Genetic diversity among wild populations of pomegranate in Tibet by SSR analyses

GE Dapeng, REN Yuan, ZHAO Jun, WANG Yuting, LIU Xueqing, YUAN Zhaohe

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2022, Vol. 46 ›› Issue (3) : 127-133.

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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 ›› 2022, Vol. 46 ›› Issue (3) : 127-133. DOI: 10.12302/j.issn.1000-2006.202105011

Genetic diversity among wild populations of pomegranate in Tibet by SSR analyses

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Abstract

【Objective】Wild pomegranate (Punica granatum) accessions were found in Tibet. To facilitate the conservation and use of wild pomegranate germplasm, the genetic diversity and population structure of three wild pomegranate populations from Tibet were studied.【Method】Primers for 13 SSR loci were used for PCR amplification of 42 wild individuals from from populations, and the amplified fragment length was determined using capillary electrophoresis. SSR data were analyzed using GenAlEx and Arlequin softwares.【Result】A total of 44 alleles were detected using 13 pairs of primers with an average of 3.835 alleles per locus. The mean values for the effective number of alleles (Ne), Shannon’s Information Index (I), expected heterozygosity (He) and the polymorphism information content (PIC) per locus were 1.971, 0.771, 0.481 and 0.393, respectively. The mean Ne, I and He of three wild populations were 1.867, 0.646 and 0.421, respectively. In the three populations of wild pomegranate accessions, the genetic diversity of the LZb population was higher than that of the CD and LZa populations. The AMOVA results showed that the percentage of genetic variation within populations was 88.43%, whereas the variance among populations was 11.57%. The Fst among the three wild populations was 0.116. Cluster analysis grouped the 42 accessions into three distinct clusters. Cluster analysis was found to be correlated with geographic origin. The most appropriate number of subpopulations was found to be K=4 using structure analysis.【Conclusion】A total of 13 SSR primers were found to be suitable for genetic diversity analysis of wild pomegranate accessions in Tibet. The genetic variance of wild pomegranate accessions in Tibet was mainly within populations. With having the highest genetic diversity and rich sampling sites, the LZb population merits should be a conservation priority.

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wild populations of pomegranate (Punica granatum) / SSR / genetic diversity / genetic structure / Tibet

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GE Dapeng , REN Yuan , ZHAO Jun , et al . Genetic diversity among wild populations of pomegranate in Tibet by SSR analyses[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2022, 46(3): 127-133 https://doi.org/10.12302/j.issn.1000-2006.202105011

