Abstract
Simple sequence repeat (SSR) markers are very useful for genetic applications in plants, but SSR resource for the important tree genus Casuarina L. ex Adans. is still limited. In this study, we report a novel set of 223 SSR markers in Casuarina developed from expressed sequence tag (EST) resource of GenBank. The 223 EST-SSR markers were polymorphic among 10 unrelated individuals of C. equisetifolia L. Johnson, with the number of alleles per locus (Na), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphic information content (PIC) averaging at 5.5, 0.72, 0.86, and 0.63, respectively. The rates of cross-species transferability ranged from 96.9% (C. glauca Sieber ex Sprengel) through 97.8% (C. cunninghamiana Miquel) to 99.1% (C. junghuhniana Miquel). Fifty-five C. equisetifolia clones widely planted in China were successfully genotyped with a subset of 20 EST-SSRs. These newly developed markers will have a great potential for genetic and breeding applications in Casuarina species and related taxa.
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Blair MW, Torres MM, Giraldo MC, Pedraza F (2009) Development and diversity of Andean-derived, gene-based microsatellites for common bean (Phaseolus vulgaris L.). BMC Plant Biol 9:100. https://doi.org/10.1186/1471-2229-9-100
Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331
Decroocq V, Favé MG, Hagen L, Bordenave L, Decroocq S (2003) Development and transferability of apricot and grape EST microsatellite markers across taxa. Theor Appl Genet 106:912–922. https://doi.org/10.1007/s00122-002-1158-z
De-Lucas AI, Cantana JC, Recio P, Hidalgo E (2008) SSR-based tool for identification and certification of commercial Populus clones in Spain. Ann For Sci 65:107p1–107p7. https://doi.org/10.1051/forest:2007079
Diem HG, Dommergues YR (1990) Current and potential uses and management of Casuarinaceae in the tropics and subtropics. In: Schwintzer CR, Tjepkema JD (eds) The biology of Frankia and actinorhizal plants. Academic Press, San Diego, pp 317–341
Dieringer D, Schlötterer C (2003) Microsatellite analyzer (MSA): a platform independent analysis tool for large microsatellite data sets. Mol Ecol Notes 3:167–169. https://doi.org/10.1046/j.1471-8286.2003.00351.x
Elavazhagan T, Ramakrishnan M, Jayakumar S, Chitravadivu C, Balakrishnan V (2009) DNA finger printing analysis in Casurina equisetifolia by using RAPD markers. Bot Res Int 2:244–247
Ellis JR, Burke JM (2007) EST-SSRs as a resource for population genetic analyses. Heredity 99:125–132. https://doi.org/10.1038/sj.hdy.6801001
Fossati T, Zapelli I, Bisoffi S, Micheletti A, Vietto L, Sala F, Castiglione S (2005) Genetic relationships and clonal identity in a collection of commercially relevant poplar cultivars assessed by AFLP and SSR. Tree Genet Genomes 1:11–19. https://doi.org/10.1007/s11295-004-0002-9
Gan S, Shi J, Li M, Wu K, Wu J, Bai J (2003) Moderate density molecular maps of Eucalyptus urophylla S. T. Blake and E. tereticornis Smith genomes based on RAPD markers. Genetica 118:59–67. https://doi.org/10.1023/A:1022966018079
Götz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talon M, Dopazo J, Conesa A (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36:3420–3435. https://doi.org/10.1093/nar/gkn176
He X, Wang Y, Li F, Weng Q, Li M, Xu L, Shi J, Gan S (2012) Development of 198 novel EST-derived microsatellites in Eucalyptus (Myrtaceae). Am J Bot 99:e134–e148. https://doi.org/10.3732/ajb.1100442
Ho KY, Lee SC (2011) ISSR-based genetic diversity of Casuarina spp. in coastal windbreaks of Taiwan. Afr J Agric Res 6:5664–5671. https://doi.org/10.5897/AJAR10.864
