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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

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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 CORE Metadata, citation and similar papers at core.ac.uk Provided by Nature Precedings Interspecific differences in single n ucleotide polymorp his ms (SNPs) and indels in expressed sequence tag libraries of oil palm Elaeis guineensis and E. oleifera Aikkal Riju 1 and Vadivel Arunachalam 2* (1)Aikkal , Kanul, Kannur , Kerala - 670564,India (2) Central Plantation Crops Research Institute, Kudlu P.O, Kasaragod – 671124, Kerala, In- dia. more than E. oleifera. We provide the re - ABSTRACT sults of the study as online database (http:/ / riju.byethost31.com /oilpalm /) Oil palm is the second largest source for use by oil palm breeders. of edible oil, which meets one- fifth of global demands of oils and fats. Ex- Keywords: Mutation, Nucleotide, Transi - tion, Trans- version, Single Nucleotide Poly- pressed sequence tag (EST) sequencing morphisms & Indel programs have provided a wealth of in- INTRODUCTION formation, identifying novel genes from a broad range of organisms and provid - The Oil palm a tropical palm tree ing an indication of gene expression lev- originated in West Africa but has since el in particular tissues. It also provides been planted successfully in tropical re - the richest source of biologically useful gions within 20 degrees of the equator. SNPs due to the relatively high redun - Oil palm is the second largest source of dancy of gene sequence, the diversity of edible oil next only to soybean, which genotypes represented within databases. contributes approximately 20% of the EST based SNPs are potential molecular world's production of oils and fats. Oil Nature Precedings : hdl:10101/npre.2009.3593.1 Posted 12 Aug 2009 markers and aid in genetic improve - is extracted from both the pulp of the ment. A total of 21062 and 2053 poly - fruit (palm oil, edible oil) and the kernel morphic (SNP and Indel) sites in E. (palm kernel oil, used mainly for soap guineensis species and in E. oleifera , manufacture). Both palm oil and palm 4955 SNPs and 1172 Indels were detect - kernel oil are high in olefins, a poten - ed. SNP(17.5/kbp) and Indel(4.1/kbp) tially valuable chemical group that can frequency was higher in E. oleifera than be processed into many non- food prod - E. guineensis species (16.8/kbp , ucts as well. There are cultivated two 1.6/kbp). E. oleifera showed higher species of oil palm, Elaeis guineensis transition to transversion ratio (1.40) Jacq. from tropical western Africa and E. than in E. guineensis (1.02). The ratio of oleifera from Americas. African oil palm Ts vs Tv showed, the genetic divergence is widely cultivated and American oil is occurring in this crops in different palm is important in terms of compact fashion and E. guineensis had diverged growth habit and resistance to diseases. Oil palm has a large diploid genome of Riju and Arunachalam 1 K.Takahashi et al. 3400 MB distributed in 32 chromo - of a crop species. Single Nucleotide somes. polymorphisms (SNPs) possess desirable Expressed Sequence Tags or ESTs properties as molecular markers. Bial- provide researchers with a quick and in- lelism makes them easy to score in high expensive route for discovering new throughput genotyping assays. Molecu - genes, for obtaining data on gene ex- lar genetic markers developed from pression and regulation, and for the ESTs can be used to examine a group of construction of the Genome maps. A individuals or populations to estimate single nucleotide polymorphism, or SNP various diversity measures and genetic (pronounced snip ), is a DNA sequence distances, infer genetic structure and variation occurring when a single nu - clustering patterns, test for Hardy- cleotide - A, T, C, or G - in the genome Weinberg equilibrium and multi- locus differs between members of a species equilibrium, and to test polymorphic (or between paired chromosomes in an loci for evidence of selective neutrality. individual). Single Nucleotide Polymor - They are useful to plant breeders, phisms may fall within coding se - germplasm managers, and population quences of genes, non- coding regions of geneticists. The use of EST sequence genes, or in the intergenic regions. SNPs data for the identification of SNPs has within a coding sequence will not neces - many advantages that can be exploited sarily change the amino acid sequence to facilitate the development of highly of the protein that is produced, due to dense genetic maps and markers assist - degeneracy of the genetic code. If DNA ed breeding programs [Varshney et. al., sequence in which any change in the 2005]. SNPs can be used to saturate ge- base pairs do not result in the change of netic maps in plants [Bhattramakki and polypeptide sequence, then it is termed Rafalski, 2001]. synonymous (sometimes called a silent Recently EST resources of oil palm mutation) - if a different polypeptide are being developed at