A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize

Autoři: Clément Cuello aff001;  Aurélie Baldy aff001;  Véronique Brunaud aff002;  Johann Joets aff004;  Etienne Delannoy aff002;  Marie-Pierre Jacquemot aff001;  Lucy Botran aff001;  Yves Griveau aff001;  Cécile Guichard aff002;  Ludivine Soubigou-Taconnat aff002;  Marie-Laure Martin-Magniette aff002;  Philippe Leroy aff006;  Valérie Méchin aff001;  Matthieu Reymond aff001;  Sylvie Coursol aff001
Působiště autorů: Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France aff001;  Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France aff002;  Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Gif-sur-Yvette, France aff003;  Génétique Quantitative et Evolution—Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-Sur-Yvette, France aff004;  UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, Paris, France aff005;  GDEC, INRA, UCA, Clermont-Ferrand, France aff006
Vyšlo v časopise: PLoS ONE 14(12)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0227011


Understanding the mechanisms triggering variation of cell wall degradability is a prerequisite to improving the energy value of lignocellulosic biomass for animal feed or biorefinery. Here, we implemented a multiscale systems approach to shed light on the genetic basis of cell wall degradability in maize. We demonstrated that allele replacement in two pairs of near-isogenic lines at a region encompassing a major quantitative trait locus (QTL) for cell wall degradability led to phenotypic variation of a similar magnitude and sign to that expected from a QTL analysis of cell wall degradability in the F271 × F288 recombinant inbred line progeny. Using DNA sequences within the QTL interval of both F271 and F288 inbred lines and Illumina RNA sequencing datasets from internodes of the selected near-isogenic lines, we annotated the genes present in the QTL interval and provided evidence that allelic variation at the introgressed QTL region gives rise to coordinated changes in gene expression. The identification of a gene co-expression network associated with cell wall-related trait variation revealed that the favorable F288 alleles exploit biological processes related to oxidation-reduction, regulation of hydrogen peroxide metabolism, protein folding and hormone responses. Nested in modules of co-expressed genes, potential new cell-wall regulators were identified, including two transcription factors of the group VII ethylene response factor family, that could be exploited to fine-tune cell wall degradability. Overall, these findings provide new insights into the regulatory mechanisms by which a major locus influences cell wall degradability, paving the way for its map-based cloning in maize.

Klíčová slova:

Cell walls – Gene expression – Genetic loci – Genomics – Maize – Plant cell walls – Plant genomics – Quantitative trait loci


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2019 Číslo 12
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