|
|
Botanical Research 2024
基于叶绿体全基因组核苷酸变异位点的大豆属(Glycine Willd.)植物的分子鉴定新方法
|
Abstract:
高通量测序技术大幅降低了获得基因组序列的成本，为大豆属植物资源多样性的精准鉴定提供了新的数据来源。我们利用来自大豆属7个近缘种的叶绿体全基因组的2363个核苷酸变异位点作为分子性状编制分子鉴定检索表，成功鉴定7个近缘种。这些特有变异位点的数量及核苷酸构成存在种间差异。大豆(Glycine max (L.) Merr.)、白毛烟豆(G. stenophita B.E.Pfeil & Tindale)、镰荚烟豆(G. falcata Benth.)、绢毛烟豆(G. canescens F. J. Herm.)以及扁豆荚大豆(G. dolichocarpa Tateishi & H. Ohashi)的特有变异位点中，A或T的比例(26.74%~42.62%)均高于C或G(9.84%~21.31%)；短绒野大豆(G. tomentella Hayata)中，A、T或C的比例(26.36%~27.91%)均高于G的比例(19.38%)；玫红野大豆(G. syndetika B. E. Pfeil & Craven)中，T或G的比例(30.00%)均高于A或C的比例(18.33%~21.67%)。结果显示叶绿体基因组的单核苷酸变异位点信息，可用于大豆属植物的分子鉴定。本研究对于大豆属植物种质资源的分类鉴定、保护和利用具有重要价值。
High-throughput sequencing technology has greatly decreased the experimental cost for yielding genome sequences and provided a new source of data for accurate identification of plant resource diversity in genus Glycine. 2363 species-specific variable nucleotide characters in the complete chloroplast genome of 7 Glycine species were used as molecular traits to identify Glycine plants and compile a molecular classification key for the first time. There are differences in aspects of amount and base composition of variable nucleotide characters between the species. The proportion of A or T (26.74%~42.62%) is higher than that of C or G (9.84%~21.31%) in Glycine max (L.) Merr., G. stenophita B.E.Pfeil & Tindale, G. falcata Benth., G. canescens F.J.Herm. and G. dolichocarpa Tateishi & H. Ohashi. The proportion of A or T or C (26.36%~27.91%) is higher with that of G (19.38%) in G .tomentella Hayata. The proportion of T or G (30.00%) is higher than that of A or C (18.33%~21.67%) in G. syndetika B. E. Pfeil & Craven. Our results indicated that species-specific variable nucleotide characters from the chloroplast genomes could be used for discrimination of different genotypes in Glycine. This study is valuable for identification, conservation and utilization of plant germplasm resources of Glycine.
| [1] | 中国科学院中国植物志编辑委员会. 中国植物志第41卷: 大豆属(豆科) [M]. 北京: 科学出版社, 1995.
https://www.iplant.cn/info/Glycine?t=z |
| [2] | Wu, Z.Y., Hong, D.Y. and Raven, P.H. (2010) Flora of China, Vol. 10, Glycine (Fabaceae). Science Press, Beijing and Missouri Botanical Garden Press, St. Louis, 33-37. https://www.iplant.cn/info/Glycine?t=foc |
| [3] | 郭顺堂, 徐婧婷. 我国大豆食品产业发展现状及存在的问题[J]. 食品科学技术学报, 2023, 41(3): 1-8.
https://doi.org/10.12301/spxb202201131 |
| [4] | 王超凡, 张大健. 基因编辑技术在大豆种质资源研究中的利用[J]. 植物遗传资源学报, 2020, 21(1): 26-32.
https://doi.org/10.13430/j.cnki.jpgr.20191028004 |
| [5] | 刘美辰. 线性回归和动力学方程在大豆原油储存品质预测上的应用[J]. 食品科技, 2019, 44(3): 183-187.
https://doi.org/10.13684/j.cnki.spkj.2019.03.033 |
| [6] | 曹天一. 不同品种大豆豆乳及豆腐加工特性的研究[D]: [博士学位论文]. 北京: 中国农业大学, 2018. |
| [7] | 陈辰, 郭顺堂, 李景妍, 徐婧婷, 王睿粲, 张新艳, 谢来超, 施小迪, 张惠, 王曙明, 王谦玉. 不同品种大豆加工豆浆的品质分析及评价模型[J]. 农业工程学报, 2018, 34(8): 291-302.
