Using single‐plant‐omics in the field to link maize genes to functions and phenotypes. Issue 12 (21st December 2020)

• Record Type: Journal Article
• Authors: Cruz, Daniel Felipe; De Meyer, Sam; Ampe, Joke; Sprenger, Heike; Herman, Dorota; Van Hautegem, Tom; De Block, Jolien; Inzé, Dirk; Nelissen, Hilde; Maere, Steven
• Is Part Of: Molecular systems biology. Volume 16:Issue 12(2020)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2020-12-21
• Subjects: field trial -- lab‐field gap -- predictive modeling -- single‐plant ‐omics -- Zea mays; Molecular biology -- Periodicals; Systems biology -- Periodicals; 572.8
• DOI: 10.15252/msb.20209667
• Languages: English
• ISSNs: 1744-4292

Abstract

Abstract: Most of our current knowledge on plant molecular biology is based on experiments in controlled laboratory environments. However, translating this knowledge from the laboratory to the field is often not straightforward, in part because field growth conditions are very different from laboratory conditions. Here, we test a new experimental design to unravel the molecular wiring of plants and study gene–phenotype relationships directly in the field. We molecularly profiled a set of individual maize plants of the same inbred background grown in the same field and used the resulting data to predict the phenotypes of individual plants and the function of maize genes. We show that the field transcriptomes of individual plants contain as much information on maize gene function as traditional laboratory‐generated transcriptomes of pooled plant samples subject to controlled perturbations. Moreover, we show that field‐generated transcriptome and metabolome data can be used to quantitatively predict individual plant phenotypes. Our results show that profiling individual plants in the field is a promising experimental design that could help narrow the lab‐field gap. SYNOPSIS: A new experimental design based on profiling individual plants of the same inbred line under uncontrolled field conditions produces gene function and phenotype predictions that complement predictions gathered from traditional lab‐based experiments. There is substantial variability in the transcriptomes, metabolomes and phenotypes of individual plants of the same genetic background grown in the same field. This variability can be used to predict gene functions and phenotypes of individual plants. Profiling individual field‐grown plants enables mapping of gene networks and phenotypes, and may help close the lab‐field gap. Abstract : A new experimental design based on profiling individual plants of the same inbred line under uncontrolled field conditions produces gene function and phenotype predictions that complement predictions gathered from traditional lab‐based experiments.