Genetic diversity analyses of Quercus acutissima based on SSR markers

LYU Feng, XIE Xiaoman, HAN Biao, LU Yizeng, WANG Lei, DONG Xin, WANG Yan, LU Lu, LIU Li, ZONG Shaoning, LI Wenqing

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2022, Vol. 46 ›› Issue (3) : 109-116.

PDF(1909 KB)
南京林业大学学报（自然科学版）
PDF(1909 KB)
JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2022, Vol. 46 ›› Issue (3) : 109-116. DOI: 10.12302/j.issn.1000-2006.202101025

Genetic diversity analyses of Quercus acutissima based on SSR markers

Author information +
History +

Abstract

【Objective】To provide a theoretical basis for the protection and use of Quercus acutissima germplasm resources, 150 individuals of Q. acutissima from eight natural populations distributed in seven provinces of China were selected as the research objects. Their genetic diversity and genetic structure were analyzed based on SSR molecular markers.【Method】A total of 18 pairs of SSR primers were screened and used to study the genetic diversity, molecular variance, genetic distance and genetic structure of Q. acutissima populations and corresponding individuals using AMOVA analysis, principal component analysis, cluster analysis and structure analysis. Software such as GenAIEx 6.51, MEGA 7.0.26 and Structure 2.3.4 were used in the data analysis.【Result 】 The average number of alleles (Na), effective alleles (Ne), the Shannon index (I) and observed heterozygosity (Ho) of the 18 SSR loci were 5.625, 4.104, 1.338 and 0.895, respectively. The average expected heterozygosity (He) was 0.645, and the 18 pairs of SSR primers that were screened showed abundant polymorphism. The genetic distance of the eight populations ranged from 0.222 to 1.587. The genetic consistency ranged from 0.205 to 0.801, the average coefficient of genetic differentiation (Fst) was 0.252, the average gene flow (Nm) was 1.140, and the average fixed index (F) was negative and was -0.441. The genetic diversity of the populations was high, the genetic differentiation was small, and there was heterozygote residues among the populations. A total of 98% of the variation came from within the population and 2% came from among the populations. UPGMA cluster analysis and structure analysis divided the eight populations into two groups, respectively. There were some differences in the individual composition of the two groups. The results of the principal component analysis were consistent with other results. The phenomena of cross introduction and gene introgression was present between the groups.【Conclusion】 The level of genetic diversity of Q. acutissima population is high, and the level of genetic differentiation is low. The genetic difference mainly exists in the population and presents the law of geographical variations in a southwest to northeast direction. For the protection of this species, areas with high genetic diversity should be protected as a priority, and the protection strategy of in situ conservation should be combined with ex situ breeding and preservation is proposed.

Key words

Quercus acutissima / natural population / simple-sequence-repeat (SSR) / genetic diversity / genetic structure

Cite this article

EndNote

Ris (Procite)

Bibtex

Download Citations
LYU Feng , XIE Xiaoman , HAN Biao , et al . Genetic diversity analyses of Quercus acutissima based on SSR markers[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2022, 46(3): 109-116 https://doi.org/10.12302/j.issn.1000-2006.202101025

