Comparative RNA-Seq analysis unfolds a complex regulatory network imparting yellow mosaic disease resistance in mungbean [Vigna radiata (L.) R. Wilczek]

Abstract

Yellow Mosaic Disease (YMD) in mungbean [Vigna radiata (L.) R. Wilczek] is one of the most damaging diseases in Asia. In the northern part of India, the YMD is caused by Mungbean Yellow Mosaic India Virus (MYMIV), while in southern India this is caused by Mungbean Yellow Mosaic Virus (MYMV). The molecular mechanism of YMD resistance in mungbean remains largely unknown. In this study, RNA-seq analysis was conducted between a resistant (PMR-1) and a susceptible (Pusa Vishal) mungbean genotype under infected and control conditions to understand the regulatory network operating between mungbean-YMV. Overall, 76.8 million raw reads could be generated in different treatment combinations, while mapping rate per library to the reference genome varied from 86.78% to 93.35%. The resistance to MYMIV showed a very complicated gene network, which begins with the production of general PAMPs (pathogen-associated molecular patterns), then activation of various signaling cascades like kinases, jasmonic acid (JA) and brassinosteroid (BR), and finally the expression of specific genes (like PR-proteins, virus resistance and R-gene proteins) leading to resistance response. The function of WRKY, NAC and MYB transcription factors in imparting the resistance against MYMIV could be established. The string analysis also revealed the role of proteins involved in kinase, viral movement and phytoene synthase activity in imparting YMD resistance. A set of novel stress-related EST-SSRs are also identified from the RNA-Seq data which may be used to find the linked genes/QTLs with the YMD resistance. Also, 11 defence-related transcripts could be validated through quantitative real-time PCR analysis. The identified gene networks have led to an insight about the defence mechanism operating against MYMIV infection in mungbean which will be of immense use to manage the YMD resistance in mungbean.

Insights into the Host-Pathogen Interaction Pathways through RNA-Seq Analysis of Lens culinaris Medik. in Response to Rhizoctonia bataticola Infection

“…[ 23 ]. For PHI-base analysis, Dasgupta et al [ 24 ] identified many transcripts as gene homologues which were found to be associated with both compatible and incompatible host-pathogen interactions (reduced virulence, unaffected pathogenicity, loss of pathogenicity, etc.) which is similar to what we have recorded in lentil when infected with Rhizoctonia .…”

“…Thus, comparative RNA-seq analysis has become a comprehensive approach for the identification of DEGs under infected and control conditions that help in the identification of the precise gene networks that are operating under infection, especially in the susceptible genotype [ 20 , 21 ]. This method has been widely applied to identify the plant-pathogen interactions in several crops such as rice [ 22 ], peanut [ 23 ], mungbean [ 24 ], and lentil [ 25 , 26 ].…”

“…The defense response by the plant is also regulated by several interconnected pathways which get triggered when PAMPs (pathogen-associated molecular patterns) are recognized by the transmembrane pattern recognition receptors (PRRs); which are known as PAMP-triggered immunity (PTI). Pathogens can overcome the PTI by way of secreting small molecules of pathogenic effectors into the host [ 23 , 24 ].…”

“…miR156, miR159, miR167, miR169, miR482), and several secondary metabolites. Thus, RNA-Seq analysis can be very effectively used as a tool to find the genome-wide transcriptional changes to the genes and proteins functions during plant-pathogen interaction [ 23 , 24 , 31 ]. Now, reports are appearing that demonstrate the differential expression of various genes as a result of the host-pathogen interactions in different crops including Ascochyta lentis infection (in lentil) [ 31 ].…”

The New Putative Type III Effector SkP48 in Bradyrhizobium sp. DOA9 is Involved in Legume Nodulation

“…The primer sets used for qRT-PCR are listed in Table S4. The transcript levels of selected V. radiata DEGs were normalized to the expression of the housekeeping gene β-actin as previously mentioned [39][40][41][42][43][44] .…”