Integrative transcriptomic and gene co-expression network analysis of host responses upon Verticillium dahliae infection in Gossypium hirsutum

Abstract

Worldwide, Verticillium wilt is among the major harmful diseases in cotton production, causing substantial reduction in yields. While this disease has been extensively researched at the molecular level of the pathogen, the molecular basis of V. dahliae host response association is yet to be thoroughly investigated. In this study, RNA-seq analysis was carried out on V. dahliae infected two Gossypium hirsutum L. cultivars, Xinluzao-36 (susceptible) and Zhongzhimian-2 (disease resistant) for 0 h, 24 h, 72 h and 120 h time intervals. Statistical analysis revealed that V. dahliae infection elicited differentially expressed gene responses in the two cotton varieties, but more intensely in the susceptible cultivar than in the resistant cultivars. Data analysis revealed 4241 differentially expressed genes (DEGs) in the LT variety across the three treatment timepoints whereas 7657 in differentially expressed genes (DEGs) in the Vd592 variety across the three treatment timepoints. Six genes were randomly selected for qPCR validation of the RNA-Seq data. Numerous genes encompassed in disease resistance and defense mechanisms were identified. Further, RNA-Seq dataset was utilized in construction of the weighted gene co-expression network and 11 hub genes were identified, that encode for different proteins associated with lignin and immune response, Auxin response factor, cell wall and vascular development, microtubule, Ascorbate transporter, Serine/threonine kinase and Immunity and drought were identified. This significant research will aid in advancing crucial knowledge on virus-host interactions and identify key genes intricate in G. hirsutum L. resistance to V. dahliae infection.

Antifungal effects of volatile organic compounds produced by Trichoderma koningiopsis T2 against Verticillium dahliae

“…The pathogenic mechanism of V. dahliae includes two theories, one of which is vascular bundle blockage theory (Ma et al, 2021). Studies have shown that V. dahliae has more enzymatic genes that degrade cell walls than other plant pathogenic fungi (Jeffress et al, 2020).…”

“…Due to the stable dormant structure microsclerotia, longterm variability, and coevolution with host plants (Ju et al, 2020;Höfer et al, 2021;Starke et al, 2021), controlling the spread of Verticillium wilt in plants remains challenging using currently available methods, such as chemical control, genetic breeding, and optimization of the cropping pattern (Ostos et al, 2020;Ramirez-Gil and Morales-Osorio, 2021;Zhang Y. L. et al, 2021). Disease resistance breeding is limited by a long breeding cycle and a lack of natural resistance resources, and chemical control has no beneficial effect on the control of soil-borne diseases (Diaz-Rueda et al, 2021;Hanika et al, 2021;Sunico et al, 2022).…”

“…are being successfully used and commercialized to combat a wide range of soil phytopathogenic fungi, such as Fusarium oxysporum, Rhizoctonia solani, Sclerotium rolfsii, S. cepivorum, and Alternaria alternate (Rabinal and Bhat, 2020;Godara and Singh, 2021;Khalil et al, 2021;Álvarez-García et al, 2022). The mechanisms of Trichoderma-based plant disease biocontrol include their capacity for nutrient and space competition, parasitism, secretion of antimicrobial metabolites (Cubilla-Ríos et al, 2019;da Silveira et al, 2021;Kamaruzzaman et al, 2021), activation of defense responses, and promotion of plant growth (Zehra et al, 2017;Chen et al, 2021). Among these approaches, the application of VOCs is considered a promising biocontrol strategy for the management of plant diseases, particularly soilborne diseases.…”

Revealing Genetic Differences in Fiber Elongation between the Offspring of Sea Island Cotton and Upland Cotton Backcross Populations Based on Transcriptome and Weighted Gene Coexpression Networks

“…However, few studies have focused on the use of extreme cotton fiber material in backcross populations to study elongation. In addition, Weighted gene coexpression network analysis (WGCNA) is very quick and efficient for mining functionally relevant genes in coexpression modules, and it has been widely used in a variety of crops to mine the corresponding candidate genes [ 77 , 78 , 79 , 80 ].…”

Transcriptome Analysis of a Cotton Cultivar Provides Insights into the Differentially Expressed Genes Underlying Heightened Resistance to the Devastating Verticillium Wilt

“…RNA-seq has been widely applied to monitor the gene expression profiles and describe the response characteristics of cotton roots under V. dahliae infection [ 17 , 28 , 29 , 30 , 31 , 32 ], and has a great potential to enrich our understanding of how cotton has elaborated various defense mechanisms against pathogen attacks. Therefore, in the current work, we conducted RNA-seq to discover the genes expressed in the roots of Gossypium hirsutum resistant cultivar Liaomian No.…”