Genome-wide association mapping of leaf mass traits in a Vietnamese rice landrace panel

Hoang Giang Thi, Gantet Pascal, Nguyen Kien Huu, Phung Nhung Thi Phuong, Ha Loan Thi, Nguyen Tuan Thanh, Lebrun Michel, Courtois Brigitte, Pham Xuan Hoi. 2019. Genome-wide association mapping of leaf mass traits in a Vietnamese rice landrace panel. PloS One, 14 (7):e0219274, 18 p.

Journal article ; Article de revue à facteur d'impact Revue en libre accès total
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Thème(s) HCERES des revues (en SHS) : Psychologie-éthologie-ergonomie; Staps

Abstract : Leaf traits are often strongly correlated with yield, which poses a major challenge in rice breeding. In the present study, using a panel of Vietnamese rice landraces genotyped with 21,623 single-nucleotide polymorphism markers, a genome-wide association study (GWAS) was conducted for several leaf traits during the vegetative stage. Vietnamese landraces are often poorly represented in panels used for GWAS, even though they are adapted to contrasting agrosystems and can contain original, valuable genetic determinants. A panel of 180 rice varieties was grown in pots for four weeks with three replicates under nethouse conditions. Different leaf traits were measured on the second fully expanded leaf of the main tiller, which often plays a major role in determining the photosynthetic capacity of the plant. The leaf fresh weight, turgid weight and dry weight were measured; then, from these measurements, the relative tissue weight and leaf dry matter percentage were computed. The leaf dry matter percentage can be considered a proxy for the photosynthetic efficiency per unit leaf area, which contributes to yield. By a GWAS, thirteen QTLs associated with these leaf traits were identified. Eleven QTLs were identified for fresh weight, eleven for turgid weight, one for dry weight, one for relative tissue weight and one for leaf dry matter percentage. Eleven QTLs presented associations with several traits, suggesting that these traits share common genetic determinants, while one QTL was specific to leaf dry matter percentage and one QTL was specific to relative tissue weight. Interestingly, some of these QTLs colocalize with leaf- or yield-related QTLs previously identified using other material. Several genes within these QTLs with a known function in leaf development or physiology are reviewed.

Mots-clés Agrovoc : Oryza, Feuille, Morphologie végétale, Photosynthèse, Chloroplaste

Mots-clés géographiques Agrovoc : Viet Nam

Mots-clés libres : Leaves, Quantitative trait loci, Rice, Genome-wide association study, Chloroplasts, Leaf development, Panicles, Photosynthesis

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

Champ stratégique Cirad : CTS 1 (2019-) - Biodiversité

Auteurs et affiliations

  • Hoang Giang Thi, Agricultural Genetic Institute (VNM)
  • Gantet Pascal, UM2 (FRA)
  • Nguyen Kien Huu, Agricultural Genetic Institute (VNM)
  • Phung Nhung Thi Phuong, Agricultural Genetic Institute (VNM)
  • Ha Loan Thi, Agricultural Genetic Institute (VNM)
  • Nguyen Tuan Thanh, VNUA (VNM)
  • Lebrun Michel, IRD (FRA)
  • Courtois Brigitte, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-2118-7102
  • Pham Xuan Hoi, Agricultural Genetic Institute (VNM) - auteur correspondant

Source : Cirad-Agritrop (

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