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Abstract:Microsatellites are the most promising co-dominant markers, widely distributed throughout the genome. Identification of these repeating genomic subsets is a tedious and iterative process making computational approaches highly useful for solving this biological problem. Here 38,083 microsatellites were localized in palm sequences. A total of 2, 97,023 sequences retrieved from public domains were used for this study. The sequences were unstained using the tool Seqclean and consequently clustered using CAP3. SSRs are located in the sequences using the microsatellite search tool, MISA. Repeats were detected in 33,309 sequences and more than one SSR had appeared in 3,943 sequences. In the present study, dinucleotide repeats (49%) were found to be more abundant followed by mononucleotide (30%) and trinucleotide (19%). Also among the dinucleotides, AG/GA/TC/CT motifs (55.8%) are predominantly repeating within the palm sequences. Thus in future this study will lead to the development of specific algorithm for mining SSRs exclusively for palms.

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Abstract: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.

Single Nucleotide Polymorphism (SNP) is a mutation where, a single base in the DNA differs from the usual base at that position. SNPs are the marker of choice in genetic analysis and also useful in locating genes associated with diseases. SNPs are important and frequently occurring point mutations in genomes and have many practical implications. In silico methods are easy to study the SNPs that are occurring in known genomes or sequences of a species of interest during the post genomic era. There are many on-line and stand alone tools to analyse the SNPs. We intend to guide the reader with the software details such as algorithmic background, file requirements, operating system specificity and species specificity, if any, for the tools of SNPs detection in plants and animals. We also list many databases and resources available today to describe SNPs in wide range of organisms.

Coconut palm is a multipurpose crop cultivated in tropics. Diversity in this crop is rich in South Pacific Ocean and Indian Ocean Islands. Foliar traits have not been studied extensively to understand the diversity. Seven traits relevant to wind tolerance, dry matter production and taxonomic discrimination known in palms are used in the study. An attempt was made using Shannon-Weaver index with an objective to understand the level of diversity for these traits in a germplasm collection from diversity hotspot areas. Seven tall groups and four dwarf groups representing seven island territories were studied using 206 individuals. Diversity estimate was the highest in Nicobar tall group whereas it was low in tall genotypes of Fiji and Tonga. Thickness of leaf sheath fiber of weft and warp strands had shown high diversity estimates. Results obtained in this study were analyzed in relation to adaptation, geographical affinity, mating system and taxonomic forms (typica and nana) along with the importance of foliar traits in diversity of coconut.

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