基于简化基因组技术的云南蓝果树群体遗传分析

doi:10.7525/j.issn.1673-5102.2019.06.013

植物研究 ›› 2019, Vol. 39 ›› Issue (6): 899-907.doi: 10.7525/j.issn.1673-5102.2019.06.013

基于简化基因组技术的云南蓝果树群体遗传分析

张珊珊, 康洪梅, 杨文忠

云南省林业科学院, 云南省森林植物培育与开发利用重点实验室/国家林业局云南珍稀濒特森林植物保护和繁育国家林业局重点实验室, 昆明 650201

收稿日期:2019-02-14 出版日期:2019-11-05 发布日期:2019-11-16
通讯作者: 杨文忠 E-mail:wzyang2004@126.com
作者简介:张珊珊(1984-),女,博士,副研究员,主要从事保护生物学的研究工作。
基金资助:
国家自然科学基金项目（31960278，31660164）；国家科技基础资源调查专项项目（2017FY100100）；国家林业和草原野生植物保护管理项目（2016YB1038，2017YB1010）；云南省林业科学院创新基金项目（QN2018-05）；云南省应用基础研究青年项目（2016FD079）

Population Genetic Analysis of Nyssa yunnanensis by Reduced-representation Sequencing Technique

ZHANG Shan-Shan, KANG Hong-Mei, YANG Wen-Zhong

Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry, Kunming 650201

Received:2019-02-14 Online:2019-11-05 Published:2019-11-16
Supported by:
National Natural Science Foundation of China(31960278,31660164);National Science and Technology Fundamental Resources Investigation Project(2017FY100100);State Forestry and Grassland Administration of China(2016YB1038,2017YB1010);Innovation Fund Project of Yunnan Academy of Forestry(QN2018-05);Youth Project of Applied Basic Research in Yunnan Province(2016FD079)

摘要/Abstract

摘要： 极小种群野生植物云南蓝果树是国家和云南省实施极小种群野生植物保护工程的代表性物种。为有效保护其遗传资源，本研究通过二代测序技术，对其进行简化基因组测序，开发一批特异性高的单核苷酸多态性标记，分析现存群体的遗传结构和遗传多样性。经过遗传变异检测，本次研究中共获得SNP位点98 498个，通过样品最低测序深度>2，样品缺失率<0.5，次要基因型频率（MAF）>0.05筛选以后，得到有效SNP位点6 309个。基于过滤后的SNP，运用生物信息学分析方法，对云南蓝果树完成了群体的遗传分析，其中：系统进化树分析将云南蓝果树划分为3大类，研究分析了云南蓝果树各分类的私人等位基因数目（Private）、平均观测杂合度（H_o）、平均期望杂合度（H_e）、核苷酸多样性（π）和平均近交系数（F_IS）5个遗传多样性参数；群体结构和主成分分析进一步证明了，云南蓝果树现存植株之间亲缘关系较远，遗传多样性差异较大，具有很高的遗传资源保存价值。本研究结果将为基于遗传管理的云南蓝果树就地保护、遗传资源保存和种群重建等保护工程提供科学依据。

关键词: 云南蓝果树, 简化基因组测序, SNP, 群体遗传分析, 遗传管理

Abstract: Nyssa yunnananesis, a plant species with extremely small populations(PSESP), has become the flagship species in national and provincial conservation programs of PSESP. For effectively preserving the existing genetic resources, the recently developed technology restriction-site associated DNA sequencing(RAD-seq), which is based on next-generation sequencing(NGS), was used to develop a batch of highly specific single nucleotide polymorphism(SNP) markers and analyze genetic structure and genetic diversity of existing populations. After detection of genetic variation, a total of 98 498 SNPs were got. Under these conditions, the minimum sequencing depth of samples>2, sample missing rate < 0.5 and MAF > 0.05 screening from all 98 498 SNPs, 6 309 effective SNPs were obtained. Population genetics analysis of N.yunnananesis was analyzed using bioinformatic method with screening SNPs. Results demonstrated that the phylogenetic tree was divided into three clusters, in which the genetic diversity parameters, such as private, the nucleotide diversity(π), observed heterozygosity(H_o), expected heterozygosity(H_e) and inbreeding coefficient(F_IS) were elucidated. Population structure and PCA analysis further proved that N.yunnananesis had far relationships and quite different genetic diversity between the existing plants. Therefore, preserving genetic resources was of very high value. This study will give scientific evidences to protection engineering in particular the in-situ conservation, genetic resource preservation and population reestablishment with genetic management related methods and techniques.

