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Bolger, A.M.* ; Poorter, H.* ; Dumschott, K.* ; Bolger, M.E.* ; Arend, D.* ; Osorio, S.* ; Gundlach, H. ; Mayer, K.F.X. ; Lange, M.* ; Scholz, U.* ; Usadel, B.*

Computational aspects underlying genome to phenome analysis in plants.

Plant J. 97, 182-198 (2018)
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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.
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Publication type Article: Journal article
Document type Scientific Article
Keywords Plant Genomes ; Plant Bioinformatics ; Plant Genome Annotation ; Phenotyping; Short Read Alignment; Wide Association; Next-generation; Sequence; Stress; Phenotype; Genotype; Accurate; Reconstruction; Architecture
Language
Publication Year 2018
HGF-reported in Year 2018
ISSN (print) / ISBN 0960-7412
e-ISSN 1365-313X
Journal Plant Journal, The
Quellenangaben Volume: 97, Issue: 1, Pages: 182-198 Article Number: , Supplement: ,
Publisher Wiley
Publishing Place 111 River St, Hoboken 07030-5774, Nj Usa
Reviewing status Peer reviewed
Institute(s) Research Unit Plant Genome and Systems Biology (PGSB)
POF-Topic(s) 30202 - Environmental Health
Research field(s) Environmental Sciences
PSP Element(s) G-503500-002
DOI 10.1111/tpj.14179
WOS ID WOS:000455506600013
Scopus ID 85059882668
PubMed ID 30500991
Erfassungsdatum 2018-12-12
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