IRD, Montpellier sequence is produced, they are non- France and MPOB, Kuala Lumpur synonymous. SNPs that are not in pro - Malaysia tein- coding regions may still have con - (http:/ / palmoils.mpob.gov.my/palm - sequences for gene splicing, transcrip - genes.html ) and deposited at dbEST. Expressed sequence tag (EST) sequenc - Nature Precedings : hdl:10101/npre.2009.3593.1 Posted 12 Aug 2009 tion factor binding, or the sequence of non- coding RNA. The study of single ing programs have provided a wealth of nucleotide polymorphisms is also im - information, identifying novel genes portant in crop and livestock breeding from a broad range of organisms and programs. Expressed sequence tags providing an indication of gene expres - (ESTs) are an important resource for sion level in particular tissues [Adams identifying polymorphisms in tran - et. al., 1995]. EST sequence data may scribed regions. provide the richest source of biologically Single nucleotide polymorphisms useful SNPs due to the relatively high (SNPs) have been shown to be the most redundancy of gene sequence, the diver - abundant source of DNA polymorphism sity of genotypes represented within in human, animal and plant genomes. databases, and the fact that each SNP SNPs are the most common type of alle- would be associated with an expressed les found within and between varieties gene [Picoult- Newberg et. al., 1999]. Re- 2 In Interspecific differences in single nucleotide polymorphisms (SNPs) and indels in expressed sequence tag libraries of oil palm Elaeis guineensis and E. oleifera cent study of Oil palm EST libraries for Zap libraries hold very few ESTs, so we SNP detection showed that the genome ignored those libraries for this study. has the SNP frequency 1.36/100bp [Riju Majority of the sequences represents et. al., 2007 ]. We have used updated root, mesocarp tissue, young flower and EST libraries of Oil palm species for this mature flower. We have used the contig analysis to find the Interspecific differ - building package Cap3 [Huang and ences in SNP / Indel polymorphisms. Madan, 1999] server (http:/ / mobyle. - SNP detection perl script AutoSNP ver - pasteur.fr/cgibin/MobylePortal/por - sion.1.0 were used to find the SNP site tal.py#) to cluster the ESTs and made information and transition vs transver - necessary ace files of each tissue. Au- sion analysis [Barker et. al., 2003]. EST- toSNP version.1.0 was used to find the SNP can be detected by using other pro - candidate SNPs from these contigs. The grams or servers such as SEAN [Huntley transition(Ts) vs transversion(Tv) ratio et. al., 2006 ], PolyPhred [Nickerson et. of all the libraries to find the DNA sub - al., 1997], PolyBayes [Marth et. al., 1999], stitution in Oil palm genome was also TRACE_DIFF [Bonfield et. al.,1998 ], Hap - calculated. loSNPer [Tang et. al., 2008] and RESULTS AND DISCUSSION HarvEST(http:/ / harvest.ucr.edu) but Au- We found 21062 SNPs and 2053 In- toSNP provides user friendly approach dels sites in E. guineensis (Table 1). In E. and interpretable result as html file. oleifera 4955 SNPs and 1172 Indels were SNPs can be classified based on their found (Table 2). Considering those SNP nucleotide substitution as either transi - site by nucleotide substitution, , a total tion (G↔A or C↔T) or of 10635 transitions(Ts), 10427 transversion(C↔G, A↔T, C↔A or transversions(Tv) and 2053 indel poly - T↔G). Indel sites can classified to four morphisms were detected in E. guineen - groups based on the nucleotide involved sis, where as in E. oleifera a total of (A/T/C/G). Thus there are ten kinds of 2891 transition, 2064 transversion and SNP/indel (two types of transition, four 1172 indel polymorphisms were detect - types of transversion and four groups of ed. SNPs occurred at a frequency of indels) are possible in genomes. 16.8/1kbp in E. guineensis species and MATERIALS AND METHODS 17.5/1kbp in E. oleifera species. Indel Nature Precedings : hdl:10101/npre.2009.3593.1 Posted 12 Aug 2009 frequency 1.6/1kbp and 4.1/1kbp ob - EST database, dbEST of NCBI release served in E. guineensis and E. oleifera re - 121407 contains 16,999 Elaeis guineen - spectively. While finding the substitu - sis (GenBank: EL680966 - EL695503 and tion comparison, tissues like mature EE593287 - EE593337) and 3,205 Elaeis flower and suspension cell libraries oleifera (GenBank: EL563704 - ES414798 shows higher transversion sites than and BM402088, BM402089 and transition. The Indel polymorphism ratio EB643519 - EB643628) expressed se - (4.1/1kbp) found to be high in mesocarp quence tags. We have used five (root, tissue than other tissue libraries ob - mature flower, shoot apical meristems, served. The overall transition vs suspension cells and young flower) EST transversion ratio in E. oleifera is 1.4, libraries of Elaeis guineensis [Jouannic which shows that the relative increase of et. al., 2005], [Chai- Ling et. al., 2007] transition over transversion. Though in and one EST library (mesocarp) of Elaeis case of E.
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