Genetic diversity and genetic structure of Tilia miqueliana population

WANG Huanli, YAN Lingjun, HUANG Xi, WANG Zhongwei, TANG Shijie

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2023, Vol. 47 ›› Issue (1) : 145-153.

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南京林业大学学报（自然科学版）
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JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2023, Vol. 47 ›› Issue (1) : 145-153. DOI: 10.12302/j.issn.1000-2006.202110049

Genetic diversity and genetic structure of Tilia miqueliana population

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Abstract

【Objective】 Tilia miqueliana is an important native tree species in Jiangsu Province, and its wild germplasm resources are particularly scarce. Exploration of the genetic diversity and the genetic structure of T. miqueliana in the field population provides the scientific basis for its resource protection, variety breeding and genetic improvement.【Method】 Fifteen polymorphic EST-SSR primers were used to analyze the genetic diversity and population structure of 93 individuals from five natural populations of T. miqueliana located on Baohua Mountain (Jiangsu Province, P1), Niushou Mountain (Jiangsu Province, P2), Huangcangyu Nature Reserve (Anhui Province, P3), Shu Mountain (Anhui Province, P4) and Tiantai Mountain (Zhejiang Province, P5). 【Result】 (1) A total of 96 alleles (A) were detected using 15 EST-SSR primer pairs. The average allelic richness at a locus was 6.4. The total number of tetraploid genotypic richness (G) and tetraploid specific genotypes (Gi) were 441 and 251, respectively. The average of the specific genotype ratio (R1) and the germplasm identification rate (R2) were 45.73% and 17.99%, respectively. (2) In the five populations, the mean number of alleles per locus (Aloc) and the tetraploid genotypic richness (Gloc) were 5.50 ± 2.43 and 9.41 ± 4.29, respectively. The mean observed heterozygosity (Ho) and the mean expected heterozygosity (He) were 0.61 ± 1.43 and 0.62 ± 0.14, respectively. Based on the values for Gloc and He, the P1 and P3 populations were identified as having high genetic diversity. (3) The genetic differentiation coefficient (Gst) was 0.030, indicating a low genetic differentiation among the five populations. Analysis of molecular variance (AMOVA) showed that the variation in genetic diversity predominantly came from within the population (96%). (4) Cluster analysis and genetic structure analysis by structure showed that the five tested populations could be divided into two groups (Group1. P1, P2 and P5; Group2. P3 and P4). The Mantel test results showed that there was no significant correlation between the genetic differentiation and the geographic distance. 【Conclusion】 High levels of genetic diversity were found within the five populations of T. miqueliana, among which Baohua Mountain population and Huangcangyu Nature Reserve population showed considerably higher genetic diversity than that the other populations showed. Combined with the results from the clustering and genetic structure analysis, we can infer that population expansion may have been centered on these two populations and migrated to other regions through human activities. There was no pronounced genetic differentiation among the different geographic populations, which may be due to the long life of individuals, the lack of natural regeneration of populations, and seed dispersal among populations through human activities. Therefore, we propose to establish isolation areas, identify priority populations for protection, increase plant outcrossing, and use artificial breeding and germplasm regeneration to protect the wild populations.

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Tilia miqueliana / SSR marker / genetic structure / genetic diversity

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WANG Huanli , YAN Lingjun , HUANG Xi , et al . Genetic diversity and genetic structure of Tilia miqueliana population[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2023, 47(1): 145-153 https://doi.org/10.12302/j.issn.1000-2006.202110049

