Gene regulatory network inference in soybean upon infection by Phytophthora sojae

• Published in: PloS one Vol. 18; no. 7; p. e0287590
• Main Authors: Hale, Brett, Ratnayake, Sandaruwan, Flory, Ashley, Wijeratne, Ravindu, Schmidt, Clarice, Robertson, Alison E, Wijeratne, Asela J
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 07.07.2023; Public Library of Science (PLoS)
• Subjects: Analysis; Arabidopsis - genetics; Arabidopsis thaliana; Artificial neural networks; Binding sites; Biology and Life Sciences; Cultivars; Deep learning; Deoxyribonucleic acid; Disease Resistance - genetics; DNA; DNA binding proteins; DNA sequencing; Drug resistance in microorganisms; Engineering and Technology; Flowers & plants; Gene expression; Gene Regulatory Networks; Genes; Genetic aspects; Genetic transcription; Genomes; Genomics; Glycine max; Glycine max - metabolism; Health aspects; Humans; Immune response; Infections; Inoculation; Instrument industry; Kinases; Machine learning; Neural networks; Next-generation sequencing; Pathogens; Phytophthora - genetics; Phytophthora sojae; Plant Diseases - genetics; Research and Analysis Methods; Soybean; Soybeans; Stem rot; Transcription factors; Transcriptomes; Virulence; United States
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0287590

Phytophthora sojae is a soil-borne oomycete and the causal agent of Phytophthora root and stem rot (PRR) in soybean (Glycine max [L.] Merrill). Yield losses attributed to P. sojae are devastating in disease-conducive environments, with global estimates surpassing 1.1 million tonnes annually. Historically, management of PRR has entailed host genetic resistance (both vertical and horizontal) complemented by disease-suppressive cultural practices (e.g., oomicide application). However, the vast expansion of complex and/or diverse P. sojae pathotypes necessitates developing novel technologies to attenuate PRR in field environments. Therefore, the objective of the present study was to couple high-throughput sequencing data and deep learning to elucidate molecular features in soybean following infection by P. sojae. In doing so, we generated transcriptomes to identify differentially expressed genes (DEGs) during compatible and incompatible interactions with P. sojae and a mock inoculation. The expression data were then used to select two defense-related transcription factors (TFs) belonging to WRKY and RAV families. DNA Affinity Purification and sequencing (DAP-seq) data were obtained for each TF, providing putative DNA binding sites in the soybean genome. These bound sites were used to train Deep Neural Networks with convolutional and recurrent layers to predict new target sites of WRKY and RAV family members in the DEG set. Moreover, we leveraged publicly available Arabidopsis (Arabidopsis thaliana) DAP-seq data for five TF families enriched in our transcriptome analysis to train similar models. These Arabidopsis data-based models were used for cross-species TF binding site prediction on soybean. Finally, we created a gene regulatory network depicting TF-target gene interactions that orchestrate an immune response against P. sojae. Information herein provides novel insight into molecular plant-pathogen interaction and may prove useful in developing soybean cultivars with more durable resistance to P. sojae.