References

List( Publishing order | Descend order by publishing year | Descend order by cited within ) Chart analysis
[1]
DENK T, GRIMM G W, MANOS P S, et al. An updated infrageneric classification of the iaks:review of previous taxonomic schemes and synthesis of evolutionary patterns[C]// Oaks physiological ecology exploring functional diversity genus Quercus L. Switzerland: Springer International Publishing, 2017:13-38.DOI: 10.1007/978-3-319-69099-5_2.
https://doi.org/10.1007/978-3-319-69099-5_2
Cited in this article [1]
[2]
徐立安. 栎属群体与进化遗传研究进展[J]. 南京林业大学学报(自然科学版), 2002, 26(6):73-77.
XU L A. Developments in population and evolutionary genetics within the genus Quercus L[J]. J Nanjing For Univ (Nat Sci Ed), 2002, 26(6):73-77.DOI: 10.3969/j.issn.1000-2006.2002.06.019.
https://doi.org/10.3969/j.issn.1000-2006.2002.06.019
Cited in this article [2]
[3]
刘志龙, 虞木奎, 唐罗忠, 等. 麻栎资源研究进展及开发利用对策[J]. 中国林副特产, 2009(6):93-96.
LIU Z L, YU M K, TANG L Z, et al. Progress and utilization countermeasure of Quercus acutissima[J]. For Prod Speciality China, 2009(6):93-96.DOI: 10.3969/j.issn.1001-6902.2009.06.045.
https://doi.org/10.3969/j.issn.1001-6902.2009.06.045
Cited in this article [1]
[4]
袁久志, 孙启时. 麻栎叶的化学成分研究[J]. 沈阳药科大学学报, 1999, 16(1):60-62.
YUAN J Z, SUN Q S. A study on the chemical constituents of the leaves of Quercus acutissima Carruth[J]. J Shenyang Pharm Univ, 1999, 16(1):60-62.DOI: 10.3969/j.issn.1006-2858.1999.01.015.
https://doi.org/10.3969/j.issn.1006-2858.1999.01.015
Cited in this article [1]
[5]
赵丹. 麻栎组培和扦插繁殖技术研究[D]. 南京: 南京林业大学, 2010.
ZHAO D. The research of propagation technique of tissue culture and cutting of Quercus acutissima[D]. Nanjing: Nanjing Forestry University, 2010.
Cited in this article [1]
[6]
董章凯, 邢世岩, 王亚明, 等. 麻栎半同胞家系苗期特性分析[J]. 东北林业大学学报, 2011, 39(4):27-28,36.
DONG Z K, XING S Y, WANG Y M, et al. Seedling traits of Quercus acutissima from different half-sib families[J]. J Northeast For Univ, 2011, 39(4):27-28,36.DOI: 10.13759/j.cnki.dlxb.2011.04.036.
https://doi.org/10.13759/j.cnki.dlxb.2011.04.036
Cited in this article [1]
[7]
董玉峰. 麻栎群体内变异性和优良家系、无性系选择研究[D]. 泰安: 山东农业大学, 2008.
DONG Y F. Study on variation among Quercus acutissima population and selection of its families and clones[D]. Taian: Shandong Agricultural University, 2008.
Cited in this article [1]
[8]
叶青雷, 曾宪云. 麻栎SRAP-PCR体系优化与遗传多样性分析[J]. 生物技术, 2009, 19(3):24-27.
YE Q L, ZENG X Y. Optimization of SRAP-PCR system and genetic diversity analysis in Quercus acutissima Carr[J]. Biotechnology, 2009, 19(3):24-27.DOI: 10.16519/j.cnki.1004-311x.2009.03.028.
https://doi.org/10.16519/j.cnki.1004-311x.2009.03.028
Cited in this article [2]
[9]
彭礼琼, 金则新, 祁彩虹, 等. 麻栎ISSR-PCR扩增条件的优化[J]. 江苏农业科学, 2011, 39(4):30-32.
PENG L Q, JIN Z X, QI C H, et al. Optimization of ISSR-PCR amplification conditions of Quercus acutissima[J]. Jiangsu Agric Sci, 2011, 39(4):30-32.DOI: 10.15889/j.issn.1002-1302.2011.04.180.
