A Database of Simple Sequence Repeats from Cereal and Legume Expressed Sequence Tags Mined in silico: Survey and Evaluation

Simple sequence repeats (SSRs) or microsatellites are an important class of molecular markers for genome analysis and plant breeding applications. In this paper, the SSR distributions within ESTs from the legumes soybean (Glycine max, representing 135.86 Mb), medicago (Medicago truncatula, 121.1 Mb) and lotus (Lotus japonicus, 45.4 Mb) have been studied relative to the distributions in cereals such as sorghum (Sorghum bicolor, 98.9 Mb), rice (Oryza sativa, 143.9 Mb) and maize (Zea mays, 183.7 Mb). The relative abundance, density, composition and putative annotations of di-, tri-, tetra- and penta-nucleotide repeats have been compared and SSR containing ESTs (SSR-ESTs) have been clustered to give a non-redundant set of EST-SSRs, available in a database. Further, a subset of such candidate EST-SSRs from sorghum have been tested for their ability to detect polymorphism between Striga-susceptible, stay-green drought tolerant mapping population parent 'E 36-1' and its Striga-resistant, non-stay-green counterpart 'N13'. Primer sets for 64% of the EST-SSRs tested produced a clear and specific PCR product band and 34% of these detected scorable polymorphism between the N13 and E 36-1 parental lines. Over half of these markers have been genotyped on 94 RILs from the (N13 x E 36-1)-based mapping population, with 42 markers mapping onto the ten sorghum linkage groups. This establishes the value of this database as a resource of molecular markers for practical applications in cereal and legume genetics and breeding. The primer pairs for non-redundant EST-SSRs have been designed and are freely available through the database (http://intranet.icrisat.org/gt1/ssr/ssrdatabase.html).

[1]  P. Langridge,et al.  Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice , 2005 .

[2]  J. Jurka,et al.  Simple repetitive DNA sequences from primates: Compilation and analysis , 1995, Journal of Molecular Evolution.

[3]  S. Decroocq,et al.  Development and transferability of apricot and grape EST microsatellite markers across taxa , 2003, Theoretical and Applied Genetics.

[4]  R. Henry,et al.  Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. , 2001, Plant science : an international journal of experimental plant biology.

[5]  A. Hoelzel,et al.  Detection of mitochondrial DNA fragments. , 1992 .

[6]  M. Morgante,et al.  Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes , 2002, Nature Genetics.

[7]  J. Weber,et al.  Human whole-genome shotgun sequencing. , 1997, Genome research.

[8]  R. Van der Hoeven,et al.  Identification, Analysis, and Utilization of Conserved Ortholog Set Markers for Comparative Genomics in Higher Plants Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010479. , 2002, The Plant Cell Online.

[9]  C. Feuillet,et al.  High transferability of bread wheat EST-derived SSRs to other cereals , 2005, Theoretical and Applied Genetics.

[10]  E. Nevo,et al.  Microsatellites within genes: structure, function, and evolution. , 2004, Molecular biology and evolution.

[11]  Ju-Kyung Yu,et al.  Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley , 2005, BMC Genomics.

[12]  L. Lipovich,et al.  Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. , 2001, Genome research.

[13]  N. Seetharama,et al.  Construction of a combined sorghum linkage map from two recombinant inbred populations using AFLP, SSR, RFLP, and RAPD markers, and comparison with other sorghum maps , 2002, Theoretical and Applied Genetics.

[14]  Thomas Lübberstedt,et al.  Functional markers in plants. , 2003, Trends in plant science.

[15]  Jianxin Ma,et al.  Consistent over-estimation of gene number in complex plant genomes. , 2004, Current opinion in plant biology.

[16]  D. Tautz,et al.  Cryptic simplicity in DNA is a major source of genetic variation , 1986, Nature.

[17]  H Green,et al.  Codon reiteration and the evolution of proteins. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Kazuo Shinozaki,et al.  Effects of free proline accumulation in petunias under drought stress. , 2005, Journal of experimental botany.