References

List( Publishing order | Descend order by publishing year | Descend order by cited within ) Chart analysis
[1]
史锋厚. 椴树属分子系统学与南京椴保育遗传学研究[D]. 南京: 南京林业大学, 2009.
SHI F H. Study on molecular phylogenetic of genus Tilia L. and conservation genetics of Tilia miqueliana Maxim[D]. Nanjing: Nanjing Forestry University, 2009.
Cited in this article [1]
[2]
汤诗杰, 郑玉红, 汤庚国. 基于ISSR标记的5个南京椴种群的遗传多样性分析[J]. 南京林业大学学报(自然科学版), 2009, 33(5):51-54.
TANG S J, ZHENG Y H, TANG G G. Study on genetic diversity of five populations of Tilia miqueliana Maxim.by using ISSR marker[J]. J Nanjing For Univ(Nat Sci Ed), 2009, 33(5):51-54.
Cited in this article [3]
[3]
汤诗杰, 郑玉红, 汤庚国. 基于RAPD标记的5个南京椴居群遗传多样性分析[J]. 植物资源与环境学报, 2013, 22(3):70-74.
TANG S J, ZHENG Y H, TANG G G. Genetic diversity analysis on five populations of Tilia miqueliana based on RAPD marker[J]. J Plant Resour Environ, 2013, 22(3):70-74.DOI:10.3969/j.issn.1674-7895.2013.03.11.
https://doi.org/10.3969/j.issn.1674-7895.2013.03.11
Cited in this article [3]
[4]
PONCET V, RONDEAU M, TRANCHANT C, et al. SSR mining in coffee tree EST databases:potential use of EST-SSRs as markers for the Coffea genus[J]. Mol Genet Genomics, 2006, 276(5):436-449.DOI:10.1007/s00438-006-0153-5.
https://doi.org/10.1007/s00438-006-0153-5
http://link.springer.com/10.1007/s00438-006-0153-5
Cited in this article [1]
[5]
杨梦婷, 黄洲, 干建平, 等. SSR分子标记的研究进展[J]. 杭州师范大学学报(自然科学版), 2019, 18(4):429-436.
YANG M T, HUANG Z, GAN J P, et al. Research progress of SSR molecular markers[J]. J Hangzhou Norm Univ(Nat Sci Ed), 2019, 18(4):429-436.DOI:10.3969/j.issn.1674-232X.2019.04.013.
https://doi.org/10.3969/j.issn.1674-232X.2019.04.013
Cited in this article [1]
[6]
陈思, 吴广文, 吴建忠, 等. 植物EST-SSR研究进展[J]. 黑龙江农业科学, 2018(12):148-152.
CHEN S, WU G W, WU J Z, et al. Research progress of EST-SSR in plants[J]. Heilongjiang Agric Sci, 2018(12):148-152.DOI:10.11942/j.issn1002-2767.2018.12.0148.
https://doi.org/10.11942/j.issn1002-2767.2018.12.0148
Cited in this article [1]
[7]
LI Y C, KOROL A B, FAHIMA T, et al. Microsatellites within genes:structure,function,and evolution[J]. Mol Biol Evol, 2004, 21(6):991-1007.DOI:10.1093/molbev/msh073.
https://doi.org/10.1093/molbev/msh073
https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msh073
Cited in this article [1]
[8]
FAVILLE M J, VECCHIES A C, SCHREIBER M, et al. Functionally associated molecular genetic marker map construction in perennial ryegrass(Lolium perenne L.)[J]. Theor Appl Genet, 2004, 110(1):12-32.DOI:10.1007/s00122-004-1785-7.
https://doi.org/10.1111/j.1601-5223.2001.00145.x
http://link.springer.com/10.1007/s00122-004-1785-7
Cited in this article [1]
[9]
KOTA R, VARSHNEY R K, THIEL T, et al. Generation and comparison of EST-derived SSRs and SNPs in barley(Hordeum vulgare L.)[J]. Hereditas, 2001, 135(2/3):145-151.DOI:10.1111/j.1601-5223.2001.00145.x.
Cited in this article [1]
[10]
杨翠, 刘凯, 谈红艳, 等. 贵州地方红米品种的遗传多样性分析[J]. 种子, 2021, 40(3):15-22.
YANG C, LIU K, TAN H Y, et al. Genetic diversity analysis of local red rice varieties in Guizhou[J]. Seed, 2021, 40(3):15-22.DOI:10.16590/j.cnki.1001-4705.2021.03.015.
https://doi.org/10.16590/j.cnki.1001-4705.2021.03.015
Cited in this article [1]
[11]
刘红云, 周强, 李淑梅, 等. 豫南地区野生大豆种质资源的SSR遗传多样性分析[J]. 种子, 2021, 40(3):64-67.
LIU H Y, ZHOU Q, LI S M, et al. Genetic diversity analysis of wild soybean germplasms in southern He’nan by SSR markers[J]. Seed, 2021, 40(3):64-67.DOI:10.16590/j.cnki.1001-4705.2021.03.064.
https://doi.org/10.16590/j.cnki.1001-4705.2021.03.064
Cited in this article [1]
[12]
彭丽娟, 牟柯澴, 张健伟, 等. 基于SSR及ISSR标记的菜豆遗传多样性分析[J] .分子植物育种, 2022, 20(21):7161-7173.
PENG L J, MOU K X, ZHANG J W, et al. Genetic diversity analysis of Phaseolus Vulgaris based on SSR and ISSR markers[J]. Mol Plant Breed, 2022, 220(21):7161-7173. DOI:10.13271/j.mpb.020.007161.
https://doi.org/10.13271/j.mpb.020.007161
Cited in this article [1]
[13]
