Abstract
BackgroundSimple Sequence Repeats or microsatellites are resourceful molecular genetic markers. There are only few reports of SSR identification and development in pineapple. Complete genome sequence of pineapple available in the public domain can be used to develop numerous novel SSRs. Therefore, an attempt was made to identify SSRs from genomic, chloroplast, mitochondrial and EST sequences of pineapple which will help in deciphering genetic makeup of its germplasm resources.ResultsA total of 359511 SSRs were identified in pineapple (356385 from genome sequence, 45 from chloroplast sequence, 249 in mitochondrial sequence and 2832 from EST sequences). The list of EST-SSR markers and their details are available in the database.ConclusionsPineElm_SSRdb is an open source database available for non-commercial academic purpose at http://app.bioelm.com/ with a mapping tool which can develop circular maps of selected marker set. This database will be of immense use to breeders, researchers and graduates working on Ananas spp. and to others working on cross-species transferability of markers, investigating diversity, mapping and DNA fingerprinting.Electronic supplementary materialThe online version of this article (doi:10.1186/s41065-016-0019-8) contains supplementary material, which is available to authorized users.
Highlights
Simple Sequence Repeats or microsatellites are resourceful molecular genetic markers
Total 5978 expressed sequence tags (ESTs) sequences of pineapple were downloaded from NCBI http://www.ncbi.nlm. nih.gov/nucest/?term=ananas+comosus in FASTA format
Genomic sequence of Ananas comosus (L.) Merrill is available as 3133 scaffolds of 381,905,120 bp length
Summary
Simple Sequence Repeats or microsatellites are resourceful molecular genetic markers. There are only few reports of SSR identification and development in pineapple. Complete genome sequence of pineapple available in the public domain can be used to develop numerous novel SSRs. an attempt was made to identify SSRs from genomic, chloroplast, mitochondrial and EST sequences of pineapple which will help in deciphering genetic makeup of its germplasm resources. Among all the markers till date, Simple Sequence Repeats (SSRs) are the most ideal, powerful and reliable markers for molecular plant breeding applications because of their high abundance, co-dominant inheritance and multiple alleles [7]. BES-SSR markers serve a useful resource for integrating genetic and physical maps [8,9]
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