Development And Identification Of Novel EST-SSR Markers From De Novo Transcriptome Data Of Cranberry Fruit

Cranberry(Vaccinium macrocarpon Ait.) is an important small fruit in a great value of research and promising prospects due to its abundant anthocyannis,flavonoid components, which has demonstrated high antioxidant and antimicrobial capacity.However, very rare improved varieties are suitable for application. Thus, novel EST-SSR marker are developed and identified of 13 cranberry cultivars in this study,which are based on de novo transcriptome data of cranberry fruit.1. A total of 1,462 EST containing 7,448 SSRs were obtained from cranberry fruit transcriptome library, the frequency of EST-SSR was 2.55%. It indicated that trinucleotide was the most abundant(54.30%) type of SSR repeats,followed by dinucleotide(39.29%) and hexanucleotide(3.13%). This study also identified that42 SSR motifs in total, among which AG/CT dinucleotide was the most abundant(16.51%) motif, followed by GAA/TTC trinucleotide(4.78%).2. Putative function annotation results showed that, out of 1,462 Unigenes, 640 unigenes were annotationed by GO database, and classified into biological process,metabolic function and cellular component. There 35 secondary categories totally could be obtained on the 2ndlevel. The result of COG analysis showed that 428 sequences can be classified into 24 categories.3. All high quality 47 primer pairs(related to response to stimulus/chemicals,162)were designed using Primer3.0, and out of them 7 primer pairs displayed polymorphism among the 13 cranberry cultivars. The level of polymorphism were18.42%, and 7~12 alleles/locus were amplified with a mean of 10.29 alleles/locus.4. Genetic similar coefficient of 13 cranberry genotypes is about 0.28~1.00 with a mean value of 0.76, UPGMA-based cluster analysis showed that all cranberries fall into four clades on 0.74 level.