RICE panicle branching

Molecular and genetics determinants of panicle branching diversity in rice.


PIs: Dr. TA Kim Nhung (AGI) - Dr. KHONG Ngan Giang (AGI) - Dr. Stefan JOUANNIC (IRD)

Other people: Dr. Hélène ADAM (IRD), Dr. James TREGEAR (IRD), Pr. Pascal GANTET (UM), Dr. Alain GHESQUIERE (IRD), Dr. LA Tuan Nghia (PRC), Dr. TRAN Thu Hoai (PRC),Nguyen Thi Nhu, Tran Vu Hang

PhD student : LUONG Ai My (French Embassy scholarship 2016-2019)


Scientific Background

Structure of panicle (rice inflorescence) is a key morphological trait in the process of domestication and improvement, as directly related to the yield (i.e. seed number). An understanding of the molecular and genetic determinants involved in rice panicle development is an important issue for breeding programs related to yield, through the identification of functional nucleotide polymorphisms (FNPs) suitable for marker-assisted selection (MAS). Improvement or sustainability of rice yield in Vietnam is a big challenge in the context of growing population, extending urbanization and climatic changes. Vietnam possesses a huge diversity of traditional rice varieties due to its geographical situation and ecosystem panel. These Vietnamese resources still constitute a largely untapped and highly valuable genetic resource for local breeding programs. Genome wide association study (GWAS) becomes a powerful methodology to increase the range of natural variation and the number of significant loci, especially for complex agronomic traits such as yield. This methodology enables to valorize locally well-adapted traditional varieties.

Scientific Objectives

The main objective of this project is to identify new determinants of the panicle architecture and to assess their function under various conditions. The first part of the project is based on GWAS using a collection of Vietnamese landraces established in LMI/AGI in collaboration with the Plant Resource Centre in Vietnam (PRC). The second part of the project is related to the analysis of the functional diversity of genes related to panicle development.


field trial for panicle structure of the Vietnamese landrace collection



1. Genome-wide associated study:


    A core-collection of 159 Vietnamese accessions has been characterized through genotyping by sequencing (GBS) (Phung et al. 2014) and phenotyping. A detailed phenotying of mature panicle using P-TRAP software in field conditions has been done over two years. The GWAS methodology will allow identifying genomic regions associated to phenotypic diversity of panicle architecture and other yield component traits (e.g. tiller number). A detailed analysis of these regions will be carried out in order to identify putative FNPs and associated genes. This will lead also to select landraces of interest for these traits and to define genetic markers, both suitable for marker-assisted selection (MAS). A comparative analysis with African rice O. glaberrima will be carried out. This work is conducted in Vietnam (LMI/AGI, Hanoi), in collaboration with PRC (Hanoi) and EDI group in UMR DIADE-IRD (France).        

spread panicle of a vietnamese landrace analyzed using the P-TRAP software (Al Tam et al., 2013)               

2. Functional diversity of panicle architecture-related genes:

    To determine that genes identified through GWAS and transcriptomic analyses performed by the EDI group are related to panicle development and to the contrasted phenotypes observed in Vietnamese landraces, we will conduct functional analysis of these genes through transgenic approaches. In this context, optimization of genetic transformation of non-conventional rice varieties is undergoing. Furthermore, functional characterization of mutants affected in their panicle development is carried out. All these activities will be supported by the Rice Functional Genomics Platform at AGI (Hanoi), in collaboration with the EDI group (UMR DIADE-IRD) in France.

illustration of panicle structure diversity in the Vietnamese landrace panel


Phung N, Mai C, Mournet P, Frouin J, Droc G, Ta N, Jouannic S, Lê L, Do V, Gantet P, Courtois B (2014) Characterization of a panel of Vietnamese rice varieties using DArT and SNP markers for association mapping purposes. BMC Plant Biol 14:371.

Ta KN, Sabot F, Adam H, Vigouroux Y, De Mita S, Ghesquiere A, Do NV, Gantet P, Jouannic S (2016) miR2118-triggered phased siRNAs are differentially expre
ssed during the panicle development of wild and domesticated African rice species. Rice (N Y) 9:10.

Harrop TWR, Ud Din I, Gregis V, Osnato M, Jouannic S, Adam H, Kater MM (2016) Gene expression profiling of reproductive meristem types in early rice inflorescences by laser microdissection. The Plant Journal 86:75–88.

Ta KN, Khong NG, Phung TPN, Le HH, Do NV, Jouannic S (2016) Genome wide association study (GWAS): potential applications and challenges for rice breeding programe. VNUA (accepted)

Mobility Planning

This project will be conducted on two sites: IRD-Montpellier (EDI group_UMR DIADE) and LMI/AGI-Hanoi.

  • Ms LUONG Ai My, a PhD student from Vietnam will be involved in this project. She will share her time between France (9 months/year) and Vietnam (3 months/year) from 11/2016 to 10/2019. 
  • A 2-month stay for Dr H. ADAM is planned in 2017.