https://doi.org/10.15889/j.issn.1002-1302.2011.04.180
Cited in this article [2]
[10]
孟旭. 麻栎的谱系地理学和遗传多样性研究[D]. 西安: 西北大学, 2017.
MENG X. Study on phylogeography and population genetics structure of Quercus acutissima Carr[D]. Xi’an: Northwest University, 2017.
Cited in this article [1]
[11]
徐小林, 徐立安, 黄敏仁, 等. 栓皮栎天然群体SSR遗传多样性研究[J]. 遗传, 2004, 26(5):683-688.
XU X L, XU L A, HUANG M R, et al. Genetic diversity of microsatellites(SSRs)of natural populations of Quercus variabilis[J]. Hereditas, 2004, 26(5):683-688.DOI: 10.16288/j.yczz.2004.05.023.
https://doi.org/10.16288/j.yczz.2004.05.023
Cited in this article [1]
[12]
秦英英, 韩海荣, 康峰峰, 等. 基于SSR标记的山西省辽东栎自然居群遗传多样性分析[J]. 北京林业大学学报, 2012, 34(2):61-65.
QIN Y Y, HAN H R, KANG F F, et al. Genetic diversity in natural populations of Quercus liaotungensis in Shanxi Province based on nuclear SSR markers[J]. J Beijing For Univ, 2012, 34(2):61-65.DOI: 10.13332/j.1000-1522.2012.02.022.
https://doi.org/10.13332/j.1000-1522.2012.02.022
Cited in this article [1]
[13]
王雁红, 俞琦, 杨佳, 等. 基于核微卫星的短柄枹栎居群遗传多样性和遗传结构[J]. 林业科学, 2015, 51(12):121-131.
WANG Y H, YU Q, YANG J, et al. Genetic diversity and population structure of Quercus serrata var.brevipetiolata revealed by nSSR markers[J]. Sci Silvae Sin, 2015, 51(12):121-131.DOI: 10.11707/j.1001-7488.20151215.
https://doi.org/10.11707/j.1001-7488.20151215
Cited in this article [1]
[14]
李文英, 顾万春, 周世良. 蒙古栎天然群体遗传多样性的AFLP分析[J]. 林业科学, 2003, 39(5):29-36.
LI W Y, GU W C, ZHOU S L. AFLP analysis on genetic diversity of Quercus mongolica populations[J]. Sci Silvae Sin, 2003, 39(5):29-36.DOI: 10.3321/j.issn:1001-7488.2003.05.005.
https://doi.org/10.3321/j.issn:1001-7488.2003.05.005
Cited in this article [1]
[15]
陈怀琼, 隋春, 魏建和. 植物SSR引物开发策略简述[J]. 分子植物育种, 2009, 7(4):845-851.
CHEN H Q, SUI C, WEI J H. Summary of strategies for developing SSR primer[J]. Mol Plant Breed, 2009, 7(4):845-851.DOI: 10.3969/mpb.007.000845.
https://doi.org/10.3969/mpb.007.000845
Cited in this article [1]
[16]
SULLIVAN A R, LIND J F, MCCLEARY T S, et al. Development and characterization of genomic and gene-based microsatellite markers in north American red oak species[J]. Plant Mol Biol Report, 2013, 31(1):231-239.DOI: 10.1007/s11105-012-0495-6.
https://doi.org/10.1007/s11105-012-0495-6
http://link.springer.com/10.1007/s11105-012-0495-6
Cited in this article [1]
[17]
PEAKALL R, SMOUSE P E. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research: an update[J]. Bioinformatics, 2012, 28(19): 2537-2539. DOI: 10.1093/bioinformatics/bts460.
https://doi.org/10.1093/bioinformatics/bts460
https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bts460
Cited in this article [1]
[18]
SLATKIN M, BARTON N H. A comparison of three indirect methods for estimating average levels of gene flow[J]. Evolution, 1989, 43(7):1349-1368. DOI: 10.2307/2409452.
https://doi.org/10.2307/2409452
https://onlinelibrary.wiley.com/toc/15585646/43/7
[19]
