Laboratoire Mixte International - “Functional Genomics and Biotechnology for Plants and associated Microorganisms”
1. History and Objectives
The International Joint Laboratory « Rice Functional Genomics and Plant Biotechnology » (LMI Rice) was set up in 2011 for a first period of 4 years within the scope of an agreement between different Vietnamese and French partners, and renewed as LMI RICE-2 for a period of 5 years starting in 2015. The Minister of Agriculture and Rural Development promulgated on May 2014 the plan to promote researches and applications of science and technology in agriculture sector to serve restructuring agriculture towards enhancing the added values and sustainable development.
Within this frameshift, LMI RICE-2 focuses on three major orientations:
1- Combining both functional genomics and association genetics approaches in rice to unravel mechanisms for the improvement of agronomical traits. The LMI Rice collection of ca 200 genotyped vietnamese rice lines is a unique resource and a pivotal tool to characterize rice determinants of the adaptation to various abiotic and biotic stresses to implement association genetic studies to propose pre-breeding varieties with improved agronomical traits. Projects that are already engaged in the frame of the first phase of the LMI Rice are continuing on: (i) abiotic stress resistance (salt, drought) and yield maintenance via the study of the genetics determinants of root system and panicle structure, (ii) biotic stresses resistance to pathogens (virus, nematodes, Xanthomonas), the mechanisms of interaction between rice and these pathogens and design of resistance engineering. New avenues will be explored in the: (i) research of QTL for nematode resistance and root development, (ii) role of aquaporine and water flux in relation with drought tolerance, (iii) mobilization of transposon in response to environmental constraints, (iv) interaction with beneficial microorganisms (endophytic and PGPR rhizobacteria) in relation with water stress and mineral nutrition. The sequencing of the vietnamese rice collection will be a priority. It will require a stronger anchoring with international programs and organizations (IRRI, CIAT,…) as well as the development of bioinformatics tools. The latter is of paramount importance for the formation in relation with USTH.
2- Setting up and developing a research project on coffee. Current partnerships (see below) between IRD, AGI, VAAS, USTH, UM have been opened to new partners: CIRAD that will establish the coffee project and UMR LSTM that will develop projects on rice and coffee interactions with soil beneficial microorganisms. The objectives are: (i) to introduce some coffee genetic resources, improved for tolerance to drought and heat as well as adapted to low levels of fertilizer, to use as root-stocks that will be assessed for nematode resistance in the Vietnam context, (ii) improve the growth of coffee by a better adaptation to nematodes and drought conditions through arbuscular mycorrhizal fungi (AM) interactions with the coffee root system in test cropping systems.
3- Capacity building and formation in plant breeding. The creation of the LMI Rice was associated with the new French-Vietnamese University of Sciences and Technology of Hanoi (USTH). The LMI RICE-2 organizes several teaching units in the master program “USTH Pharmacological, Medical & Agronomical Biotechnology” at USTH that includes plant biotechnology. LMI RICE-2 is continuously supporting capacity building in the field of plant biology with a special emphasis on plants breeding and the development of associated bioinformatic tools. The LMI is the research support of the local master program “USTH Pharmacological, Medical & Agronomical Biotechnology”. It has trained master and PhD students as well as young researchers.
2. Equipment
Most of the basic equipment are available to analyze from the gene to the plant.. Histology platform is a more specific tool developped in the LMI
No Equipment
1 Molecular biology: qPCR, PCR, Nanodrop, electroporator, centrifuge, electrophoresis, microplates analyzing, chemical hood, image analysis,…
2 Cellular biology, tissue culture, bacteriology: histology equipment, epifluo microscope and binoculary, contolled growth chambers, controlled growth room, -80C -20C storage, laminary hoods, ovens, autoclaves, …
3 Genetic: nethouse, field station, database storage,…
3. Current research activities
The two main axes of the research conducted at LMI RICE-2 are:
A- to capitalize on the unique LMI RICE collection of ca 200 genotyped Vietnamese rice to develop adaptation to biotic and biotic stresses, Yield and quality by GWAS, QTLs and functional genomics to identify favourable markers and release of pre-breeding material to the breeders.
- Ongoing rice projects that will continue: Root development and abiotic stress tolerance, Diversity of rice panicle architecture, Engineering of virus resistance, Rice Nematode interactions, Function and regulation of aquaporins
- New rice emerging projects: Rice endophytic Bradyrhizobia and adaptation to environment (PI: M. Lebrun, UM), Rice / Xanthomonas interaction (PI: S. Cunnac, IRD; Tuan Thu Tran, AGI), The rice-Mobilomes project: using active transposable elements to perform a large-scale comparative study of the response of Vietnamese rice genomes to stress (PI: M. Mirouze, IRD)
- An important aspect linked with the development of these projects will be the increase of the bioinformatics capacity (P. Larmande, BioInfo Eng IRD, 2016 LMI Hanoi). The capacity to set up high throughput phenotyping is scrutinized through the connection with the IRRI Rice Global Array program.
B- to set up and develop a new strategic project on coffee improvement: coffee genomics, genetics, micro-propagation and culture system in order to improve adaptation of new robusta varieties to biotic (nematodes) and abiotic (drought) stresses and quality improvement:
- First version of a research and technology transfer program on coffee in Vietnam, to create a Vietnamese national Robusta root-stock breeding program for nematode tolerance and improve Arabica lines for Vietnam. This project is established in the frame of the partnership of LMI RICE-2 with CIRAD (Benoit Bertrand (Chercheur CIRAD, IPME)  and Philippe Vaast (CIRAD, Ecosols), through two H2020 projects that are actually evaluated.
- Managing the native arbuscular mycorrhizal fungal communities to sustainably increase the productivity of coffee plantations in Vietnam in order to stimulate the establishment of the AM symbiosis and to promote the impacts of AM fungi on the development of coffee outplants (i.e. improvement of health status and mineral status) (Robin Duponnois (DR IRD, LSTM).
4. Five recent selected representative publications 
No Publication Authors Journal Article Year
1 Characterization of a panel of Vietnamese rice varieties using DArT and SNP markers for association mapping purposes HUNG N.T.P., MAI C.D., MOURNET P., FROUIN J., DROC G., TA N.K.,  JOUANNIC S., LE L.T., DO V.N., GANTET P., COURTOIS B. BMC Plant Biology, 14:371.
2 Meloidogyne incognita - rice (Oryza sativa) interaction: a new model system to study plant-root-knot nematode interactions in monocotyledons NGUYEN V.P., BELLAFIORE S., PETITOT A-S., HAIDAR R., BAK A., ABED A., GANTET P., MEZZALIRA I., de ALMEIDA-ENGLER J., FERNANDEZ D. Rice, 7, 23-36
3 p2 of Rice grassy stunt virus (RGSV) and p6 and p9 of Rice ragged stunt virus (RRSV) isolates from Vietnam exert suppressor activity on the RNA silencing pathway. NGUYEN T.D. LACOMBE S., BANGRATZ M., TA H.A., DO N.V., GANTET P., BRUGIDOU C.   Virus Genes, 51(2):267-275 2015
4 OsMADS26 Negatively Regulates Resistance to Pathogens and Drought Tolerance in Rice. P KHONG G.N., PATI P.K., RICHAUD F., PARIZOT B., BIDZINSKI P., MAI C.D., BÈS M., BOURRIÉ I., MEYNARD D., BEECKMAN T., SELVARAJ M.G., MANABU I., GENGA A.M., BRUGIDOU C., DO N.V., GUIDERDONI E., MOREL J.B., GANTET P. Plant Physiol., 169(4):2935-49. 2015
5 miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species. TA K.N., SABOT F., ADAM H., VIGOUROUX Y., DE MITA S., GHESQUIERE A., DO N.V., GANTET P., JOUANNIC S. Rice, 9(1):10 2016

