RICE / nematodes Interactions




(The illustration shows a rice root system after infection by nematodes, we can observe galls and enlargement of roots that result of an induced modification of root morphogenesis by nematodes)




Project leaders: Dr. Stephane Bellafiore (IRD), Dr. Ngo Thi Xuyen (HUA), To Thi Mai Huong (USTH).

With: Nguyen Thi Hue, Kieu Thi Hanh
, Phung Thi Phuong Nhung, Elodie Chapuis (IRD), Jamel Aribi (IRD), Francois Anthony (IRD), Antony Champion (IRD), Guillaume Besnard (CNRS), Florent Tivet (Cirad)

PhD Student: Malyna Suong (IRD Scholarship), Trang Hieu Nguyen (French embassy Scholarship from

Scientific Background


   Plant parasitic nematodes are economically damaging pests on horticultural and field crops. Rice (Oryza sativa) can experience severe losses from Meloidogyne graminicola and Hirschmanniella oryzae in Asia. Meloidogyne graminicola is an obligate sedentary endoparasite particularly adapted to flooded conditions. Therefore, it can be found both in upland (rainfed) and lowland (irrigated) rice. Infection by nematodes alters the root’s vascular system disrupting the water and nutrient transport, all of which result in poor growth. In South East Asian countries such as Indonesia, Myanmar, Philippines, Thailand or Vietnam, we have generally observed a yield loss of 15 to 20 % in infested fields. Control of M. graminicola is possible with chemical nematicides. However, these are often too expensive, may be toxic and are under increasing legislative pressure (Montreal protocol, 2010). Damage due to M.graminicola can be limited by growing constantly under flooded conditions. However, rice-producing countries are being urged to change their water management practices to limit their impact on global warming caused by methane production in rice fields. As a result, cultivation of aerobic rice is largely
promoted but this system has its drawbacks as it is particularly favourable to Meloidogyne infection.

    In this context several approaches are conducted at the Joint International Laboratory “LMI-Rice” in order to understand pest behaviour and propose alternative strategies to control their impact for a sustainable agriculture.

Rice fields infected by nematods. A: presence of symptoms B: absence of symptoms

Scientific Objectives

The objectives of this project are as follows:

  • Develop DNA markers (SCAR, SNP, SSR) as useful tools for species identification and study of nematode genetic structure.
  •  Reveal the nematodes populations’ distribution, study their morphological and molecular diversity, and compare the aggressiveness of the identified isolated.
  •  Study the allelic diversity of nematodes effectors known to be key factors controlling the pathogenicity.
  •  Screen for natural resistant rice varieties (O. sativa and O. glaberrima) and characterize the resistance thanks to histological and molecular analysis. Positional cloning of the resistance genes.


  Our LMI-team belongs to the Nefonev team from the UMR IPME at IRD Montpellier (http://umr-ipme.ird.fr/). The main interests of the Nefonev team (Functional and evolutive nematology) are the diversity and the structure of the populations of plant parasitic nematodes (PPN). Our research projects are conducted in tropical and subtropical environments and are based on the interactions between plants and nematodes. In addition to our main site in Montpellier, we are also present in Vietnam (LMI RICE), Reunion (CIRAD 3P) and Martinique (CAEC).

    To this day, more than 4,100 species of PPN have been identified and amongst them are the root-knot nematodes from the genus Meloidogyne known to be one of the most damaging in agriculture (rice, coffee, etc…). In order to find new solutions for infestation control, our priority field of study is the interaction rice/M. graminicola as a biological model as it is so widely distributed and causes important yield losses (15 to 20%) in most of Asia’s rice agro-ecosystems. Our projects also integrate other nematodes species because of their aggressiveness on rice (Hirschmanniella oryzae, M. incognita, M. javanica, M. oryzae and M. salasi) and on coffee trees (M. exigua, M. incognita and M. javanica).

            Juvenile nematods seen under microscope    

    Our objectives are to reveal the nematodes populations’ distribution, to study their morphological and molecular diversity, and to compare the aggressiveness of the identified isolates. The parasitism is followed under different crop managements in order to propose sustainable practices with low nematode impact. A collection of the studied isolates is maintained at the LMI Rice and at Montpellier. The complete sequencing of several species and populations allows us to analyse the allelic diversity of nematodes effectors, as well as to develop SNP and SSR markers for better species identification and study of genetic structure. In combination with those investigations, we also study the morphological variability between our populations.


