ISSN: 2155-952X

Journal of Biotechnology & Biomaterials
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  • Research Article   
  • J Biotechnol Biomater 2016, Vol 6(3): 241
  • DOI: 10.4172/2155-952X.1000241

SSR Marker-based Genetic Diversity Analysis of Tidal and Flood Prone Areas in Rice (Oryza sativa L.)

ASM Masuduzzaman1, Maksudul Haque1*, MM Emam Ahmed1 and Chandan Kumar Mohapatra2
1Plant Breeding Division, Bangladesh Rice research Institute (BRRI), , Regional Station, Habiganj-3300, Bangladesh
2Fenchuganj, , Sylhet, Bangladesh
*Corresponding Author : Maksudul Haque, Scientific Officer (Golden rice), Plant Breeding Division, Bangladesh Rice research Institute (BRRI), Gazipur-1701, Bangladesh, Tel: 008801723778056, Email: maksudulhq@gmail.com

Received Date: Jul 24, 2016 / Accepted Date: Aug 04, 2016 / Published Date: Aug 11, 2016

Abstract

One hundred and sixty rice varieties from the tidal and flood prone areas of south and south East Asian countries were analyzed. Samples sizes were: 50 varieties from Bangladesh (deepwater, tidal and flood prone rice and modern varieties), 14 varieties from India (flood prone rice), 16 varieties from Sri Lanka (flood prone rice), 7 varieties from Vietnam (tidal varieties), 69 varieties from Indonesia (tidal varieties) and 4 check varieties from IRRI. All 30 primer pairs created polymorphic bands among the 160 rice varieties from flood and tidal prone areas, which indicated that the microsatellites used were suitable for diversity analysis. A total of 337 alleles were detected with an average of 11 alleles per locus and the number of alleles per locus varied from 4 to 21. The highest PIC values were observed for the primer of RM474 (0.91), followed by RM5 (0.82), RM484 (0.81), RM214 (0.81), and RM19 (0.79). Cluster analysis divided the genotypes into four main clusters and six sub-clusters based on geographical origins and ecotypes. Microsatellite clustering (over 30 polymorphic loci) and submergence screening data indicated greater genetic diversity among 160 genotypes for molecular loci and for submergence tolerance. Tolerant genotypes in Cluster-1 are expected to have different tolerance genes. Finding relationship between tolerance and country of origin, highly tolerant varieties (FR13A and FR43B) were found from east India. Genetic diversity analysis among flood prone rice will be useful for identifying the varieties having maximum diversity with submergence tolerance and selected varieties will be useful for further studies.

Keywords: SSR, Genetic diversity, Tidal, Flood prone, Submergence, Rice (Oryza sativa L.)

Citation: Masuduzzaman ASM, Haque M, Ahmed MME, Mohapatra CK (2016) SSR Marker-based Genetic Diversity Analysis of Tidal and Flood Prone Areas in Rice (Oryza sativa L.). J Biotechnol Biomater 6:241. Doi: 10.4172/2155-952X.1000241

Copyright: © 2016 Masuduzzaman ASM, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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