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Benchmarking database systems for Genomic Selection implementation

Nti-Addae Yaw, Matthews Dave, Ulat Victor Jun, Syed Raza, Sempere Guilhem, Petel Adrien, Renner Jon, Larmande Pierre, Guignon Valentin, Jones Elizabeth, Robbins Kelly. 2019. Benchmarking database systems for Genomic Selection implementation. Database, 2019:baz096, 10 p.

Journal article ; Article de revue à facteur d'impact Revue en libre accès total
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Quartile : Q2, Sujet : MATHEMATICAL & COMPUTATIONAL BIOLOGY

Abstract : Motivation: With high-throughput genotyping systems now available, it has become feasible to fully integrate genotyping information into breeding programs. To make use of this information effectively requires DNA extraction facilities and marker production facilities that can efficiently deploy the desired set of markers across samples with a rapid turnaround time that allows for selection before crosses needed to be made. In reality, breeders often have a short window of time to make decisions by the time they are able to collect all their phenotyping data and receive corresponding genotyping data. This presents a challenge to organize information and utilize it in downstream analyses to support decisions made by breeders. In order to implement genomic selection routinely as part of breeding programs, one would need an efficient genotyping data storage system. We selected and benchmarked six popular open-source data storage systems, including relational database management and columnar storage systems. Results: We found that data extract times are greatly influenced by the orientation in which genotype data is stored in a system. HDF5 consistently performed best, in part because it can more efficiently work with both orientations of the allele matrix.

Mots-clés Agrovoc : Génotype, Banque de données, Logiciel, amélioration génétique

Mots-clés complémentaires : génotypage, benchmarking

Classification Agris : U10 - Computer science, mathematics and statistics
C30 - Documentation and information
F30 - Plant genetics and breeding
L10 - Animal genetics and breeding

Champ stratégique Cirad : CTS 1 (2019-) - Biodiversité

Auteurs et affiliations

  • Nti-Addae Yaw, Cornell University (USA) - auteur correspondant
  • Matthews Dave, Boyce Thompson Institute (USA)
  • Ulat Victor Jun, CIMMYT
  • Syed Raza, Cornell University (USA)
  • Sempere Guilhem, CIRAD-BIOS-UMR INTERTRYP (FRA)
  • Petel Adrien, CIRAD-BIOS-UMR PVBMT (REU)
  • Renner Jon, University of Minnesota (USA)
  • Larmande Pierre, IRD (FRA)
  • Guignon Valentin, Bioversity International (FRA)
  • Jones Elizabeth, Cornell University (USA)
  • Robbins Kelly, Cornell University (USA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/593557/)

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