A genome-wide association study using a Vietnamese landrace panel of rice (Oryza sativa) reveals new QTLs controlling panicle morphological traits

Ta Nhung Kim, Khong Ngan Giang, Ha Thi Loan, Nguyen Dieu Thu, Mai Chung Duc, Hoang Thi Giang, Phung Nhung Thi Phuong, Bourrié Isabelle, Courtois Brigitte, Tran Thi Thu Hoai, Dinh Bach Yen, La Tuan Nghia, Do Vinh Nang, Lebrun Michel, Gantet Pascal, Jouannic Stefan. 2018. A genome-wide association study using a Vietnamese landrace panel of rice (Oryza sativa) reveals new QTLs controlling panicle morphological traits. BMC Plant Biology, 18 (1):282, 15 p.

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Quartile : Q1, Sujet : PLANT SCIENCES

Abstract : Context: Yield improvement is an important issue for rice breeding. Panicle architecture is one of the key components of rice yield and exhibits a large diversity. To identify the morphological and genetic determinants of panicle architecture, we performed a detailed phenotypic analysis and a genome-wide association study (GWAS) using an original panel of Vietnamese landraces. Results: Using a newly developed image analysis tool, morphological traits of the panicles were scored over two years: rachis length; primary, secondary and tertiary branch number; average length of primary and secondary branches; average length of internode on rachis and primary branch. We observed a high contribution of spikelet number and secondary branch number per panicle to the overall phenotypic diversity in the dataset. Twenty-nine stable QTLs associated with seven traits were detected through GWAS over the two years. Some of these QTLs were associated with genes already implicated in panicle development. Importantly, the present study revealed the existence of new QTLs associated with the spikelet number, secondary branch number and primary branch number traits. Conclusions: Our phenotypic analysis of panicle architecture variation suggests that with the panel of samples used, morphological diversity depends largely on the balance between indeterminate vs. determinate axillary meristem fate on primary branches, supporting the notion of differences in axillary meristem fate between rachis and primary branches. Our genome-wide association study led to the identification of numerous genomic sites covering all the traits studied and will be of interest for breeding programs aimed at improving yield. The new QTLs detected in this study provide a basis for the identification of new genes controlling panicle development and yield in rice.

Mots-clés Agrovoc : riz, Oryza sativa, genomic features [EN], Locus des caractères quantitatifs, Panicule, amélioration génétique

Mots-clés géographiques Agrovoc : Viet Nam

Mots-clés complémentaires : QTL, Architecture végétale

Classification Agris : F30 - Plant genetics and breeding
F50 - Plant structure

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Ta Nhung Kim, Agricultural Genetics Institute (VNM)
  • Khong Ngan Giang, Université de Montpellier (FRA)
  • Ha Thi Loan, Université de Montpellier (FRA)
  • Nguyen Dieu Thu, Université de Montpellier (FRA)
  • Mai Chung Duc, Université de Montpellier (FRA)
  • Hoang Thi Giang, Université de Montpellier (FRA)
  • Phung Nhung Thi Phuong, Université de Montpellier (FRA)
  • Bourrié Isabelle, Université de Montpellier (FRA)
  • Courtois Brigitte, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-2118-7102
  • Tran Thi Thu Hoai, PRC (VNM)
  • Dinh Bach Yen, PRC (VNM)
  • La Tuan Nghia, PRC (VNM)
  • Do Vinh Nang, Université de Montpellier (FRA)
  • Lebrun Michel, Université de Montpellier (FRA)
  • Gantet Pascal, UM2 (FRA)
  • Jouannic Stefan, IRD (FRA) - auteur correspondant

Source : Cirad-Agritrop (

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