Informative genomic microsatellite markers for efficient genotyping applications in sugarcane

• Published in: Theoretical and applied genetics 2009-01, Vol.118 (2), p.327-338
• Main Authors: Parida, Swarup K, Kalia, Sanjay K, Kaul, Sunita, Dalal, Vivek, Hemaprabha, G, Selvi, Athiappan, Pandit, Awadhesh, Singh, Archana, Gaikwad, Kishor, Sharma, Tilak R, Srivastava, Prem Shankar, Singh, Nagendra K, Mohapatra, Trilochan
• Format: Article
• Language: English
• Subjects: Agriculture; Base Sequence; Biochemistry; Biological and medical sciences; Biomedical and Life Sciences; Biotechnology; Classical genetics, quantitative genetics, hybrids; Cloning; Cultivars; Design; Fundamental and applied biological sciences. Psychology; Genetic diversity; Genetic Markers; Genetics of eukaryotes. Biological and molecular evolution; Genomes; Genomic Library; Genotype; Life Sciences; Microsatellite Repeats; Molecular Sequence Data; Original Paper; Phylogeny; Plant Biochemistry; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Polymerase Chain Reaction; Polymorphism; Polymorphism, Genetic; Pteridophyta, spermatophyta; Saccharum - genetics; Sequence Alignment; Sequence Analysis, DNA - methods; Sugarcane; Vegetals
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-008-0902-4

Genomic microsatellite markers are capable of revealing high degree of polymorphism. Sugarcane (Saccharum sp.), having a complex polyploid genome requires more number of such informative markers for various applications in genetics and breeding. With the objective of generating a large set of microsatellite markers designated as Sugarcane Enriched Genomic MicroSatellite (SEGMS), 6,318 clones from genomic libraries of two hybrid sugarcane cultivars enriched with 18 different microsatellite repeat-motifs were sequenced to generate 4.16 Mb high-quality sequences. Microsatellites were identified in 1,261 of the 5,742 non-redundant clones that accounted for 22% enrichment of the libraries. Retro-transposon association was observed for 23.1% of the identified microsatellites. The utility of the microsatellite containing genomic sequences were demonstrated by higher primer designing potential (90%) and PCR amplification efficiency (87.4%). A total of 1,315 markers including 567 class I microsatellite markers were designed and placed in the public domain for unrestricted use. The level of polymorphism detected by these markers among sugarcane species, genera, and varieties was 88.6%, while cross-transferability rate was 93.2% within Saccharum complex and 25% to cereals. Cloning and sequencing of size variant amplicons revealed that the variation in the number of repeat-units was the main source of SEGMS fragment length polymorphism. High level of polymorphism and wide range of genetic diversity (0.16-0.82 with an average of 0.44) assayed with the SEGMS markers suggested their usefulness in various genotyping applications in sugarcane.