Genomics of Crucifer’s Host-Pathosystem at a Glance

Abstract

Crucifer’s crops are very important crop commodity with very significant contribution in the world’s need of human and animals yielding edible and industrial oil along with vegetables and forage crops of economic, trade, and food security. These groups of crops are challenged by numerous pathogens threatening their production at global level. Some of them have been exploited to reveal genomics of host–pathogen interaction to comprehend the molecular mechanisms of infection and pathogenesis for better management of diseases they cause and influence yield and quality losses. The genome of six Brassica crops has been sequenced after the sequencing of Arabidopsis thaliana genome. The genome size of A. thaliana is smallest with 125 Mb and B. napus genome is largest with 925 Mb. To get deeper insight into the molecular and biological functions of host–pathogen interaction, genome of major pathogens of crucifers has been sequenced and analyzed. Among pathogens, P. brassicae genome is compact and smallest with 24.2–25.5 Mb and G. orontii genome causing powdery mildew is largest with 160 Mb in size. The genome analysis of pathogens has facilitated phylogenetic, host specificity, pathogenicity factors/genes, and molecular events during crucifer’s host–pathogen interactions. The perception and understanding of molecular and genetical mechanisms of host–pathogen recognition and events of pathogenesis are regulated by genomics modulation of interacting host and pathogen. Pathogenomics have revealed host specificity, change of host range, and evolution of pathogenic variability. The R genes regulate functions, and molecular mechanisms of host–pathogen interactions. The timing of the induction of genes in R, and S varieties is crucial for mounting effective host defense to the pathogens. Transcriptomic analysis has revealed genes strongly associated with pathogenesis. The genes involved in cell response signaling, cell wall degradation, protein degradation, enzymes production, host transcriptional, and hormonal regulation are differentially expressed. The virulence mechanisms are transition period from biotrophy to necrotrophy to facilitate the acquisition of host nutrients by the pathogen. Differential expression of up and down regulated genes, and functional groups has been identified during host–pathogen interaction. The whole genome analysis of host and pathogen offers potential unbiased insight into the molecular mechanisms of host-pathosystem in crucifers.

For rapid, accuracy, less laborious, and less expensive way of detection and identification of crucifer’s pathogens, pathotypes, and effectors genes, molecular protocols have been used at field, and controlled laboratory conditions. The distinct lineages that had diverged from each other have also been detected. Molecular markers (RAPD, ESTs) have been used for detection and identification of genetical, and pathological variation and clades of pathogens. The molecular approaches have been allowed detection, identification, and quantification of pathogens host cell entry, area covered by pathogens in host tissues, seed, and soil. The RT-PCR protocols have been developed to detect, and discriminate AGs of R. solani from field, soil, and viruses along with their strains from Brassica species. High degree of genetic diversity has been recorded in major pathogens of crucifers in the form of pathotypes/races/strains differing in virulence, and host range on Brassica species and genotypes. The evolution of new virulence’s of pathogens is more common in areas where crops with major gene resistance coupled with genetic uniformity have been sown. The genomes of P. brassicae pathotypes Pb2, Pb5, and Pb8 have been sequenced to gain insight into genome variations and its correlations with host specificity. Phylogenetics of pathotypes has been assessed. The changes in pathotypes structure under field conditions have been analyzed through whole genome DNA similarity sequences. The infection of pathogens in Brassica species activates host metabolism to regulate carbohydrates, respiration, lipid profile, enzymes, toxins, H₂O₂, OH, phenols, hormones, nucleic acid, proteins, electrolytes, GSL, ROS, and other metabolites which affects crucifer’s physiology, biochemistry, and molecular events leading to pathogenesis. Several genes are differentially expressed during host–pathogen interaction for virulence at different stages of host infection and disease development. The genomics of crucifers host-pathosystem has been studies with simple, reproducible, and standardized methodology to elaborate genome sequencing of host as well as pathogen, events of host and pathogen interaction, signaling pathways, expression of different genes, analysis of transcriptome, biochemical changes, pathogenic variability, molecular markers, transition period from biotrophy to necrotrophy, detection, and identification of pathogens, pathotypes, and genes during the process of infection and pathogenesis of crucifer cops.