PRITCHARD J K, STEPHENS M, DONNELLY P. Inference of Population structure using multilocus genotype data[J]. Genetics, 2000, 155(4):9197-9201. DOI: 10.1093/genetics/155.2.945.
https://doi.org/10.1093/genetics/155.2.945
Cited in this article [1]
[20]
SUDHIR K, GLEN S, KOICHIRO T. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets[J]. Mo Biol & Evol, 2016(7):1870. DOI: 10.1093/molbev/msw054.
https://doi.org/10.1093/molbev/msw054
Cited in this article [1]
[21]
张昊. 中国栎属麻栎组三个近缘物种的群体遗传学和种群动态历史研究[D]. 西安: 西北大学, 2018.
ZHANG H. Study on population genetics and demographic history of the three closely related species of Section Aegilops occurred in China[D]. Xi’an: Northwest University, 2018.
Cited in this article [1]
[22]
GAO J, LIU Z L, ZHAO W, et al. Combined genotype and phenotype analyses reveal patterns of genomic adaptation to local environments in the subtropical oak Quercus acutissima[J]. J Syst Evol, 2021, 59(3):541-556.DOI: 10.1111/jse.12568.
https://doi.org/10.1111/jse.12568
https://onlinelibrary.wiley.com/toc/17596831/59/3
Cited in this article [1]
[23]
杨梅, 张敏, 师守国, 等. 武当木兰种群遗传结构的ISSR分析[J]. 林业科学, 2014, 50(1):76-81.
YANG M, ZHANG M, SHI S G, et al. Analysis of genetic structure of Magnolia sprengeri populations based on ISSR markers[J]. Sci Silvae Sin, 2014, 50(1):76-81.DOI: 10.11707/j.1001-7488.20140112.
https://doi.org/10.11707/j.1001-7488.20140112
Cited in this article [1]
[24]
巨苗苗. 基于SLAF-seq技术的高山栎组植物系统发育和群体遗传学研究[D]. 西安: 西北大学, 2020.
JU M M. Research on the phylogeny and population genetics of Quercus Sect. Heterobalanus based on the SLAF-seq[D]. Xi’an: Northwest University, 2020.
Cited in this article [1]
[25]
MURAWSKI D A, HAMRICK J L. The effect of the density of flowering individuals on the mating systems of nine tropical tree species[J]. Heredity, 1991, 67(2):167-174.DOI: 10.1038/hdy.1991.76.
https://doi.org/10.1038/hdy.1991.76
https://doi.org/10.1038/hdy.1991.76
Cited in this article [1]
[26]
MURAWSKI D A, HAMRICK J L. The mating system of Cavanillesia platanifolia under extremes of flowering-tree density: a test of predictions[J]. Biotropica, 1992, 24(1):99.DOI: 10.2307/2388478.
https://doi.org/10.2307/2388478
https://www.jstor.org/stable/2388478?origin=crossref
Cited in this article [1]
[27]
文亚峰, UCHIYAMA K, 韩文军, 等. 微卫星标记中的无效等位基因[J]. 生物多样性, 2013, 21(1):117-126.
https://doi.org/10.3724/SP.J.1003.2013.10133
Abstract
微卫星标记以其独有的优点广泛应用于遗传学研究, 但无效等位基因(null alleles)的存在与潜在影响是其最大缺陷之一, 在研究工作中并未得到足够重视。本文在综述国内外相关文献的基础上, 明确了微卫星无效等位基因的概念与特点, 对其可能的产生原因、频率估算方法、相关分析软件及其对群体遗传学、亲本分析等研究结果的影响进行述评, 以期对无效等位基因有较为全面、深入的了解。微卫星无效等位基因的产生与SSR侧翼序列的变异(点突变、插入或缺失)及引物结合位点有关, 其与同工酶标记中的无效等位基因有本质区别, 并非基因本身的自然属性。虽然微卫星无效等位基因具有普遍性、复杂性和隐匿性等特点, 但完全可以通过Hardy-Weinberg平衡检验、亲子代基因型分析和重新设计引物等方法认识、检测并估算其频率。无效等位基因会对遗传学相关研究结果造成显著影响, 如降低群体遗传多样性, 加大群体间遗传分化; 降低亲本分析排除率, 甚至可能造成亲本分析结果的错误与混乱。今后研究工作中, 我们应对无效等位基因予以足够重视并谨慎对待, 从标记位点选择、无效等位基因数据调整及重新设计引物分析等多个方面尽可能减少和避免其影响, 以获得最真实的分析结果。