Key words: Nyssa yunnanensis, restriction-site associated DNA sequencing, SNP, population genetic analysis, genetic management

中图分类号:

S727.28

张珊珊, 康洪梅, 杨文忠. 基于简化基因组技术的云南蓝果树群体遗传分析[J]. 植物研究, 2019, 39(6): 899-907.

ZHANG Shan-Shan, KANG Hong-Mei, YANG Wen-Zhong. Population Genetic Analysis of Nyssa yunnanensis by Reduced-representation Sequencing Technique[J]. Bulletin of Botanical Research, 2019, 39(6): 899-907.

参考文献

1. 杨文忠,向振勇,张珊珊,等. 极小种群野生植物的概念及其对我国野生植物保护的影响[J]. 生物多样性,2015,23(3):419-425. Yang W Z,Xiang Z Y,Zhang S S,et al. Plant species with extremely small populations(PSESP) and their significance in China's national plant conservation strategy[J]. Biodiversity Science,2015,23(3):419-425.
2. 孙宝玲,张长芹,周凤林,等. 极度濒危植物——云南蓝果树的种子形态和不同处理条件对种子萌发的影响[J]. 云南植物研究,2007,29(3):351-354. Sun B L,Zhang C Q,Zhou F L,et al. Seed morphology and effects of different treatments on germination of the critically endangered Nyssa yunnanensis(Nyssaceae)[J]. Acta Botanica Yunnanica,2007,29(3):351-354.
3. 孙宝玲,张长芹. 极度濒危植物云南蓝果树的形态修订[J]. 云南植物研究,2007,29(2):173-175. Sun B L,Zhang C Q. A revised description of Nyssa yunnanensis(nyssaceae)[J]. Acta Botanica Yunnanica,2007,29(2):173-175.
4. 张珊珊,康洪梅,杨文忠,等. 干旱胁迫下AMF对云南蓝果树叶片解剖结构的影响[J]. 广西植物,2016,36(10):1265-1274. Zhang S S,Kang H M,Yang W Z,et al. Effects of arbuscular mycorrhizal fungi on anatomical structure of Nyssa yunnanensis leaves under drought stress[J]. Guihaia,2016,36(10):1265-1274.
5. 张珊珊,康洪梅,杨文忠,等. 干旱胁迫下AMF对云南蓝果树幼苗生长和光合特征的影响[J]. 生态学报,2016,36(21):6950-6862. Zhang S S,Kang H M,Yang W Z,et al. Effects of arbuscular mycorrhizal fungi on growth and photosynthetic characteristics of Nyssa yunnanensis seedlings under drought stress[J]. Acta Ecologica Sinica,2016,36(21):6950-6862.
6. Zhang S S,Kang H M,Yang W Z,et al. Climate change-induced water stress suppresses the regeneration of the critically endangered forest tree Nyssa yunnanensis[J]. PLoS ONE,2017,12(8):e0182012.
7. 杨文忠,康洪梅,向振勇,等. 极小种群野生植物保护的主要内容和技术要点[J]. 西部林业科学,2014,43(5):24-29. Yang W Z,Kang H M,Xiang Z Y,et al. Methods and techniques for conserving wild plant species with extremely small populations[J]. Journal of West China Forestry Science,2014,43(5):24-29.
8. Yang W Z,Zhang S S,Wang W B,et al. A sophisticated species conservation strategy for Nyssa yunnanensis,a species with extremely small populations in China[J]. Biodiversity and Conservation,2017,26(4):967-981.
9. 王云生,黄宏文,王瑛. 植物分子群体遗传学研究动态[J]. 遗传,2007,29(10):1191-1198. Wang Y S,Huang H W,Wang Y. Recent progress in plant molecular population genetics[J]. Hereditas,2007,29(10):1191-1198.
10. 张笑,郑骑坚,李忠虎,等. 绞股蓝的遗传多样性和群体结构研究[J]. 中草药,2015,46(13):1958-1965. Zhang X,Zheng Q J,Li Z H,et al. Genetic diversity and population structure of Gynostemma pentaphyllun[J]. Chinese Traditional and Herbal Drugs,2015,46(13):1958-1965.
11. Hartl D L,Clark G C. Principles of population genetics[M]. 4th ed. Sunderland,Massachusetts:Sinauer Associates,2007.
12. 邹喻苹,葛颂,王晓东. 系统与进化植物学中的分子标记[M]. 北京:科学出版社,2001. Zou Y P,Ge S,Wang X D. Molecular markers in systematic and evolutionary botany[M]. Beijing:Science Press,2001.
13. Vucetich J A,Burnham D,Macdonald E A,et al. Just conservation:What is it and should we pursue it?[J]. Biological Conservation,2018,221:23-33.
14. Whitlock R,Hipperson H,Thompsonb D B A,et al. 2016. Consequences of in-situ strategies for the conservation of plant genetic diversity[J]. Biological Conservation,2018,203:134-142.
15. Davey J W,Blaxter M L. RADSeq:next-generation population genetics[J]. Briefings in Functional Genomics,2010,9(5-6):416-423.
16. Etter P D,Bassham S,Hohenlohe P A,et al. SNP discovery and genotyping for evolutionary genetics using RAD sequencing[M].//Rockman M. Methods in Molecular Biology. Totowa:Humana Press,2012,772:157-178.
17. Lozier J D. Revisiting comparisons of genetic diversity in stable and declining species:assessing genome-wide polymorphism in North American bumble bees using RAD sequencing[J]. Molecular Ecology,2014,23(4):788-801.
