Genetic Resources and Crop Evolution

, Volume 63, Issue 7, pp 1113–1126 | Cite as

Genetic diversity analysis of Pakistan rice (Oryza sativa) germplasm using multiplexed single nucleotide polymorphism markers

  • Shahid Masood Shah
  • Muhammad Arif
  • Kashif Aslam
  • Ghulam Shabir
  • Michael J. Thomson
Research Article


A broad base of genetic diversity is crucial to provide variation to withstand biotic and abiotic stresses and to continue to make yield improvements. Pakistan has a wide range of climates and rice is ranked second as a staple food; however, very little is known in terms of rice genetic diversity in Pakistan with respect to global germplasm. This research was performed to investigate the genetic diversity and structure of the most commonly grown rice varieties in Pakistan, including the aromatic Basmati varieties, along with accessions from other countries. One hundred and five rice accessions were analyzed, including 21 Pakistan accessions, 44 IRRI lines, 6 wild rices, and 34 global accessions representing all five groups of rice as a reference in this study. These accessions were genotyped with 373 multiplexed SNP markers using the Illumina GoldenGate assay RiceOPA2.1 run at the Genotyping Services Lab at IRRI. The overall call percentage of the 373 SNPs across 105 accessions was 98.7 %. Structure analysis, principal coordinate analysis, and clustering with Neighbor Joining and UPGMA separated the genotypes in five major groups: indica, japonica, wild, aromatic and aus, while the Structure analysis at K = 7 further divided the indica cluster into 4 indica sub-groups. The Pakistan varieties were found in both the indica and aromatic clusters, but with an overall lower genetic diversity than seen in germplasm from other countries. Information on the diversity of rice germplasm can help guide future initiatives to widen the genetic base of rice cultivation in Pakistan.


Basmati Multiplexed SNP marker genotyping Oryza sativa Pakistan Rice diversity 



International Rice Research Institute


Minor allele frequency




Oligo pool assay


Single nucleotide polymorphism



We gratefully acknowledge the technical assistance of Maria Ymber Reveche, Christine Jade Dilla-Ermita, Dennis Nicuh Lozada, Erwin Tandayu, Pauline Capistrano, and Geraldine Ann M. Layaoen in the Genotyping Services Lab at IRRI. Also special thanks to Yoo Jin Lee for provision of wild rice from her research work. This study was funded in part by the Higher Education Commission (HEC) of Pakistan, the Global Rice Science Partnership and the International Rice Research Institute, Philippines. This research forms part of the Ph.D. thesis study of S.M.S.

Author contribution

S.M.S. analyzed data and wrote the manuscript. K.A. and G.S. assisted with data analysis and provided insight during manuscript preparation. M.A. provided rice germplasm, conceived of the study and provided guidance for manuscript writing. M.J.T. provided guidance for data analysis and helped with editing the manuscript. All authors read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest. This research does not involve human participants or animals.

Supplementary material

10722_2015_304_MOESM1_ESM.docx (167 kb)
Supplementary material 1 (DOCX 166 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  1. 1.Department of Environmental SciencesCOMSATS Institute of Information TechnologyAbbottabadPakistan
  2. 2.Institute of Molecular Biology and BiotechnologyBahauddin Zakariya UniversityMultanPakistan
  3. 3.National Institute for Biotechnology and Genetic Engineering (NIBGE)FaisalabadPakistan
  4. 4.International Rice Research Institute (IRRI)Los BañosPhilippines
  5. 5.Department of Soil and Crop SciencesTexas A&M UniversityCollege StationUSA

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