Regulatory architecture of transcription factors underlying common bean response to anthracnose: integrating scientometrics, genomics, and interaction networks

Abstract

The common bean (Phaseolus vulgaris L.) is a legume of major importance in the diet of the Brazilian population, and diseases such as anthracnose are among the main factors limiting crop productivity. Understanding the molecular interactions within the bean– anthracnose pathosystem is essential for the development of sustainable disease management strategies. In this context, transcription factors (TFs) play a central role in regulating transcriptional programs involved in plant responses to biotic stresses. TF families such as MYB, NAC, WRKY, and ERF are widely recognized as important components of plant immunity. The analysis of these families within interaction networks allows the identification of central genes (hubs) that coordinate regulatory responses associated with plant defense. Among these families, WRKY transcription factors are well characterized in the model organism Arabidopsis thaliana, whose members participate in mechanisms of pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), regulating genes involved in the production of phenolic compounds, antimicrobial molecules, resistance proteins, and hormonal signaling pathways such as those mediated by salicylic acid (SA) and jasmonic acid (JA). In this context, this thesis aimed to analyze transcription factors differentially expressed in response to infection by Colletotrichum lindemuthianum race 65 in common bean through the construction of protein–protein interaction (PPI) networks, here referred to as the “Factorome,” as well as to perform a genome-wide characterization and expression analysis of the WRKY gene family in P. vulgaris. To achieve this objective, the thesis was structured into three complementary chapters. First, the Factorome was analyzed to identify TF families involved in the immune response of common bean to anthracnose. Next, a scientometric study was conducted to characterize the global research landscape related to WRKY transcription factors and plant resistance. Finally, a genome-wide analysis of the WRKY family in common bean was performed, together with the evaluation of its gene expression during anthracnose infection. Network analysis revealed the WRKY, NAC, and AP2/ERF families as central hubs in the response to infection and indicated a temporal dynamic in the activation and suppression of hormonal pathways associated with SA, JA, and ethylene at 48 and 96 hours after inoculation. The scientometric study identified the main researchers, institutions, and research trends related to the WRKY family, reinforcing its relevance in plant resistance studies. Genome-wide analysis identified 89 WRKY genes in P. vulgaris, revealing their structural diversity, repertoire of cis-regulatory elements, and evolutionary dynamics. The results indicate the presence of genes with expression patterns associated with resistance, whereas others display profiles consistent with susceptibility to anthracnose.