Transcription Factor Networks in Leaves of Cichorium endivia: New Insights into the Relationship between Photosynthesis and Leaf Development

Abstract

Cichorium endivia is a leafy crop closely related to Lactuca sativa that comprises two major botanical varieties characterized by a high degree of intraspecific morphological variation: var. latifolium with broad leaves (escarole) and var. crispum 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 C. endivia 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.

The Regulation of CIN-like TCP Transcription Factors

“…The downregulation of LsTCP4 by the insertion led to the severer leaf serration in Empire type cultivars [ 61 ]. However, differential expression analysis between broad- and curly-leaved plants of Cichorium endivia , a close relative of L. sativa that also displayed wavy or serrated leaves, did not identify TCP4-like homologous genes as differentially expressed in leaves with different morphologies, and the two transcripts were abundant in both leaf types [ 62 ]. Tomato forms compound leaves regulated by LACEOLATE ( LA ) homologous to CIN- like TCPs .…”

A Comparative Transcriptomic Meta-Analysis Revealed Conserved Key Genes and Regulatory Networks Involved in Drought Tolerance in Cereal Crops

“…To identify putative upstream regulators of the differentiation between tolerant and sensitive responses, we selected the TF-encoding DEGs of the four species ( Supplementary File S3 ) and we performed a k-means cluster analysis of the gene expression profiles of the CDT genes together with the TF–DEGs for each species. The optimum cluster number was determined based on converging results of the sum of squared errors (SSE) estimate and the Calinsky criterion, as described by Testone et al [ 58 ]. The analysis defined the presence of four different expression clusters for each species ( Figure 4 , Supplementary File S4 ).…”

“…These genes were positively correlated to SGR ( Table S8 ), fully corroborating the k-means clustering data. Node degree, which, in a GCN network, is the number of neighbours to which a node directly connects, is an important centrality parameter that identifies essential genes in the network [ 58 , 60 ]. In this respect, the GCN analysis identified PsaO, PsaK , and LHCB , with node degrees of 429, 418, and 410 respectively, as hub central genes in the osmotic stress response.…”

“…Each gene was indexed according to the species (Bd: B. distachyon; Hv: H. vulgare; Os: O. sativa; Zm: Z. mays ). The optimum number of clusters was determined as described by Testone et al (2019) [ 58 ]. Data scaling, k-means clustering, and visualization were performed in R according to the methods of Morgan et al [ 111 ].…”

Chromosome-Level Genome Assembly for Acer pseudosieboldianum and Highlights to Mechanisms for Leaf Color and Shape Change

“…Leaf shape is a complex trait controlled by multiple genes and is of great significance for plant photosynthetic energy storage and resistance to stress ( Testone et al, 2019 ; He P. et al, 2020 ). Teosinte branched1, cycloidea, and proliferating cell factors (TCPs), belonging to the bHLH transcription factor family, are widely involved in leaf morphology regulation ( Aggarwal et al, 2010 ; Zhao M. L. et al, 2020 ; Lan et al, 2021 ).…”