EST-SSR markers for gerbera (Gerbera hybrida)

Abstract

Gerbera (Gerbera hybrida) is one of the most important cut and pot flowers marketed worldwide. Few molecular markers and no SSR (simple sequence repeat) markers were available for gerbera breeding and genetic studies. Through in silico analysis of 8,670 unigene sequences assembled from 16,998 gerbera expressed sequence tags (ESTs) in the GenBank, we identified 893 SSR loci, corresponding to 10.3% of the gerbera unigene sequences or one SSR in every 5.16 kb of the ESTs in the gerbera transcriptome. The majority of SSR loci contain dinucleotide (42.8%) or trinucleotide (25.6%) repeats, while fewer contain tetranucleotide (6.4%), pentanucleotide (9.1%) and hexanucleotide (16.1%) repeats. AG (37%) and AAT (7.3%) were the most abundant motifs identified. Out of 115 primer pairs designed, 99 (86.1%) amplified discrete PCR products of the expected sizes, while 67 (67.7%) detected polymorphism among seven gerbera cultivars representing three plant types (cut flower, pot, and garden) propagated by two methods (seed or tissue culture). The number of alleles at these SSR loci ranged from 2 to 6, with an average of 2.7 alleles per locus. The PIC value of 67 polymorphic SSR markers was 0.13–0.80, with an average of 0.51. Sixty-eight ESTs targeted by the 115 SSR markers have putative gene functions, and two marker loci may have potential to be associated with disease resistance or flowering time. The availability of these gerbera EST-SSR markers should facilitate the use of molecular markers in gerbera breeding and genetic studies.