1. History, Objectives and Research results

The International Joint Laboratory « Rice Functional Genomics and  Biotechnology for Plants and associated Microorganisms» (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, panicle structure and hormone effects, (ii) biotic stresses resistance to pathogens (nematodes, Xanthomonas, Magnaporthe), 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) root development in condition of phosphate depletion, (iv) mobilization of transposon in response to environmental constraints, (v) interaction with beneficial microorganisms (endophytic PGPR rhizobacteria and endomycorhiza) in relation with water stress, mineral nutrition and pathogens. The valorization of the sequenced 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 a new partner: 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 assess the conditions of adaptation of elite high quality Arabica coffee in Vietnamese environmental condition. This project is realized within the frame of a H2020 European Union program (“Breedcafs”), (ii) to improve the growth of robusta coffee grown in the center region of Vietnam 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. Partnership 

• Vietnamese partners 

1. Agricultural Genetics Institute (AGI)
2. Vietnam Academy of Agricultural Science (VAAS)
3. Plant Protection Research Institute (PPRI)
4. Plant Resource Center (PRC)

• International partners 

1. Institut de Recherche pour le Développement (IRD), France
2. University Montpellier (UM), France
3. Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), France
4. 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).

3. Funding sources

Type of funding	Period	Amount
USTH, GUST-VAST	2015-2020	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 2016/3years)	2017-2019	60KUSD(3years)
Nafosted 2 (accepted 2016/3years)	2017-2019	60KUSD(3years)
MOST-“HoaSen” (accepted in 2018/2years)	2018-2020	110KUSD (2 years)
ANR	2016-2019	120Keuros total
Open Science-Agropolis Fondation	2016-2018	40Keuros total
H2020 “Breedcafs”	2017-2021	4200keuros total for 19 participants

 

4. Equipment

Most of the basic equipment are available to analyze from the gene to the plant. Histology platform is a more specific tool developed 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,…

 

5. Ongoing 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 (PI: Hoang Thi Giang, AGI; Gantet P., UM, UMR DIADE), Diversity of rice panicle architecture (PI: Khong Ngan Giang, AGI; Jouannic S., IRD, UMR DIADE), Sensitivity to jasmonate (PI: To Thi Mai Huong, USTH; Champion A., IRD, UMR DIADE), Rice Nematode interactions (PI: Bellafiore S., IRD, UMR IPME), Function and regulation of aquaporins (PI: Hoang Thi Giang, AGI; Doan Trung Luu, CNRS, UMR BPMP)

- New rice emerging projects: Rice endophytic rhizobacteria and adaptation to environment (PI: Nguyen Van Phuong, USTH; M. Lebrun, UM/IRD/USTH), Rice / Xanthomonas interaction (PI: Cunnac S., IRD; Nguyen Duy Phuong, 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: Mirouze M., IRD, UMR DIADE), Characterization of rice plant adaptation to phosphate starvation (PI: Mai Thi Phuong Nga, USTH), Characterization of new resistance genes to blast disease (Magnaporthe oryzae) (PI: Hoang Thi Giang, AGI; Fournier E., INRA, UMR BGPI)

- An important aspect linked with the development of these projects will be the increase of the bioinformatics capacity (Larmande P., IRD/USTH). 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 elites high quality arabica varieties to vietnamese environmental conditions. This project is supported by a funding of the European Union H2020 “Breedcafs” program. (PI: Marraccini P., CIRAD)

- Managing the native arbuscular mycorrhizal fungal communities to sustainably increase the productivity of robusta coffee plantations in the central area of 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 (PI: Lebrun M., UM/IRD/USTH; Duponnois R., IRD, UMR LSTM).

6. Members

No	Full name	Position	University/Institute	Remark
Vietnamese members
1	Hoang Thi Giang	R	AGI
2	Ta Kim Nhung	R	AGI	Post-Doc in Japan
3	Do Nang Vinh	R	AGI
4	Mai Duc Chung	R	AGI
5	To Thi Mai Huong	L	USTH
6	Khong Ngan Giang	R	AGI
7	Nguyen Van Phuong	L	USTH
8	Mai Thi Phuong Nga	L	USTH
International members
1	Marraccini Pierre	R	CIRAD
2	Larmande Pierre	R	IRD/USTH	Pro parte ICT-USTH
3	Lebrun Michel	R	UM/IRD/USTH
4	Duong Benoît	VIA	IRD

 

7. Featured publications

No	Publications	Authors	Journal	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.	2014
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	2014
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
6	Differences in meristem size and expression of branching genes are associated with variation in panicle phenotype in wild and domesticated African rice.	TA K.N., ADAM H., STAEDLER Y.M., SHÖNENBERGER J., HARROP T., TREGEAR J., DO N.V., GANTET P., GHESQUIERE A., JOUANNIC S.	EvoDevo: 8, 1–14	2017
7	Hypersensitivity-Like Response to Meloidogyne graminicola in Rice (Oryza sativa).	PHAN N.T., DE WAELE D., LORIEUX M., XIONG L., BELLAFIORE S.	Phytopathology,108: 521–528	2018

 

8. Research outcomes or featured results have been achieved

The LMI Rice collection of ca 200 genotyped and sequenced vietnamese rice lines is a recognized 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.