WEN Y F, UCHIYAMA K, HAN W J, et al. Null alleles in microsatellite markers[J]. Biodivers Sci, 2013, 21(1):117-126.DOI: 10.3724/SP.J.1003.2013.10133.
https://doi.org/10.3724/SP.J.1003.2013.10133
http://pub.chinasciencejournal.com/article/getArticleRedirect.action?doiCode=10.3724/SP.J.1003.2013.10133
Cited in this article [1]
[28]
JACQUEMYN H, HONNAY O, GALBUSERA P, et al. Genetic structure of the forest herb Primula elatior in a changing landscape[J]. Mol Ecol, 2004, 13(1):211-219.DOI: 10.1046/j.1365-294x.2003.02033.x.
https://doi.org/10.1046/j.1365-294x.2003.02033.x.
http://doi.wiley.com/10.1046/j.1365-294X.2003.02033.x
Cited in this article [1]
[29]
KREMER A, PETIT R J. Gene diversity in natural populations of oak species[J]. Ann For Sci, 1993,50(Supplement):186s-202s.DOI: 10.1051/forest:19930717.
https://doi.org/10.1051/forest:19930717
Cited in this article [1]
[30]
HAMRICK J, GODT M. Allozyme diversity in plant species[C]// BROWN A,CLEGG M.Plant population genetics, breeding and genetic resources, Sunderland M A: Sinauer, 1990:43-63.
Cited in this article [1]
[31]
伊贤贵, 陈洁, 尤禄祥, 等. 山樱花群体遗传多样性的SSR分析[J]. 南京林业大学学报(自然科学版), 2018, 42(5):25-31.
YI X G, CHEN J, YOU L X, et al. Genetic divertsity of Cerasus serrulata populations assessed by SSR markers[J]. J Nanjing For Univ (Nat Sci Ed), 2018, 42(5):25-31.DOI: 10.3969/j.issn.1000-2006.201702036.
https://doi.org/10.3969/j.issn.1000-2006.201702036
Cited in this article [1]
[32]
臧明月, 李璇, 方炎明. 基于SSR标记的白栎天然居群遗传多样性分析[J]. 南京林业大学学报(自然科学版), 2021, 45(1):63-69.
ZANG M Y, LI X, FANG Y M. Genetic diversity analysis among natural populations of Quercus fabri based on SSR markers[J]. J Nanjing For Univ (Nat Sci Ed), 2021, 45(1):63-69.DOI: 10.12302/j.issn.1000-2006.202004049.
https://doi.org/10.12302/j.issn.1000-2006.202004049
Cited in this article [1]
[33]
SHI X M, WEN Q, CAO M, et al. Genetic diversity and structure of natural Quercus variabilis population in China as revealed by microsatellites markers[J]. Forests, 2017, 8(12):495.DOI: 10.3390/f8120495.
https://doi.org/10.3390/f8120495
http://www.mdpi.com/1999-4907/8/12/495
Cited in this article [1]
[34]
徐小林. 栓皮栎群体遗传结构研究[D]. 南京: 南京林业大学, 2003.
XU X L. Study on genetic structure of Quercus variabilis natural populations[D]. Nanjing: Nanjing Forestry University, 2003.
Cited in this article [1]
PDF(1909 KB)

Accesses

Citation

Detail
Sections
Recommended
The full text is translated into English by AI, aiming to facilitate reading and comprehension. The core content is subject to the explanation in Chinese.

Author

Reader

Reviewer

www.nldxb.njfu.edu.cn

Edited ＆ Published by Editorial Department of Nanjing Forestry University(Natural Sciences Edition)
Address： No.159 Longpan Road,Nanjing 210037 Jiangsu,P.R.China
E-mail ：xuebao@njfu.edu.cn , xuebao@njfu.com.cn
Telephone +86-25-85428247,85427076
Distributed by China International Book Trading Corporation P.O. Box 399, Beijing ,P.R. China

/

〈 〉