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Genetic diversity, population structure and association study using TE-AFLP markers in Pongamia pinnata (L.) Pierre germplasm

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Abstract

Genetic diversity of Pongamia pinnata, a plant species emerging as biodiesel source, was assessed using three endonuclease (TE)-amplified fragment length polymorphism (AFLP) markers. A total of 275 accessions from different Indian geographical regions were collected. High level of polymorphism (62.6%) was observed in 334 loci amplified using six primer combinations. The Jaccard’s dissimilarity coefficient ranged from 0.17 to 0.80. Based on the neighbour joining method of clustering, accessions were grouped into six major clusters congruent with their respective geographical locations. The mean values of effective multiplex ratio, polymorphic information content, marker index and resolving power were 34.83, 0.286, 9.700 and 14.29 respectively. In addition, a core collection consisting of 20 accessions was identified. Population STRUCTURE analysis produced the highest log likelihood score when the number of populations (K) was set at 2, which was not consistent with clustering analysis based on genetic diversity. Two TE-AFLP markers, E_ac x P_a04 and E_ac x P_a39, were significantly associated with oil content (at P = 0.005). The extent of genetic diversity detected and core germplasm of CPT identified in this study could be selected and used for tree breeding, germplasm conservation and suitable feed stock for biofuel.

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Acknowledgements

The authors sincerely acknowledge the funding received from the Department of Science and Technology, Government of India, for the project (grant number SR/SO/PS-08/2006). Mr. Shyam Sundar Sharma thanks the Council of Scientific and Industrial Research, Government of India, for providing fellowship for this work.

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Authors and Affiliations

  1. The Energy and Resources Institute, IHC Complex, Lodhi Road, New Delhi, 110003, India

    Shyam Sundar Sharma, Md Aminul Islam, Vivek Kumar Singh, Madan Singh Negi & Shashi Bhushan Tripathi

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  1. Shyam Sundar Sharma
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  2. Md Aminul Islam
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  3. Vivek Kumar Singh
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  4. Madan Singh Negi
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  5. Shashi Bhushan Tripathi
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Correspondence to Shashi Bhushan Tripathi.

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The authors declare that they have no conflict of interest.

Data archiving statement

The data consisting of raw data and primary information of 275 individuals will be archived in Dryad (http://datadryad.org/).

Additional information

Responsible editor: J. L. Wegrzyn

Electronic supplementary material

ESM 1

List of Pongamia accessions used in the study (DOC 289 kb)

ESM 2

(A) Map showing the geographical locations of collection sites of Pongamia accessions used in this study. The four red dots represent accessions from different regions of Delhi, two orange dots represent East and South NCR. (B) The yellow dots showing the collection sites in other states of India (DOC 113 kb)

ESM 3

Representative autoradiogram of TE-AFLP fingerprints of Pongamia pinnata accessions using E-AG x P-C primer combination (DOC 976 kb)

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Sharma, S.S., Islam, M.A., Singh, V.K. et al. Genetic diversity, population structure and association study using TE-AFLP markers in Pongamia pinnata (L.) Pierre germplasm. Tree Genetics & Genomes 13, 6 (2017). https://doi.org/10.1007/s11295-016-1088-6

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  • DOI: https://doi.org/10.1007/s11295-016-1088-6

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