References

List( Publishing order | Descend order by publishing year | Descend order by cited within ) Chart analysis
[1]
YUAN Z H, YIN Y L, QU J L, et al. Population genetic diversity in Chinese pomegranate (Punica granatum L.) cultivars revealed by fluorescent-AFLP markers[J]. J Genet Genomics, 2007, 34(12):1061-1071.DOI: 10.1016/S1673-8527(07)60121-0.
https://doi.org/10.1016/S1673-8527(07)60121-0
https://linkinghub.elsevier.com/retrieve/pii/S1673852707601210
Cited in this article [1]
[2]
赵丽华, 李名扬, 王先磊, 等. 石榴种质资源遗传多样性及亲缘关系的ISSR分析[J]. 果树学报, 2011, 28(1):66-71.
ZHAO L H, LI M Y, WANG X L, et al. Genetic diversity and genetic relationship of pomegranate (Punica granatum) germplasm evaluated by ISSR markers[J]. J Fruit Sci, 2011, 28(1):66-71.DOI: 10.13925/j.cnki.gsxb.2011.01.010.
https://doi.org/10.13925/j.cnki.gsxb.2011.01.010
Cited in this article [1]
[3]
张四普, 汪良驹, 曹尚银, 等. 23个石榴基因型遗传多样性的SRAP分析[J]. 果树学报, 2008, 25(5):655-660.
ZHANG S P, WANG L J, CAO S Y, et al. Analysis of genetic diversity of 23 pomegranate genotypes by SRAP[J]. J Fruit Sci, 2008, 25(5):655-660.
Cited in this article [1]
[4]
洪文娟, 郝兆祥, 刘康佳, 等. 基于石榴全基因组序列的SSR标记开发及鉴定[J]. 北京林业大学学报, 2019, 41(8):38-47.
HONG W J, HAO Z X, LIU K J, et al. Development and identification of SSR molecular markers based on whole genomic sequences of Punica granatum[J]. J Beijing For Univ, 2019, 41(8):38-47.DOI: 10.13332/j.1000-1522.20190167.
https://doi.org/10.13332/j.1000-1522.20190167
Cited in this article [2]
[5]
HASNAOUI N, BUONAMICI A, SEBASTIANI F, et al. Molecular genetic diversity of Punica granatum L.(pomegranate) as revealed by microsatellite DNA markers (SSR)[J]. Gene, 2012, 493(1):105-112.DOI: 10.1016/j.gene.2011.11.012.
https://doi.org/10.1016/j.gene.2011.11.012
https://linkinghub.elsevier.com/retrieve/pii/S0378111911006688
Cited in this article [1]
[6]
LUO X, CAO S Y, HAO Z X, et al. Analysis of genetic structure in a large sample of pomegranate (Punica granatum L.) using fluorescent SSR markers[J]. J Hortic Sci Biotechnol, 2018, 93(6):659-665.DOI: 10.1080/14620316.2018.1432994.
https://doi.org/10.1080/14620316.2018.1432994
https://www.tandfonline.com/doi/full/10.1080/14620316.2018.1432994
Cited in this article [1]
[7]
胡颂杰. 西藏农业概论[M]. 成都: 四川科学技术出版社, 1995:500-503.
HU S J. An introduction to agriculture of Tibet[M]. Chengdu: Sichuan Science and Technology Publishing House, 1995:500-503.
Cited in this article [1]
[8]
段盛烺, 宗学普, 刘效义, 等. 西藏果树资源考察初报[J]. 园艺学报, 1983, 10(4):217-224.
DUAN S L, ZONG X P, LIU X Y, et al. Preliminary report on the fruit germplasm resources in the autonomous region of Xizang[J]. Acta Hortic Sin, 1983, 10(4):217-224.
Cited in this article [1]
[9]
李乡旺, 毛品一, 尹秉高, 等. 西藏古树的初步研究[J]. 西南林学院学报, 1991, 11(2):134-138.
LI X W, MAO P Y, YIN B G, et al. A preliminary study on ancient trees of Tibet[J]. J Southwest For Coll, 1991, 11(2):134-138.
Cited in this article [1]
[10]
曹尚银, 李好先, 郝兆祥. 中国石榴地方品种图志[M]. 北京: 中国林业出版社, 2018.
CAO S Y, LI H X, HAO Z X. Chinese local varieties of pomegranate map[M]. Beijing: China Forestry Publishing House, 2018.
Cited in this article [1]
[11]
AZIZ S, FIRDOUS S, RAHMAN H, et al. Genetic diversity among wild pomegranate (Punica granatum) in Azad Jammu and Kashmir region of Pakistan[J]. Electron J Biotechnol, 2020, 46:50-54.DOI: 10.1016/j.ejbt.2020.06.002.
