Computational aspects underlying genome to phenome analysis in plants

Anthony M. Bolger, Hendrik Poorter, Kathryn Dumschott, Marie E. Bolger, Daniel Arend, Sonia Osorio, Heidrun Gundlach, Klaus F. X. Mayer, Matthias Lange, Uwe Scholz, Björn Usadel

Research output: Contribution to journalReview article

15 Citations (Scopus)
1 Downloads (Pure)

Abstract

Recent advances in genomics technologies have greatly accelerated the progress in both fundamental plant science and applied breeding research. Concurrently, high-throughput plant phenotyping is becoming widely adopted in the plant community, promising to alleviate the phenotypic bottleneck. While these technological breakthroughs are significantly accelerating quantitative trait locus (QTL) and causal gene identification, challenges to enable even more sophisticated analyses remain. In particular, care needs to be taken to standardize, describe and conduct experiments robustly while relying on plant physiology expertise. In this article, we review the state of the art regarding genome assembly and the future potential of pangenomics in plant research. We also describe the necessity of standardizing and describing phenotypic studies using the Minimum Information About a Plant Phenotyping Experiment (MIAPPE) standard to enable the reuse and integration of phenotypic data. In addition, we show how deep phenotypic data might yield novel trait-trait correlations and review how to link phenotypic data to genomic data. Finally, we provide perspectives on the golden future of machine learning and their potential in linking phenotypes to genomic features.

Original languageEnglish
Pages (from-to)182-198
Number of pages17
JournalPlant Journal
Volume97
Issue number1
DOIs
Publication statusPublished - Jan 2019

Bibliographical note

Copyright the Author(s) 2018. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Keywords

  • Genetic Association Studies
  • Genome, Plant/genetics
  • Genomics
  • Machine Learning
  • Phenomics
  • Phenotype
  • Plants/genetics
  • Quantitative Trait Loci/genetics
  • plant bioinformatics
  • plant genomes
  • plant genome annotation
  • phenotyping

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