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

doi:10.7525/j.issn.1673-5102.2019.06.013

Abstract

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

CLC Number:

S727.28

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.

References

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.

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