Development of EST-SSR and genomic-SSR in Chinese fir

doi:10.3969/j.issn.1000-2006.2014.01.002

XU Yang, CHEN Jinhui, LI Ya, HONG Zhou, WANG Ying, ZHAO Yaqi, WANG Xinmin, SHI Jisen

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2014, Vol. 38 ›› Issue (01) : 9-14.

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JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2014, Vol. 38 ›› Issue (01) : 9-14. DOI: 10.3969/j.issn.1000-2006.2014.01.002

Development of EST-SSR and genomic-SSR in Chinese fir

XU Yang, CHEN Jinhui, LI Ya, HONG Zhou, WANG Ying, ZHAO Yaqi, WANG Xinmin, SHI Jisen^*

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Abstract

In order to develop SSR primers of Cunninghamia lanceolata(Lamb.)Hook based on EST-SSR and genomic SSR, 292 non-repeated Chinese fir EST-sequences were assembled by removing low-quality and redundant fragments depend upon 444 ESTs sequences from NCBI Public database, and 143 genome-sequences were assembled by removing redundant fragments in 1 142 genome sequences. All those non-redundant sequences of Cunninghamia lanceolata(Lamb.)Hook was searched for mono-to hexa-nucleotide simple sequence repeats(SSR or microsatellite)with software MISA, and the type,size and frequency of these SSRs were determined. Totally, There were 109 SSRs to be picked out among EST-sequences, the distribution density was 964.58 SSR/Mbp; and 39 SSRs were found in genome sequences, accounting for the higher density of 1 037.24 SSR/Mbp. In both Genomic and EST sequence library, the Hexanucleotides repeats, especially AT-rich repeat, was the most repeated type, and the AGC/CTG was the most trinucleotides repeats, The 37 and 95 pairs of SSR primers were designed based on EST library and Genomic by Primer 3.0, respectively. Ten EST-SSR primers and eight pairs of gSSR primers were selected randomly to perform PCR amplification with 12 individuals. There were four pairs of primers showed polymorphism both in EST-SSR and gSSR, with polymorphic rate of 40% and 50%, respectively. Twenty-five polymorphic alleles were amplified by 8 SSR primer pairs, which showed an average 3.125 polymorphism alleles for each primer, the average effective alleles(Na)2.399 5, average PIC 0.519 1, average Hot 0.307 4. There were more polymorphism alleles from gSSR markers than EST-SSR among groups. More allelic loci were amplified with four pairs of primer from gSSR than the four pairs of primer from EST-SSR, and the former had higher PIC value also.

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XU Yang, CHEN Jinhui, LI Ya, HONG Zhou, WANG Ying, ZHAO Yaqi, WANG Xinmin, SHI Jisen. Development of EST-SSR and genomic-SSR in Chinese fir[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2014, 38(01): 9-14 https://doi.org/10.3969/j.issn.1000-2006.2014.01.002

