Hybridization-Based Enrichment and Next Generation Sequencing to Explore Genetic Diversity in Plants

Irma Terracciano, Concita Cantarella and Nunzio D’Agostino ()
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Irma Terracciano: Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Centro di ricerca per l’orticoltura
Concita Cantarella: Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Centro di ricerca per l’orticoltura
Nunzio D’Agostino: Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) - Centro di ricerca per l’orticoltura

A chapter in Dynamics of Mathematical Models in Biology, 2016, pp 117-136 from Springer

Abstract: Abstract In plant research, targeted re-sequencing of enriched genomic DNA regions has become a scalable and cost-effective method for the discovery of genome-wide sequence variations to be exploited to address different biological questions. In this manuscript, we describe the main strategies to reduce genome complexity in plants with a special focus on hybridization-based enrichment methods. Then, we provide an overview of applications of target enrichment-based next generation sequencing (NGS) protocols in plant genetics and illustrate major bioinformatic approaches and tools for the analysis of NGS data, the identification of sequence polymorphisms, and their annotation to predict possible biological effects. Finally, we introduce our research activity on the use of hybridization-based target enrichment system for the identification of interesting sequence variations at candidate genes controlling carotenoid biosynthesis in tomato.

Keywords: Sequence capture; Target enrichment; Sequence polymorphisms; Variant calling; Allele mining (search for similar items in EconPapers)
Date: 2016
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Persistent link: https://EconPapers.repec.org/RePEc:spr:sprchp:978-3-319-45723-9_10

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DOI: 10.1007/978-3-319-45723-9_10

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