Mining for single nucleotide polymorphisms and insertions / deletions in expressed sequence tag libraries of oil palm

The oil palm is a tropical oil bearing tree. Recently EST-derived SNPs and SSRs are a free by-product of the currently expanding EST (Expressed Sequence Tag) data bases. The development of high-throughput methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion / deletion) has led to a revolution in their use as molecular markers. Available (5452) Oil palm EST sequences were mined from dbEST of NCBI. CAP3 program was used to assemble EST sequences into contigs. Candidate SNPs and Indel polymorphisms were detected using the perl script auto_snip version 1.0 which has used 576 ESTs for detecting SNPs and Indel sites. We found 1180 SNP sites and 137 indel polymorphisms with frequency 1.36 SNPs / 100 bp. Among the six tissues from which the EST libraries had been generated, mesocarp had high frequency of 2.91 SNPs and indels per 100 bp whereas the zygotic embryos had lowest frequency of 0.15 per 100 bp. We also used the Shannon index to analyze the proportion of ten possible types of SNP/indels. ESTs from tissues of normal apex showed highest values of Shannon index (0.60) whereas abnormal apex had least value (0.02). The present report deals the use of Shannon index for comparing SNP/ indel frequencies mined from ESTlibraries and also confirm that the frequency of SNP occurrence in oil palm to use them as markers for genetic studies

Interspecific Analysis for SNPs in EST Libraries of Oil Palm- Elaeis Guineensis and E. Oleifera

Oil palm is the second largest source of edible oil, which contributes to approximately 20% of the world's production 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, and the fact that each SNP would be associated with an expressed gene. There are cultivated two species of oil palm, Elaeis guineensis Jacq. from tropical western Africa and E. oleifera from Americas. Interspecific SNP detection carried but by choosing Lambda Zap II libraries of both species. Auto_snp perl script was used to cluster the ESTs and detect SNPs. A total of 163 EST sequences belong to Lambda zap libraries analysed here, interestingly we have found 60 SNP site (35 Transition transversion 25 ) in this species specific sequences. Labda Zap tissue also shows the similar pattern of SNPs, such as transition type mutation is higher than trasnversion type in Oil palm (Riju et al, 2007)

Interspecific Analysis for SNPs in EST Libraries of Oil Palm- Elaeis Guineensis and E. Oleifera

Oil palm is the second largest source of edible oil, which contributes to approximately 20% of the world's production 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, and the fact that each SNP would be associated with an expressed gene. There are cultivated two species of oil palm, Elaeis guineensis Jacq. from tropical western Africa and E. oleifera from Americas. Interspecific SNP detection carried but by choosing Lambda Zap II libraries of both species. Auto_snp perl script was used to cluster the ESTs and detect SNPs. A total of 163 EST sequences belong to Lambda zap libraries analysed here, interestingly we have found 60 SNP site (35 Transition transversion 25 ) in this species specific sequences. Labda Zap tissue also shows the similar pattern of SNPs, such as transition type mutation is higher than trasnversion type in Oil palm (Riju et al, 2007)