Ho KY, Yang JC, Hsiao JY (2002) An assessment of genetic diversity and documentation of hybridization of Casuarina grown in Taiwan using RAPD markers. Int J Plant Sci 163:831–836. https://doi.org/10.1086/341826
Huang G, Zhong C, Su X, Zhang Y, Pinyopusarerk K, Franche C, Bogusz D (2009) Genetic variation and structure of native and introduced Casuarina equisetifolia (L. Johnson) provenances. Silvae Genet 58:79–85
Kullan ARK, Kulkarni AV, Kumar RS, Rajkumar R (2016) Development of microsatellite markers and their use in genetic diversity and population structure analysis in Casuarina. Tree Genet Genomes 12:49. https://doi.org/10.1007/s11295-016-1009-8
Li F, Gan S (2011) An optimised protocol for fluorescent-dUTP based SSR genotyping and its application to genetic mapping in Eucalyptus. Silvae Genet 60:18–25
Libby WJ (1985) Potential of clonal forestry. In: Zsuffa L, Rauter RM and eatman CW (eds) Clonal forestry: its impact on tree improvement and our future forests. Proceedings of the nineteenth meeting of the Canadian Tree Improvement Association, Part 2, Toronto, pp 1–11
Mariotti R, Cultrera NGM, Mousavi S, Baglivo F, Rossi M, Albertini E, Alagna F, Carbone F, Perrotta G, Baldoni L (2016) Development, evaluation, and validation of new EST-SSR markers in olive (Olea europaea L.). Tree Genet Genomes 12:120. https://doi.org/10.1007/s11295-016-1077-9
Mignone F, Gissi C, Liuni S, Pesole G (2002) Untranslated regions of mRNAs. Genome Biol 3:reviews0004.1–0004.10. http://genomebiology.com/2002/3/3/reviews/0004.1
Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data II: gene frequency data. J Mol Evol 19:153–170. https://doi.org/10.1007/BF02300753
Paetkau D, Calvert W, Stirling I, Strobeck C (1995) Microsatellite analysis of population structure in Canadian polar bears. Mol Ecol 4:347–354. https://doi.org/10.1111/j.1365-294X.1995.tb00227.x
Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539. https://doi.org/10.1093/bioinformatics/bts460
Powell W, Machray GC, Provan J (1996) Polymorphisms revealed by simple sequence repeats. Trends Plant Sci 1:215–222. https://doi.org/10.1016/1360-1385(96)86898-1
Rohlf FJ (1998) NTSYS-pc. Numerical taxonomy and multivariate analysis system, version 2.02. Exeter Software, New York
Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386
Schwencke J, Bureau J-M, Crosnier M-T, Brown S (1998) Cytometric determination of genome size and base composition of tree species of three genera of Casuarinaceae. Plant Cell Rep 18:346–349. https://doi.org/10.1007/s002990050584
Sharma RK, Bhardwaj P, Negi R, Mohapatra T, Ahuja PS (2009) Identification, characterization and utilization of unigene derived microsatellite markers in tea (Camellia sinensis L). BMC Plant Biol 9:53. https://doi.org/10.1186/1471-2229-9-53
Sokal RR, Michener CD (1958) Statistical method for evaluating systematic relationships. Univ Kansas Sci Bull 38:1409–1438
Song Z, Zhang M, Li F, Weng Q, Zhou C, Li M, Li J, Huang H, Mo X, Gan S (2016) Genome scans for divergent selection in natural populations of the widespread hardwood species Eucalyptus grandis (Myrtaceae) using microsatellites. Sci Rep 6:34941. https://doi.org/10.1038/srep34941
Turnbull JW (1990) Taxonomy and genetic variation in casurinas. In: El-Lakany MH, Turnbull JW, Brewbaker JL (eds) Advances in casuarina research and utilization, Proceedings of the Second International Casuarina Workshop, Cairo, pp 1–11
Varshney R, Granner A, Sorrells M (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55. https://doi.org/10.1016/j.tibtech.2004.11.005