https://doi.org/10.11975/j.issn.1002-6819.2018.08038 |
| [8] | Wang, R.C. and Guo, S.T. (2021) Phytic Acid and Its Interactions: Contributions to Protein Functionality, Food Processing and Safety. Comprehensive Reviews in Food Sci-ence and Food Safety, 20, 2081-2105.
https://doi.org/10.1111/1541-4337.12714 |
| [9] | 吴元浩. 植物基牛肉饼质构特性研究: 基质蛋白与拉丝蛋白复合效果分析[D]: [博士学位论文]. 北京: 中国农业大学, 2021. |
| [10] | 蒲艳艳, 宫永超, 李娜娜, 刘艳, 王秋玲, 宋东涛, 颜廷进, 丁汉凤. 中国大豆种质资源遗传多样性研究进展[J]. 大豆科学, 2018, 37(2): 315-321. https://doi.org/10.11861/j.issn.1000-9841.2018.02.0315 |
| [11] | 卢江杰. 大豆Soja亚属基因组变异与人工进化特征研究[D]: [博士学位论文]. 南京: 南京农业大学, 2014. |
| [12] | Zhuang, Y.B., Li, X.M., Hu, J.M., Li, X.M., Hu, J.M., Xu, R. and Zhang, D.J. (2022) Expanding the Gene Pool for Soybean Improvement with Its Wild Relatives. aBI-OTECH, 3, 115-125. https://doi.org/10.1007/s42994-022-00072-7 |
| [13] | Zuo, Y.J., Wen, J. and Zhou, S.L. (2017) Intercontinental and Intracontinental Biogeography of the Eastern Asian-Eastern North American Disjunct Panax (the Ginseng Genus, Araliaceae), Emphasizing Its Diversification Processes in Eastern. Molecular Phylogenetics and Evolu-tion, 117, 60-74. https://doi.org/10.1016/j.ympev.2017.06.016 |
| [14] | Suo, Z.L., Zhang, C.H., Zheng, Y.Q., He, L.X., Jin, X.B., Hou, B.X. and Li, J.J. (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 |
| [15] | 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 |
| [16] | Suo, Z.L., Li, W.Y., Jin, X.B. and Zhang, H.J. (2016) A New Nu-clear 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 |
| [17] | 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 |
| [18] | Dong, W.P., Xu, C., Li, D.L., Jin, X.B., Li, R.L., Lu, Q. and Suo Z.L. (2016) Comparative Analysis of the Complete Chloroplast Genome Sequences in Psammophytic Haloxylon Species (Amaranthaceae). PeerJ, 4, e2699.
https://doi.org/10.7717/peerj.2699 |
| [19] | Dong, W.P., Xu, C., Li, W.Q., Xie, X.M., Lu, Y.Z., Liu, Y.L., Jin, X.B. and Suo, Z.L. (2017) Phylogenetic Resolution in Juglans Based on Complete Chloroplast Genomes and Nuclear DNA Sequences. Frontiers in Plant Science, 8, Article No. 1148. https://doi.org/10.3389/fpls.2017.01148 |
| [20] | Xu, C., Dong, W.P., Li, W.Y., Lu, Y.Z., Xie, X.M., Jin, X.B., Shi, J.P., He, K.H. and Suo, Z.L. (2017) Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes. Frontiers in Plant Science, 8, Article No. 15.
https://doi.org/10.3389/fpls.2017.00015 |
| [21] | Li, W.Q., Liu, Y.L., Yang, Y., Xie, X.M., Lu, Y.Z., Yang, Z.R., Jin, X.B., Dong, W.P. and Suo, Z.L. (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 |
| [22] | Dong, W.P., Xu, C., Liu, Y.L., Shi, J.P., Li, W.Y. and Suo, Z.L. (2021) Chloroplast Phylogenomics and Divergence Times of Lagerstroemia (Lythraceae). BMC Genomics, 22, Article No. 434.
https://doi.org/10.1186/s12864-021-07769-x |
| [23] | Guo, C., Liu, K.J., Li, E.Z., Chen, Y.F., He, J.Y., Li, W.Y., Dong, W.P. and Suo, Z.L. (2023) Maternal Donor and Genetic Variation of Lagerstroemia indica Cultivars. Internation-al Journal of Molecular Sciences, 24, Article No. 3606.
