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Background  The oil palm ( Elaeis guineensis , 2n = 32) has the highest oil yield of any crop species, as well as comprising the richest dietary source of provitamin A. For the tropical species, the best mean growth temperature is about 27°C, with a minimal growth temperature of 15°C. Hence, the plantation area is limited into the geographical ranges of 10°N to 10°S. Enhancing cold tolerance capability will increase the total cultivation area and subsequently oil productivity of this tropical species. Developing molecular markers related to cold tolerance would be helpful for molecular breeding of cold tolerant  Elaeis guineensis .    Results  In total, 5791 gene-based SSRs were identified in 51,452 expressed sequences from  Elaeis guineensis  transcriptome data: approximately one SSR was detected per 10 expressed sequences. Of these 5791 gene-based SSRs, 916 were derived from expressed sequences up- or down-regulated at least two-fold in response to cold stress. A total of 182 polymorphic markers were developed and characterized from 442 primer pairs flanking these cold-responsive SSR repeats. The polymorphic information content (PIC) of these polymorphic SSR markers across 24 lines of  Elaeis guineensis  varied from 0.08 to 0.65 (mean = 0.31 ± 0.12). Using  in-silico  mapping, 137 (75.3%) of the 182 polymorphic SSR markers were located onto the 16  Elaeis guineensis  chromosomes. Total coverage of 473 Mbp was achieved, with an average physical distance of 3.4 Mbp between adjacent markers (range 96 bp - 20.8 Mbp). Meanwhile, Comparative analysis of transcriptome under cold stress revealed that one  ICE1  putative ortholog, five  CBF  putative orthologs, 19  NAC  transcription factors and four cold-induced orhologs were up-regulated at least two fold in response to cold stress. Interestingly, 5′ untranslated region of both Unigene21287 ( ICE1 ) and CL2628.Contig1 ( NAC ) both contained an SSR markers.    Conclusions  In the present study, a series of SSR markers were developed based on sequences differentially expressed in response to cold stress. These EST-SSR markers would be particularly useful for gene mapping and population structure analysis in  Elaeis guineensis . Meanwhile, the EST-SSR loci were inducible expressed in response to low temperature, which may have potential application in identifying trait-associated markers in oil palm in the future.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-014-0384-2) contains supplementary material, which is available to authorized users.

bmc plant biology

Exploiting transcriptome data for the development and characterization of gene-based SSR markers related to cold tolerance in oil palm (Elaeis guineensis)