[19]  John M. Hancock.  The contribution of slippage-like processes to genome evolution , 1995, Journal of Molecular Evolution.

[20]  A. Hoelzel.  Molecular genetic analysis of populations: a practical approach. , 1993 .

[21]  T. Mohapatra,et al.  Unigene derived microsatellite markers for the cereal genomes , 2006, Theoretical and Applied Genetics.

[22]  W Miller,et al.  Analysis of the quality and utility of random shotgun sequencing at low redundancies. , 1998, Genome research.

[23]  D. Marshall,et al.  Computational and experimental characterization of physically clustered simple sequence repeats in plants. , 2000, Genetics.

[24]  J T Finch,et al.  Glutamine repeats as polar zippers: their possible role in inherited neurodegenerative diseases. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[25]  M. Sorrells,et al.  Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat , 2002, Plant Molecular Biology.

[26]  G. Singer,et al.  Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. , 2000, Molecular biology and evolution.

[27]  C. Robin Buell,et al.  The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants , 2004, Nucleic Acids Res..

[28]  F. Taddei,et al.  Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions? , 2002, Nucleic acids research.

[29]  A. McClung,et al.  Microsatellites and a single-nucleotide polymorphism differentiate apparentamylose classes in an extended pedigree of US rice germ plasm , 1997, Theoretical and Applied Genetics.

[30]  Martin F. W Ojciechowski.  RECONSTRUCTING THE PHYLOGENY OF LEGUMES (LEGUMINOSAE): AN EARLY 21 ST CENTURY PERSPECTIVE , 2003 .

[31]  K. Edwards,et al.  Microsatellite repeats in common bean (Phaseolus vulgaris ): isolation, characterization, and cross-species amplification in Phaseolus ssp. , 2002 .

[32]  N. Seetharama,et al.  QTL mapping of stay-green in two sorghum recombinant inbred populations , 2002, Theoretical and Applied Genetics.

[33]  H. Zoghbi,et al.  Trinucleotide repeats: mechanisms and pathophysiology. , 2000, Annual review of genomics and human genetics.

[34]  X. Huang,et al.  CAP3: A DNA sequence assembly program. , 1999, Genome research.

[35]  W. Powell,et al.  Polymorphism revealed by simple sequence repeats , 1996 .

[36]  E. Trifonov.  Tuning Function of Tandemly Repeating Sequences: A Molecular Device for Fast Adaptation , 2004 .

[37]  N. Saunders,et al.  Diversity in coding tandem repeats in related Neisseria spp. , 2003, BMC Microbiology.

[38]  John M. Hancock,et al.  Amino Acid Reiterations in Yeast Are Overrepresented in Particular Classes of Proteins and Show Evidence of a Slippage-Like Mutational Process , 1999, Journal of Molecular Evolution.

[39]  J. Jurka,et al.  Microsatellites in different eukaryotic genomes: survey and analysis. , 2000, Genome research.

[40]  G. May,et al.  Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. , 2004, Theoretical and Applied Genetics.

[41]  Snehasis Mukhopadhyay,et al.  Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. , 2005, Genome.

[42]  L Pinsky,et al.  Evidence for a repressive function of the long polyglutamine tract in the human androgen receptor: possible pathogenetic relevance for the (CAG)n-expanded neuronopathies. , 1995, Human molecular genetics.

[43]  S. Lincoln.  Constructing genetic maps with MAPMAKER/EXP 3.0. , 1992 .

[44]  B. Reddy,et al.  Genomic regions influencing resistance to the parasitic weed Striga hermonthica in two recombinant inbred populations of sorghum , 2004, Theoretical and Applied Genetics.

[45]  K. Devos,et al.  Genome Relationships: The Grass Model in Current Research , 2000, Plant Cell.

[46]  Andreas Graner,et al.  Genic microsatellite markers in plants: features and applications. , 2005, Trends in biotechnology.