C. Akkasaeng

ESAP plus: a web-based server for EST-SSR marker development

BackgroundSimple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence Tags (ESTs), which can be obtained from the plant mRNA (converted to cDNA), must be utilized. With the advent of high-throughput sequencing technology, huge EST sequence data have been generated and are now accessible from many public databases. However, SSR marker identification from a large in-house or public EST collection requires a computational pipeline that makes use of several standard bioinformatic tools to design high quality EST-SSR primers. Some of these computational tools are not users friendly and must be tightly integrated with reference genomic databases.ResultsA web-based bioinformatic pipeline, called EST Analysis Pipeline Plus (ESAP Plus), was constructed for assisting researchers to develop SSR markers from a large EST collection. ESAP Plus incorporates several bioinformatic scripts and some useful standard software tools necessary for the four main procedures of EST-SSR marker development, namely 1) pre-processing, 2) clustering and assembly, 3) SSR mining and 4) SSR primer design. The proposed pipeline also provides two alternative steps for reducing EST redundancy and identifying SSR loci. Using public sugarcane ESTs, ESAP Plus automatically executed the aforementioned computational pipeline via a simple web user interface, which was implemented using standard PHP, HTML, CSS and Java scripts. With ESAP Plus, users can upload raw EST data and choose various filtering options and parameters to analyze each of the four main procedures through this web interface. All input EST data and their predicted SSR results will be stored in the ESAP Plus MySQL database. Users will be notified via e-mail when the automatic process is completed and they can download all the results through the web interface.ConclusionsESAP Plus is a comprehensive and convenient web-based bioinformatic tool for SSR marker development. ESAP Plus offers all necessary EST-SSR development processes with various adjustable options that users can easily use to identify SSR markers from a large EST collection. With familiar web interface, users can upload the raw EST using the data submission page and visualize/download the corresponding EST-SSR information from within ESAP Plus. ESAP Plus can handle considerably large EST datasets. This EST-SSR discovery tool can be accessed directly from: http://gbp.kku.ac.th/esap_plus/.

Simple sequence repeat (SSR)-based genetic variability among peanut genotypes different in specific leaf weight and relative water content

The objective of this study was to compare if simple sequence repeat (SSR) markers could correctly identify peanut genotypes with difference in specific leaf weight (SLW) and relative water content (RWC). Four peanut genotypes and two water regimes (FC and 1/3 available water; 1/3 AW) were arranged in factorial randomized complete block design with six replications. The data were recorded for specific leaf weight (SLW) and relative water content (RWC), and 256 SSR markers were used to detect genetic difference. 89 SSR markers could detect polymorphism among peanut genotypes (48.9%). The numbers of alleles ranged from 1 to 6 with a mean of 2.7 alleles per locus. The polymorphic information content (PIC) values varied from 0.38 to 0.75 with a mean of 0.48. The genetics relationship among peanut genotypes was estimated. KK 4 was clustered distinct from the others genotypes, whereas ICGV 98324 and ICGV 98303 were grouped in the same cluster furthest from the KK 4. The results from this study could be useful as a source of variation for development of mapping population for drought tolerance in peanut breeding program. Keywords : Drought, water regime, polymorphism, genetic relationship, SSR markers African Journal of Biotechnology Vol. 12(26), pp. 4053-4064, 26 June, 2013