Development of Novel Polymorphic EST-SSR Markers from the Cranberry Fruit Transcriptome

Cranberry (Vaccinium macrocarpon Ait.) has high developmental prospects and great research value. Cranberry has a narrow genetic base, however, its morphological characteristics are not easily distinguishable. Besides, traditional breeding methods are limited, and breeding progress on cranberry cultivars has been slow.

The objective of this study was to assess polymorphic EST-SSR markers developed from a cranberry fruit transcriptomic sequencing library to provide candidate EST-SSR sequences for future research on stress resistance breeding of cranberry.

Thirteen cranberry accessions were used for EST-SSR analysis, and 16 accessions of other Vaccinium species were used to test primer transferability. Genomic DNA was extracted from young leaves of 6-year-old cranberry plants and subjected to PCR amplification. A binary matrix was established and analyzed in NTSYS-pc v.2.10e for calculation of the genetic similarity of cranberry cultivars and construction of a cluster dendrogram.

A total of 47 stress-resistance-related primer pairs were designed, of which 7 pairs showed polymorphism. The average number of effective alleles was 1.844, and the average expected heterozygosity was 0.455. The average transfer rate was 63.39%. Genetic similarity coefficients ranged from 0.28 to 1.00, with an average of 0.76. UPGMA clustering divided the 13 cranberry accessions into four groups at a genetic similarity of 0.74.

The seven polymorphic EST-SSR markers were able to reveal genetic relationships among 13 cranberry accessions and can be used for future research on stress resistance breeding of cranberry.