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Practical Workflow from High-Throughput Genotyping to Genomic Estimated Breeding Values (GEBVs)

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Crop Breeding

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2264))

Abstract

The global climate is changing, resulting in significant economic losses worldwide. It is thus necessary to speed up the plant selection process, especially for complex traits such as biotic and abiotic stresses. Nowadays, genomic selection (GS) is paving new ways to boost plant breeding, facilitating the rapid selection of superior genotypes based on the genomic estimated breeding value (GEBV). GEBVs consider all markers positioned throughout the genome, including those with minor effects. Indeed, although the effect of each marker may be very small, a large number of genome-wide markers retrieved by high-throughput genotyping (HTG) systems (mainly genotyping-by-sequencing, GBS) have the potential to explain all the genetic variance for a particular trait under selection. Although several workflows for GBS and GS data have been described, it is still hard for researchers without a bioinformatics background to carry out these analyses. This chapter has outlined some of the recently available bioinformatics resources that enable researchers to establish GBS applications for GS analysis in laboratories. Moreover, we provide useful scripts that could be used for this purpose and a description of key factors that need to be considered in these approaches.

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Acknowledgment

The authors thank the BRESOV (Breeding for resilient, efficient and sustainable organic vegetable production) and TomGEM (A holistic multi-actor approach toward the design of new tomato varieties and management practices to improve yield and quality in the face of climate change) projects founded by the European Union Horizon 2020 research and innovation program under grant agreement No. 774244 and No. 679796, respectively. We also thank D’Acunzo D.M. for editing the manuscript.

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Authors and Affiliations

  1. CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano Faiano, Italy

    Felice Contaldi & Salvatore Esposito

  2. Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy

    Elisa Cappetta

Authors
  1. Felice Contaldi
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  2. Elisa Cappetta
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  3. Salvatore Esposito
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Editors and Affiliations

  1. Council for Agricultural Research and Economics - Research Centre for Vegetable and Ornamental Crops (CREA-OF), Pontecagnano, Salerno, Italy

    Pasquale Tripodi

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Contaldi, F., Cappetta, E., Esposito, S. (2021). Practical Workflow from High-Throughput Genotyping to Genomic Estimated Breeding Values (GEBVs). In: Tripodi, P. (eds) Crop Breeding. Methods in Molecular Biology, vol 2264. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1201-9_9

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  • DOI: https://doi.org/10.1007/978-1-0716-1201-9_9

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1200-2

  • Online ISBN: 978-1-0716-1201-9

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