1. bookVolume 62 (2013): Issue 1-6 (December 2013)
Journal Details
License
Format
Journal
eISSN
2509-8934
First Published
22 Feb 2016
Publication timeframe
1 time per year
Languages
English
access type Open Access

Development and characterization of 28 polymorphic EST-SSR markers for Cunninghamia lanceolata (Taxodiaceae) based on transcriptome sequences

Published Online: 01 Jul 2017
Volume & Issue: Volume 62 (2013) - Issue 1-6 (December 2013)
Page range: 137 - 141
Received: 09 Nov 2012
Journal Details
License
Format
Journal
eISSN
2509-8934
First Published
22 Feb 2016
Publication timeframe
1 time per year
Languages
English
Abstract

The Chinese fir (Cunninghamia lanceolata) is a very important plantation species that is mainly distributed in Southern China. However, genomic analyses of C. lanceolata have lagged significantly behind those of other conifer species due to a lack of suitable markers. To address this issue, we examined 27,666,670 reads from C. lanceolata transcriptome sequences recorded in the SRA database. Assembly produced 35,633 contigs, 1,822 (5.11%) of which contained one or more SSRs. In total, 2,156 SSRs were identified, giving an average SSR density of 68.4 SSRs/Mb. The most common SSR types were tri-SSRs (41.7%), followed by hexa-(29.8%), penta- (12.7%), di-(11.1%) and tetra-(4.7%) SSRs. EST-SSR markers based on the 1,822 SSR-containing contigs were developed using the CMiB pipeline and primer pairs were designed to target 35 loci. Polymorphism was observed in 28 of these loci, for which the number of alleles per locus ranged from 3 to 12 over 16 plus-tree individuals. The observed heterozygosity (Ho), expected heterozygosity (He) and fixation index (FIS) values for the targeted loci ranged from 0.125 to 0.938, 0.225 to 0.891 and -0.368 to 0.456, respectively. The corres - ponding PIC values ranged from 0.210 to 0.881, with an average of 0.573. Some of these markers have since been used in our ongoing genetic diversity analyses of C. lanceolata. To our knowledge, this is the first analysis of SSRs and EST-SSR markers in C. lanceolata, and the identified EST-SSR markers will be useful in future genetic analyses of C. lanceolata and related species.

Keywords

BÉRUBÉ, Y., J. ZHUANG, D. RUNGIS, S. RALPH, J. BOHLMANN and K. RITLAND (2007): Characterization of EST-SSRs in loblolly pine and spruce. Tree Genetics & Genomes 3: 251-259.10.1007/s11295-006-0061-1Search in Google Scholar

BLACKET, M. J., C. ROBIN, R. T. GOOD, S. F. LEE and A. D. MILLER (2012): Universal primers for fluorescent labelling of PCR fragments - an efficient and cost-effective approach to genotyping by fluorescence. Molecular Ecology Resources 12: 456-463.10.1111/j.1755-0998.2011.03104.xSearch in Google Scholar

BOTSTEIN, D., R. L. WHITE, M. SKOLNICK and R. W. DAVIS (1980): Construction of a genetic linkage map in man using restriction fragment length polymorphism. Am J Hum Genet 32: 314-331.Search in Google Scholar

CASTELO, A. T., W. MARTINS and G. R. GAO (U2002): Trolltandem repeat occurrence locator. Bioinformatics Applications Note 18: 634-636.10.1093/bioinformatics/18.4.634Search in Google Scholar

CHUNG, J. D., T. P. LIN, Y. C. TAN, M. Y. LIN, S. Y. HWANG (2004): Genetic diversity and biogeography of Cunninghamia konishii (Cupressaceae), an island species in Taiwan: a comparison with Cunninghamia lanceolata, a mainland species in China. Molecular Phylogenetics and Evolution 33: 792-801.10.1016/j.ympev.2004.08.011Search in Google Scholar

CONESA, A., S. GOTZ, J. M. GARCIA-GOMEZ, J. TEROL, M. TALON and M. ROBLES (2005): Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.10.1093/bioinformatics/bti610Search in Google Scholar

