RICE panicle branching

Functional diversity of genes involved in rice panicle architecture.


PIs: Dr. Stefan JOUANNIC (IRD) - Dr Le Thuy Ham (AGI)

Other peoples: Dr. Hélène Adam (IRD), Pr. Pascal Gantet (IRD/UM2), Dr. Khong Ngan Giang (AGI) Dr. Alain Ghesquières (IRD), Dr. La Tuan Nghia (PGRI), Dr Mai Duc Chung (AGI),  Msc. Nguyen Van Cuu (AGI), Msc Le Thi Loan (PGRI),


PhD student : Ta Kim Nhung (scholarships from 322 programme and GRiSP)


Scientific Background:


Inflorescence structure is a key character in the process of domestication, which often involves a change in the pattern and timing of branching, and ultimately the yield, since it directly affects the numbers of flowers and seeds produced. An understanding of the molecular mechanisms involved in panicle development in Asian rice species is an important issue for yield improvement breeding programs, through the identification of functional nucleotide polymorphisms (FNPs) suitable for marker-assisted selection (MAS). Cellular events associated to panicle development and genes affecting the panicle architecture and the seed number per panicle have already been described in O. sativa. Nevertheless, FNPs associated to these genes in O. sativa and/or other AA genome rice species have not been reported. Moreover, little is known about developmental and molecular mechanisms associated to panicle architecture in African rice.


Scientific Objectives:


The main objective of this project is to identify the determinants of the panicle architecture and function under optimal conditions and to assess their allelic diversity in both Asian and African species (cultivated and wild-relative species). The first part of the project will concern the analysis of the inter-specific diversity between cultivated and wild-relatives in Asia and Africa. The second part of the project will be specifically dedicated to the analysis of the panicle diversity of traditional Vietnamese accessions.




1.       Detailed characterization of the cellular processes at the origin of differential panicle architecture and functioning in various rice species: O. sativa, O. rufipogon, O. glaberrima and O. barthii selected among the set of accessions identified for deep resequencing. This approach will be sustained by the characterisation of expression pattern of key genes involved in O. sativa panicle development. This work will be conducted in France (IRD, Montpellier)

2.     Characterisation of the intra-specific diversity of traditional accessions of O. sativa from Vietnam through association mapping. A core-collection of Vietnamese accessions will be established through genotyping and phenotyping. In this context, the mature panicles from 270 accessions will be phenotyped in detail. This approach will identify contrasted accessions that will be further characterised in #1. This work will be conducted in Vietnam (IGA and PRC, Hanoi)

3.     Search for allelic diversity and FNPs through the analysis of O. sativa panicle-associated candidate gene allelic diversity in the AA genome rice species. This work will be conducted in Vietnam (IGA, Hanoi) and in France (IRD, Montpellier). Functional analysis of the FNPs identified will be conducted through transgenic approaches and will be supported by the Rice Functional Genomics Platform at CIRAD (France) and the IGA (Hanoi).


Evaluation of plantlets of the rice collection in the Plant Genetic Ressource Institute, Vietnam, July 2011

Mobility Planning

This project will be conducted on both sites: IRD-Montpellier and LMI/IAG-Hanoi. A PhD student from Vietnam will be involved in this project (Ms. Ta Kim Nhung). She will share her time between FR (9 months/year) and VN (3 months/year) over 3 years.

During the first year, a stays of 3 months are planned for Ta Kim Nhung (PhD student) and Dr. Stefan Jouannic (IRD) at the same time in order to initiate the activities concerning the diversity of panicule architecture of VN rice cultivars, and to plan the activities concerning the optimization of rice genetic transformation protocol.