ISHS Acta Horticulturae 849: II International Symposium on Guava and other Myrtaceae
DEVELOPMENT OF GUAVA MICROSATELLITE (SSR) MARKERS USING THE SAT SOFTWARE |
| Authors: | A.M. Risterucci, G. Nansot, R. Grangeon, V. Lepitre, A. de Reeper, X. Argout, M. Ruiz, N. Billotte |
| Keywords: | Psidium guajava L., enriched genomic library, PCR primer design |
| DOI: | 10.17660/ActaHortic.2010.849.12 |
| Abstract:
Among the various PCR-based techniques, the simple sequence repeats (SSRs) or microsatellites are characterized by the co-dominant mode of inheritance which permits easy transfer of markers between genetic maps of different crosses in contrast to dominant PCR markers types such as RAPD or AFLP. Microsatellites detect multiple alleles at a single locus and a high level of polymorphism within cultivars; thus they are a powerful tool for the estimation of heterozygosity. A method for establishing genomic libraries enriched for microsatellites was developed, and results obtained on Psidium guava are presented. Designing optimal SSR markers from bulk sequence data is a laborious and time-consuming process. SAT (SSR Analysis Tool) is a user-friendly Web application developed to minimize tedious manual operations and reduce errors. This tool facilitates the integration, analysis, and display of sequence data from SSR-enriched libraries. SAT is designed to successively perform base calling and quality evaluation of chromatograms, eliminate cloning vector, adaptors and low quality sequences, detect chimera or partially digested sequences, search for SSR motifs, cluster and assemble the redundant sequences, and design SSR primer pairs. An additional virtual PCR step establishes primer specificity. Users may modify the different parameters of each step of the SAT analysis. Although certain steps are compulsory, such as SSR motif search and sequence assembly, users do not have to run the entire pipeline, and they can choose selectively which steps to perform. A database allows users to store and query results, and to redo individual steps of the workflow. | |
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