    Finally, in order to identify resistant varieties, the screening of a group of rice accessions including Asian and African species (Oryza sativa and O. glaberrima respectively) is being carried out. The histological and molecular analysis of rice plants resistant to the root-knot nematodes, as well as the positional cloning of the resistance genes are in progress.

Upcoming project

  • Discovery of QTLs associated with the sensitivity to Jasmonic acid that links to plant growth and stress tolerance in Vietnamese rice collection using Genome Wide Association Study

    Jasmonates (JA) is a central phyto-hormone which plays a crucial role in host immunity, stress response and is also an important regulator of plant growth and development. Many studies have investigated the important role of this hormone in response to wounding, pathogens and abiotic stress. It is also well known that JA negatively impacts the plant fitness in order to protect the plant from stresses resulting therefore in significant plant yield reduction.

    These contrasting activities of the hormone imply a broader role for the JAs in regulating a compromise between growthand defense-oriented metabolisms, thereby optimizing plant fitness in rapidly changing environments. In this study, we aim at discovering some significant QTLs linked to the JA sensitivity using Genome-Wide Association Studies (GWAS) approach. We will attempt to evaluate the correlation between the sensitivity to JA of these accessions and their tolerance to stress. In complement to GWAS, we will also evaluate the local and systemic response to salt stress and to wounding in rice using specific markers associated with JA sensitivity or JA biosensor in rice.

    Understanding the involvement of JA-expressed-genes in very early stages of their perception will allow us to directly target these factors. This is an effective way to reduce the energy loss due to activation of JA pathway, thus improving stress tolerance in rice

The fundings comes from Nafosted (Ministry Of Sciences and Technologies).

People involved: To Thi Mai Huong (PI), Phung Thi Phuong Nhung, Nguyen Thi Hue, Kieu Thi Hanh

Mobility Planning

Ms. Malyna Suong (PhD supported by an ARTS-IRD scholarship): Malyna works 2 months a year in France and 10 months a year between Cambodia (field experiments) and Vietnam (LMI Rice). Her work is on the “Molecular epidemiology of plant-parasitic nematode, Meloidogyne spp. associated with rice in Southeast Asia”

Mr. Nguyen Trang Hieu (PhD student, French Embassy scholarship): Hieu works 10 months a year in France (IRD-Montpellier) and 2 months a year at LMI Rice on the « Analyse quantitative et dynamique de la perception de l’hormone jasmonate en réponse aux stress environnementaux chez le riz ».

LMI Rice nematology publications

Mantelin S., Bellafiore S., and Kyndt T. Meloidogyne graminicola a major threat to rice agriculture. Molecular Plant Pathology (2016) in press DOI: 10.1111/mpp.12394

AL-Tam F., Dos Anjos A., Bellafiore S, Shahbazkia H.R. Detection of Root Knot Nematodes in Microscopy Images. Proceedings of the International Conference on Bioimaging (2015). doi.org/10.5220/000520900076 0081.

Bellafiore S., Jougla C., Chapuis E., Besnard G., Suong M., Nguyen Vu P., De Waele D., Gantet P., and Ngo Thi X. Characterization of Rice Root-knot Nematode (Meloidogyne graminicola) from Vietnamese Rice fields reveals intraspecific variability. C. R. Biologies (2015) 338:471-483.

Nguyen Vu P., Bellafiore S., Petitot A.S., Haidar R., Aurélie B.,Abed A., Gantet P., Almeida-Engler J., and Fernandez D. Histological and molecular analysis of Meloidogyne incognita development in rice (Oryza sativa). Rice (2014) 7 doi:10.1186/s12284-014- 0023-4.

Besnard G., Jühling F., Chapuis E., Zedane L., Lhuillier E., Mateille T., and Bellafiore S. Fast assembly of the mitochondrial genome of a plant parasitic nematode (Meloidogyne graminicola) using next generation sequencing. C. R. Biologies (2014) 337: 295-301.

Cabasan MTN., Kumar A., Bellafiore S., and De Waele D. Histopathology of the rice root-knot nematode, Meloidogyne graminicola, on Oryza sativa and O. glaberrima. Nematology (2014) 16:73-81.

Ngô Thị X., Nguyễn Tài Đ., Nguyễn Thị Mai H., Nguyễn Trung Đ., Gantet P., and Bellafiore S. Study on
Rice Root knot Nematode (Meloidogyne spp.) in Vietnam. Plant Protection Journal (2012) 1: 25-30.