18. Bruneaux M,Johnston S E,Herczeg G,et al. Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach[J]. Molecular Ecology,2013,22(3):565-582.
19. Baird N A,Etter P D,Atwood T S,et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers[J]. PLoS One,2008,3(10):e3376.
20. Hohenlohe P A,Amish S J,Catchen J M,et al. Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout[J]. Molecular Ecology Resources,2011,11(S1):117-122.
21. Ogden R,Gharbi K,Mugue N,et al. Sturgeon conservation genomics:SNP discovery and validation using RAD sequencing[J]. Molecular Ecology,2013,22(11):3112-3123.
22. 王久利,朱明星,徐明行,等. 基于RAD-seq技术的异型花SSR信息分析[J]. 植物研究,2017,37(3):447-452,460. Wang J L,Zhu M X,Xu M X,et al. Analysis on SSR in Sinoswertia tetraptera base on RAD-seq[J]. Bulletin of Botanical Research,2017,37(3):447-452,460.
23. 段义忠,王建武,杜忠毓,等. 基于SLAF-seq简化基因组技术的沙冬青SNP位点开发及遗传分析[J]. 植物研究,2018,38(1):141-147. Duan Y Z,Wang J W,Du Z Y,et al. SNP sites developed by specific length amplification fragment sequencing(SLAF-seq) and genetic analysis in Ammopitanthus mongolicus[J]. Bulletin of Botanical Research,2018,38(1):141-147.
24. Wang X Q,Sun G L,Gong X L,et al. Application of RAD sequencing for evaluating the genetic diversity of domesticated Panax notoginseng(Araliaceae)[J]. PLoS One,2016,11(11):e0166419.
25. 孙宝玲. 中国蓝果树属分类学与极度濒危植物云南蓝果树保护生物学[D]. 中国科学院昆明植物研究所,2008. Sun B L. Taxtonomy of Nyssa L. (Nyssaceae) and conservation biology of Nyssa yunnanensis,a critically endangered species[D]. Kunming Institute of Botany,Chinese Academy of Sciences,2008.
26. 向振勇,张珊珊,杨文忠,等. 基于ISSR遗传多样性分析的云南蓝果树保护措施探索[J]. 植物遗传资源学报,2015,16(3):664-669. Xiang Z Y,Zhang S S,Yang W Z,et al. Conservation of Nyssa yunnanensis based on genetic diversity analysis using ISSR markers[J]. Journal of Plant Genetic Resources,16(3):664-669.
27. Kobayashi M. The Ipomoea trifida complex closely related to sweet potato[C].//Shideler S F,Rincon H,et al. Proceedings of the 6th symposium of the intemational society of tropical root crop. Lima,Peru:CIE,1984:561-568.
28. Roullier C,Duputié A,Wennekes P,et al. Disentangling the origins of cultivated sweet potato(Ipomoea batatas(L.)Lam.)[J]. PLoS One,2013,8(5):e62707.
29. 褚延广,苏晓华. 单核苷酸多态性在林木中的研究进展[J]. 遗传,2008,30(10):1272-1278. Chu Y G,Su X H. Research progress of single nucleotide polymorphisms in forest trees[J]. HEREDITAS,2008,30(10):1272-1278.
30. Miller M R,Atwood T S,Eames B F,et al. RAD marker microarrays enable rapid mapping of zebrafish mutations[J]. Genome Biology,2007,8(6):R105.
31. 石璇,王茹嫒,唐君,等. 利用简化基因组技术分析甘薯种间单核苷酸多态性[J]. 作物学报,2016,42(5):641-647. Shi X,Wang R Y,Tang J,et al. Analysis of interspecific SNPs in sweetpotato using a reduced-representation genotyping technology[J]. Acta Agronomica Sinica,2016,42(5):641-647.
32. Talebi R,Naji A M,Fayaz F. Geographical patterns of genetic diversity in cultivated chickpea(Cicer arietinum L.) characterized by amplified fragment length polymorphism[J]. Plant,Soil and Environment,2008,54(10):447-452.
33. Catchen J,Bassham S,Wilson T,et al. The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing[J]. Molecular Ecology,2013,22(11):2864-2883.
34. Frankham R,Ballou J D,Briscoe D A. Introduction to conservation genetics[M]. Cambridge:Cambridge University Press,2010.
35. Hamilton M B. Population genetics[M]. West Sussex:Wiley-Blackwell,2009.
36. Wright S I,Lauga B,Charlesworth D. Subdivision and haplotype structure in natural populations of Arabidopsis lyrata[J]. Molecular Ecology,2003,12(5):1247-1263.
37. Shi F X,Li M R,Li Y L,et al. The impacts of polyploidy,geographic and ecological isolations on the diversification of Panax(Araliaceae)[J]. BMC Plant Biology,2015,15:297.
38. Hamrick J L,Godt M J W. Allozyme diversity in plant species[C].//Brown A H D,Clegg M T,Kahler A L,et al. Plant population genetics,breeding and genetic resources. Sunderland:Sinauer Associates Inc,1990:43-63.
39. Frankham R,Ballou J D,Briscoe D A. Introduction to conservation genetics[M]. Cambridge:Cambridge University Press,2002.

