Universität zu Köln

Fernandes, Joel ORCID: 0000-0002-8557-0015 (2024). Analysis of immunity signalling pathways in rice (Oryza sativa). PhD thesis, Universität zu Köln.

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Abstract

Major crop innovations in agriculture rely on understanding how crop immune systems are controlled and how immunity receptors defend against pathogens. Plant pathogens translocate effectors (virulence factors) into plant cells to dampen immunity and increase pathogen growth inside the plant. Research efforts are focused mainly on understanding defence networks in the model plant Arabidopsis thaliana (A. thaliana). Probing and verifying the conservation of A. thaliana gene networks in crop genomes is an important step towards generating the next generation of crops that are resilient to environmental changes and not compromising on yield. Polymorphic nucleotide-binding leucine-rich repeat (NLR) receptors control effector triggered immunity (ETI). NLRs are divided into coiled-coil (CC) domain NLRs (CNLs) and Toll-Interleukin1 Receptor (TIR) domain NLRs (TNLs). The EDS1 lipase-like protein family (EDS1, PAD4 and SAG101) is well studied in Arabidopsis thaliana (A. thaliana) as essential signal transducers for TNLs and to transcriptionally reprogram defence and stress hormone pathways in ETI. TNLs and the downstream immunity genes SAG101 and NRG1s which act as a helper NLRs, have a central role in eudicot immunity but have been lost in monocots. Why co-functioning immunity genes (ADR1, EDS1and PAD4) are retained with only CNL sensors and some TIR-domain proteins in monocots, such as Oryza sativa (O. sativa), is not understood and represents the central research question I addressed in my PhD project. Rice has a diverse CNL receptor repertoire to defend against pathogens such as the blast fungus Magnaporthe oryzae pv oryzae (Mo), and other pathogens such as Xanthomonas oryzae to test my PhD question. Based on knowledge from A. thaliana immunity hubs, I generated rice CRISPR-Cas9 mutants in OsEDS1, OsPAD4, OsADR1 and OsICS1 genes. These mutant lines were crossed to generate combinatorial mutants in order to investigate immunity networks in rice. I first assessed physiological and developmental traits of my mutants under non-triggered conditions (unstressed greenhouse grown plants). Oseds1pad4 double mutant lines exhibited stunting and autoimmunity, which is not observed in A. thaliana eds1pad4 double mutants. I performed RNA-seq analysis of the rice mutants which revealed immunity gene modulation (CNLs and phytohormone pathway genes) as well as genes affecting development in Oseds1pad4 plants. Basal immunity to virulent Mo and Xanthomonas oryzae isolates required EDS1 and PAD4 as demonstrated by infection assays of single mutants. All tested CRISPR-Cas9 mutants were not compromised in CNL ETI to Mo effector AVRPia but were susceptible to a weakly recognized effector variant AVRPiaR43G, suggesting that the OsEDS1, OsPAD4 and OsADR1 genes are needed for full tissue-level immunity. Heterologous expression of OsEDS1, OsPAD4 and OsADR1 did not cause host cell death was not observed when these proteins were expressed. The results presented in this thesis provide new insights into the genetic and molecular architecture of a conserved hub (EDS1-family genes with ADR1) in rice innate immunity. Functional, structural and molecular insights and identification of upstream and downstream processes are important to understand this module better towards engineering sustainable crops

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Fernandes, Joel joel.lars.fernandes@gmail.com orcid.org/0000-0002-8557-0015 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-720928
Date:	2024
Place of Publication:	Cologne
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Außeruniversitäre Forschungseinrichtungen > MPI for Plant Breeding Research
Subjects:	Agriculture
Uncontrolled Keywords:	Keywords Language Rice basal immunity English Immunity signalling pathways English
Date of oral exam:	15 February 2023
Referee:	Name Academic Title Parker, Jane Prof. Dr. Kopriva, Stanislav Prof. Dr.
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/72092