5. Partnership

*) Vietnamese partners:
Agricultural Genetics Institute (AGI), Vietnam
University of Science and Technology of Hanoi (USTH), Vietnam
Vietnam Academy of Agricultural Science (VAAS), Vietnam
Plant Protection Research Institute (PPRI), Vietnam
Plant Resource Center (PRC), Vietnam

*) International partners:
Institut de Recherche pour le Développement (IRD), France
University Montpellier (UM), France
Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), France
LMI Constitutive Research Units: DIADE (UM/IRD), IPME (IRD/UM/CIRAD), LSTM (IRD, UM, CIRAD, INRA, SupAgro),
 and also strong partnership with:
AGAP (CIRAD, INRA, SupAgro), BPMP (CNRS, INRA, UM, SupAgro) and BGPI (INRA, CIRAD, SupAgro).

6. Available fundings
Type of funding Period Amount
USTH 2015-2019 Variable on project basis/year
IRD 2015-2019 ca. 40Keuros/year
University of Montpellier 2015-2019 15Keuros/year
Hoa Sen Lotus (French) 2015-2016 5 Keuros/year
Nafosted 1 (accepted 2016/3 years) 2017-2019 60KUSD(3 years)
Nafosted 2 (accepted 2016/3 years) 2017-2019 60KUSD(3 years)
MOST - “HoaSen” (accepted in 2016/2 years) 2017-2018 120KUSD (2 years)
ANR 2016-2019 120Keuros total
Open Science-Agropolis Fondation 2016-2018 40Keuros total
7. LMI RICE-2 Staffs
No Full name Position University/Institute Remark
Vietnamese Institutions researchers
1 Hoang Thi Giang R AGI  
2 Mai Duc Chung R AGI  
3 Ta Kim Nhung R AGI  
4 Do Nang Vinh R AGI  
6 To Thi Mai Huong L USTH  
7 Khong Ngan Giang R AGI  
International Institutions researchers
1 Bellafiore Stéphane R IRD  
2 Jouannic Stéphane R IRD Pro parte
3 Gantet Pascal R UM Pro parte
4 Larmande Pierre R IRD  
5 Lebrun Michel R UM  
PhD Students
1 Phung Nhung Phuong   AGI  
3 Nguyen Le Khanh   ARTS-IRD  
4 Malyna Suong   ARTS-IRD  
5 Nguyen Trang Hieu   French Ambassy  
6 Luong Ai My   French Ambassy