, 215:17 | Cite as

Novel biotic stress responsive candidate gene based SSR (cgSSR) markers from rice

  • Kutubuddin Ali MollaEmail author
  • T. P. Muhammed Azharudheen
  • Soham Ray
  • Sutapa Sarkar
  • Alaka Swain
  • Mridul Chakraborti
  • Joshitha Vijayan
  • Onkar Nath Singh
  • Mirza Jaynul Baig
  • Arup Kumar Mukherjee


Developing host resistance is an effective measure to minimize the yield losses caused by biotic stresses in crop plants. Generation of genomic resources greatly facilitates the development of resistant plants. Microsatellite markers speed up the selection procedure and introgression of resistant alleles in rice breeding programme. Candidate gene based SSR (cgSSR) markers are preferred over genomic SSR due to their tighter linkage with the trait governing loci. This study describes the identification and analysis of cgSSR markers from biotic stress responsive genes of rice. Among the selected 308 different biotic stress responsive genes of rice, 176 gene sequences were found to harbour a total of 364 SSR loci. Tri-nucleotide motif was found to be the most abundant (51.09%), followed by di- (45.05%) and tetra-nucleotide (3.84%). Intron and CDS are the two locations where most of the cgSSR loci were found, followed by 5′UTR and 3′UTR. In order to validate, polymorphism survey was done in 25 Oryza sativa genotypes using 35 cgSSR primer pairs. Among the 35 cgSSR, 27 cgSSR exhibited loci specific amplification with an average allele number of 5.66 per primer and mean PIC value of 0.226. Further, out of 27, 21 cgSSRs were found to be cross transferable to the wild species belonging to the Sativa complex; while 19 were found to be transferable to the species belonging to the Officinalis complex. The novel biotic stress-responsive cgSSR markers developed here could be used in marker-assisted introgression and pyramiding of resistant allele into elite rice cultivars from other rice germplasm as well as from wild relatives of rice.


Genic SSR Trait specific marker Wild rice Cross species transferability Genomic resources Biotic stress of rice 



Simple sequence repeat


Sequence tagged microsatellite site


Candidate gene based SSR


Untranslated region


Polymorphism information content


Quantitative trait loci


Expressed sequence tag


Coding DNA sequence


Polymerase chain reaction


Annealing temperature


Ethylenediaminetetraacetic acid


Principal coordinates analysis


Bacterial leaf blight


Rice dwarf virus


Rice stripe virus


Sheath blight


Gene ontology



Authors are thankful to the Director, ICAR-National Rice Research Institute for encouragement and providing all facilities to carry out research work. Thanks are due to the Genebank of ICAR-NRRI, Cuttack for providing the germplasm.

Author’s contribution

KAM conceptualized, designed and planned the study. KAM, TPMA, SR, AS and SS performed the experiments. KAM, TPMA, SR, SS, MC, JV, ONS, MJB and AKM analysed the data. KAM wrote the manuscript. TPMA, MC, SR and SS edited the manuscript. JV, ONS, MJB and AKM critically revised the manuscript. KAM, TPMA, SR and AS are responsible for preparing different tables and figures. All authors read and approved the final manuscript.


The work was funded by Indian Council of Agricultural Research (ICAR), New Delhi. The Funding body has no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Availability of data and materials

All data generated or analysed during this study are included in this published article and in additional files (Additional file 1-6).

Supplementary material

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Kutubuddin Ali Molla
    • 1
    Email author
  • T. P. Muhammed Azharudheen
    • 1
  • Soham Ray
    • 1
  • Sutapa Sarkar
    • 1
  • Alaka Swain
    • 1
  • Mridul Chakraborti
    • 1
  • Joshitha Vijayan
    • 2
  • Onkar Nath Singh
    • 1
  • Mirza Jaynul Baig
    • 1
  • Arup Kumar Mukherjee
    • 1
  1. 1.ICAR-National Rice Research InstituteCuttackIndia
  2. 2.Faculty Centre of Integrated Rural Development and ManagementRamakrishna Mission Vivekananda Educational & Research InstituteKolkataIndia

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