https://doi.org/10.1016/j.ejbt.2020.06.002
https://linkinghub.elsevier.com/retrieve/pii/S0717345820300269
Cited in this article [2]
[12]
KHADIVI A, MIRHEIDARI F, MORADI Y, et al. Morphological variability of wild pomegranate (Punica granatum L.) accessions from natural habitats in the Northern parts of Iran[J]. Sci Hortic, 2020, 264:109165.DOI: 10.1016/j.scienta.2019.109165.
https://doi.org/10.1016/j.scienta.2019.109165
https://linkinghub.elsevier.com/retrieve/pii/S0304423819310519
Cited in this article [1]
[13]
MAHAJAN R, JAVED A, KAPOOR N. Characterization of genetic diversity of wild pomegranate collected from Himachal Pradesh,India[J]. Ann Pl Sci, 2018, 7(2):2042.DOI: 10.21746/aps.2018.7.2.10.
https://doi.org/10.21746/aps.2018.7.2.10
Cited in this article [1]
[14]
ÇALIŞKAN O, BAYAZIT S, ÖKTEM M, et al. Evaluation of the genetic diversity of pomegranate accessions from Turkey using new microsatellite markers[J]. Turk J Agric For, 2017, 41:142-153.DOI: 10.3906/tar-1606-124.
https://doi.org/10.3906/tar-1606-124
https://journals.tubitak.gov.tr/agriculture/vol41/iss2/7
Cited in this article [1]
[15]
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]
[16]
EXCOFFIER L, LISCHER H E L. Arlequin suite ver 3.5:a new series of programs to perform population genetics analyses under Linux and Windows[J]. Mol Ecol Resour, 2010, 10(3):564-567.DOI: 10.1111/j.1755-0998.2010.02847.x.
https://doi.org/10.1111/j.1755-0998.2010.02847.x.
https://onlinelibrary.wiley.com/toc/17550998/10/3
Cited in this article [1]
[17]
LIU K J, MUSE S V. PowerMarker:an integrated analysis environment for genetic marker analysis[J]. Bioinformatics, 2005, 21(9):2128-2129.DOI: 10.1093/bioinformatics/bti282.
https://doi.org/10.1093/bioinformatics/bti282
https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bti282
Cited in this article [1]
[18]
LETUNIC I, BORK P. Interactive Tree Of Life (iTOL) v4:recent updates and new developments[J]. Nucleic Acids Res, 2019, 47(1):256-259.DOI: 10.1093/nar/gkz239.
https://doi.org/10.1093/nar/gkz239
Cited in this article [1]
[19]
PRITCHARD J K, STEPHENS M, DONNELLY P. Inference of population structure using multilocus genotype data[J]. Genetics, 2000, 155(2):945-959.DOI: 10.1093/genetics/155.2.945.
https://doi.org/10.1093/genetics/155.2.945
https://academic.oup.com/genetics/article/155/2/945/6048111
Cited in this article [1]
[20]
EARL D A, VONHOLDT B M. STRUCTURE HARVESTER:A website and program for visualizing Structure output and implementing the Evanno method[J]. Conserv Genet Resour, 2012, 4(2):359-361.DOI: 10.1007/s12686-011-9548-7.
https://doi.org/10.1007/s12686-011-9548-7
http://link.springer.com/10.1007/s12686-011-9548-7
Cited in this article [1]
[21]
JAKOBSSON M, ROSENBERG N A. CLUMPP:a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure[J]. Bioinformatics, 2007, 23(14):1801-1806.DOI: 10.1093/bioinformatics/btm233.
https://doi.org/10.1093/bioinformatics/btm233
https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btm233
Cited in this article [1]
[22]
ROSENBERG N A. Distruct:a program for the graphical display of population structure[J]. Mol Ecol Notes, 2004, 4(1):137-138.DOI: 10.1046/j.1471-8286.2003.00566.x.
https://doi.org/10.1046/j.1471-8286.2003.00566.x.
http://doi.wiley.com/10.1046/j.1471-8286.2003.00566.x
