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


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Article Info

DATE

2017-02

AUTHORS

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

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. More... »

PAGES

6

References to SciGraph publications

  • 1999-01. A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars in THEORETICAL AND APPLIED GENETICS
  • 2000-04. AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.) in MOLECULAR BREEDING
  • 2007-12. Genetic variability and association studies in pod and seed traits of Pongamia pinnata (L.) Pierre in Haryana, India in GENETIC RESOURCES AND CROP EVOLUTION
  • 2010-07. Analysis of Genetic Diversity in Pongamia [Pongamia pinnata (L) Pierrre] using AFLP Markers in JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY
  • 2009-10. Estimation of population structure in coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] using allozyme and microsatellite markers in TREE GENETICS & GENOMES
  • 2010-08. AFLP-Based Genetic Diversity Assessment of Commercially Important Tea Germplasm in India in BIOCHEMICAL GENETICS
  • 2014-02. Genetic analysis of Pongamia pinnata (L.) Pierre populations using AFLP markers in TREE GENETICS & GENOMES
  • 2016-04. Seed traits, fatty acid profile and genetic diversity assessment in Pongamia pinnata (L.) Pierre germplasm in PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
  • 2012-06. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method in CONSERVATION GENETICS RESOURCES
  • 1999-07. Assessment of genetic diversity in Azadirachta indica using AFLP markers in THEORETICAL AND APPLIED GENETICS
  • 2010-03. Inter and intra-population variability of Pongamia pinnata: a bioenergy legume tree in PLANT SYSTEMATICS AND EVOLUTION
  • 1996-09. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis in MOLECULAR BREEDING
  • 2011-03. Assessment of Genetic Diversity of Biodiesel Species Pongamia pinnata Accessions using AFLP and Three Endonuclease-AFLP in PLANT MOLECULAR BIOLOGY REPORTER
  • 2008-03. Pongamia pinnata: An Untapped Resource for the Biofuels Industry of the Future in BIOENERGY RESEARCH
  • Journal

    TITLE

    Tree Genetics & Genomes

    ISSUE

    1

    VOLUME

    13

    Author Affiliations

    Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s11295-016-1088-6

    DOI

    http://dx.doi.org/10.1007/s11295-016-1088-6

    DIMENSIONS

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    33 schema:description 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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