Barley microsatellites: allele variation and mapping

Microsatellites have developed into a powerful tool for mapping mammalian genomes and first reports about their use in plants have been published. A database search of 228 barley sequences from GenBank and EMBL was made to determine which simple sequence repeat (SSR) motif prevails in barley. Nearly all types of SSRs were found. The (A)n and (T)n SSRs occurred more often than (C)n and (G)n for n≥10. Among the dinucleotide repeats, the (CG)n SSRs occurred least often. Trinucleotide repeats did not occur with n>7 and there is no correlation between the GC content in the trinucleotide motifs and the number of observed SSRs. Analysing 15 different microsatellites with 11 barleys yielded 2.1 alleles per microsatellite. Sequencing 25 putative microsatellites showed that the resolution capacity of highquality agarose gels was sufficient to determine differences of only three base paris. Five microsatellites were mapped on three different chromosomes of a barley RFLP map.

[1]  H. Hamada,et al.  A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[2]  D. Brunel.  A microsatellite marker in Helianthus annuus L. , 2004, Plant Molecular Biology.

[3]  S. Tingey,et al.  Genetic diagnostics in plant breeding: RAPDs, microsatellites and machines. , 1993, Trends in genetics : TIG.

[4]  D. Tautz,et al.  Simple sequences are ubiquitous repetitive components of eukaryotic genomes. , 1984, Nucleic acids research.

[5]  K. Davies.  Protection and susceptibility , 1993, Nature.

[6]  Xinping C. Zhao,et al.  Characterization and genetic mapping of a short, highly repeated, interspersed DNA sequence from rice (Oryza sativa L.) , 1992, Molecular and General Genetics MGG.

[7]  T. Close,et al.  A cDNA-based comparison of dehydration-induced proteins (dehydrins) in barley and corn , 1989, Plant Molecular Biology.

[8]  R. Jorgensen,et al.  Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[9]  D. Culley,et al.  Analysis of barley nitrate reductase cDNA and genomic clones , 1991, Molecular and General Genetics MGG.

[10]  R. Zielinski,et al.  Organization and expression of two tandemly oriented genes encoding ribulosebisphosphate carboxylase/oxygenase activase in barley. , 1991, The Journal of biological chemistry.

[11]  M. Thomas,et al.  Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs) , 1993, Theoretical and Applied Genetics.

[12]  S. Kauppinen.  Structure and expression of the Kas12 gene encoding a beta-ketoacyl-acyl carrier protein synthase I isozyme from barley. , 1992, The Journal of biological chemistry.

[13]  H. H. Kramer,et al.  Orienting Linkage Maps on the Chromosomes of Barley 1 , 1961 .

[14]  S. Weissman,et al.  Construction of libraries enriched for sequence repeats and jumping clones, and hybridization selection for region-specific markers. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[15]  A. Schulman,et al.  BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.) , 1993, Plant Molecular Biology.

[16]  D. Tautz.  Hypervariability of simple sequences as a general source for polymorphic DNA markers. , 1989, Nucleic acids research.

[17]  W. Crosby,et al.  Nucleotide sequence of a complete barley alcohol dehydrogenase 1 cDNA. , 1988, Nucleic acids research.

[18]  L. Andersson,et al.  The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. , 1993, Nucleic acids research.

[19]  P. Cregan,et al.  Length polymorphisms of simple sequence repeat DNA in soybean. , 1992, Genetics.

[20]  A. Graner,et al.  Construction of an RFLP map of barley , 1991, Theoretical and Applied Genetics.

[21]  G. Kochert,et al.  Phylogenetic distribution and genetic mapping of a (GGC)n microsatellite from rice (Oryza sativa L.) , 1993, Plant Molecular Biology.

[22]  P. Goodfellow,et al.  Variation is now the theme , 1992, Nature.

[23]  S. Tanksley,et al.  Abundance, polymorphism and genetic mapping of microsatellites in rice , 1993, Molecular and General Genetics MGG.

[24]  R. Rodriguez,et al.  The isolation and characterization of a barley 1,3‐1,4‐β‐glucanase gene , 1990 .

[25]  J. Ecker,et al.  Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. , 1994, Genomics.

[26]  E S Lander,et al.  A genetic map of the mouse suitable for typing intraspecific crosses. , 1992, Genetics.

[27]  M. Daly,et al.  MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. , 1987, Genomics.

[28]  M. Senior,et al.  Mapping maize microsatellites and polymerase chain reaction confirmation of the targeted repeats using a CT primer. , 1993, Genome.

[29]  K. Davies.  Of mice and men (and cows and cats) , 1993, Nature.

[30]  J. L. Weber,et al.  Survey of plant short tandem DNA repeats , 1994, Theoretical and Applied Genetics.

[31]  S. Tanksley,et al.  Genetic and physical mapping of barley telomeres , 1993, Molecular and General Genetics MGG.

[32]  P. J. Maughan,et al.  RFLP and microsatellite mapping of a gene for soybean mosaic virus resistance , 1994 .

[33]  L. Alexander,et al.  A microsatellite linkage map of the porcine genome. , 1994, Genetics.

[34]  C. Aragoncillo,et al.  Genetics of CM-proteins (A-hordeins) in barley , 1984, Theoretical and Applied Genetics.

[35]  A. Graner,et al.  Assessment of the degree and the type of restriction fragment length polymorphism in barley (Hordeum vulgare) , 1990, Theoretical and Applied Genetics.

[36]  F. Salamini,et al.  Structure of a chalcone synthase gene from Hordeum vulgare , 1991, Plant Molecular Biology.

[37]  S. Tanksley,et al.  Construction of a restriction fragment length polymorphism map for barley (Hordeum vulgare) , 1991 .

[38]  J. Devereux,et al.  A comprehensive set of sequence analysis programs for the VAX , 1984, Nucleic Acids Res..

[39]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[40]  S. Hubbell,et al.  Abundance and DNA sequence of two-base repeat regions in tropical tree genomes. , 1991, Genome.

[41]  G. Gyapay,et al.  A second-generation linkage map of the human genome , 1992, Nature.

[42]  D. Kudrna,et al.  A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome , 1993, Theoretical and Applied Genetics.

[43]  J. Rine,et al.  Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[44]  J. Beckmann,et al.  Toward a Unified Approach to Genetic Mapping of Eukaryotes Based on Sequence Tagged Microsatellite Sites , 1990, Bio/Technology.

[45]  F. Salamini,et al.  Structural analysis of the waxy locus from Hordeum vulgare. , 1988, Nucleic acids research.

[46]  M. Morgante,et al.  PCR-amplified microsatellites as markers in plant genetics. , 1993, The Plant journal : for cell and molecular biology.

[47]  J. Weber,et al.  Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. , 1989, American journal of human genetics.