Genomics of Crucifer’s Host-Pathosystem: Prologue

Abstract

Crucifer’s belong to the family Cruciferae containing over 3660 species which includes very important crops of human and animal needs yielding quality edible oil, industrial oilseeds, vegetables, and fodder crops. The largest group of crops contains 39 species of Brassicaceae grown all over the world including Arabidopsis thaliana which has been used widely for dissecting molecular mechanisms of crucifer’s host-pathosystem through multiomics approaches. Under natural and cultivated conditions, crucifer’s are challenged by several abiotic and biotic stresses viz., Albugo (White rust), Alternaria (Alternaria blight), Colletotrichum (Anthracnose), Erysiphe (Powdery mildew), Fusarium (Fusarium wilt), Hyaloperonospora (Downy mildew), Leptosphaeria (Blackleg), Plasmodiophora (Clubroot), Pseudocercosporella (White leaf spot), Pyrenopeziza (Light leaf spot), Sclerotinia (Stem rot), Turnip mosaic virus (TuMV), Verticillium (Verticillium wilt), Xanthomonas (Black rot), and Heterodera (Cyst nematode). These pathogens have been used as model host-pathosystem to reveal genomics of crucifer’s host-pathosystem. The genomics of plants was initiated after the sequencing of A. thaliana genome for the first time in 1990. The genome size of A. thaliana is 125 Mbp containing 25,498 genes encoding proteins from 11,000 families. Now, the genome of all the six Brassica species has been sequenced. The sequence analysis has revealed genome size of B. carinata 642 Mb, B. juncea 922 Mb, B. napus 925 Mb, B. nigra 591 Mb, B. oleracea 584.60 Mb, and B. rapa 485 Mb. The genome of major pathogens of crucifer’s has also been sequenced. The availability of genome sequence analysis of both host and pathogen has allowed rapid identification of candidate genes during different events of host–pathogen interaction to understand genes governing pathogenesis and host resistance. The application of omics technologies like NGS, Pangenomics, SNP, In Silico, BSA, Ren Seq, Effectoromics, Transcriptomics, Proteomics, Secretomics, Interactomics, and Metabolomics has benefitted greatly in revealing the complex biological, genetical, and molecular mechanisms of crucifer’s host-pathosystem. Crucifers have developed molecular mechanisms in response to multiple stresses which are activated through complex signaling pathways for the expression of genes to overcome these stresses. Several genes are differentially expressed in response to multiple stresses. At global level, 16 pathogens causing crucifers diseases are considered as of major consequences based on their geographical distribution, host range, losses caused, and resources spend to manage them. Using crucifer’s host-pathosystem with these pathogens, several genes have been identified, mapped on Brassica chromosomes with functional characterization, isolation, and cloning to produce resistant cultivars of Brassica. In recent years, QRT-PCR, a powerful and efficient technique has become the first choice in quantitative gene expression in crucifer’s host-pathosystem for various biological and molecular functions. However, data normalization is essential for reliable output of QRT-PCR assays to avoid unsuitable choice of reference genes.