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

BACKGROUND: 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. OBJECTIVE: 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. MATERIALS AND METHODS: 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. RESULTS: 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. CONCLUSIONS: 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.