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Genome-wide association study of a panel of vietnamese rice landraces reveals new QTLs for tolerance to water deficit during the vegetative phase

Hoang Giang Thi, Van Dinh Lam, Nguyen Thom Thi, Ta Nhung Kim, Gathignol Floran, Mai Chung Duc, Jouannic Stefan, Tran Khanh Dang, Khuat Trung Huu, Do Vinh Nang, Lebrun Michel, Courtois Brigitte, Gantet Pascal. 2019. Genome-wide association study of a panel of vietnamese rice landraces reveals new QTLs for tolerance to water deficit during the vegetative phase. Rice, 12:4, 20 p.

Journal article ; Article de revue à facteur d'impact
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Quartile : Q1, Sujet : AGRONOMY

Abstract : Background: Drought tolerance is a major challenge in breeding rice for unfavorable environments. In this study, we used a panel of 180 Vietnamese rice landraces genotyped with 21,623 single-nucleotide polymorphism markers to perform a genome-wide association study (GWAS) for different drought response and recovery traits during the vegetative stage. These landraces originate from different geographical locations and are adapted to different agrosystems characterized by contrasted water regimes. Vietnamese landraces are often underrepresented in international panels used for GWAS, but they can contain original genetic determinants related to drought resistance. Results: The panel of 180 rice varieties was phenotyped under greenhouse conditions for several drought-related traits in an experimental design with 3 replicates. Plants were grown in pots for 4 weeks and drought-stressed by stopping irrigation for an additional 4 weeks. Drought sensitivity scores and leaf relative water content were measured throughout the drought stress. The recovery capacity was measured 2 weeks after plant rewatering. Several QTLs associated with these drought tolerance traits were identified by GWAS using a mixed model with control of structure and kinship. The number of detected QTLs consisted of 14 for leaf relative water content, 9 for slope of relative water content, 12 for drought sensitivity score, 3 for recovery ability and 1 for relative crop growth rate. This set of 39 QTLs actually corresponded to a total of 17 different QTLs because 9 were simultaneously associated with two or more traits, which indicates that these common loci may have pleiotropic effects on drought-related traits. No QTL was found in association with the same traits in both the indica and japonica subpanels. The possible candidate genes underlying the quantitative trait loci are reviewed. Conclusions: Some of the identified QTLs contain promising candidate genes with a function related to drought tolerance by osmotic stress adjustment.

Mots-clés Agrovoc : Oryza sativa, Variété indigène, Tolérance à la sécheresse, Taux de croissance, Locus des caractères quantitatifs, Carte génétique

Mots-clés géographiques Agrovoc : Viet Nam

Mots-clés complémentaires : QTL, génotypage

Mots-clés libres : Association mapping, Drought tolerance, Genotyping by sequencing, Quantitative trait loci, Rice, Vietnamese landraces

Classification Agris : F30 - Plant genetics and breeding
F62 - Plant physiology - Growth and development

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

Auteurs et affiliations

  • Hoang Giang Thi, HUST (VNM) - auteur correspondant
  • Van Dinh Lam, Agricultural Genetics Institute (VNM)
  • Nguyen Thom Thi, Université de Montpellier (FRA)
  • Ta Nhung Kim, Agricultural Genetics Institute (VNM)
  • Gathignol Floran, Université de Montpellier (FRA)
  • Mai Chung Duc, HUST (VNM)
  • Jouannic Stefan, IRD (FRA)
  • Tran Khanh Dang, Agricultural Genetics Institute (VNM)
  • Khuat Trung Huu, Agricultural Genetics Institute (VNM)
  • Do Vinh Nang, Agricultural Genetics Institute (VNM)
  • Lebrun Michel, Université de Montpellier (FRA)
  • Courtois Brigitte, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-2118-7102
  • Gantet Pascal, UM2 (FRA) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/593266/)

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