Abstract
Inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) techniques were successfully applied, for the first time, to analyze genetic diversity among 92 ginger landraces collected from north-western Himalayan region of India. Six IRAP primer/combinations generated 75 loci with an average of 12 loci/primer displaying an overall polymorphism of 95.95 %. On the other hand, twenty five REMAP primer combinations produced 414 loci with 96.5 % polymorphism. IRAP showed maximum Rp (5.39) and PIC (0.28) values, while the same in REMAP was observed to be 10.92 and 0.34. Cluster analysis using Jaccard’s similarity coefficient for IRAP and REMAP data ranged between 0.21 to 1.0 and 0.21 to 0.85, respectively distinguishing all the genotypes with diverse genetic makup. The results also confirmed the presence of sukkula retrotransposon (RT6) in the ginger genome which effectively acted as genetic marker revealing high regional genetic diversity in the ginger gene pool. The study will help in giving insight to the genetic constitution of vegetatively grown ginger crop and for its further utilization in improvement, conservation and management programmes.
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Abbreviations
- IRAP:
-
Inter-retrotransposon amplified polymorphism
- REMAP:
-
Retrotransposon-microsatellite amplified polymorphism (REMAP)
- RTN:
-
Retrotransposon
- PIC:
-
Polymorphic information content
- Rp:
-
Resolving power
- AE1:
-
Assay efficiency index
- UPGMA:
-
Unweighted pair-group method with arithmetic averages
- PCO:
-
Principal coordinate analysis
- DI:
-
Diversity index
- SAHN:
-
Sequential agglomerative, hierarchical, and nested clustering
- COPH:
-
Cophenetic value matrix
- MXCOMP:
-
Matrix Comparison Plot
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Acknowledgements
The authors gratefully acknowledge Director, Dr Ram Vishwakarma, Indian Institute of Integrative Medicine (IIIM-CSIR), Jammu for providing the necessary facilities. Department of Biotechnology (DBT), Government of India, New Delhi is acknowledged for funding the research grant (BT/PR9218/AGR/05/376/2007). Authors Pankaj Pandotra and MK Husain are thankful to CSIR for the award of Senior Research fellowship and Research Associate ship.
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IIIM/1527/2013
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ESM 1
Sequences of Retrotransposon, Simple sequence repeats and Inter simple sequence repeats of primers used in the study. (DOC 68 kb)
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Pandotra, P., Husain, M.K., Ram, G. et al. Retrotransposon based genetic status of North-West Himalayan Zingiber officinale revealed high heterogeneity. J. Plant Biochem. Biotechnol. 23, 211–216 (2014). https://doi.org/10.1007/s13562-013-0196-8
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DOI: https://doi.org/10.1007/s13562-013-0196-8