Molecular screening and diversity analysis of rice (Oryza sativa L.) genotypes for biotic and abiotic stresses using SSR markers


Pragati Randive1 *, Gokhale NB1 , Sawardekar SV 1 , Kunkerkar RL2 , Bhagwat SS1 , Kelkar VG1

1 Dr.BalasahebSawant Konkan KrishiVidyapeeth, Dapoli – 415 712, Dist-Ratnagiri, Maharashtra, India. 

2 RARS, Dr.BalasahebSawant Konkan KrishiVidyapeeth, Karjat, Dist-Raigad, Maharashtra, India. 

*Corresponding author e-mail:

Received: 16th March 2019; Accepted: 26th May 2019


In this study, rice germplasms were screened for biotic (blast, bacterial blight, brown planthopper, gall midge) and abiotic stress tolerance (drought, salinity) in 50 rice genotypes using 19 trait linked SSR markers.Among the genotypes; B 40 showed amplification of the resistance/tolerance specific alleles for multiple traits, viz., blast, bacterial blight, gall midge, saltol and IRBB 57 showed presence of resistance/tolerance specific alleles for blast, bacterial blight, gall midge and drought. Moreover the genotypes, IR 11 A 546, IR 11 A 581, IR 11 N 169, IRBB 2, IRBB 4, IRBB 5, IRBB 13, IRBB 64, IRBB 12 DS-GMEI-22, IR 64, IRBB 55, IRBB 62, IRBB 14, IRBB 50, IR 11 N 223 showed presence of resistance specific alleles for blast, bacterial blight, gall midge, brown planthopper and drought, Saltol by combination of any of the above three traits. The rice line IRBB 10 showed presence of resistance linked alleles for two gall midge resistance genes,Gm4 (270bp) and Gm8 (170bp). Genotypes IRBB 61 and IRBB 62 showed presence of resistance linked alleles for two of the Saltol linked loci. The rice genotypes displaying amplification of resistance/tolerance linked alleles for multiple traits can be used as donors for these traits after their validation through phenotypic screening. All the nineteen SSR primers used in this study amplified and showed the polymorphism among the rice genotypes. With an average of 5.42 alleles per locus, a total of 103 alleles were detected. The polymorphism information content (PIC) values ranged from 0.40 to 0.90 with an average PIC value of 0.65 per primer. Rice genotypes were grouped into two main clusters by UPGMA, which were further divided into two sub-clusters. Through Marker Assisted Selection (MAS), this study will assist in selection of parental lines and also for development of new breeding population that will be tolerant to specific biotic and abiotic stresses.

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