JARNE, P and P. J. LAGODA (1996): Microsatellites, from molecules to populations and back. Trends in Ecology and Evolution 11: 424-429.10.1016/0169-5347(96)10049-5Search in Google Scholar

PARK, S. D. E. (2001): Trypanotolerance in West African cattle and the population genetic effects of election [Ph.D. thesis]. University of Dublin.Search in Google Scholar

PEAKALL, R. and P. E. SMOUSE (2006): GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288-295.10.1111/j.1471-8286.2005.01155.xSearch in Google Scholar

QI, M. (2008): Genetic diversity of wide cross population of Cunninghamia lanceolata and platycladu orientalis. Bulletin of botanical research 28: 299-303.Search in Google Scholar

SARMAH, R., J. SAHU, B. DEHURY, K. SARMA, S. SAHOO, M. SAHU, M. BAROOAH, P. SEN and M. K. MODI (2012): ESMP: A high-throughput computational pipeline for mining SSR markers from ESTs. Bioinformation 8: 206-208.10.6026/97320630008206330200422419843Search in Google Scholar

RAYMOND, M. and F. ROUSSET (1995): Genepop (Version-1.2): Population genetics software for exact tests and ecumenicism. Journal of Heredity 86: 248-249.10.1093/oxfordjournals.jhered.a111573Search in Google Scholar

SELKOE, K. A. and R. J. TOONEN (2006): Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecology Letters 9: 615-629.10.1111/j.1461-0248.2006.00889.x16643306Search in Google Scholar

SQUIRRELL, J., P. M. HOLLONGSWORTH, M. WOODHEAD, J. RUSSELL, A. J. LOWE, M. GIBBY and W. POWELL (2003): How much effort is required to isolate nuclear microsatellites from plants? Molecular Ecology 12: 1339-1348.10.1046/j.1365-294X.2003.01825.x12755865Search in Google Scholar

THIEL, T., W. MICHALEK, R. K. VARSHNEY and A. GRANER (2003): Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106: 411-422.10.1007/s00122-002-1031-012589540Search in Google Scholar

TSUMURA, Y., K. YOSHIMURA, N. TOMARU and K. OHBA (1995): Molecular phylogeny of conifers using RFLP analysis of PCR-amplified specific chloroplast genes. Theoretical and Applied Geneticst 91: 1222-1236.10.1007/BF0022093324170050Search in Google Scholar

UENO, S., Y. MORIGUCHI, K. UCHIYAMA, T. U. IHARA, N. FUTAMURA, T. SAKURAI, K. SHINOHARA and Y. TSUMURA (2012): A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica. BMC Genomics 13: 136.10.1186/1471-2164-13-136342412922507374Search in Google Scholar

VAN OOSTERHOUT, C., W. F. HUTCHINSON, D. P. M. WILLS and P. SHIPLEY (2004): MICRO CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4: 535-538.10.1111/j.1471-8286.2004.00684.xSearch in Google Scholar

YANG, Y. L., X. Q. MA and M. Q. Z. (2009): Molecular polymorphicanalysis for different geographic provenances of Chinese fir. Journal of Tropical and Subtropical Botany 17: 183-189.Search in Google Scholar

YOU, Y. and J. S. HONG (1998): Application of RAPD marker of genetic variation of Chinese fir provenances. Scientia Silvae Sinicae 34: 33-38.Search in Google Scholar

ZALAPA, J. E., H. CUEVAS, H. ZHU, S. STEFFAN, D. SENALIK, E. ZELDIN and B. MCCOWN et al. (2012): Using next-generation sequencing approaches for the isolation of simple sequence repeat (SSR) loci in the plant sciences. American Journal of Botany 99: 193-208.10.3732/ajb.110039422186186Search in Google Scholar

ZANE, L., L. BARGELLONI and T. PATARNELLO (2002): Strategies for microsatellite isolation: A review. Molecular Ecology 11: 1-16.10.1046/j.0962-1083.2001.01418.x11903900Search in Google Scholar

Recommended articles from Trend MD

Plan your remote conference with Sciendo