1. Genome-wide Association Study of a Panel of Vietnamese Rice Landraces Reveals New QTLs for Tolerance to Water Deficit During the Vegetative Phase
- Author
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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, Hanoi University of Science and Technology (HUST), LMI RICE, Agronomical Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, Université de Montpellier (UM), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Agricultural Genetics Institute, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), French Ministry of Foreign Affairs and International Development, Ministry of Science and Technology of Vietnam, Global Rice Science Partnership (2011-2016), CGIAR Research Program (CRP) on rice agri-food systems (RICE, 2017-2022), and Agricultural Genetics Institute (AGI)
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Locus des caractères quantitatifs ,Quantitative trait loci ,Tolérance à la sécheresse ,F62 - Physiologie végétale - Croissance et développement ,Oryza sativa ,lcsh:Plant culture ,F30 - Génétique et amélioration des plantes ,Association mapping ,Drought tolerance ,Genotyping by sequencing ,Rice ,Vietnamese landraces ,Variété indigène ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,lcsh:SB1-1110 ,Vegetal Biology ,fungi ,food and beverages ,Taux de croissance ,Carte génétique ,Original Article ,Biologie végétale - 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. Electronic supplementary material The online version of this article (10.1186/s12284-018-0258-6) contains supplementary material, which is available to authorized users.
- Published
- 2019
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