陈春艳, 马杰, 屈雯, 等. 基于转录组序列的胡萝卜EST-SSR标记开发及遗传多样性分析[J/OL]. 分子植物育种, 2021:1-12 [2021-03-18].
CHEN C Y, MA J, QU W, et al. Development of EST-SSR markers based on transcriptome sequencing and genetic diversity analysis of carrot[J/OL]. Mol Plant Breed, 2021:1-12 [2021-03-18].
http://kns.cnki.net/kcms/detail/46.1068.S.20210318.1142.016.html
Cited in this article [1]
[14]
FINESCHI S, SALVINI D, TAURCHINI D, et al. Chloroplast DNA variation of Tilia cordata(Tiliaceae)[J]. Can J For Res, 2003, 33(12):2503-2508.DOI:10.1139/x03-179.
https://doi.org/10.1139/x03-179
http://www.nrcresearchpress.com/doi/10.1139/x03-179
Cited in this article [1]
[15]
LIESEBACH H, SINKÓ Z. A contribution to the systematics of the genus Tilia with respect to some hybrids by RAPD analysis[J]. Dendrobiology, 2008, 59:13-22.DOI:10.1007/978-1-4020-8476-8_13.
https://doi.org/10.1007/978-1-4020-8476-8_13
Cited in this article [1]
[16]
FILIZ E, BIRBILENER S, OZYIGIT I I, et al. Assessment of genetic variations of silver lime(Tilia tomentosa Moench.) by RAPD markers in urban and forest ecosystems[J]. Biotechnol Biotechnol Equip, 2015, 29(4):631-636.DOI:10.1080/13102818.2015.1042049.
https://doi.org/10.1080/13102818.2015.1042049
http://www.tandfonline.com/doi/full/10.1080/13102818.2015.1042049
Cited in this article [1]
[17]
COLAGAR A H, YUSEFI M, ZAREI M, et al. Assessment of genetic diversity of Tilia rubra DC. by RAPD analysis in the Hyrcanian forests,north of Iran[J]. Pol J Ecol, 2013, 61(2):341-348.DOI:10.3354/mesp10346.
https://doi.org/10.3354/mesp10346
Cited in this article [1]
[18]
王欢利, 汤诗杰, 王仲伟, 等. 基于转录组的椴树属EST-SSR引物及其筛选方法和应用: 201911380003.1[P]. 2020-10-23.
WANG H L, TANG S J, WANG Z W, et al. Screening methods and applications of EST-SSR primers in Tilia miqueliana based on transcriptome:201911380003.1[P]. 2020-10-23.
Cited in this article [1]
[19]
ESSELINK G D, NYBOM H, VOSMAN B. Assignment of allelic configuration in polyploids using the MAC-PR(microsatellite DNA allele counting-peak ratios) method[J]. Theor Appl Genet, 2004, 109(2):402-408.DOI:10.1007/s00122-004-1645-5.
https://doi.org/10.1007/s00122-004-1645-5
http://link.springer.com/10.1007/s00122-004-1645-5
Cited in this article [1]
[20]
THRALL P H, YOUNG A. AUTOTET:a program for analysis of autotetraploid genotypic data[J]. J Hered, 2000, 91(4):348-349.DOI:10.1093/jhered/91.4.348.
https://doi.org/10.1093/jhered/91.4.348
https://academic.oup.com/jhered/article-lookup/doi/10.1093/jhered/91.4.348
Cited in this article [1]
[21]
梁玉琴. 河南省柿种质资源遗传多样性研究[D]. 北京: 中国林业科学研究院, 2015.
LIANG Y Q. Study on genetic diversity of persimmon germplasms in Henan Province[D]. Beijing: Chinese Academy of Forestry, 2015.
Cited in this article [1]
[22]
范英明, 张登荣, 于大德, 等. 河北省华北落叶松天然群体遗传多样性分析[J]. 植物遗传资源学报, 2014, 15(3):465-471.
FAN Y M, ZHANG D R, YU D D, et al. Genetic diversity and population structure of Larix principis-rupprechtii Mayr. in Hebei province[J]. J Plant Genet Resour, 2014, 15(3):465-471.DOI:10.13430/j.cnki.jpgr.2014.03.002.
https://doi.org/10.13430/j.cnki.jpgr.2014.03.002
Cited in this article [1]
[23]
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/28/19/2537/288671
Cited in this article [2]
[24]
ROHLF F J, JENSEN R J. NTSYS-pc[J]. Q Rev Biol, 1989, 64(2):250-252.DOI: 10.1086/416356.
https://doi.org/10.1086/416356
Cited in this article [1]
[25]
GOWER J C. Some distance properties of latent root and vector methods used in multivariate analysis[J]. Biometrika, 1966, 53(3/4):325-338.DOI:10.1093/biomet/53.3-4.325.
https://doi.org/10.1093/biomet/53.3-4.325
https://academic.oup.com/biomet/article-lookup/doi/10.1093/biomet/53.3-4.325
Cited in this article [1]
[26]
EVANNO G, REGNAUT S, GOUDET J. Detecting the number of clusters of individuals using the software STRUCTURE:a simulation study[J]. Mol Ecol, 2005, 14(8):2611-2620.DOI:10.1111/j.1365-294X.2005.02553.x.
https://doi.org/10.1111/j.1365-294X.2005.02553.x
