Development and genetic analysis of novel chloroplast microsatellite markers of Clematis

doi:10.3969/j.issn.1004-1524.2017.12.10

›› 2017, Vol. 29 ›› Issue (12): 2023-2031.DOI: 10.3969/j.issn.1004-1524.2017.12.10

• Horticultural Science • Previous Articles Next Articles

Development and genetic analysis of novel chloroplast microsatellite markers of Clematis

CHEN Wenchao, SU Wanhan, LIU Zhigao^*, JI Mengcheng

College of Landscape Architecture, Zhejiang A & F University, Lin'an 311300, China

Received:2017-05-12 Online:2017-12-20 Published:2018-01-08

Abstract

Abstract: The whole chloroplast genome sequence of Clematis fusca var. coreana from GeneBank database was analyzed, and 11 cpSSR primer pairs were designed based on that. In addition, the transferability of the 11 pairs of cpSSR primer in different species and cultivars of Clematis were studied. The results showed that 67 cpSSRs were distributed across the whole chloroplast genome, and most of them located in the area 1 088-41 445 bp and 50 135-127 217 bp, which generally consisted of a single base A/T. All of the 11 pairs of cpSSR primer could be successfully cross-amplified in different species and cultivars of Clematis, which indicated that the 11 primer pairs for cpSSR markers had good transferability in Clematis. The average number of alleles (Na) was 10.91, effective number of alleles (Ne) was 5.40, major allele frequency (MAF) was 0.31, and polymorphism information content (PIC) was 0.79. In addition, clustering result of UPGMA of 55 samples based on cpSSR data was discussed.

Key words: Clematis, cpSSR, primer development, allele

CLC Number:

S567.23⁺9

CHEN Wenchao, SU Wanhan, LIU Zhigao, JI Mengcheng. Development and genetic analysis of novel chloroplast microsatellite markers of Clematis[J]. , 2017, 29(12): 2023-2031.

