Characterisation of microsatellite markers from sugarcane (Saccharum sp.), a highly polyploid species.

Cultivated sugarcane varieties (Saccharum spp) are derived from complex interspecific hybridisations between the species S. spontaneum (2n=40-128) and S. officinarum (2n=60 or 80). To analyse this complex genome, the potential of microsatellite repeats as genetic markers in sugarcane with respect to their abundance, variability and ability to detect polymorphisms was investigated. A set of microsatellite markers for genome analysis in cultivated sugarcane was identified from an enriched genomic DNA library constructed from Saccharum sp. cv Q124. Sequencing of 798 sugarcane genomic DNA clones from an enriched microsatellite library, yielded 457 inserts containing microsatellite repeat motifs. Just over 84% of the microsatellites contained dinucleotide or trinucleotide repeats averaging 15 and 13 repeat motifs, respectively. Primer sets were designed and synthesised for over 100 microsatellite sequences and tested on a set of five sugarcane cultivars. Both, heterozygosity as witnessed by the number of alleles, and length polymorphisms as seen in the differences in PCR product size for a particular allele were observed. Microsatellite markers are likely to have many applications in sugarcane genetics and breeding including germplasm analysis, cultivar identification, parent evaluation and marker assisted breeding.

[1]  Jonathan D. G. Jones,et al.  Germinal transpositions of the maize element Dissociation from T-DNA loci in tomato. , 1995, Genetics.

[2]  M. Smulders,et al.  Use of short microsatellites from database sequences to generate polymorphisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species , 1997, Theoretical and Applied Genetics.

[3]  P. Gupta,et al.  Microsatellites in plants: a new class of molecular markers , 2002 .

[4]  R. Bothmer,et al.  Characterization and analysis of microsatellite loci in Elymus caninus (Triticeae: Poaceae) , 1998, Theoretical and Applied Genetics.

[5]  W. Powell,et al.  Discriminating between barley genotypes using microsatellite markers. , 1997, Genome.

[6]  C. Chevalet,et al.  Interactions of selection, linkage and drift in the dynamics of polygenic characters. , 1996, Genetical research.

[7]  K. Edwards,et al.  Microsatellite libraries enriched for several microsatellite sequences in plants. , 1996, BioTechniques.

[8]  M. Maroof,et al.  Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations, and population dynamics. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[9]  J. Doyle,et al.  Isolation of plant DNA from fresh tissue , 1990 .

[10]  J. Glaszmann,et al.  RFLP mapping in cultivated sugarcane (Saccharum spp.): genome organization in a highly polyploid and aneuploid interspecific hybrid. , 1996, Genetics.

[11]  S. Kresovich,et al.  An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPS and pedigree , 1997, Theoretical and Applied Genetics.

[12]  M. Sorrells,et al.  Frequencies and sequence characteristics of di-, tri-, and tetra-nucleotide microsatellites in wheat. , 1996, Genome.

[13]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[14]  G. Bryan,et al.  Isolation and characterisation of microsatellites from hexaploid bread wheat , 1997, Theoretical and Applied Genetics.

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

[16]  H. Lafitte,et al.  Genetic analysis of adaptation differences between highland and lowland tropical maize using molecular markers , 1999, Theoretical and Applied Genetics.

[17]  K. Tsunewaki,et al.  Restriction fragment length polymorphism (RFLP) analysis in wheat. I. Genomic DNA library construction and RFLP analysis in common wheat. , 1990, Idengaku zasshi.

[18]  G. Bryan,et al.  Fifty new microsatellite loci for the wheat genetic map , 1998, Theoretical and Applied Genetics.

[19]  J. Glaszmann,et al.  A molecular approach to unraveling the genetics of sugarcane, a complex polyploid of the Andropogoneae tribe. , 1994, Genome.

[20]  S. Mccouch,et al.  Comparative evaluation of within-cultivar variation of rice (Oryza sativa L.) using microsatellite and RFLP markers. , 1997, Genome.

[21]  J. Irvine.  Saccharum species as horticultural classes , 1999, Theoretical and Applied Genetics.

[22]  C. Hackett,et al.  Identification of AFLP and SSR markers associated with quantitative resistance to Globodera pallida (Stone) in tetraploid potato (Solanum tuberosum subsp. tuberosum) with a view to marker-assisted selection , 1998, Theoretical and Applied Genetics.

[23]  G. Churchill,et al.  Optimizing parental selection for genetic linkage maps. , 1993, Genome.

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

[25]  M. Senior,et al.  Maize simple repetitive DNA sequences: abundance and allele variation. , 1996, Genome.

[26]  K. Edwards,et al.  Abundance and polymorphism of microsatellite markers in the tea tree (Melaleuca alternifolia, Myrtaceae) , 1999, Theoretical and Applied Genetics.

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

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