Cited in this article [1]
[23]
EVANNO G, REGNAUT S, GOUDET J. Detecting the number of clusters of individuals using the software sturcture: 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]
[24]
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.
Cited in this article [1]
[25]
陈芸, 王继莲, 丁晓丽, 等. 新疆石榴种质资源遗传多样性的SRAP分析[J]. 西北植物学报, 2016, 36(5):916-922.
CHEN Y, WANG J L, DING X L, et al. Genetic diversity of germplasm collection of pomegranate in Xinjiang using SRAP markers[J]. Acta Bot Boreali Occidentalia Sin, 2016, 36(5):916-922.DOI: 10.7606/j.issn.1000-4025.2016.05.0916.
https://doi.org/10.7606/j.issn.1000-4025.2016.05.0916
Cited in this article [1]
[26]
马丽, 王庆军, 罗华, 等. 枣庄石榴种质资源遗传多样性的ISSR分析[J]. 北方园艺, 2018(24):35-40.
MA L, WANG Q J, LUO H, et al. Genetic diversity analysis of pomegranate germplasm resources from Zaozhuang by ISSR markers[J]. North Hortic, 2018(24):35-40.DOI: 10.11937/bfyy.20181599.
https://doi.org/10.11937/bfyy.20181599
Cited in this article [1]
[27]
FRANKHAM R, BALLOU J D, BRISCOE D A. A primer of conservation genetics[M]. Cambridge: Cambridge University Press, 2004:52-75.
Cited in this article [1]
[28]
赵丽华. 中国石榴居群遗传结构的ISSR分析[J]. 北方园艺, 2011(10):103-107.
ZHAO L H. Population genetics structure of pomegranate Punica granatum L. revealed by ISSR markers in China[J]. North Hortic, 2011(10):103-107.
Cited in this article [1]
[29]
赵丽华, 李名扬, 王先磊. 川滇石榴品种遗传多样性及亲缘关系的AFLP分析[J]. 林业科学, 2010, 46(11):168-173.
ZHAO L H, LI M Y, WANG X L. Genetic diversity and genetic relationship of pomegranate(Punica granatum)in Sichuan and Yunnan evaluated by AFLP markers[J]. Sci Silvae Sin, 2010, 46(11):168-173.
Cited in this article [1]
[30]
王庆军, 罗华, 赵丽娜, 等. 24个山东石榴品种遗传多样性的ISSR分析[J]. 中国果树, 2018(2):18-22.
WANG Q J, LUO H, ZHAO L N, et al. Genetic diversity analysis of 24 pomegranate cultivars in Shandong by ISSR markers[J]. China Fruits, 2018(2):18-22.DOI: 10.16626/j.cnki.issn1000-8047.2018.02.005.
https://doi.org/10.16626/j.cnki.issn1000-8047.2018.02.005
Cited in this article [1]
[31]
李菁, 张小飞, 陈珏屹, 等. 基于ISSR分子标记的西藏杓兰种群遗传多样性分析[J]. 西北植物学报, 2020, 40(6):969-977.
LI J, ZHANG X F, CHEN J Y, et al. Genetic diversity of Cypripedium tibeticum populations revealed by ISSR analysis[J]. Acta Bot Boreali Occidentalia Sin, 2020, 40(6):969-977.DOI: 10.7606/j.issn.1000-4025.2020.06.0969.
https://doi.org/10.7606/j.issn.1000-4025.2020.06.0969
Cited in this article [1]
[32]
叶兴状, 张明珠, 刘益鹏, 等. 基于SRAP标记半枫荷天然种群的遗传多样性分析[J]. 植物资源与环境学报, 2021, 30(4):60-68.
YE X Z, ZHANG M Z, LIU Y P, et al. Analysis on genetic diversity of natural populations of Semiliquidambar cathayensis based on SRAP marker[J]. J Plant Resour Environ, 2021, 30(4):60-68. DOI: 10.3969 /j.issn.1674-7895.2021.04.07.
https://doi.org/10.3969 /j.issn.1674-7895.2021.04.07
Cited in this article [1]
[33]
刘硕, VERONIQUE D, 张玉军, 等. 普通杏和西伯利亚杏野生居群遗传多样性与其地理分布关系研究[J]. 植物遗传资源学报, 2020, 21(6):1527-1538.
LIU S, VERONIQUE D, ZHANG Y J, et al. Study on the relationship between genetic diversity and geographical distribution of wild common apricots and Siberian apricots[J]. J Plant Genet Resour, 2020, 21(6):1527-1538.DOI: 10.13430/j.cnki.jpgr.20200417001.
https://doi.org/10.13430/j.cnki.jpgr.20200417001
Cited in this article [1]
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