Development of guava microsatellite (SSR) markers using the SAT software

Risterucci Ange-Marie, Nansot Grégoire, Grangeon Romain, Lepitre Vincent, Dereeper Alexis, Argout Xavier, Ruiz Manuel, Billotte Norbert. 2010. Development of guava microsatellite (SSR) markers using the SAT software. In : Proceedings of the Second International Symposium on guava and other Myrtaceae, Mérida, Mexico, November 10-13, 2008, Aguascalientes, Mexico, November 17-18, 2008. Rohde Wolfgang (ed.), Fermin Gustavo (ed.). ISHS. Louvain : ISHS [Belgique], 113-119. (Acta Horticulturae, 849) ISBN 978-90-6605-018-1 International Symposium on Guava and other Myrtaceae. 2, Mérida, Mexique, 10 Novembre 2008/18 Novembre 2008.

Résumé : The development and application of molecular genetic markers provide the opportunity to establish and evaluate measures for the quality of genetic resources collections. In particular, DNA-based polymorphisms are a powerful tool for the assessment of genetic diversity. Among the various molecular markers, RFLPs were the first to be used for plant genome studies, mapping and diversity analysis. However, RFLPs are labour-intensive, timeconsuming, and depend on large quantities of DNA which in instances such as some species requires purification by ultracentrifugation. PCR-based techniques can be readily used to detect polymorphisms with small amounts of DNA and are, therefore, convenient for genetic analysis of plants at early stages of development. Among the various PCR-based techniques, the simple sequence repeats (SSRs or microsatellites) are characterized by the codominant 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 polymorphisms within cultivars; thus they are a powerfull tool for the estimation of heterozygosity. A method for establishing genomic libraries enriched for microsatellites was developed, and results obtained on Psidium guava will be 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 motifs 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. The SAT Web application is available at http://sat.cirad.fr/sat.

Mots-clés Agrovoc : Psidium guajava

Classification Agris : F30 - Génétique et amélioration des plantes

Auteurs et affiliations

• Risterucci Ange-Marie, CIRAD-BIOS-UMR DAP (FRA)
• Nansot Grégoire
• Grangeon Romain
• Lepitre Vincent
• Dereeper Alexis
• Argout Xavier, CIRAD-BIOS-UMR DAP (FRA) ORCID: 0000-0002-0100-5511
• Ruiz Manuel, CIRAD-BIOS-UMR DAP (FRA) ORCID: 0000-0001-8153-276X
• Billotte Norbert, CIRAD-BIOS-UMR DAP (FRA)

Source : Cirad - Agritrop (https://agritrop.cirad.fr/549009/)

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