References

[1] RAJENDRAKUMAR P, BISWAL A S, SRINIVASARAO K, et al. Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions[J]. Bioinformatics , 2007, 23(1): 1-4.
[2] TAMBARUSSI E V, MELOTTOPASSARIN D M, GONZALEZ S G, et al. In silico analysis of Simple Sequence Repeats from chloroplast genomes of Solanaceae species[J]. Crop Breeding & Applied Biotechnology , 2009, 9(4): 344-352.
[3] PROVAN J, SORANZO N, WILSON N J, et al. A low mutation rate for chloroplast microsatellites[J]. Genetics , 1999, 153(2): 943.
[4] BRYAN G J, MCNICOLL J, RAMSAY G, et al. Polymorphic simple sequence repeat markers in chloroplast genomes of Solanaceous plants[J]. Theoretical & Applied Genetics , 1999, 99(5): 859-867.
[5] HAO D C, GU X J, XIAO P G, et al. Chemical and biological research of Clematis medicinal resources [M]// Medicinal Plants , [S.l.]: [s.n.], 2013: 341-371.
[6] GREY W C. Clematis the genus [M]. Portland: Timber Press, 2000: 36-40.
[7] WANG W T, LI L Q. A new system of classification of the genus Clematis (Ranunculaceae)[J]. Acta Phytotaxonomica Sinica , 2005, 43: 431-488.
[8] 王文采. 毛茛科六新种[J]. 广西植物, 2016, 36(11): 1303-1311.
WANG W T. Six new species of Ranunculaceae from China[J]. Guihaia , 2016, 36(11): 1303-1311. (in Chinese with English abstract)
[9] 王文采. 迭部铁线莲, 甘肃毛茛科一新种[J]. 植物研究, 2015, 35(1): 1-3.
WANG W T. Clematis diebuensis, a new specis of Ranunculaceae from Gansu[J]. Bulletin of Botanical Research , 2015, 35(1): 1-3. (in Chinese with English abstract)
[10] WANG W T. A new species of the genus Clematis (Ranunculaceae) from Yunnan, China[J]. Plant Diversity and Resources , 2015, 37(2): 139-140.
[11] WANG W T. A revision of Clematis sect. Viticella (Ranunculaceae)[J]. Guihaia , 2007, 27(1): 1-28.
[12] 王文采. 云南毛茛科新分类群[J]. 云南植物研究, 2008, 30(5): 519-524.
WANG W T. New taxa of Ranunculaceae from Yunnan[J]. Acta Botanica Yunnanica , 2008, 30(5): 519-524. (in Chinese with English abstract)
[13] WANG W T, XIE L. A revision of Clematis sect. Tubulosae (Ranunculaceae)[J]. Acta Phytotaxonomica Sinica , 2007, 45(4): 425-457.
[14] GARDNER N, HOKANSON S C. Intersimple sequence repeat fingerprinting and genetic variation in a collection of Clematis cultivars and commercial germplasm[J]. Hortscience : A Publication of the American Society for Horticultural Science , 2005, 40(7): 1982-1987.
[15] TAO Y, WANG L Y, ROH M S. Confirmation of Clematis hybrids using molecular markers[J]. Scientia Horticulturae , 2010, 125(2): 136-145.
[16] SLOMBA J M, GAREY J R, ESSIG F B. The actin I intron: a phylogenetically informative DNA region in Clematis (Ranunculaceae)[J]. Sida Contributions to Botany , 2004, 21(2): 879-886.
[17] MIIKEDA O, KITA K, HANDA T, et al. Phylogenetic relationships of Clematis (Ranunculaceae) based on chloroplast and nuclear DNA sequences[J]. Botanical Journal of the Linnean Society , 2006, 152(2): 153-168.
[18] 蒋明,周英巧,李嵘嵘. 铁线莲属8种药用植物ITS序列分析[J]. 中草药, 2011, 42(9): 1802-1806.
JIANG M, ZHOU Y Q, LI R R. ITS sequence analysis of eight medicinal plants in Clematis L.[J]. Chinese Traditional and Herbal Drugs , 2011, 42(9): 1802-1806. (in Chinese with English abstract)
[19] 李骁, 王佩, 赵龙, 等. 铁线莲属蒙药材的rDNA-ITS序列分析[J]. 内蒙古医学院学报, 2012, 34(4): 325-330.
LI X, WANG P, ZHAO L, et al. rDNA-ITS sequence analysis of the traditional Mongolian medicinal plants in Clematis L.[J]. Journal of Inner Mongolia Medical College , 2012, 34(4): 325-330. (in Chinese with English abstract)
[20] SAITOU N, NEI M. The neighbor-joining method: a new method for reconstructing phylogenetic trees[J]. Molecular Biology & Evolution , 1987, 4(4): 406-425.
[21] 龚桂芝,洪棋斌,彭祝春,等. 枳属种质遗传多样性及其与近缘属植物亲缘关系的SSR和cpSSR分析[J]. 园艺学报, 2008, 35(12): 1742-1750.
