Abstract
Length variations in simple sequence tandem repeats are being given increased attention in plant genetics. Some short tandem repeats (STRs) from a few plant species, mainly those at the dinucleotide level, have been demonstrated to show polymorphisms and Mendelian inheritance. In the study reported here a search for all of the possible STRs ranging from mononucleotide up to tetranucleotide repeats was carried out on EMBL and GenBank DNA sequence databases of 3026 kb nuclear DNA and 1268 kb organelle DNA in 54 and 28 plant species (plus algae), respectively. An extreme rareness of STRs (4 STRs in 1268 kb DNA) was detected in organelle compared with nuclear DNA sequences. In nuclear DNA sequences, (AT)n sequences were the most abundant followed by (A)n · (T)n, (AG)n · (CT)n, (AAT)n · (ATT)n, (AAC)n · (GTT), (AGC)n · (GCT)n, (AAG)n · (CTT)n, (AATT)n · (TTAA)n, (AAAT)n · (ATTT)n and (AC)n · (GT)n sequences. A total of 130 STRs were found, including 49 (AT)n sequences in 31 species, giving an average of 1 STR every 23.3 kb and 1 (AT)n STR every 62 kb. An abundance comparable to that for the dinucleotide repeat was observed for the tri- and tetranucleotide repeats together. On average, there was 1 STR every 64.6 kb DNA in monocotyledons versus 1 every 21.2 kb DNA in dicotyledons. The fraction of STRs that contained G-C basepairs increased as the G+C contents went up from dicotyledons, monocotyledons to algae. While STRs of mono-, di- and tetranucleotide repeats were all located in non coding regions, 57% of the trinucleotide STRs containing G-C basepairs resided in coding regions.
Similar content being viewed by others
References
Akkaya MS, Bhagwat AA, Cregan PB (1992) Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 132:1131–1139
Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218
Beckmann JS, Weber JL (1992) Survey of human and rat microsatellites. Genomics 12:627–631
Brook JD, McCurrach ME, Harley HG, Buckler AJ, Church D, Aburatani H, Hunter K, Stanton VP, Thirion JP, Hudson T, Sohn R, Zemelman B, Snell RG, Rundle SA, Crow S, Davies J, Shelbourne P, Buxton J, Jones C, Juvonen V, Johnson K, Harper PS, Shaw DJ, Housman DE (1992) Molecular basis of myotonic dystrophy: expansion of a trinucleotide (CTG) repeat at the 3'end of a transcript encoding a protein kinase family member. Cell 68:799–808
Condit R, Hubbell SP (1991) Abundance and DNA sequence of 2-base repeat regions in tropical tree genomes. Genome 34:66–71
Economou EP, Bergen AW, Warren AC, Antonarakis SE (1990) The polydeoxyadenylate tract of Alu repetitive elements is polymorphic in the human genome. Proc Natl Acad Sci USA 87:2951–2954
Fu Y-H, Pizzuti A, Fenwick RG, King J Jr, Rajnarayan S, Dunne PW, Dubel J, Nasser GA, Ashizawa T, de Jong P, Wieringa B, Korneluk R, Perryman MB, Epstein HF, Caskey CT (1992) An unstable triplet repeat in a gene related to myotonic muscular dystrophy. Science 255:1256–1258
Kremer EJ, Pritchard M, Lynch M, Yu S, Holman K, Baker E, Waren ST, Schlessinger D, Sutherland GR, Richards RI (1991) Map** of DNA instability at the fragile X to a trinucleotide repeat sequence p(CCG)n. Science 252:1711–1714
Luty JA, Guo Z, Willard HF, Ledbetter DH, Ledbetter S, Litt M (1990) Five polymorphic microsatellite VNTRs on the human X chromosome. Am J Hum Genet 46:776–783
McAleer MA, Aitman TJ, Cornall RJ, Ghosh S, Hall JRS, Hearne CM, Love JM, Prins JB, Ramachandran S, Rodrigues N, DeLarato NH, Peterson LB, Wicker LS, Todd JA (1992) Linkage analysis of 84 microsatellite markers in intra and interspecific backcrosses. Mamm Genome 3:457–460
Messeguer R, Ganal MW, Steffens JC, Tanksley SD (1991) Characterization of the level, target sites and inheritance of cytosin methylation in tomato nuclear DNA. Plant Mol Biol 16:753–770
Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3:175–182
NIH/CEPH Collaborative Map** Group (1992) A comprehensive genetic linkage map of the human genome. Science 258:67–86
Serikawa T, Kuramoto T, Hilbert P, Mori M, Yamada J, Dubay CJ, Lindpainter K, Ganten D, Genenet J-L, Lathrop M, Beckmann JS (1992) Rat gene map** using PCR-analyzed microsatellites. Genetics 131:701–721
Smeets HJM, Brunner HG, Ropers HH, Wieringa B (1989) Use of variable simple sequence motifs as genetic markers: Application to study of myotonic dystrophy. Hum Genet 83:245–251
Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of aukaryotic genomes. Nucleic Acids Res 12:4127–4138
Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388–396
Weising K, Weigand F, Driesel AJ, Kahl G, Zischler H, Epplen JT (1989) Polymorphic simple GATA/GACA repeats in plant genomes. Nucleic Acids Res 17:10128
Weissenbach J, Gyapay G, Dib C, Vignal A, Morissette J, Millasseau P, Vaysseix G, Lathrop M (1992) A second-generation linkage map of the human genome. Nature 359:794–801
Wu K, Tanksley SD (1993) Abundances, polymorphisms and genetic map** of microsatellites in rice. Mol Gen Genet (in press)
Zhao X, Kochert G (1992) Characterization and genetic map** of a short, highly repeated, interspersed DNA sequence from rice (Oryza sativa L.). Mol Gen Genet 231:353–359
Zuliani G, Hobbs HH (1990) A high frequency of length polymorphisms in repeated sequences adjacent to Alu sequences. Am J Hum Genet 46:963–969
Author information
Authors and Affiliations
Additional information
Communicated by F. Salamini
Rights and permissions
About this article
Cite this article
Wang, Z., Weber, J.L., Zhong, G. et al. Survey of plant short tandem DNA repeats. Theoret. Appl. Genetics 88, 1–6 (1994). https://doi.org/10.1007/BF00222386
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00222386