Study of the growth parameters of Polymyxa graminis f. sp. colombiana on rice roots and identification of the first candidate effectors through bioinformatics

Details

Supervisors

Legrève, Anne ; Genard, Margaux

Faculty

Faculté des bioingénieurs

Degree label

Master [120] : bioingénieur en sciences agronomiques, à finalité spécialisée

Abstract

Polymyxa graminis f. sp. colombiana is the vector of the Rice stripe necrosis virus and infects rice (Oryza sativa). Rice in a major staple food for global consumption, particularly in developing countries, and the RSNV threatens its production by reducing its yield to up to 40%. As of today, the only efficient control against the virus is the use of resistant cultivars and the adoption of culture rotation practices. A key parameter involved in the infection of host plants by parasites and pathogens is the expression of effectors. Effectors are defined as proteins and small molecules that alter host cell structures and functions, thereby facilitating the colonization of pathogens. As some of these effectors are essential for infection of the host, disturbing their function could lead to novels way of disease control. Therefore, this study aims at identifying candidate effectors responsible for host infection through comparison of genomic data with other relatives of the Plasmodiophorid family. Identification of candidate effectors is two step process. The first aims at identifying effectors through bioinformatics and the second aims at confirming their presence in a pathosystem involving Pgcol and rice. For that reason, Pgcol first had to be produced on rice. In this study Pgcol was grown on rice without much success. Consequently, several bioassays were made to study the ecological parameters involved in the development of Pgcol in rice. The influence of the nutritive solution pH, the type of watering system (collective or individual), the life form serving as inoculum and the dynamic of infection were studied. Additionally, the extraction of sporosores and the disinfection of rice seeds were studied. At the end of this study, no bioassay successfully produced satisfactory amounts of Pgcol. Our results indicate that using individual system over collective is more appropriate for Pgcol production. Several other parameters are hypothesized to potentially improve its production, but more study should be addressed to confirm them. Predicting candidate effectors was made by using BLAST software by comparing genomic data of Pgcol with three other plasmodiophorids: Pollymyxa betae, Plasmodiophora brassicae, and Spongospora subterranea. One hundred and nine candidate effectors were identified for the first time for Pgcol. Eleven of them correspond to candidate effectors of Pbras and are described in the literature. Interestingly, one is involved with the disruption of the chitin-triggered immunity of the host plant. Further study of the candidate effectors should be made to confirm their presence and function in planta.