[1]	尹一卜, 李吉祥, 郭樱杰, 芦子廷, 肖英, 刘华领, 詹亚光, 曾凡锁. 白蜡属种间杂交子代木质素含量变异及FmPAL核苷酸多态性关联分析[J]. 植物研究, 2022, 42(2): 191-199.
[2]	余静雅, 夏铭泽, 徐浩, 张发起. 青藏高原地区3种蒿属植物转录组比较分析[J]. 植物研究, 2022, 42(2): 200-210.
[3]	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.
[4]	张序, 张秀姣, 马永鹏, 李正红, 万友名, 马宏. 基于GBS简化基因组技术的宽杯杜鹃遗传多样性分析[J]. 植物研究, 2021, 41(3): 429-435.
[5]	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.
[6]	杨赟, 陈梦娇, 杜庆鑫, 朱景乐, 杜红岩, 杨绍彬. 基于全基因组重测序技术的‘红叶’杜仲SNP位点开发[J]. 植物研究, 2019, 39(6): 947-954.
[7]	王久利, 陈世龙, 邢睿, 宋相杰, 朱明星, 张发起. 椭圆叶花锚简化基因组的SSR信息分析及SSR引物开发[J]. 植物研究, 2018, 38(2): 292-297.
[8]	段义忠, 王建武, 杜忠毓, 亢福仁. 基于SLAF-seq简化基因组技术的沙冬青SNP位点开发及遗传分析[J]. 植物研究, 2018, 38(1): 141-147.
[9]	王久利, 朱明星, 徐明行, 陈世龙, 张发起. 基于RAD-seq技术的异型花SSR信息分析[J]. 植物研究, 2017, 37(3): 447-452.
[10]	王艳红1,2；贾庆斌1；张磊1；张含国1*. 长白落叶松4CL基因单核苷酸多态性及其与木材材性的关联分析[J]. 植物研究, 2016, 36(2): 242-251.
[11]	高刚；邓家彬；苟学梅；王茜；张艳；杨瑞武. 14个赖草属植物DREB2*基因的克隆与SNP分析[J]. 植物研究, 2015, 35(1): 47-51.

基于简化基因组技术的云南蓝果树群体遗传分析

Population Genetic Analysis of Nyssa yunnanensis by Reduced-representation Sequencing Technique

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 11

编辑推荐

Metrics

本文评价