Genome-wide identification and characterization of defense-signaling network in bread wheat (Triticum aestivum L.)

Sethi, Avinash (2019) Genome-wide identification and characterization of defense-signaling network in bread wheat (Triticum aestivum L.). PhD thesis, Indian Institute of Science Education and Research Kolkata.

Text (PhD thesis of Avinash Sethi (13RS043)) 13RS043.pdf - Submitted Version Restricted to Repository staff only Download (4MB)

Abstract

Bread wheat (Triticum aestivum L.) is an important staple food worldwide, yet in-depth information on important components of defense signaling networks and small RNA (smRNA) pathways in wheat genomes (and most other grasses) has been critically limiting. Here, we have identified 54 gene families of defense-related phytohormone signaling and secondary metabolism pathways in wheat. We have performed genome-wide characterization, chromosome organization, gene structure analysis, and analysis of expression of these components in wheat. Wheat homologs were further mapped to other 15 Poaceae members; their phylogenetic maps were constructed and evolutionary studies were conducted. We also evaluated the contribution of tandem and segmental duplications in the generation of these gene families in Poaceae. In wheat, highest numbers of defense-related gene loci were localized on B sub-genome, specifically on chromosome 5BL while highest numbers of smRNA pathway genes were localized on A subgenome. Meta-analysis of wheat expression arrays showed complex pattern of gene expression in various plant tissues and during exposure to stress conditions. Evolutionary analysis showed that during the expansion of gene families of defense-signaling networks, many species specific group/subgroups have evolved. We have compiled all the information in form of the ‘wheat phylogenomics and signalling resource’ (WPSR), a user-friendly web-interface that facilitates easy sequence retrieval, alignment, visualization and interpretation of gene expression, coexpression networks and phylogenies. Role of defense signaling network and reprograming of smRNAs were elucidated in wheat during spot blotch and powdery mildew infection. SmRNA sequencing of wheat during spot blotch infection lead the identification of 390 conserved and 205 novel miRNAs which further strengthen our understanding on regulation of smRNAmediated defense responses. Non-conventional features of plant miRNA-mRNA interaction were employed to achieve accurate target prediction in non-model species. Further, miRNA-mRNA interactome associated with spot blotch infection in wheat was constructed. Collectively, this work provides a comprehensive annotated catalogue of signaling network and smRNAs. Functional characterization of plant defenses in wheat show a central role of SA and JA signaling in plant defenses against phytopathogens.

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