.L., Chen, L.N., Pei, D., Jin, X.B. and Zhang, H.J. (2015) A New Nuclear DNA Marker from Ubiquitin Ligase Gene Region for Genetic Diversity Detection of Walnut Germplasm Resources. Biotechnology Reports, 5, 40-45.
https://doi.org/10.1016/j.btre.2014.11.003 |
| [9] | Suo, Z.L., Li, W.Y., Jin, X.B. and Zhang, H.J. (2016) A New Nuclear DNA Marker Revealing Both Microsatellite Variations and Single Nucleotide Polymorphic Loci: A Case Study on Classification of Cultivars in Lagerstroemia indica L. Journal of Microbial & Biochemical Technology, 8, 266-271. https://doi.org/10.4172/1948-5948.1000296 |
| [10] | 李文清, 杨勇, 解孝满, 鲁仪增, 常青, 靳晓白, 索志立. E3泛素-蛋白连接酶UPL3 DNA序列揭示德阳柿和油柿为栽培柿的最近缘物种[J]. 农业科学, 2018, 8(6): 657-673. https://doi.org/10.12677/hjas.2018.86100 |
| [11] | LePage, B.A. and Basiger, J.F. (1995) The Evolutionary History of the Genus Larix (Pinaceae). United States Department of Agriculture, Forest Service, Intermountain Research Station, General Technical Report GTR-INT-319, U.S. Department of Agriculture Forest Service, Washington DC, 19-29. |
| [12] | 毛子军, 王秀华, 周丹, 杨永富. 落叶松属系统学研究概况[J]. 东北林业大学学报, 1999, 27(2): 39-44.
https://doi.org/10.3969/j.issn.1000-5382.1999.02.010 |
| [13] | 洪德元. 生物多样性事业需要科学、可操作的物种概念[J]. 生物多样性, 2016, 24(9): 979-999.
https://doi.org/10.17520/biods.2016203 |
| [14] | Bondar, E.I., Putintseva, Y.A., Oreshkova, N.V. and Krutovsky, K.V. (2019) Siberian Larch (Larix sibirica Ledeb.) Chloroplast Genome and Development of Polymorphic Chloroplast Markers. BMC Bioinformatics, 20, Article No. 38.
https://doi.org/10.1186/s12859-018-2571-x |
| [15] | Kim, S.-C., Lee, J.-W., Lee, M.-W., Baek, S.-H. and Hong, K.-N. (2018) The Complete Chloroplast Genome Sequences of Larix kaempferi and Larix olgensis var. koreana (Pinaceae). Mitochondrial DNA Part B, 3, 36-37.
https://doi.org/10.1080/23802359.2017.1419092 |
| [16] | Li, B., Lin, F.R., Huang, P., Guo, W. and Zheng, Y. (2022) Development of Nuclear SSR and Chloroplast Genome Markers in Diverse Liriodendron chinense Germplasm Based on Low-Coverage Whole Genome Sequencing. BMC Biological Research, 53, Article No. 21. https://doi.org/10.1186/s40659-020-00289-0 |
| [17] | Dong, W.P., Xu, C., Li, D.L., et al. (2016) Comparative Analysis of the Complete Chloroplast Genome Sequences in Psammophytic Haloxylon Species (Amaranthaceae). PeerJ, 4, e2699. https://doi.org/10.7717/peerj.2699 |
| [18] | Dong, W.P., Xu, C., Li, W.Q., et al. (2017) Phylogenetic Resolution in Juglans Based on Complete Chloroplast Genomes and Nuclear DNA Sequences. Frontiers in Plant Science, 8, Article 1148.
https://doi.org/10.3389/fpls.2017.01148 |
| [19] | Xu, C., Dong, W.P., Li, W.Y., et al. (2017) Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes. Frontiers in Plant Science, 8, Article 15. https://doi.org/10.3389/fpls.2017.00015 |
| [20] | Li, W.Q., Liu, Y.L., Yang, Y., et al. (2018) Interspecific Chloroplast Genome Sequence Diversity and Genomic Resources in Diospyros. BMC Plant Biology, 18, Article No. 210. https://doi.org/10.1186/s12870-018-1421-3 |
| [21] | Dong, W.P., Xu, C., Liu, Y.L., et al. (2021) Chloroplast Phylogenomics and Divergence Times of Lagerstroemia (Lythraceae). BMC Genomics, 22, Article No. 434. https://doi.org/10.1186/s12864-021-07769-x |
| [22] | Guo, C., Liu, K.J., Li, E.Z., et al. (2023) Maternal Donor and Genetic Variation of Lagerstroemia indica Cultivars. International Journal of Molecular Sciences, 24, Article No. 3606. https://doi.org/10.3390/ijms24043606 |
| [23] | Katoh, K. and Standley, D.M. (2013) MAFFT Multiple Se-quence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution, 30, 772-780. https://doi.org/10.1093/molbev/mst010 |
| [24] | Kumar, S., Stecher, G. and Tamura, K. (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular Biology and Evolution, 33, 1870-1874. https://doi.org/10.1093/molbev/msw054 |
| [25] | Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J.C., et al. (2017) DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Molecular Biology and Evolution, 34, 3299-3302. https://doi.org/10.1093/molbev/msx248 |
| [26] | 张晓放, 董茜, 罗明哲, 于朝龙, 吕晓亮. 日本落叶松育种研究现状及趋势[J]. 林业科技, 2005, 30(3): 10-11.
http://doi.org/10.3969/j.issn.1001-9499.2005.03.004 |
| [27] | 王若森, 倪伯春. 日本杂交落叶松引种研究[J]. 林业勘探设计, 2009, 152(4): 58-60. |
| [28] | 卢思聪, 张毓, 石雷, 赵世伟, 等. 世界栽培兰花百科图鉴[M]. 北京: 中国农业大学出版社, 2014: 50-51. |
| [29] | Goodwin, Z.A., Harris, D.J., Filer, D., et al. (2015) Wide Spread Mistaken Identity in Tropical Plant Collections. Current Biology, 25, R1057-R1069. https://doi.org/10.1016/j.cub.2015.10.002 |
| [30] | 索志立, 顾翠花, 左云娟, 杨志荣, 孙忠民, 杨强发, 靳晓白. 利用叶绿体基因组大单拷贝区的单核苷酸多态位点鉴定紫薇属和马尾藻属植物[J]. 植物学研究, 2022, 11(2): 218-228. https://doi.org/10.12677/br.2022.112026 |
| [31] | 刘儒, 潘文婷, 李斌, 靳晓白, 李锐丽, 索志立. 利用叶绿体全基因组的单核苷酸多态位点对鹅掌楸和北美鹅掌楸的分子鉴定[J]. 农业科学, 2022, 12(11): 1098-1108. https://doi.org/10.12677/hjas.2022.1211151 |
| [32] | 王文采, 等. 世界植物简志[M]. 北京: 北京出版集团北京出版社, 2021: 1-172. |
