Plant Molecular Biology Reporter

, Volume 36, Issue 3, pp 373–386 | Cite as

Genome-Wide Analysis in Wild and Cultivated Oryza Species Reveals Abundance of NBS Genes in Progenitors of Cultivated Rice

  • Hukam C. Rawal
  • S. V. Amitha Mithra
  • Kirti Arora
  • Vishesh Kumar
  • Neha Goel
  • Dwijesh Chandra Mishra
  • K. K. Chaturvedi
  • Anil Rai
  • S. Vimala Devi
  • T. R. Sharma
  • Amolkumar U. SolankeEmail author
Original Paper


NBS-encoding genes play a critical role in the plant defense system. Wild relatives of crop plants are rich reservoirs of plant defense genes. Here, we performed a stringent genome-wide identification of NBS-encoding genes in three cultivated and eight wild Oryza species, representing three different genomes (AA, BB, and FF) from four continents. A total of 2688 NBS-encoding genes were identified from 11 Oryza genomes. All the three progenitor species of cultivated rice, namely O. barthii, O. rufipogon, and O. nivara, were the richest reservoir of NBS-encoding genes (214, 313, and 307 respectively). Interestingly, the two Asian cultivated species showed a contrasting pattern in the number of NBS-encoding genes. While indica subspecies maintained nearly equal number of NBS genes as its progenitor (309 and 313), the japonica subspecies had retained only two third in the course of evolution (213 and 307). Other major sources for NBS-encoding genes could be (i) O. longistaminata since it had the highest proportion of NBS-encoding genes and (ii) O. glumaepatula as it clustered distinctly away from the rest of the AA genome species. The present study thus revealed that NBS-encoding genes can be exploited from the primary gene pool for disease resistance breeding in rice.


NBS genes NB-ARC domain NBS-LRR Genome-wide analysis Disease resistance Evolution 


Author Contributions

AS and AM: conceived and designed the experiments; HR and NG: developed the pipelines and analyzed data; KA and VK: PCR validation; HR and AS: finalized tables and figures; DM, KC, and AR: provided the bioinformatic support; VD: supplied plant material; AM, AS, and TS: drafted and finalized the manuscript; and all the authors read and approved the manuscript.

Funding Information

This research received financial support from the Centre for Agricultural Bioinformatics Scheme (CABin) funded by the Indian Council of Agricultural Research (ICAR), New Delhi, India.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Hukam C. Rawal
    • 1
  • S. V. Amitha Mithra
    • 1
  • Kirti Arora
    • 1
  • Vishesh Kumar
    • 1
  • Neha Goel
    • 1
  • Dwijesh Chandra Mishra
    • 2
  • K. K. Chaturvedi
    • 2
  • Anil Rai
    • 2
  • S. Vimala Devi
    • 3
  • T. R. Sharma
    • 1
    • 4
  • Amolkumar U. Solanke
    • 1
    Email author
  1. 1.ICAR-National Research Centre on Plant BiotechnologyNew DelhiIndia
  2. 2.ICAR-Indian Agricultural Statistics Research InstituteNew DelhiIndia
  3. 3.ICAR-National Bureau of Plant Genetic ResourcesNew DelhiIndia
  4. 4.National Agri-Food Biotechnology InstituteMohaliIndia

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