基于SCoT分子标记的裸果木遗传多样性分析

doi:10.7525/j.issn.1673-5102.2018.05.012

摘要/Abstract

摘要： 为了揭示裸果木的遗传多样性和遗传结构，采用SCoT分子标记对新疆7个裸果木自然种群201个植株进行分析。结果表明12条引物共扩增出145个位点，在物种和种群水平上裸果木多态位点百分率分别为97.24%和76.45%，Nei's遗传多样性指数分别为0.263 8和0.213 7，Shannon's信息多样性指数分别为0.408 1和0.331 6，说明裸果木具有较高的遗传多样性，且物种水平遗传多样性略高于种群水平；遗传分化系数为0.183 9，说明其遗传变异主要来自种群内，种群间存在一定程度的分化；Mantel检验结果表明裸果木种群地理距离与遗传距离不存在显著相关性；运用主坐标分析（PCoA）和STRUCTURE分析对裸果木个体间亲缘关系聚类分析的结果存在一定差异，但总体上结果是一致的。裸果木的遗传多样性和遗传结构可能与进化历史、繁育系统、地理隔离和人为干扰有关。

关键词: 裸果木, SCoT, 遗传多样性, 遗传分化, 遗传距离

Abstract: The experiment was conducted to study the genetic diversity and genetic structure of Gymnocarpos przewalskii with 201 individuals sampled from 7 G.przewalskii populations in Xinjiang by using tart codon targeted(SCoT) markers. The 12 random primers were amplified to 145 loci. The percentage of polymorphic bands, Nei's genetic diversity index and Shannon's information index of species and population leve were 97.24% and 76.45%, 0.2638 and 0.2137, 0.4081 and 0.3316, respectively. These results indicated that the genetic diversity of G.przewalskii was higher, and the genetic diversity of the species level was slightly higher than the population level. The genetic differentiation coefficient was 0.1839, indicating that the genetic variation of G.przewalskii mainly existed in populations, differentiation among populations exists partly. The results of Mantel test showed that there were no significant correlation between geographical distance and genetic distance. The results of principal coordinate analysis(PCoA) and genetic structure analysis were some differences, but basically consistent with each other. Therefore, the present status of genetic diversity and genetic structure of G.przewalskii might be related to its evolutionary history, breeding system, geographical isolation and human disturbance.

Key words: Gymnocarpos przewalskii, SCoT, genetic diversity, genetic differentiation, genetic distance

中图分类号:

Q945.5

狄林楠, 李新蓉, 宋楠. 基于SCoT分子标记的裸果木遗传多样性分析[J]. 植物研究, 2018, 38(5): 725-732.

DI Lin-Nan, LI Xin-Rong, SONG Nan. Genetic Diversity of Gymnocarpos przewalskii Based on SCoT Markers[J]. Bulletin of Botanical Research, 2018, 38(5): 725-732.

