Molecular profiling in relation to drought tolerance in advance breeding lines of rice using microsatellite markers

  • Shuchi Shankar Choudhary
  • V. K. SharmaEmail author
  • Pankaj Kumar
  • Mithilesh Kumar
Original Article


Using agro-morphological characters and microsatellite markers, advance breeding lines of rice were discriminated for their ability to tolerate drought stress at reproductive stage. Experimental materials consisting of 17 advance breeding lines and a check were evaluated in randomized block design with three replications under irrigated condition and drought condition created under rainout shelter during three consecutive years. An analysis of variance revealed significant differences among the genotypes for all the ten agro-morphological characters evaluated under both the conditions across the years. Principal component analysis showed the relative importance of root length, number of tillers per plant, number of grains per panicle, harvest index and grain yield per plant among agro-morphological characters and stress tolerance level, stress susceptibility index, stress tolerance index and drought tolerance efficiency among drought tolerance indices as the important classification variables. Relative mean performance in respect of grain yield as well as drought tolerance indices reflected remarkably greater degree of drought tolerance in 11 advance breeding lines and the check, discriminating them from remaining entries under evaluation. Utilizing a panel of 32 microsatellite primers, selective amplification of targeted genomic regions revealed that the primers RM 72, RM 163, RM 212, RM 225, RM 231, RM 302, RM 327, RM 518, RM 521, RM 555, RM 1349, RM 3549 and RM 5443 were highly informative with greater gene diversity and discrimination ability. Hierarchical cluster analysis based on molecular profiles discriminated the entries into five genotypic groups and drought tolerant entries were accommodated into three distinct groups with remarkably greater efficiency (85.7%). Principal coordinate analysis based two dimensional plots of microsatellites dependent genetic profiles displayed a very close correspondence with the genotypic clustering pattern revealed from a perusal of dendrogram. Sequential exclusion of primers in cluster analysis led to identification of RM 212, RM 231, RM 324, RM 431, RM 521, RM 3549 and RM 6374 as the most useful primers for discrimination of drought tolerant and susceptible lines of rice. Molecular profiling based on these markers can be utilized as efficient tools for discrimination and identification of drought tolerant lines.


Rice Drought tolerance Principal component analysis Microsatellite markers Principal coordinate analysis Genetic divergence 



Stress tolerance level


Stress susceptibility index


Stress tolerance index


Drought tolerance efficiency


Principal component analysis


Principal coordinate analysis



The authors gratefully acknowledge the Department of Plant Breeding and Genetics, Dr. Rajendra Prasad Central Agricultural University Pusa, Bihar, India for providing the seed of rice genotypes used in the study.

Author’s contribution

VKS conceived and designed the experiments, SSC carried out the field evaluation and molecular characterization, VKS, SSC and PK analyzed the data, SSC, VKS, MK and PK interpreted the results. All authors have read the manuscript and agree with its content.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


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Copyright information

© Society for Plant Biochemistry and Biotechnology 2019

Authors and Affiliations

  • Shuchi Shankar Choudhary
    • 1
  • V. K. Sharma
    • 1
    Email author
  • Pankaj Kumar
    • 1
  • Mithilesh Kumar
    • 1
  1. 1.Department of Agricultural Biotechnology and Molecular BiologyDr. Rajendra Prasad Central Agricultural UniversityPusa, SamastipurIndia

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