Transcription Factor Networks in Leaves of <i>Cichorium endivia:</i> New Insights into the Relationship Between Photosynthesis and Leaf Development

• Main Authors: Giulio Testone, Elena Baldoni, M. Adelaide Iannelli, Chiara Nicolodi, Elisabetta Di Giacomo, Fabrizio Pietrini, Giovanni Mele, Donato Giannino, Giovanna Frugis
• Format: Article
• Language: English
• Published: MDPI AG 2019-11-01
• Series: Plants
• Subjects: transcription factors; photosynthesis; leaf shape; plant development; <i>cichorium endivia</i>; rna-seq; cluster analysis; gene co-expression networks
• Online Access: https://www.mdpi.com/2223-7747/8/12/531

<i>Cichorium endivia</i> is a leafy crop closely related to <i>Lactuca sativa </i>that comprises two major botanical varieties characterized by a high degree of intraspecific morphological variation: var. <i>latifolium</i> with broad leaves (escarole) and var. <i>crispum</i> with narrow crisp curly leaves (endive). To investigate the relationship between leaf morphology and photosynthetic activity, escaroles and endives were used as a crop model due to the striking morphological diversity of their leaves. We constructed a leaf database for transcription factors (TFs) and photosynthesis-related genes from a refined <i>C. endivia</i> transcriptome and used RNA-seq transcriptomic data from leaves of four commercial endive and escarole cultivars to explore transcription factor regulatory networks. Cluster and gene co-expression network (GCN) analyses identified two main anticorrelated modules that control photosynthesis. Analysis of the GCN network topological properties identified known and novel hub genes controlling photosynthesis, and candidate developmental genes at the boundaries between shape and function. Differential expression analysis between broad and curly leaves suggested three novel TFs putatively involved in leaf shape diversity. Physiological analysis of the photosynthesis properties and gene expression studies on broad and curly leaves provided new insights into the relationship between leaf shape and function.