References

[1] 叶志宏, 施季森, 翁玉榛, 等. 杉木地理种源变异模式[J]. 南京林业大学学报, 1990, 14(4):15-22.Ye Z H, Shi J S, Weng Y Z, et al. The geographical provenance variation pattern of Cunninghamia lanceolata[J]. Journal of Nanjing Forestry University, 1990, 14(4):15-22.
[2] 施季森, 叶志宏, 翁玉榛, 等. 杉木生长与材性联合遗传改良研究[J].南京林业大学学报, 1993, 17(1):1-8.Shi J S, Ye Z H, WengY Z, et al. Research on the joint genetic improvement of growth and wood properties in Chinese fir(Cunninghamia lanceolata(Lamb.)Hook.)[J]. Journal of Nanjing Forestry University, 1993, 17(1):1-8.
[3] 施季森. 福建省杉木遗传改良现状与发展技术对策[J]. 福建林业科技, 1994,21(3):28-31.Shi J S. The present situation of Chinese fir genetic improvement in Fujian province and the technical countermeasures of developing it[J]. Journal of Fujian Forestry Science and Technology, 1994,21(3):28-31.
[4] 郑仁华, 施季森. 福建省杉木良种繁育现状与对策[J]. 林业科技开发, 2004, 18(2):3-7.Zheng R H, Shi J S. The present situation and the counter measures of Cunninghamia lanceolata breeding in Fujian province[J]. China Forestry Science and Technology, 2004,18(2):3-7.
[5] 郑仁华, 施季森. 福建杉木良种繁育现状与展望[R].南宁:第三届南方林木育种研讨会, 2006.
[6] 施季森. 林木生物技术育种未来10年若干科学问题展望[J]. 南京林业大学学报:自然科学版, 2012, 36(5):1-13.Shi J S. Prospection on some topics of forest genetic improvement through modern biotechnology for the next-ten-years in China[J]. Journal of Nanjing Forestry University:Natural Sciences Edition. 2012, 36(5):1-13.
[7] Morgante M, Olivieri M. PCR-amplified microsatellites as markers in plant genetics[J]. Plant J, 1993, 3(1):175-182.
[8] Varshney R K, Graner A, Sorrells M E. Genic microsatellite markers in plants:features and applications[J]. Trends in Biotechnology, 2005, 23(1):48-55.
[9] Prakash C Sharma, Grover A, Gunter K. Mining microsatellites in eukaryotic genomes[J]. Trends in Biotechnology, 2007, 25(11):490-498.
[10] Wang G F, Gao Y, Yang L, et al. Identification and analysis of differentially expressed genes in differentiating xylem of Chinese fir(Cunninghamia lanceolata)by suppression subtractive hybridization[J]. Genome, 2007, 50(12):1141-1155
[11] 李亚. 杉木CpG文库的构建及全基因组DNA甲基化检测[D]. 南京:南京林业大学, 2011. Li Y. The construction of CpG library and genome-wide DNA methylation detection in Chinese fir[D]. Nanjing:Nanjing Forestry University, 2011.
[12] Doyle J. DNA protocols for plants CTAB total DNA isolation[C]//Hewitt G M, Johnston A. Molecular Techniques in Taxonomy. Berlin:Springer-Verlag, 1991.
[13] Yeh F C, Boyle T. Population genetic analysis of co-dominant and dominant markers and quantitative traits[J]. Belgian Journal of Botany, 1997,129:57
[14] Kimura M, Crow J F. The number of alleles that can be maintained in a finite population[J]. Genetics, 1964, 49:725-738.
[15] Yin T M, Zhang X Y, Gunter L E, et al. Microsatellite primer resource for Populus developed from the mapped sequence scaffolds of the Nisqually-1 genome[J]. New Phytologist, 2009,181:498-503
[16] Cavagnaro P F, Senalik D A, Yang L M, et al. Genome-wide characterization of simple sequence repeats in cucumber(Cucumis sativus L.)[J]. BMC Genomics, 2010, 11(1):569.
[17] Echt C S, Saha S, Deemer D L, et al. Microsatellite DNA in genomic survey sequences and UniGenes of loblolly pine[J]. Tree Genetics & Genomes, 2011, 7(4):773-780.
[18] Berube Y, Zhuang J, Rungis D, et al. Characterization of EST SSRs in loblolly pine and spruce[J]. Tree Genetics & Genomes, 2007, 3(3):251-259.
[19] 樊洪泓, 李廷春, 李正鹏, 等. 银杏EST序列中微卫星的分布特征[J]. 基因组学与应用生物学, 2009, 5(5):869-873.Fan H H, Li T C, Li Z P, et al. Characteristics of microsatellite in ginkgo EST sequences[J]. Genomics and Applied Biology, 2009, 5(5):869-873.
[20] Cho Y G, Ishii, Temnykh S, et al. Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice(Oryza sativa)[J]. Theor Appl Genet, 2000, 100(7):13-722.
[21] Eujayl I, Sorrells M, Baum M, et al. Assessment of genotypic variation among cultivated durum wheat based on EST-SSRS and genomic SSRS[J]. Euphytica, 2001, 119(1-2):39-43.
[22] Tuskan G A, Gunter L E, Yang, et al. Characterization of microsatellites revealed by genomic sequencing of Populus trichocarpa [J]. Canadian Journal of Forest Research-Revue Canadienne De Recherche Forestiere, 2004, 34(1):85-93.
[23] Dutta S, Kumawat G, Singh B P, et al. Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea[Cajanus cajan (L.)Millspaugh][J]. BMC Plant Biol, 2011, 11(1):17.
[24] Heuertz M, De Paoli E, Kallman T, et al. Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce[Picea abies(L.)Karst][J]. Genetics, 2006, 174(4):2095-2105.
[25] Li X G, Wu H X, Southerton S G. Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants[J]. BMC Evolutionary Biology, 2010, 10:190.
[26] Nystedt B, Street N R, Wetterbom A, et al. The Norway spruce genome sequence and conifer genome evolution[J]. Nature, 2013, 497(7451):579-84.
[27] Buschiazzo E, Ritland C, Bohlmann J, et al. Slow but not low:genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms[J]. BMC Evolutionary Biology, 2012, 12(1):8.
[28] Liewlaksaneeyanawin C, Ritland C E, El-Kassaby Y A, et al. Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs[J]. Theoretical and Applied Genetics, 2004,109(2):361-369.
[29] Chagne D, Chaumeil P, Ramboer A, et al. Cross-species transferability and mapping of genomic and cDNA SSRs in pines[J]. Theoretical and Applied Genetics, 2004, 109(6):1204-1214.
[30] Rungis D, Berube Y, Zhang J, et al. Robust simple sequence repeat markers for spruce(Picea spp.)from expressed sequence tags[J]. Theoretical and Applied Genetics, 2004,109(6):1283-1294.
[31] Rajora O P, Rahman M H, Dayanandan S, et al. Isolation, characterization, inheritance and linkage of microsatellite DNA markers in white spruce (Picea glauca)and their usefulness in other spruce species[J]. Mol Gen Genet, 2000,264:871-882.
[32] Moriguchi Y, Ueno S, Ujino-Ihara T, et al. Characterization of EST-SSRs from Cryptomeria japonica[J]. Conserv Genet Resour, 2009, 1(1):373-376.
[33] Li S X, Yin T M, Wang M X, et al. Characterization of microsatellites in the coding regions of the Populus genome [J]. Molecular Breeding, 2011, 27(1):59-66.
[34] Echt C S, Saha S, Krutovsky K V, et al. An annotated genetic map of loblolly pine based on microsatellite and cDNA markers [J]. BMC Genetics, 2011, 12(1):17.

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