基于SSR标记的麻栎天然群体遗传多样性分析

吕锋; 解孝满; 韩彪; 鲁仪增; 王磊; 董昕; 王艳; 陆璐; 刘莉; 宗绍宁; 李文清

doi:10.12302/j.issn.1000-2006.202101025

吕锋, 解孝满, 韩彪, 鲁仪增, 王磊, 董昕, 王艳, 陆璐, 刘莉, 宗绍宁, 李文清

南京林业大学学报（自然科学版） ›› 2022, Vol. 46 ›› Issue (3) : 109-116.

PDF(1909 KB)

国家林草科技领军期刊
中国精品科技期刊
中国高校百佳科技期刊
江苏省新闻出版政府奖期刊奖
RCCSE林学权威期刊（A+）
CSCD核心期刊
Scopus数据库收录期刊
中文核心期刊
SCD核心期刊

作者加群：102861116

微信公众号：南京林业大学学报

高级检索

PDF(1909 KB)

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

研究论文

基于SSR标记的麻栎天然群体遗传多样性分析

吕锋 ¹ ,
解孝满 ¹^,² ,
韩彪 ² ,
鲁仪增 ² ,
王磊 ² ,
董昕 ² ,
王艳 ² ,
陆璐 ² ,
刘莉 ¹ ,
宗绍宁 ² ,
李文清 ¹^,²^,^*

作者信息 +

Genetic diversity analyses of Quercus acutissima based on SSR markers

LYU Feng ¹ ,
XIE Xiaoman ¹^,² ,
HAN Biao ² ,
LU Yizeng ² ,
WANG Lei ² ,
DONG Xin ² ,
WANG Yan ² ,
LU Lu ² ,
LIU Li ¹ ,
ZONG Shaoning ² ,
LI Wenqing ¹^,²^,^*

Author information +

文章历史 +

摘要

【目的】基于SSR分子标记对麻栎天然群体遗传多样性与遗传结构进行分析,为麻栎种质资源的保护和利用提供理论基础。【方法】以分布于我国7个省8个麻栎天然群体的150个个体为研究对象,利用筛选出的18对SSR引物,使用GenAIEx 6.51、MEGA 7.0.26和Structure 2.3.4等软件,采用AMOVA分析、主成分分析、聚类分析和Structure分析等方法,对麻栎群体及相应个体的遗传多样性、分子方差、遗传距离及遗传结构进行研究。【结果】18个SSR位点的等位基因数(N_a)平均为5.625个,有效等位基因数(N_e)平均为4.104个,Shannon指数(I)平均为1.338,观测杂合度(H_o)平均为0.895,期望杂合度(H_e)平均为0.645,筛选出的18对麻栎SSR引物具有丰富的多态性。8个麻栎群体的遗传距离为0.222~1.587,遗传一致度为0.205~0.801,遗传分化系数(F_st)平均为0.252,基因流(N_m)平均为1.140,固定指数(F)均为负值且平均为-0.441。麻栎群体的遗传多样性水平较高,遗传分化小,且群体间存在杂合子剩余;其98%的变异来自群体内, 2%的变异来自群体间。UPGMA聚类分析、Structure分析均将8个群体分为2组,二者的个体组成成分存在一定差异;主成分分析结果与上述基本一致,存在一定的交叉引种及基因渐渗现象。【结论】麻栎群体遗传多样性水平较高,遗传分化水平较低,遗传差异主要存在于群体内部,并呈现出沿“西南—东北”方向地理变异规律。因此,对麻栎天然群体的保护应该采取原地保护和异地繁育保存相结合的措施。

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 (N_a), effective alleles (N_e), the Shannon index (I) and observed heterozygosity (H_o) of the 18 SSR loci were 5.625, 4.104, 1.338 and 0.895, respectively. The average expected heterozygosity (H_e) 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 (F_st) was 0.252, the average gene flow (N_m) 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.

导出引用

吕锋, 解孝满, 韩彪, 等. 基于SSR标记的麻栎天然群体遗传多样性分析[J]. 南京林业大学学报（自然科学版）. 2022, 46(3): 109-116 https://doi.org/10.12302/j.issn.1000-2006.202101025

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

中图分类号： S722;S792.181

参考文献

列表( 原文顺序 | 文献年度倒序 | 文中引用次数倒序 ) 可视化分析

[1]

DENK

, 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

本文引用 [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.

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

本文引用 [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

本文引用 [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

本文引用 [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. 本文引用 [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

本文引用 [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. 本文引用 [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.

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

本文引用 [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

本文引用 [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. 本文引用 [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.

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

本文引用 [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

本文引用 [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

, YANG

, 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

本文引用 [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.

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

本文引用 [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 本文引用 [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

本文引用 [1]

[17]

PEAKALL

, 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

本文引用 [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 本文引用 [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 本文引用 [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. 本文引用 [1]

[22]

GAO

, LIU

Z L

, ZHAO

, 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

本文引用 [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

, ZHANG

, 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

本文引用 [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. 本文引用 [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 本文引用 [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 本文引用 [1]

[27]

文亚峰, UCHIYAMA

, 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

摘要

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

, 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

本文引用 [1]

[28]

JACQUEMYN

, HONNAY

, GALBUSERA

, 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

本文引用 [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 本文引用 [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. 本文引用 [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.

X G

, CHEN

, 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

本文引用 [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

, 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

本文引用 [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 本文引用 [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. 本文引用 [1]