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QTL mapping for nitrogen use efficiency and related physiological and agronomical traits during the vegetative phase in rice under hydroponics

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Abstract

Breeding crops for better nitrogen use efficiency (NUE) is one of the primary objectives in modern agriculture to decrease nitrogen (N) fertiliser application. However, genetic information about the components of NUE is still limited. The present study aims to identify quantitative trait loci (QTLs) for agronomical NUE (agNUE) and its two components—absorption NUE (aNUE) and physiological NUE (pNUE)—and related traits. A population including 174 recombinant inbred lines derived from the cross IR64/Azucena was tested twice in hydroponics in the Yoshida solution at the vegetative phase with three different N concentrations: 1X (standard), 1/4X and 1/8X. The different components of NUE and several physiological and agronomical traits were determined after 4 weeks of N treatment. The results were submitted to composite interval mapping (CIM) and to joint QTL analysis for multiple traits. The CIM revealed 14 putative QTLs for NUE components and 63 QTLs for 12 physiological and agronomical traits. Six hotspots containing numerous QTLs were identified. All of them were confirmed through joint QTL analysis. Furthermore, four of them—(1) for aNUE and agNUE on chromosome 3; (2) for aNUE and agNUE on chromosome 8; (3) for both dry weight of stems + sheaths and dry weight of roots on chromosome 3; (4) for plant height on chromosome 1—were found repeatedly in several repetitions in our studies and have been identified also in previous studies. These finding may serve as a basis for further fine-mapping and candidate gene studies, therefore aiding the development of cultivars for sustainable agriculture.

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Acknowledgments

We thank the Institut de Recherche pour le Développement (IRD) and the Centre de Coopération internationale en Recherche agronomique pour le Développement (CIRAD) in Montpellier (France) for their collaboration in this study by providing the segregating population and the genotypic map of the markers for the recombinant inbred lines (RILs)—European project EGRAM. We are also thankful to the CUD (Commission universitaire pour le Développement) scholarship program, Belgium, for their financial contribution.

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  1. Department of Biology, Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam

    Hanh Thi Thuy Nguyen

  2. Earth and Life Institute, Unité d’Ecophysiologie et Amélioration végétale, Université catholique de Louvain, Croix du Sud 2 bte L7.05.11, 1348, Louvain-la-Neuve, Belgium

    Hanh Thi Thuy Nguyen, Duong Thuy Dang & Pierre Bertin

  3. Department of Food Crop Science, Faculty of Agronomy, Vietnam National University of Agriculture, Hanoi, Vietnam

    Cuong Van Pham

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Correspondence to Pierre Bertin.

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Nguyen, H.T.T., Dang, D.T., Van Pham, C. et al. QTL mapping for nitrogen use efficiency and related physiological and agronomical traits during the vegetative phase in rice under hydroponics. Euphytica 212, 473–500 (2016). https://doi.org/10.1007/s10681-016-1778-z

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