Agricultural Research

, Volume 5, Issue 1, pp 1–12 | Cite as

Genetic Diversity Analysis Reveals Importance of Green Revolution Gene (Sd1 Locus) for Drought Tolerance in Rice

  • Prashant Vikram
  • Suhas Kadam
  • Bikram Pratap Singh
  • You Jin lee
  • Jitendra Kumar Pal
  • Sanjay Singh
  • O. N. Singh
  • B. P. Mallikarjuna Swamy
  • Karthikeyan Thiyagarajan
  • Sukhwinder Singh
  • Nagendra K. Singh
Full-Length Research Article


Genetic diversity analysis based on genome-wide single-nucleotide polymorphism (SNP) assay of a set of Indian rice cultivars including modern high-yielding varieties and landraces revealed two broad groups, one with “Aus” and the other with “Indica” cultivars. Marker analysis of these genotypes was carried out for three major drought tolerance QTLs as well as green revolution gene, sd1. This gene collocates with a drought QTL, qDTY 1.1 . The well-known drought-tolerant landraces or traditional varieties had the “tall” allele of the sd1 gene, indicating the possibility of close linkage, pleiotropy or both associated with this gene. Profiling of rice genotypes investigated in the present study with drought QTL markers, genome-wide SNPs, and sd1 gene reveals the importance of using multiple genes rather focusing on any single major QTL/gene for drought tolerance. Our results suggested that rice genetic improvement for rain-fed areas require enhanced use of pre-green revolution varieties.


Drought Genetic diversity Landrace Rice 



Quantitative trait loci


Marker-assisted breeding


Days after sowing


Days after transplanting


Days to 50 % flowering


Plant height




Grain yield


Harvest index


Simple sequence repeats


Polymerase chain reaction



The financial support of “DBT-funded QTL to variety” project is duly acknowledged. Authors also acknowledge the support of IRRI drought breeding group.

Supplementary material

40003_2015_199_MOESM1_ESM.pdf (781 kb)
Supplementary material 1 (PDF 780 kb)


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Copyright information

© NAAS (National Academy of Agricultural Sciences) 2016

Authors and Affiliations

  • Prashant Vikram
    • 1
    • 4
  • Suhas Kadam
    • 2
  • Bikram Pratap Singh
    • 2
  • You Jin lee
    • 1
  • Jitendra Kumar Pal
    • 2
  • Sanjay Singh
    • 2
  • O. N. Singh
    • 3
  • B. P. Mallikarjuna Swamy
    • 1
  • Karthikeyan Thiyagarajan
    • 4
  • Sukhwinder Singh
    • 4
  • Nagendra K. Singh
    • 2
  1. 1.International Rice Research InstituteLos BanosPhilippines
  2. 2.National Research Centre for Plant BiotechnologyIARIPusa, New DelhiIndia
  3. 3.Central Rice Research InstituteCuttackIndia
  4. 4.International Center for Maize and Wheat Improvement (CIMMYT)El BatánMexico

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