http://www.blackwell-synergy.com/toc/mec/14/8
Cited in this article [1]
[27]
BOTSTEIN D, WHITE R L, SKOLNICK M, et al. Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J]. Am J Hum Genet, 1980, 32(3):314-331.DOI:10.1016/0165-1161(81)90274-0.
https://doi.org/10.1016/0165-1161(81)90274-0.
https://www.ncbi.nlm.nih.gov/pubmed/6247908
Cited in this article [1] Abstract
We describe a new basis for the construction of a genetic linkage map of the human genome. The basic principle of the mapping scheme is to develop, by recombinant DNA techniques, random single-copy DNA probes capable of detecting DNA sequence polymorphisms, when hybridized to restriction digests of an individual's DNA. Each of these probes will define a locus. Loci can be expanded or contracted to include more or less polymorphism by further application of recombinant DNA technology. Suitably polymorphic loci can be tested for linkage relationships in human pedigrees by established methods; and loci can be arranged into linkage groups to form a true genetic map of "DNA marker loci." Pedigrees in which inherited traits are known to be segregating can then be analyzed, making possible the mapping of the gene(s) responsible for the trait with respect to the DNA marker loci, without requiring direct access to a specified gene's DNA. For inherited diseases mapped in this way, linked DNA marker loci can be used predictively for genetic counseling.
[28]
WRIGHT S. The interpretation of population structure by F-statistics with special regard to systems of mating[J]. Evolution, 1965, 19(3):395-420.DOI:10.1111/j.1558-5646.1965.tb01731.x.
https://doi.org/10.1111/j.1558-5646.1965.tb01731.x
https://www.jstor.org/stable/2406450?origin=crossref
Cited in this article [1]
[29]
HAO L, ZHAI Y G, ZHANG G S, et al. Efficient fingerprinting of the tetraploid Salix psammophila using SSR markers[J]. Forests, 2020, 11(2):176.DOI:10.3390/f11020176.
https://doi.org/10.3390/f11020176
https://www.mdpi.com/1999-4907/11/2/176
Cited in this article [1]
[30]
HAMRICK J L, GODT M J W, SHERMAN-BROYLES S L. Factors influencing levels of genetic diversity in woody plant species[J]. New Forest, 1992, 6:95-124.DOI:10.1007/BF00120641.
https://doi.org/10.1007/BF00120641
http://link.springer.com/10.1007/BF00120641
Cited in this article [1]
[31]
汤诗杰, 汤庚国. 安徽皇藏峪自然保护区南京椴种群结构分析[J]. 植物资源与环境学报, 2007, 16(3):58-63.
TANG S J, TANG G G. Analysis on structure of Tilia miqueliana population in Huangcangyu Nature Reserve of Anhui Province[J]. J Plant Resour Environ, 2007, 16(3):58-63.DOI:10.3969/j.issn.1674-7895.2007.03.011.
https://doi.org/10.3969/j.issn.1674-7895.2007.03.011
Cited in this article [1]
[32]
汤诗杰, 彭志, 汤庚国. 宝华山南京椴群落的特征分析[J]. 扬州大学学报(农业与生命科学版), 2008, 29(1):90-94.
TANG S J, PENG Z, TANG G G. A community characteristics analysis on Tilia miqueliana in Baohua Mt.[J]. J Yangzhou Univ(Agric Life Sci Ed), 2008, 29(1):90-94.DOI:10.16872/j.cnki.1671-4652.2008.01.022.
https://doi.org/10.16872/j.cnki.1671-4652.2008.01.022
Cited in this article [1]
[33]
KOLE C. Wild crop relatives:genomic and breeding resources[M]. Berlin:Springer, 2011.DOI:10.1007/978-3-642-21250-5.
https://doi.org/10.1007/978-3-642-21250-5.
Cited in this article [1]
[34]
程庭峰, 王环, 周党卫, 等. 秦艽的遗传多样性研究进展[J]. 中草药, 2019, 50(15):3720-3728.
CHENG T F, WANG H, ZHOU D W, et al. Research advance of genetic diversity of Chinese traditional herb Gentianae macrophyllae Radix[J]. Chin Tradit herb drugs, 2019, 50(15):3720-3728.DOI:10.7501/j.issn.0253-2670.2019.15.031.
https://doi.org/10.7501/j.issn.0253-2670.2019.15.031
Cited in this article [1]
[35]
李乃伟, 束晓春, 何树兰, 等. 南方红豆杉的ISSR遗传多样性分析[J]. 西北植物学报, 2010, 30(12):2536-2541.
LI N W, SHU X C, HE S L, et al. ISSR analysis of genetic diversity of Taxus chinensis var.mairei[J]. Acta Bot Boreali Occident Sin, 2010, 30(12):2536-2541.
Cited in this article [1]
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