参考文献

1. 钱迎倩,马克平. 生物多样性研究的原理与方法[M]. 北京:中国科学技术出版社,1994:2.Qian Y Q,Ma K P. Principles and methodologies of biodiversity studies[M]. Beijing:Chinese Science and Technology Press,1994:2.
2. Saccheri I,Kuussaari M,Kankare M,et al. Inbreeding and extinction in a butterfly metapopulation[J]. Nature,1998,392(6675):491-494.
3. Soltis P S,Soltis D E. Genetic variation in endemic and widespread plant species[J]. Aliso,1991,13(1):10.
4. 葛颂,洪德元. 濒危物种裂叶沙参及其近缘广布种泡沙参的遗传多样性研究[J]. 遗传学报,1999,26(4):410-417.Ge S,Hong D Y. Studies of morphological and allozyme variation of the endangered Adenophora lobophylla and its widespread congener A. potaninii[J]. Acta Genetica Sinica,1999,26(4):410-417.
5. 张颖娟,王玉山. 珍稀濒危植物长叶红砂种群遗传多样性的ISSR分析[J]. 植物研究,2008,28(5):568-573.Zhang Y J,Wang Y S. Analysis on the population genetic diversity of endangered shrub Reaumuria trigyna by ISSR markers[J]. Bulletin of Botanical Research,2008,28(5):568-573.
6. 徐刚标,梁艳,蒋燚,等. 伯乐树种群遗传多样性及遗传结构[J]. 生物多样性,2013,21(6):723-731.Xu G B,Liang Y,Jiang Y,et al. Genetic diversity and population structure of Bretschneidera sinensis,an endangered species[J]. Biodiversity Science,2013,21(6):723-731.
7. 肖猛,李群,郭亮,等. 四川西部濒危植物桃儿七遗传多样性的RAPD分析[J]. 生态学报,2015,35(5):1488-1495.Xiao M,Li Q,Guo L,et al. RAPD analysis of genetic diversity of an endangered species Sinopodophyllum hexandrum(Royle) Ying from Western Sichuan Province,China[J]. Acta Ecologica Sinica,2015,35(5):1488-1495.
8. Collard B C Y,Mackill D J. Start Codon Targeted(SCoT) polymorphism:a simple,novel DNA marker technique for generating gene-targeted markers in plants[J]. Plant Molecular Biology Reporter,2009,27(1):86-93.
9. 熊发前,唐荣华,陈忠良,等. 目标起始密码子多态性(SCoT):一种基于翻译起始位点的目的基因标记新技术[J]. 分子植物育种,2009,7(3):635-638.Xiong F Q,Tang R H,Chen Z L,et al. SCoT:a novel gene targeted marker technique based on the translation start codon[J]. Molecular Plant Breeding,2009,7(3):635-638.
10. 龙治坚,范理璋,徐刚,等. SCoT分子标记在植物研究中的应用进展[J]. 植物遗传资源学报,2015,16(2):336-343.Long Z J,Fan L Z,Xu G,et al. Application advance of SCoT molecular markers in plants[J]. Journal of Plant Genetic Resources,2015,16(2):336-343.
11. Luo C,He X H,Hu C,et al. Analysis of diversity and relationships among mango cultivars using Start Codon Targeted(SCoT) markers[J]. Biochemical Systematics and Ecology,2010,38(6):1176-1184.
12. Al-Qurainy F,Khan S,Nadeem M,et al. SCoT marker for the assessment of genetic diversity in Saudi Arabian date palm cultivars[J]. Pakistan Journal of Botany,2015,47(2):637-643.
13. Zhang J C,Xie W G,Wang Y R,et al. Potential of Start Codon Targeted(SCoT) markers to estimate genetic diversity and relationships among Chinese Elymus sibiricus accessions[J]. Molecules,2015,20(4):5987-6001.
14. 张安世,张中海,齐秀娟,等. 猕猴桃SCoT遗传多样性分析及指纹图谱的构建[J]. 植物研究,2017,37(2):259-265.Zhang A S,Zhang Z H,Qi X J,et al. Genetic diversity and fingerprints with SCoT markers in Actinidia[J]. Bulletin of Botanical Research,2017,37(2):259-265.
15. 傅立国. 中国植物红皮书:稀有濒危植物:第1册[M]. 北京:科学出版社,1991:202.FU L G. China plant red data book:rare and endangered plants:volume 1[M]. Beijing:Science Press,1991:202.
16. Oxelman B,Ahlgren B,Thulin M. Circumscription and phylogenetic relationships of Gymnocarpos(Caryophyllaceae-Paronychioideae)[J]. Edinburgh Journal of Botany,2002,59(2):221-237.
17. 马松梅,张明理,张宏祥,等. 利用最大熵模型和规则集遗传算法模型预测孑遗植物裸果木的潜在地理分布及格局[J]. 植物生态学报,2010,34(11):1327-1335.Ma S M,Zhang M L,Zhang H X,et al. Predicting potential geographical distributions and patterns of the relic plant Gymnocarpos przewalskii using maximum entropy and genetic algorithm for rule-set prediction[J]. Chinese Journal of Plant Ecology,2010,34(11):1327-1335.
18. 李新蓉,唐欣,付文洁. 荒漠孑遗植物裸果木的花部特征及繁育系统[J]. 生态学杂志,2016,35(10):2592-2598.Li X R,Tang X,Fu W J. Floral syndrome and breeding system of Gymnocarpos przewalskii Maxim[J]. Chinese Journal of Ecology,2016,35(10):2592-2598.
19. 唐欣,李新蓉. 荒漠孑遗植物裸果木的开花物候特征[J]. 植物学报,2017,52(4):487-495.Tang X,Li X R. Flowering phenology characteristics of the desert relict Plant Gymnocarpos przewalskii[J]. Bulletin of Botany,2017,52(4):487-495.