Wagner HW, Sefc KM (1999) IDENTITY 1.0. Centre for Applied Genetics, University of Agricultural Sciences, Vienna
Weir BS (1996) Genetic data analysis II. Sinauer Associates Inc. Publishers, Sunderland
Yasodha R, Kathirvel M, Sumathi R, Gurumurthi K, Sunil A, Nagaraju J (2004) Genetic analyses of Casuarinas using ISSR and FISSR markers. Genetica 122:161–172. https://doi.org/10.1023/B:GENE.0000040938.13344.70
Yasodha R, Sumathi R, Ghosh M, Gurumurthi K (2009) Identification of simple sequence repeats in Casuarina equisetifolia. IUP J Genet Evol 2:46–55
Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16. https://doi.org/10.1046/j.0962-1083.2001.01418.x
Zhang M, Zhou C, Song Z, Weng Q, Li M, Ji H, Mo X, Huang H, Lu W, Luo J, Li F, Gan S (2018) The first identification of genomic loci in plants associated with resistance to galling insects: a case study in Eucalyptus L’Hér. (Myrtaceae). Sci Rep 8:2319. https://doi.org/10.1038/s41598-018-20780-9
Zhong C, Zhang Y, Chen Y, Jiang Q, Chen Z, Wu C, Pinyopusarerk K, Franche C, Bogusz D (2010) Casuarina research and development in China. In: Zhong C, Pinyopusarerk K, Kalinganire A, Franche C (eds) Improving smallholder livelihood through improved casuarina productivity. Proceedings of the 4th International Casuarina Workshop, Haikou, pp 5–10
Zhou C, He X, Li F, Weng Q, Yu X, Wang Y, Li M, Shi J, Gan S (2014) Development of 240 novel EST-SSRs in Eucalyptus L’Hérit. Mol Breed 33:221–225. https://doi.org/10.1007/s11032-013-9923-z
Acknowledgments
The authors would like to thank Hongxia Ji and Heyu Yang for technical assistance.
Funding
This work was financially supported by Forestry Administration of Guangdong Province, China (2014KJCX017) and National Natural Science Foundation of China (31470634).
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Data archiving statement
The primer sequences for the 223 EST-SSRs were deposited in Probe database of GenBank (http://www.ncbi.nlm.nih.gov/probe) with IDs Pr032826133–355. The allelic data of the 223 EST-SSRs against the 10 unrelated C. equisetifolia individuals and the 20 EST-SSRs against the 55 C. equisetifolia clones are available from the TreeGenes (http://treegenesdb.org) with accession no. TGDR074.
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Communicated by M. Wirthensohn
Electronic supplementary material
Online Resource 1
The sequence of forward and reverse primers and repeat motif for the 223 novel EST-SSR markers developed in Casuarina (PDF 353 kb)
Online Resource 2
Functional annotations of the 223 novel EST-SSR markers developed in Casuarina (PDF 335 kb)
Online Resource 3
Gene ontology (GO) classification of the SSR-containing ESTs into three categories, including cellular component (a), molecular function (b) and biological process (c) (PDF 748 kb)
Online Resource 4
Polymorphisms and cross-species amplification for the 223 novel EST-SSR markers developed in Casuarina (PDF 298 kb)
Online Resource 5
Nei’s genetic distance between the 55 commercial clones of C. equisetifolia (PDF 309 kb)
Online Resource 6
Alleles of uniquely fingerprinted clonal genotypes of C. equisetifolia at a minimum of six EST-SSR markers (PDF 293 kb)
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Xu, X., Zhou, C., Zhang, Y. et al. A novel set of 223 EST-SSR markers in Casuarina L. ex Adans.: polymorphisms, cross-species transferability, and utility for commercial clone genotyping. Tree Genetics & Genomes 14, 30 (2018). https://doi.org/10.1007/s11295-018-1246-0
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DOI: https://doi.org/10.1007/s11295-018-1246-0