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Interspecific differences in single nucleotide polymorphisms (SNPs) and indels in expressed sequence tag libraries of oil palm Elaeis guineensis and E. oleifera

Aikkal Riju¹ and Vadivel Arunachalam²

Correspondence: (Login to view email address)

1. Aikkal, Kanul, Kannur, Kerala 670564, India
2. Central Plantation Crops Research Institute, Kudlu P.O, Kasaragod 671124, Kerala, India

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Document Type:

Manuscript

Date:

Received 24 September 2009 05:38 UTC; Posted 24 September 2009

Subjects:

Genetics & Genomics, Bioinformatics, Evolutionary Biology

Tags:

• Transition
• Transversion
• Single Nucleotide Polymorphisms
• Indel
• mutation
• nucleotide

Abstract:

Oil palm is the second largest source of edible oil, which meets one-fifth of global demands of oils and fats. Expressed sequence tag (EST) sequencing programs have provided a wealth of information, identifying novel genes from a broad range of organisms and providing an indication of gene expression level in particular tissues. It also provides the richest source of biologically useful SNPs due to the relatively high redundancy of gene sequence, the diversity of genotypes represented within databases. EST based SNPs are potential molecular markers and aid in genetic improvement. A total of 21062 and 2053 polymorphic (SNP and Indel) sites in E. guineensis species and in E. oleifera, 4955 SNPs and 1172 Indels were detected. SNP(17.5/kbp) and Indel(4.1/kbp) frequency was higher in E. oleifera than E. guineensis species (16.8/kbp, 1.6/kbp). E. oleifera showed higher transition to transversion ratio (1.40) than in E. guineensis (1.02). The ratio of Ts vs Tv showed, the genetic divergence is occurring in this crops in different fashion and E. guineensis had diverged more than E. oleifera. We provide the results of the study as online database (http://riju.byethost31.com/oilpalm/) for use by oil palm breeders.

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This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Riju, Aikkal and Arunachalam, Vadivel. Interspecific differences in single nucleotide polymorphisms (SNPs) and indels in expressed sequence tag libraries of oil palm Elaeis guineensis and E. oleifera. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2009.3593.2> (2009)

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Version number	Document title	Date
v1	Posted 12 August 2009

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