Genetic dissection of photochemical efficiency under water-deficit stress in rice

  • David Šebela
  • Raju Bheemanahalli
  • Anandhan Tamilselvan
  • Niteen N. Kadam
  • S. V. Krishna JagadishEmail author
Short Communications


Chlorophyll fluorescence (Chl-F) measurements together with non-invasive estimations of chlorophyll content, can be used to investigate functionally rich or poor photosystem II (PSII), relating to alterations in photosynthetic performances under different abiotic stresses. The aim was to identify genetic loci that control rice capacity to cope with different soil moisture conditions such as non-stress (control), water deficit and recovery during the reproductive stage. A genome-wide association study was performed for effective quantum yield of photosystem II (QY) and chlorophyll index across all three treatments. Accessions showed significant variability in traits within each treatment. A total of 43 genetic loci associated with QY and chlorophyll index were identified. Of the total genetic loci identified, 14 were for control, 13 for water-deficit stress and 16 for recovery responses. Interestingly, the majority of the identified genetic loci were co-localized either with chlorophyll synthesis or degradation pathways, components of PSII, transcription factors, protein kinases, transporters, kinases, and antioxidants genes. Favorable alleles and donor accessions found in our study would complement efforts aimed at stacking of traits. Moreover, our results provide promising genetic information for future validation and a potential resource for improving photochemical efficiency and subsequently enhancing carbon gain in rice under water-limited conditions.


Genome-wide association study Photochemical efficiency Rice Recovery Water-deficit stress 



We thank The Federal Ministry for Economic Cooperation and Development, Germany, and the USAID-Bill and Melinda Gates Foundation for their financial support. We also thank the GRiSP (Global Rice Science Partnerships; now renamed to RICE CRP consortium) for establishing the PRAY Global Phenotyping Network.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

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Copyright information

© Indian Society for Plant Physiology 2019

Authors and Affiliations

  1. 1.International Rice Research InstituteMetro ManilaPhilippines
  2. 2.Global Change Research Institute CASBrnoCzech Republic
  3. 3.Department of AgronomyKansas State UniversityManhattanUSA

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