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Amplified fragment length polymorphism analysis to assess genetic diversity in rice

  • Asit B. MandalEmail author
  • Pranit Mukherjee
  • Anjana Bora
  • Partha Ray Choudhury
  • Sourav Dutta
  • Chiranjib Mandal
Research Articles


Amplified Fragment Length polymorphism (AFLP) was studied involving 48 diverse rice genotypes, comprising of indica, japonica, and Tongil type (indica × japonica) varieties to assess the genetic diversity. Initially 64 primer pair combinations were screened of which 5 were found to be suitable producing clear fragments (35–500 bp). In total 700 amplicons (bands) were produced with an average of 140 bands per primer pair. Maximum (207) from EcoRI AC*/MseI-CAC and minimum (75) amplicons from EcoRI TG*/MseI-CTT primer pairs were observed. Minimum (0.973) and maximum (0.990) PIC values recorded for primer pair EcoRI AC*/MseI-CAC and EcoRI AC*/MseI-CAT, respectively. Pairwise genetic similarity estimates ranged in between 0.6412 and 0.943 with a mean of 0.797. Triguna, an indica high yielding variety (HYV), and a new plant type (NPT) rice, IR 7946-46-1-3-2 having indica x japonica parentage showed minimum genetic similarity coefficient (0.641) with maximum genetic divergence, whereas ADT 41 and Sasyasree, two indica HYVs displayed maximum genetic similarity coefficient—0.953 with lowest genetic distance. All accessions could be clearly identified by using five primer pairs, offers immense scope of AFLP in assessing genetic diversity in rice. The present study also identified prospective varieties for use in selective hybridization and productive progeny selection. Most of the varieties shared distinct clusters based on varietal types, race, parentage and growing area where those are cultivated traditionally albeit with a few exceptions. The dendrogram could demarcate the varieties irrespective of race with unique traits, albeit with exceptions, which warrants further experimentation involving more number of primers in future.


Genetic diversity Rice AFLP Productive lines Superior genetics 



Authors thank the Director, Indian Institute of Seed Science (erstwhile Directorate of Seed Research) Research, Mau 275101, UP for the concept, self-involvement and guidance in executing this research work.


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Copyright information

© Society for Plant Research 2019

Authors and Affiliations

  • Asit B. Mandal
    • 1
    • 5
    Email author
  • Pranit Mukherjee
    • 2
  • Anjana Bora
    • 1
  • Partha Ray Choudhury
    • 1
    • 3
  • Sourav Dutta
    • 4
  • Chiranjib Mandal
    • 2
  1. 1.ICAR-Indian Institute of Seed ScienceMauIndia
  2. 2.ICAR- Central Research Institute for Jute and Allied FibresBarrackporeIndia
  3. 3.Seed Unit, Division of Crop SciencesICAR HeadquartersNew DelhiIndia
  4. 4.Techno India UniversityKolkataIndia
  5. 5.Biotechnology UnitICAR-Central Research Institute for Jute and Allied FibresKolkataIndia

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