Exploiting EST databases for the development and characterization of EST-SSR markers in blueberry (Vaccinium) and their cross-species transferability in Vaccinium spp

• 54 EST-SSR primer pairs were developed from 17,267 ESTs in blueberry.
• Those primer pairs exhibited a high degree of polymorphism with a mean PIC of 0.772.
• The cross-species transferability ranged from 68.5% to 88.90% in 8 species of Vaccinium.
• Relationships of materials revealed at EST-SSR level were consistent with the traditional taxonomy.

Expressed sequence tags (ESTs) databases are an increasingly valuable resource for developing SSR markers. However, to date, only a limited number of SSR markers have been developed from EST databases for blueberry. In this study, 17,267 ESTs in blueberry (Vaccinium spp.) were screened for SSRs with motif lengths varying from 2 to 6 base pairs (bp). In total, 2187 SSRs (12.67% of total screened ESTs) were identified from 1876 microsatellite-containing sequences. Dinucleotide repeats follow by trinucleotide repeats were the predominant motif. A total of 54 EST-SSR markers were characterized from 120 primer pairs designed by assaying 12 samples of the Vaccinium genus section Cyanococcus. The primer pairs exhibited a high degree of polymorphism with a mean PIC of 0.772, indicating high level informativeness within these EST-SSRs. The 54 new EST-SSR primer pairs comprising 540 alleles were used to investigate cross-species transferability among 26 accessions, which represented 8 species (three exotic cultivated species and five natural wild species from China) from 6 sections of Vaccinium. The results indicated that cross-species transferability ranged from 68.5% to 88.9%. Cluster analysis and PCoA based on 54 EST-SSR primer pairs were largely consistent with the traditional taxonomy and geographic locations among the materials tested, and both indicated that the EST-SSR primers were effective for the phylogenetic analysis in Vaccinium. Our results showed that those EST-SSR markers displayed considerable polymorphism and high transferability in both cultivated and wild species of Vaccinium, and will contribute to the studies of genetic diversity, linkage mapping, QTL and molecular assisted breeding of Vaccinium crops.

The relationships among 30 Vaccinium accessions based on cluster dendrogram using genotypic data of 54 polymorphic EST-SSR primer pairs.Figure optionsDownload as PowerPoint slide