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An Overview of Genoty** by Sequencing in Crop Species and Its Application in Pepper

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Dynamics of Mathematical Models in Biology

Abstract

The exploitation of genetic variation in crops is essential to establish innovative breeding programs in the frame of global population increase and the sustainable intensification of agriculture. The advent of next generation sequencing technologies and the availability of complete or draft genome sequences of many crops allowed the development of several methods for SNP discovery. Genoty** by sequencing (GBS) has recently emerged as a promising approach to simultaneously allow SNP identification and genoty**. GBS provides a rapid, highly informative, high-throughput and cost-effective tool for exploring plant genetic diversity on a genome-wide scale and does not require any a priori knowledge on the genome of the species of interest. The features of GBS make it an attractive technology for (1) the assessment of population structure of germplasm collections; (2) the development of high density linkage maps and (3) genetic map** studies. Herein, we present an overview of the GBS method and describe the main protocols in use, the principal methods for genetic diversity analysis and potential applications of the results in crop breeding programs. Finally, we illustrate the strategy we adopted to investigate the genetic diversity in cultivated pepper (Capsicum annuum).

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Acknowledgements

This project was supported by the ‘GenHort’ project funded by the Italian Ministry of University and Research (MIUR, PON02_00395_3215002) and the ‘PEPIC’ project funded by the Italian Ministry of Agricultural, Food and Forestry.

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  1. Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) – Centro di ricerca per l’orticoltura, Via dei Cavalleggeri 25, Pontecagnano Faiano (SA), Italy

    Francesca Taranto, Nunzio D’Agostino & Pasquale Tripodi

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  1. Francesca Taranto
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  2. Nunzio D’Agostino
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  3. Pasquale Tripodi
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Correspondence to Pasquale Tripodi .

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  1. National Research Council, Institute of Biosciences and Bioresources, Naples, Napoli, Italy

    Alessandra Rogato

  2. National Research Council, Institute of Genetics and Biophysics, ABT, Naples, Italy

    Valeria Zazzu

  3. Laboratory for Genomics, Transcriptomics and Proteomics (Lab-GTP), High Performance Computing and Networking Institute (ICAR) National Research Council (CNR), Naples, Italy

    Mario Guarracino

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Taranto, F., D’Agostino, N., Tripodi, P. (2016). An Overview of Genoty** by Sequencing in Crop Species and Its Application in Pepper. In: Rogato, A., Zazzu, V., Guarracino, M. (eds) Dynamics of Mathematical Models in Biology . Springer, Cham. https://doi.org/10.1007/978-3-319-45723-9_9

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