https://doi.org/10.3390/ijms24043606 |
| [24] | Lam, H. M., Xu, X., Liu, X., et al. (2010) Resequencing of 31 Wild and Cultivated Soybean Genomes Identifies Patterns of Genetic Diversity and Selection. Nature Genetics, 42, 1053-1059. https://doi.org/10.1038/ng.715 |
| [25] | 张彦威, 李伟, 张礼凤, 王彩洁, 戴海英, 徐冉. 基于重测序的大豆新品种齐黄34的全基因组变异挖掘[J]. 中国油料作物学报, 2016, 38(2): 150-158. https://doi.org/10.7505/j.issn.1007-9084.2016.02.003 |
| [26] | 刘方东. 中国大豆种质群体的基因组演化特征分析及其农艺性状的遗传体系解析与育种潜势预测[D]: [博士学位论文]. 南京: 南京农业大学, 2018. |
| [27] | Li, M.W., Wang, X., Sze, C.C., Yung, W.S., Wong, F.L., Zhang, G., Chung, G., Chan, T.F. and Lam, H.M. (2023) Development of a Set of Polymorphic DNA Markers for Soybean (Glycine max L.) Applications. Agronomy, 13, Article No. 2708. https://doi.org/10.3390/agronomy13112708 |
| [28] | Zhuang, Y.B., Wang, X.T., Li, X.C., Hu, J.M., Fan, L.H., Jack-son, S., Doyle, J., Zhang, X.S., Zhang, D.J. and Ma, J.X. (2022) A Super-Pangenome Framework of the Genus Glycine Unveils Polyploid Evolution and Life-Strategy Transition. Nature Plants, 8, 233-244. https://doi.org/10.21203/rs.3.rs-548382/v1 |
| [29] | Landis, J.B., Jeff, J. and Doyle, J.J. (2023) Genomic Relation-ships of Glycine remota, a Recently Discovered Perennial Relative of Soybean, within Glycine. Systematic Botany, 48, 78-87.
https://doi.org/10.1600/036364423X16758873924117 |
| [30] | Asaf, S., Khan, A.L., Aaqil Khan, M., Muhammad Imran, Q., Kang, S.M., Al-Hosni, K., et al. (2017) Comparative Analysis of Complete Plastid Genomes from Wild Soy-bean (Glycine soja) and Nine Other Glycine Species. PLOS ONE, 12, e0182281. https://doi.org/10.1371/journal.pone.0182281 |
| [31] | 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 |
| [32] | 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 |
| [33] | 李斌, 左云娟, 刘艳磊, 杨志荣, 靳晓白, 潘伯荣, 常青, 索志立. 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[J]. 植物学研究, 2023, 12(4): 227-239.
https://doi.org/10.12677/br.2023.124030 |
| [34] | Katoh, K. and Standley, D.M. (2013) MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution, 30, 772-780. https://doi.org/10.1093/molbev/mst010 |
| [35] | 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 |
| [36] | Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J.C., Guirao-Rico, S., Librado P., Ramos-Onsins, S.E. and Sánchez-Gracia, A. (2017) DnaSP 6: DNA Sequence Polymor-phism Analysis of Large Data Sets. Molecular Biology and Evolution, 34, 3299-3302. https://doi.org/10.1093/molbev/msx248 |
| [37] | Wai, N.S. (1929) A New Species of Mono-mucor, Mucor sufu, on Chinese Soybean Cheese. Science, 70, 307-308.
https://doi.org/10.1126/science.70.1813.307-a |
| [38] | 青宁生. 我国首位在Science上发表论文的微生物学先驱——魏岩寿[J]. 微生物学报, 2006(4): 509-510.
https://doi.org/10.13343/j.cnki.wsxb.2006.04.001 |
| [39] | Goodwin, Z.A., Harris, D.J., Filer, D., Wood, J.R.I. and Scotland, R.W. (2015) Wide Spread Mistaken Identity in Tropical Plant Collections. Current Biology, 25, R1057-R1069. https://doi.org/10.1016/j.cub.2015.10.002 |
| [40] | 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 |
| [41] | 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. |
| [42] | 何真, 韵晓东, 武凯, 姬虎太, 常建忠, 乔麟轶, 郑军. 大豆种质资源遗传多样性研究进展[J]. 生物技术进展, 2015, 5(2): 103-108. https://doi.org/10.3969/j.issn.2095-2341.2015.02.05 |
