Unravelling the Complex Interplay of Transcription Factors Orchestrating Seed Oil Content in Brassica napus L.

Abstract

Transcription factors (TFs) and their complex interplay are essential for directing specific genetic programs, such as responses to environmental stresses, tissue development, or cell differentiation by regulating gene expression. Knowledge regarding TF–TF cooperations could be promising in gaining insight into the developmental switches between the cultivars of Brassica napus L., namely Zhongshuang11 (ZS11), a double-low accession with high-oil- content, and Zhongyou821 (ZY821), a double-high accession with low-oil-content. In this regard, we analysed a time series RNA-seq data set of seed tissue from both of the cultivars by mainly focusing on the monotonically expressed genes (MEGs). The consideration of the MEGs enables the capturing of multi-stage progression processes that are orchestrated by the cooperative TFs and, thus, facilitates the understanding of the molecular mechanisms determining seed oil content. Our findings show that TF families, such as NAC, MYB, DOF, GATA, and HD-ZIP are highly involved in the seed developmental process. Particularly, their preferential partner choices as well as changes in their gene expression profiles seem to be strongly associated with the differentiation of the oil content between the two cultivars. These findings are essential in enhancing our understanding of the genetic programs in both cultivars and developing novel hypotheses for further experimental studies.

In Silico Identification of the Complex Interplay between Regulatory SNPs, Transcription Factors, and Their Related Genes in Brassica napus L. Using Multi-Omics Data

“…In the same way, NAC genes were upregulated after the induction of a cold shock [47]. Interestingly, we have shown that members of TF families such as GATA, DOF, NAC, or MYB are important regulators of genes with a monotonic expression pattern in both cultivars in the seed tissue by forming TF co-operations [48].…”

Transcriptional Regulation of Quinoa Seed Quality: Identification of Novel Candidate Genetic Markers for Increased Protein Content

“…Thus, large changes in the gene expression patterns associated with glycolysis can probably also affect the allocation of carbon between different storage compounds during the development of seeds. However, there is a complex interplay between different transcription factors involved in seed developmental processes that can also be of importance for metabolic switches directed to oil synthesis ( Fatihi et al, 2016 ; Rajavel et al, 2021 ).…”

Identification of the Complex Interplay Between Nematode-Related lncRNAs and Their Target Genes in Glycine max L.

“…Two distinct sets of ME-lncRNAs (with corresponding p-values) were found with ascending or descending monotonic expression patterns. To meet the efficient level of stringency for monotonicity, we defined the parameters as permut = 100, svdetimes = 100, and svdenoise = 0.1, according to (Rajavel et al, 2021). Eventually, ME-lncRNAs with a CPM >1 and sample variance for discriminating error value ≤1 were considered as significant ME-lncRNAs.…”