Inter and intra-population variability of Pongamia pinnata: a bioenergy legume tree

Sahoo, Debee Prasad; Aparajita, Subhashree; Rout, Gyana Ranjan

doi:10.1007/s00606-009-0254-9

Cited by 17 publications

(21 citation statements)

References 12 publications

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“…Prior to this study, the genotyping of Pongamia germplasm has been restricted to ISSR, RAPD and AFLP markers Sahoo et al 2010;Sujatha et al 2010;Thudi et al 2010;Kesari and Rangan 2011;Sharma et al 2011;Jiang et al 2012;Pavithra et al 2014). No codominant SSR markers have been developed for this outcrossing species.…”

Section: Discussionmentioning

confidence: 99%

“…Molecular markers, on the other hand, can provide more informative and reproducible data for germplasm selection at a juvenile stage, and they can also aid in evaluating genetic diversity of extant populations and planning conservation actions for the long-term variability of a plant species. Several types of molecular markers have already been applied in Pongamia, including inter simple sequence repeat (ISSR) Sahoo et al 2010;Sujatha et al 2010;Jiang et al 2012), random amplified polymorphic DNA (RAPD) Kesari and Rangan 2011) and amplified fragment length polymorphism (AFLP) Thudi et al 2010;Sharma et al 2011;Pavithra et al 2014). However, owing to the difficulty in marker development using conventional methods, these studies only employed a limited number of marker loci, most of which were dominantly inherited and not feasible for distinguishing between homozygotes and heterozygotes.…”

Section: Introductionmentioning

confidence: 99%

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De novo sequencing and characterization of seed transcriptome of the tree legume Millettia pinnata for gene discovery and SSR marker development

et al. 2016

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Pongamia (Millettia pinnata) is a promising biofuel crop with multiple merits. Breeding of ideal Pongamia germplasm for industrial application demands substantial progress in molecular biology of this legume species, which has been largely hampered by the paucity of its genomic data. In this study, we constructed and characterized a comprehensive seed transcriptome by the high-throughput Illumina sequencing technology. We obtained over 83 million high-quality reads, which were processed and assembled into 53,586 unigenes with a mean length of 787 bp. Among these unigenes, 39,602 (73.90 %) and 24,078 (44.93 %) showed significant similarity to proteins in the NCBI non-redundant and the SwissProt protein databases, respectively. Of the annotated unigenes, 30,619 (57.14 %) were classified into 56 Gene Ontology categories. Furthermore, 21,905 (40.88 %) unigenes were assigned to 128 pathways in the Kyoto Encyclopedia of Genes and Genomes pathway database. A set of 364 unigenes involved in five pathways closely related to oil biosynthesis and accumulation were screened out as candidates for future functional analyses. On the other hand, 5710 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified in 4951 unigenes with a density of one SSR every 7.39-kb sequence. One hundred EST-SSRs were randomly selected to validate amplification and to assess polymorphism among 12 Pongamia individuals. Eighty-two primer pairs successfully amplified DNA fragments and 17 of them detected polymorphism, in which the polymorphism information content values ranged from 0.14 to 0.57. Jianzi Huang and Xiaohuan Guo have contributed equally to this work.Electronic supplementary material The online version of this article (

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

De novo sequencing and characterization of seed transcriptome of the tree legume Millettia pinnata for gene discovery and SSR marker development

et al. 2016

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“…Bornet et al. , 2002; Levsen & Mort, 2009; Sahoo et al. , 2010; see also reviews in Mc‐Gregor et al.…”

Section: Discussionmentioning

confidence: 99%

Testing hybridization hypotheses and evaluating the evolutionary potential of hybrids in mangrove plant species

2010

J of Evolutionary Biology

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Natural hybridization is of marked importance from global to local biological diversity. In mangroves, species ranges overlap extensively with one another and species share a long overlap of flowering time. Although hybridization has been suggested, patterns of hybridization and the evolutionary potential of hybrids are not yet fully understood. This study provides molecular evidence for the parental origins and status of hybrids in the dominant mangrove genus Rhizophora based on comparisons of chloroplast and nuclear phylogenies and estimations of genetic relatedness and structure from inter‐simple sequence repeat (ISSR) markers. Phylogenetic analyses indicate that almost all species can act as maternal parents to hybrids and that hybridization can be bidirectional. Bayesian analyses indicate that hybrids are simple F1s, and no trace of backcrossing was detected within populations. Hybridization, for the most part, occurs almost only locally and dispersal of hybrid individuals is limited beyond the hybrid sites.

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“…A number of studies have been conducted on Pongamia using dominant markers such as RAPD, ISSR, AFLP and TE-AFLP (Kesari et al 2010;Sahoo et al 2010;Sharma et al 2011). However, the information content of these dominant markers is less due to presence of only two allelic states.…”

Section: Introductionmentioning

confidence: 99%

Isolation and characterization of a first set of nine polymorphic microsatellite loci in Pongamia pinnata (Fabaceae)

Sharma

Islam

Negi

et al. 2014

J Genet

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Inter and intra-population variability of Pongamia pinnata: a bioenergy legume tree

Cited by 17 publications

References 12 publications

De novo sequencing and characterization of seed transcriptome of the tree legume Millettia pinnata for gene discovery and SSR marker development

De novo sequencing and characterization of seed transcriptome of the tree legume Millettia pinnata for gene discovery and SSR marker development

Testing hybridization hypotheses and evaluating the evolutionary potential of hybrids in mangrove plant species

Isolation and characterization of a first set of nine polymorphic microsatellite loci in Pongamia pinnata (Fabaceae)

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