Abstract
Microsatellites, or simple sequence repeats (SSRs), are usually regarded as the “markers of choice” in population genetics research because they exhibit high variability. The development cost of these markers is usually high. In addition, microsatellite primers developed for one species often do not cross-amplify in related species, requiring separate development for each species. However, microsatellites found in expressed sequence tags (ESTs) might better cross-amplify as they reside in or near conserved coding DNA. In this study, we identified 14 Pinus taeda (loblolly pine) EST-SSRs from public EST databases and tested for their cross-species transferability to P. contorta ssp. latifolia, P. ponderosa, and P. sylvestris. As part of our development of a P. contorta microsatellite set, we also compared their transferability to that of 99 traditional microsatellite markers developed in P. taeda and tested on P. contorta ssp. latifolia. Compared to traditional microsatellites, EST-SSRs had higher transfer rates across pine species; however, the level of polymorphism of microsatellites derived from ESTs was lower. Sequence analyses revealed that the frequencies of insertions/deletions and base substitutions were lower in EST-SSRs than in other types of microsatellites, confirming that EST-SSRs are more conserved than traditional SSRs. Our results also provide a battery of 23 polymorphic, robust microsatellite primer pairs for lodgepole pine.
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References
Auckland LD, Bui T, Zhou Y, Shepherd M, Williams CG (2002) Conifer microsatellite handbook. Corporate Press, Raleigh, N.C.
Ayres NM, McClung AM, Larkin PD, Bligh HFJ, Jones CA, Park WD (1997) Microsatellites and a sin1gle-nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germplasm. Theor Appl Genet 94:773–781
Cabot EL, Beckenbach AT (1989) Simultaneous editing of multiple nucleic acid and protein sequences with Esee. Comput Appl Biosci 5:233–234
Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156:847–854
Chen X, Cho YG, McCouch SR (2002) Sequence divergence of rice microsatellites in Oryza and other plant species. Mol Genet Genomics 268:331–343
Chin ECL, Senior ML, Shu H, Smith JSC (1996) Maize simple repetitive DNA sequences: abundance and allele variation. Genome 39:866–873
Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722
Cordeiro GM, Casu R, McIntyre CL, Manners JM, Henry RJ (2001) Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross-transferable to erianthus and sorghum. Plant Sci 160:1115–1123
Decroocq V, Fave MG, Hagen L, Bordenave L, Decroocq S (2003) Development and transferability of apricot and grape microsatellite markers across taxa. Theor Appl Genet 106:912–922
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh tissue. Phytochem Bull 19:11–15
Dresselhaus T, Cordts S, Heuer S, Sauter M, Lorz H, Kranz E (1999) Novel ribosomal genes from maize are differentially expressed in the zygotic and somatic cell cycles. Mol Gen Genet 261:416–427
Elsik CG, Williams CG (2001) Low-copy microsatellite recovery from a conifer genome. Theor Appl Genet 103:1189–1195
Elsik CG, Minihan VT, Hall SE, Scarpa AM, Williams CG (2000) Low-copy microsatellite markers for Pinus taeda L. Genome 43:550–555
Fujimori S, Washio T, Higo K, Ohtomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Tomita M (2003) A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription. FEBS Lett 554:17–22
Hackauf B, Wehling P (2002) Identification of microsatellite polymorphisms in an expressed portion of the rye genome. Plant Breed 121:17–25
Hicks MD, Adams D, O’Keefe S, Macdonald E, Hodgetts R (1998) The development of RAPD and microsatellite markers in lodgepole pine (Pinus contorta var. latifolia). Genome 41:797–805
Karhu A, Dieterich JH, Savolainen O (2000) Rapid expansion of microsatellite sequences in pines. Mol Biol Evol 17:259–265
Kinlaw CS, Neale DB (1997) Complex gene families in pine genomes. Trends Plant Sci 2:356–359
Koch P (1996) Lodgepole pine in North America. Forest Product Society, Madison, Wis.
Krupkin AB, Liston A, Strauss SH (1996) Phylogenetic analysis of the hard pines (Pinus subgenus Pinus, Pinaceae) from chloroplast DNA restriction site analysis. Am J Bot 83:489–498
Kutil BL, Williams CG (2001) Triplet-repeat microsatellite shared among hard and soft pines. J Hered 92:327–332
Little EL Jr, Critchfield WB (1969) Subdivisions of the genus Pinus (pines). USDA For Serv Misc Publ 1144, Washington, D.C.
Oetting WS, Lee HK, Flanders DJ, Wiesner GL, Sellers TA, King RA (1995) Linkage analysis with multiplexed short tandem repeat polymorphisms using infrared fluorescence and M13 tailed primers. Genomics 30:450–458
Richard GF, Dujon B (1996) Distribution and variability of trinucleotide repeats in the genome of the yeast Saccharomyces cerevisiae. Gene 174:165–174
Scott KD (2001) Microsatellites derived from ESTs and their comparison with those derived from by other methods. In: Henry RJ (ed) Plant genotyping: the DNA fingerprinting of plants. CABI, New York, pp 225–237
Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726
Scotti I, Magni F, Fink R, Powell W, Binelli G, Hedley PE (2000) Microsatellite repeats are not randomly distributed within Norway spruce (Picea abies K.) expressed sequences. Genome 43:41–46
Shepherd M, Cross M, Maguire TL, Dieters MJ, Williams CG, Henry RJ (2002) Transspecific microsatellites for hard pines. Theor Appl Genet 104:819–827
Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712
Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR markers in the barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422
Young ET, Sloan JS, Van Riper K (2000) Trinucleotide repeats are clustered in regulatory genes in Saccharomyces cerevisiae. Genetics 154:1053–1068
Zhou Y, Bui T, Auckland LD, Williams CG (2002) Undermethylated DNA as a source of microsatellites from a conifer genome. Genome 45:91–99
Acknowledgements
This work was funded through NSERC grants to K.R. We sincerely thank D.B. Neale for providing loblolly pine EST sequences, and C.H. Newton for contributing the DNA of 24 individual lodgepole pines. We also would like to thank two anonymous reviewers and O. Savolainen for helpful comments on the manuscript.
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Liewlaksaneeyanawin, C., Ritland, C.E., El-Kassaby, Y.A. et al. Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs. Theor Appl Genet 109, 361–369 (2004). https://doi.org/10.1007/s00122-004-1635-7
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DOI: https://doi.org/10.1007/s00122-004-1635-7