![]() Simple sequence repeats (SSRs), also known as microsatellites, and single nucleotide polymorphisms (SNPs) are the modern genetic markers currently being used in plant genetic analysis, together with anonymous marker systems, such as amplified fragment length polymorphisms (AFLPs). The generation of novel markers allows the production of high-density genetic maps and enables the genotype–phenotype link to be defined with greater precision. ![]() In human studies, they are frequently used for the identification of genes underlying inherited disorders ( Thorisson et al., 2005). Markers are used in agricultural breeding programmes to incorporate genetically characterized traits in place of field trials or glasshouse screens ( Gupta et al., 2001). The association of markers with heritable traits provides a link between the genotype of an organism and the expressed phenotype. They are used to define a genotype without the requirement to sequence the entire DNA content of the genome. Molecular genetic markers are based on variation in the genome that can be assayed and monitored between individuals and across generations. Overall, autoSNPdb can provide a wealth of genetic polymorphism information for any species for which sequence data are available. An average of one SNP per 240 bp was identified, with SNPs more prevalent in the 5′ regions and simple sequence repeat (SSR) flanking sequences. The correlation between SNPs and barley cultivar, expressed tissue type and development stage has been collated for ease of exploration. SNPs can be viewed and searched by sequence, functional annotation or predicted synteny with a reference genome, in this case rice. We have applied this software to public barley expressed sequences, and the resulting database is available over the Internet. ![]() We have extended the autoSNP method to produce autoSNPdb, which integrates SNP and gene annotation information with a graphical viewer. Confidence in the predicted SNPs is based on sequence redundancy, and haplotype co-segregation scores are calculated for a further independent measure of confidence. The SNP detection method autoSNP has been developed to identify SNPs from sequence data for any species. SNPs can be identified in silico, but care must be taken to ensure that the identified SNPs reflect true genetic variation and are not a result of errors associated with DNA sequencing. Single nucleotide polymorphisms (SNPs) are the most abundant molecular genetic marker. Molecular markers are used to provide the link between genotype and phenotype, for the production of molecular genetic maps and to assess genetic diversity within and between related species.
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