Abstract
Efficacy of two dominant molecular markers, namely, amplified fragment length polymorphism (AFLP) and three endonuclease (TE)-AFLP, were assessed in 20 individuals of the biodiesel species Pongamia pinnata. Four primer combinations generated a total of 254 and 194 bands in AFLP and TE-AFLP, respectively. Both techniques could unequivocally identify each accession used in this study. The Jaccard’s similarity coefficient ranged from 0.30 to 0.90 for AFLP and from 0.25 to 0.85 for TE-AFLP. The correlation coefficient between AFLP and TE-AFLP dendrogram was 0.56 which was low but significant (P < 0.001). Values of effective multiplex ratio, marker index, and resolving power were markedly higher in AFLP than in TE-AFLP. However, the band intensities across different lanes were uniform in TE-AFLP leading to easy and accurate scoring of gels which resulted in slightly higher bootstrap values with TE-AFLP data as compared to AFLP data. Inferences based on TE-AFLP data had similar level of biological relevance as compared to AFLP data when location and diameter of trees were taken in to consideration. However, the easy scorability of TE-AFLP profiles is extremely important and especially desirable in studies requiring genotyping of large number of individuals distributed across many gels.
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Acknowledgments
The authors thank Department of Science and Technology, Government of India, for its gracious funding for the project (grant number SR/SO/PS-08/2006). We thank Mr. Bidya Bhushan Gupta and Mr. Bharatendu Gupta for their assistance during field surveys. We thank the anonymous reviewer for valuable suggestions. The authors are also thankful to Dr. R. K. Pachauri, Director General, TERI, for his kind support.
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Supplemental Figure S1
Mantel matrix plot between pairwise cophenetic distances obtained from AFLP and TE-AFLP data. R is the matrix correlation coefficient between the two matrices (PPT 31 kb)
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Sharma, S.S., Negi, M.S., Sinha, P. et al. Assessment of Genetic Diversity of Biodiesel Species Pongamia pinnata Accessions using AFLP and Three Endonuclease-AFLP. Plant Mol Biol Rep 29, 12–18 (2011). https://doi.org/10.1007/s11105-010-0204-2
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DOI: https://doi.org/10.1007/s11105-010-0204-2