20. 王立龙,王亮,张丽芳,等. 不同生境下濒危植物裸果木种群结构及动态特征[J]. 植物生态学报,2015,39(10):980-989.Wang L L,Wang L,Zhang L F,et al. Structure and dynamic characteristics of Gymnocarpos przewalskii in different habitats[J]. Chinese Journal of Plant Ecology,2015,39(10):980-989.
21. 王静,王海芳,花立民,等. 珍稀濒危植物裸果木RAPD反应体系优化研究[J]. 草原与草坪,2012,32(1):7-11.Wang J,Wang H F,Hua L M,et al. Study on optimization of RAPD reaction system for endangered plant Gymnocarpos przewalskii[J]. Grassland and Turf,2012,32(1):7-11.
22. Ma S M,Zhang M L,Sanderson S C. Phylogeography of the rare Gymnocarpos przewalskii(Caryophyllaceae):indications of multiple glacial refugia in north-western China[J]. Australian Journal of Botany,2012,60(1):20-31.
23. 徐振朋,宛涛,蔡萍,等. 裸果木种群遗传多样性及其与土壤因子的关联性研究[J]. 生态环境学报,2017,26(9):1473-1479.Xu Z P,Wan T,Cai P,et al. Study on the relevance between genetic diversity of Gymnocarpos przewalskii populations and soil factors[J]. Ecology and Environmental Sciences,2017,26(9):1473-1479.
24. Ge X J,Yu Y,Yuan M Y,et al. Genetic diversity and geographic differentiation in endangered Ammopiptanthus(Leguminosae) populations in desert regions of northwest China as revealed by ISSR analysis[J]. Annals of Botany,2005,95(5):843-851.
25. 张杰,王佳,李浩宇,等. 濒危植物蒙古扁桃不同地理种群遗传多样性的ISSR分析[J]. 生态学报,2012,32(14):4443-4452.Zhang J,Wang J,Li H Y,et al. Genetic diversity of different eco-geographical populations in endangered plant Prunus mongolica by ISSR Markers[J]. Acta Ecologica Sinica,2012,32(14):4443-4452.
26. Hamrick J L,Godt M J W. Effects of life history traits on genetic diversity in plant species[J]. Philosophical Transactions of the Royal Society B:Biological Sciences,1996,351(1345):1291-1298.
27. Nybom H. Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants[J]. Molecular Ecology,2004,13(5):1143-1155.
28. Smadja C M,Butlin R K. A framework for comparing processes of speciation in the presence of gene flow[J]. Molecular Ecology,2011,20(24):5123-5140.
29. Flaxman S M,Feder J L,NOSIL P. Genetic hitchhiking and the dynamic buildup of genomic divergence during speciation with gene flow[J]. Evolution,2013,67(9):2577-2591.
30. Evanno G,Regnaut S,Goudet J. Detecting the number of clusters of individuals using the software structure:a simulation study[J]. Molecular Ecology,2005,14(8):2611-2620.
31. 宗绪晓,关建平,王海飞,等. 世界栽培豌豆(Pisum sativum L.)资源群体结构与遗传多样性分析[J]. 中国农业科学,2010,43(2):240-251.Zong X X,Guan J P,Wang H F,et al. Population structure and genetic diversity of global pea(Pisum sativum L.) germplasm resources[J]. Scientia Agricultura Sinica,2010,43(2):240-251.
32. Souza I G B,Souza V A B,Lima P S C. Molecular characterization of Platonia insignis Mart. ("Bacurizeiro") using inter simple sequence repeat(ISSR) markers[J]. Molecular Biology Reports,2013,40(5):3835-3845.
33. Hewitt G M. Some genetic consequences of ice ages,and their role in divergence and speciation[J]. Biological Journal of the Linnean Society,1996,58(3):247-276.
34. Soltis D E,Morris A B,Mclachlan J S,et al. Comparative phylogeography of unglaciated eastern North America[J]. Molecular Ecology,2006,15(14):4261-4293.
35. Farwig N,Braun C,Böhning-Gaese K. Human disturbance reduces genetic diversity of an endangered tropical tree,Prunus africana(Rosaceae)[J]. Conservation Genetics,2008,9(2):317-326.
36. 林乐静,金楚齐,郑春豪,等. 武夷山地伯乐树种群遗传多样性的ISSR分析[J]. 植物研究,2015,35(4):559-563.Lin L J,Jin C Q,Zheng C H,et al. ISSR analysis on the genetic diversity of relic plant Bretschneidera sinensis from Wuyishan Region[J]. Bulletin of Botanical Research,2015,35(4):559-563.
37. 李龙梅,石晓蒙,蒋维昕,等. 广西境内马褂木天然群体遗传多样性的ISSR分析[J]. 广西植物,2017,37(1):22-28.Li L M,Shi X M,Jiang W X,et al. ISSR analysis on genetic diversity of Liriodendron chinense natural populations in Guangxi[J]. Guihaia,2017,37(1):22-28.
38. Ferreira D K,Nazareno A G,Mantovani A,et al. Genetic analysis of 50-year old Brazilian pine(Araucaria angustifolia) plantations:implications for conservation planning[J]. Conservation Genetics,2012,13(2):435-442.