GONG G Z, HONG Q B, PENG Z C, et al. Genetic diversity of Poncirus and it's phylogenetic relationship with relatives as revealed by nuclear and choroplast SSR[J]. Acta Horticulturae Sinica , 2008, 35(12): 1742-1750. (in Chinese with English abstract)
[22] 张扬勇, 方智远, 王庆彪, 等. 拟南芥叶绿体SSR引物在甘蓝上的应用[J]. 园艺学报, 2011, 38(3): 549-555.
ZHANG Y Y, FANG Z Y, WANG Q B, et al. Utility of Arabidopsis chloroplast simple sequence repeat (cpSSR) primers in cabbage ( Brassica oleracea L. var. capitata L.)[J]. Acta Horticulturae Sinica , 2011, 38(3): 549-555. (in Chinese with English abstract)
[23] 张君毅. 蝴蝶兰叶绿体DNA微卫星分析与标记开发[J]. 江西农业学报, 2011, 23(12): 31-33.
ZHANG J Y. Microsatellite analysis of chloroplast DNA in Phalaenopsis aphrodite subsp. formosana and it's marker exploitation[J]. Acta Agriculturae Jiangxi , 2011, 23(12): 31-33. (in Chinese with English abstract)
[24] ISHII T, MCCOUCH S R. Microsatellites and microsynteny in the chloroplast genomes of Oryza and eight other Gramineae species[J]. Theoretical and Applied Genetics , 2000, 100(8): 1257-1266.
[25] 胡建斌, 李建吾, 梁芳芳, 等. 黄瓜叶绿体基因组全序列微卫星分布特征与标记开发[J]. 细胞生物学杂志, 2009, 31(1): 69-74.
HU J B, LI J W, LIANG F F, et al. Characterization of microsatellites in complete chloroplast genome of cucumber ( Cucumis sativus ) and marker exploitation[J]. Chinese Journal of Cell Biology , 2009, 31(1): 69-74. (in Chinese with English abstract)
[26] 王化坤, 乔玉山, 娄晓鸣, 等. 拟南芥叶绿体DNA 全序列微卫星分布规律的分析[J].中国生物化学与分子生物学报, 2006, 22(10): 845-850.
WANG H K, QIAO Y S, LOU X M, et al. Distribution of microsatellite from complete sequence of Arabidopsis thaliana chloroplast DNA[J]. Chinese Journal of Biochemistry and Molecular Biology , 2006, 22(10): 845-850. (in Chinese with English abstract)
[27] 李博, 刘合霞. 叶绿体基因组微卫星标记(cpSSR)研究进展[J]. 安徽农业科学, 2012, 40(13): 7638-7639.
LI B, LIU H X. Research advances in chloroplast simple sequence repeat (cpSSR)[J]. Journal of Anhui Agriculture , 2012, 40(13): 7638-7639. (in Chinese with English abstract)
[28] 潘磊, 李依, 郭瑞, 等. 豇豆叶绿体微卫星标记的开发及其在近缘种的通用性研究[J]. 长江蔬菜, 2014 (6): 9-15.
PAN L, LI Y, GUO R, et al. Development of cpSSR markers in Vigna unguiculata and their transferability in related species[J]. Journal of Changjiang Vegetables , 2014 (6): 9-15. (in Chinese with English abstract)
[29] WOLFE K H, LI W H, SHARP P M. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs[J]. Proceedings of the National Academy of Sciences USA , 1987, 84(24): 9054-9058.
[30] DEGUILLOUX M F, DUMOLIN L S, et al. A set of primers for the amplification of chloroplast microsatellites in Quercus [J]. Molecular Ecology Notes , 2003, 3(1): 24-27.
[31] BOSTEIN D, WHITE R L, SKOLINICK M, et al. Construction of a genetic linkage map in a using restriction fragment length polymorphisms[J]. American Journal of Medical Genetics , 1980, 32(3): 314-331.

Development and genetic analysis of novel chloroplast microsatellite markers of Clematis

RichHTML

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 4

Recommended Articles

Metrics

Comments

[1]	YANG Yongjiang, WU Enyun, REN Wenwen, MA Boyan, GAO Chenghong, LI Hongxu, LIU Lixia, CAO Xin, ZANG Rongxin, YANG Jutian, ZHANG Li. SNP screening and protein function prediction of TLR2 gene in Chinese Holstein cattle [J]. , 2018, 30(8): 1321-1327.
[2]	NONG Weilun, BI Yingjie, LI Hongxu, ZHANG Li. H-FABP gene cloning, SNPs screening and bioinformatics analysis in Gansu black pig [J]. , 2018, 30(3): 378-385.
[3]	ZHU Xiao\\|li1，2，3， TAO Yue\\|zhi2， ZHOU Bo3，*. Distribution pattern of multiple alleles of rice blast resistance genes and its application in gene cloning#br# [J]. , 2015, 27(10): 1789-.
[4]	HUANG Yu-lei;LU Jia-xin;JIANG Ming;*;LI Wen-ping;ZHANG Xu-yu;ZOU Qing-chen. Callus induction and plant regeneration of Clematis henryi [J]. , 2011, 23(4): 0-735.