GinMicrosatDb: a genome-wide microsatellite markers database for sesame (Sesamum indicum L.)
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Molecular breeding in sesame is still at infancy due to limited number of microsatellite markers available and the low level of polymorphism exhibited by them. Therefore, whole genome sequencing was used for development of microsatellite markers so as to ensure availability of substantial number of polymorphic markers for use in marker assisted breeding programs. Whole genome sequencing of sesame variety ‘Swetha’ was done using Illumina paired-end sequencing and Roche 454 shotgun sequencing technologies (GCA_000975565.1 in GenBank). ‘GinMicrosatDb’, a genome-wide microsatellite marker database has been developed using the whole genome sequence data of sesame variety ‘Swetha’. The database consists of microsatellites localized on both linkage groups and scaffolds with their genomic co-ordinates. It provides five sets of forward and reverse primers for each of the microsatellite loci along with the flanking sequences, primer GC content, product size and melting temperature etc. The distribution of microsatellites can be viewed and selected through a genome browser as well as through a physical map. The newly identified microsatellite markers are expected to help sesame breeders in developing marker tags for traits of economic importance thereby bringing about greater efficiency in marker-assisted selection programs.
KeywordsLinkage group Microsatellites Physical map Sesame
This study was funded by ICAR-National Agricultural Innovation Project (No. 415501-05) and Consortium Research Platform on Genomics. The facilities provided by Indian Council of Agricultural Research, NBPGR and ICAR-IASRI are acknowledged.
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Conflict of interest
- Asp T, Frei UK, Didion T, Nielsen KK, Lubberstedt T (2007) Frequency, type, and distribution of EST-SSRs from three genotypes of Lolium perenne, and their conservation across orthologous sequences of Festuca arundinacea, Brachypodium distachyon, and Oryza sativa. BMC Plant Biol 7(1):36CrossRefPubMedPubMedCentralGoogle Scholar
- Janick J (2008) Plant breeding reviews, vol 30. Wiley, LondonGoogle Scholar
- Paetkau D (1999) Microsatellites obtained using strand extension: an enrichment protocol. Biotechniques 26(690–692):694–697Google Scholar