[1]	杨磊, 曹秋梅, 冯缨, 李文军. 珍稀濒危植物阜康阿魏的遗传多样性及遗传结构[J]. 植物研究, 2023, 43(1): 51-58.
[2]	常二梅, 刘建锋, 黄跃宁, 李红丽, 单冰燕, 江泽平, 赵秀莲. 岷江柏野生居群和迁地保护居群的遗传多样性比较[J]. 植物研究, 2022, 42(5): 772-779.
[3]	张玉洁, 石鹏霞, 赵凡, 陈晓丹, 孙坤, 张辉. rpl32-trnL片段在柳穿鱼不同地理居群遗传多样性分析中的应用[J]. 植物研究, 2022, 42(5): 780-789.
[4]	付鹏程, 韦秋前, 史明艳. 青藏高原岷县龙胆的遗传分化与种群动态历史分析[J]. 植物研究, 2022, 42(4): 556-564.
[5]	李义良, 赵奋成, 刘阳, 钟岁英, 林昌明, 谭志强, 李福明, 廖仿炎, 吴惠姗, 郭文冰, 王哲. 湿加松亲本间SNP遗传距离与生长性状杂种优势关系研究[J]. 植物研究, 2021, 41(5): 738-743.
[6]	段义忠, 王海涛, 张格格, 严伟娜. 基于ISSR分子标记的孑遗濒危植物四合木遗传结构分析[J]. 植物研究, 2021, 41(3): 466-473.
[7]	吕冬雪, 张学杰, 张洛艳, 樊守金. 基于SSR技术对黄河三角洲二色补血草遗传多样性研究[J]. 植物研究, 2020, 40(6): 923-931.
[8]	宁馨, 姜小龙, 邓敏, 徐刚标. 基于简化基因组数据开发岭南青冈微卫星引物[J]. 植物研究, 2020, 40(4): 629-634.
[9]	杨立荣, 孙秀秀, 陈加利, 云勇, 陈宣, 郑道君. 海南特有极小种群植物文昌锥的SCoT-PCR体系建立及有效引物评价[J]. 植物研究, 2020, 40(1): 66-72.
[10]	管睿婷, 刘济明, 王敏, 陈敬忠, 武梦瑶, 童炳丽. 不同天然居群小蓬竹的遗传多样性[J]. 植物研究, 2019, 39(5): 740-751.
[11]	郭文丽, 李义良, 赵奋成, 铁军, 廖仿炎, 钟岁英, 林昌明, 叶威方. 湿加松无性系表型遗传多样性研究[J]. 植物研究, 2019, 39(2): 259-266.
[12]	刘济明, 管睿婷, 王敏, 陈敬忠, 童炳丽, 武梦瑶. 不同喀斯特小生境中小蓬竹的遗传多样性[J]. 植物研究, 2019, 39(1): 69-77.
[13]	蔡年辉, 许玉兰, 王亚楠, 陈诗, 汪梦婷, 李根前. 基于SSR标记的不同优势等级云南松遗传多样性分析[J]. 植物研究, 2019, 39(1): 87-95.
[14]	肖遥, 麻文俊, 易飞, 杨桂娟, 王秋霞, 王平, 王军辉. 滇楸种质生长性状遗传变异及表型性状遗传多样性分析[J]. 植物研究, 2018, 38(6): 843-851.
[15]	刘海瑞, 高庆波, 张发起, 邢睿, 迟晓峰, 陈世龙. 基于叶绿体基因序列rbcL-accD研究莛子藨的分子遗传多样性和谱系地理结构[J]. 植物研究, 2018, 38(2): 278-283.