Abstract
We analyzed the genetic differences of 16 poplar clones between genomic-SSR and EST-SSR markers. The statistical results show that the average number of alleles detected by genomic-SSR was 4.1, Shannon’s index 1.0646, observed heterozygosity 0.4427 and expected heterozygosity 0.5523, while for the EST-SSR, the average number of alleles was 2.8, Shannon’s index 0.6985, observed heterozygosity 0.2330 and expected heterozygosity 0.4684. Cluster analysis indicated that the EST-SSR capacity of genotypic identification was more precise than that of genomic-SSR. These results reveal that EST-SSR and genomic-SSR have statistically significant genetic differences in polymorphism detection and genotypic identification. These differences could provide a theoretical basis for the rational use of SSR markers in species diversity and other related research.
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References
Ayres N M, McClung A M, Larkin P D, Bligh H F J, Jones C A, Park W D. 1997. Microsatellites and a single-nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germ plasm. Theor Appl Genet, 94: 773–781
Botstein D, White R L, Skolnick R M, Davis R W. 1980. Construction of genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet, 32: 314–331
Chang W, Zhao X, Li X, Qiu B, Han Y P, Teng W L, Li W B. 2009. Development of soybean EST-SSR marker and comparison with genomic-SSR marker. Chin J Oil Crop Sci, 31(2): 149–156 (in Chinese with English abstract)
Dellaporta S L, Wood J, Hicks J. 1983. A rapid method for DNA extraction from plant tissue. Plant Mol Biol Rep, 1: 19–21
Ellis J R, Burke J M. 2007. EST-SSRs as a resource for population genetic analyses. Heredity, 99: 125–132
Eujayl I, Sorrells M, Baum M, Wolters P, Powell W. 2001. Assessment of genotypic variation among cultivated durum wheat based on EST-SSRs and genomic-SSRs. Euphytica, 119: 39–43
Hanai L R, Santini L, Camargo L E A, Fungaro M H P, Gepts P, Tsai S M, Vieira M L C. 2010. Extension of the core map of common bean with EST-SSR, RGA, AFLP, and putative functional markers. Mol Breeding, 25: 25–45
Jia J Z, Zhang Z B, Devos K, Gale M D. 2001. Analysis of genetic diversity of 21 chromosomes of wheat by RFLP mapping lotus. Sci Chin (Ser C), 31(1): 13–21 (in Chinese)
Maynard Smith J, Haigh J. 1974. The hitch-hiking effect of a favorable gene. Genet Res, 23(1): 23–35
Moccia M D, Oger-Desfeux C, Marais G A B, Widmer A. 2009. A White Campion (Silene latifolia) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping. BMC Genom, 10: 243–257
Nei M, Li W H. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA, 76: 5269–5273
Su X H, Huang Q J, Zhang B Y, Zhang X H. 2004. The achievement and developing strategy on variety selection and breeding of poplar in China. World Forest Res, 17(1): 46–49 (in Chinese with English abstract)
Sun Q X, Huang T C, Ni Z F, Procunier J D. 1996. Study on wheat heterotic group I. Genetic diversity revealed by random amplified polymorphic DNA (RAPD) in elite wheat cultivars. J Agric Biotechnol, 4(2): 103–110 (in Chinese with English abstract)
Tuskan G A, Gunter L E, Yang Z K, Yin T M, Sewell M M, Di-Fazio S P. 2004. Characterization of microsatellites revealed by genomic sequencing of Populus trichocarpa. Can J Forest Res, 34: 85–93
Varshney R K, Graner A, Sorrells M E. 2005. Genic microsatellite markers in plants: features and applications. Trends Biotechnol, 23(1): 48–55
Wen M F, Wang H Y, Xia Z Q, Zou M L, Lu C, Wang W Q. 2010. Development of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha curcas L. BMC Res Notes, 3: 42–50
Yang X Q, Liu P, Han Z F, Ni Z F, Liu W Q, Sun Q X. 2005. Comparative analysis of genetic diversity revealed by genomic-SSR, EST-SSR and pedigree in wheat (Triticum asetivum L.). Acta Genet Sin, 32(4): 406–416 (in Chinese with English abstract)
Yang Y L, Zhang Y D, Zhang X Y. 2008. Transferability analysis of Populus SSR markers in Salix. Mol Plant Breeding, 6(6): 1134–1138 (in Chinese with English abstract)
Yin T M, DiFazio S P, Gunter L E, Zhang X Y, Sewell M M, Woolbright S A, Allan G J, Kelleher C T, Douglas C J, Wang M X, Tuskan G A. 2008. Genome structure and emerging evidence of an incipient sex chromosome in Populus. Genome Res, 18: 422–430
Zeng S H, Xiao G, Guo J, Fei Z J, Xu Y Q, Roe B A, Wang Y. 2010. Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim. BMC Genom, 11: 94–105
Zhao Y, Kong F M, Ding C Q, Li S S. 2008. Transferability of EST-SSR markers in zoysiagrasses. Chin J Grassland, 30(3): 69–73 (in Chinese with English abstract)
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Song, Yp., Jiang, Xb., Zhang, M. et al. Differences of EST-SSR and genomic-SSR markers in assessing genetic diversity in poplar. For. Stud. China 14, 1–7 (2012). https://doi.org/10.1007/s11632-012-0106-5
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DOI: https://doi.org/10.1007/s11632-012-0106-5