Identification of QTLs associated with agronomic performance under nitrogen-deficient conditions using chromosome segment substitution lines of a wild rice relative, Oryza rufipogon

  • Satoshi Ogawa
  • Milton Orlando Valencia
  • Mathias Lorieux
  • Juan David Arbelaez
  • Susan McCouch
  • Manabu Ishitani
  • Michael Gomez Selvaraj
Original Article


Improved root system architecture can enhance agronomic performance by increasing water and nitrogen (N) acquisition efficiency. However, little is known about interaction between root system architecture and agronomic performance under field environments. To gain a better understanding about the genetic basis of these relationships, we evaluated a set of chromosome segment substitution lines (CSSLs) derived from crosses between a tropical japonica rice cultivar ‘Curinga’ and a wild species Oryza rufipogon accession IRGC105491. Root system architectural traits were investigated using the CSSLs at 40 days old seedlings using the root basket method under hydroponic conditions, and agronomic performances were also tested under field conditions with different N treatments. Agronomic performances were computed as the ratio of a trait value under low to high N treatments, including grain yield and biomass yield as nitrogen-deficiency tolerance (NDT) traits. Root architecture and NDT trait QTLs were mapped using 238 SNP marker loci. A total of 13 QTLs for root system architectural, NDT and morpho-physiological traits were identified on chromosomes 1, 3, 4, 5, 7, 8, 9, 10 and 12. Interestingly, a QTL for deeper root number was identified the region of SNP markers between id1012330 and id1021697 on chromosome 1 under hydroponic conditions overlapped with a QTL for NDT trait of relative grain yield (qRGY1). These results suggest that deeper root trait is helpful to maintain grain yield under nitrogen-deficient conditions. The QTL associated root architecture could potentially be used in future rice-breeding efforts to increase agronomic performance under nitrogen-deficient conditions.


Nitrogen-deficiency tolerance Root system architecture Deeper root Quantitative trait locus Underground revolution 



Analysis of variance


Agronomic nitrogen use efficiency


International center for tropical agriculture: spanish-language name centro internacional de agricultura tropical


Chromosome segment substitution line


Day after transplant


Farmer’s practice




Nitrogen use efficiency


Nitrogen-deficiency tolerance


Quantitative trait locus


Relative biomass yield


Ratio of deeper root


Relative grain yield


Root pattern value


Root system architecture


Single nucleotide polymorphism


Soil and plant analyzer development



We thanks to Dr. Okada, University of Tokyo and Angela Joseph Fernando, Consultant CIAT for their critical evaluation of the manuscript. We thank Dr. Joe Tohme, Agro biodiversity research area director CIAT for his continuous support. We appreciate Lucia Chavez, CIAT for their technical assistance. This study was conducted as a part of SATREPS project (JICA-JST) in Colombia. SO worked as research fellow of Japan Society for the Promotion of Science and also has been received financial support from Univ. of Tokyo, Japan Public–Private Partnership Student Study Abroad Program; TOBITATE! Young Ambassador Program and grants-in-aid from Ministry of Foreign Affairs of Japan (MOFA) to do this study.

Supplementary material

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Supplementary material 1 (PPTX 176 kb)
11738_2016_2119_MOESM2_ESM.docx (29 kb)
Supplementary material 2 (DOCX 30 kb)


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Copyright information

© Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków 2016

Authors and Affiliations

  • Satoshi Ogawa
    • 1
    • 2
  • Milton Orlando Valencia
    • 1
  • Mathias Lorieux
    • 1
    • 3
  • Juan David Arbelaez
    • 4
  • Susan McCouch
    • 4
  • Manabu Ishitani
    • 1
  • Michael Gomez Selvaraj
    • 1
  1. 1.International Center for Tropical Agriculture (CIAT), A.A. 6713CaliColombia
  2. 2.Department of Global Agricultural Science, Graduate School of Agricultural and Life ScienceThe University of TokyoTokyoJapan
  3. 3.Institut de Recherche pour le Développement (IRD), DIADE Research UnitMontpellierFrance
  4. 4.Department of Plant Breeding and Genetics240 Emerson Hall, Cornell UniversityIthacaUSA

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