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Nov 30, 2018
The Plant Journal : For Cell And Molecular Biology
Recent advances in genomics technologies have greatly accelerated 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. Whilst these technological breakthroughs are significantly accelerating 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. Here 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 in order 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. This article is protected by copyright. All rights reserved.

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