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Rubus idaeus has remarkable economic and cultural value. Developing efficient simple sequence repeat (SSR) markers is necessary for the molecular breeding of red raspberry. In this study, SSR mining was performed using the de novo transcriptome sequence of R. idaeus. In total, 14,210 SSR sequences were identified from 11,158 SSR-containing unigenes. In all the SSR sequences, mononucleotide, dinucleotide, and trinucleotide repeats were the most common, and their number and percentage were 1323 (9.31%), 6752 (47.52%), and 4897 (34.46%), respectively. Of the mononucleotide and dinucleotide repeats, A/T, AG/CT, AT/AT, and AC/GT were more abundant and accounted for 9.09%, 37.82%, 6.51%, and 3.14% of the total repeat number, respectively. In the trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide repeats, the nucleotide (NT) patterns AAG/CTT, AAAG/CTTT, AAAAG/CTTTT, and AAGAGG/CCTCTT were the most frequent, and accounted for 14.11%, 0.38%, 0.57%, and 0.23% of the total SSRs, respectively. Of the 480 SSR-containing unigenes with gene ontology (GO) annotation, the classification results showed that they were mainly involved in binding, catalytic, and transporter molecular functions. Most of the 3441 SSR-containing unigenes with the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation were involved in the following top five pathways: metabolic, RNA transport, spliceosome, protein processing in the endoplasmic reticulum, and mRNA surveillance. Thirty pairs of primers derived from the red raspberry transcriptome were randomly selected to assess their polymorphism by using 15 red raspberry germplasms, in which the polymorphism information content (PIC) values ranged from 0.50 to 0.86, with a mean of 0.73, thereby indicating a high level of polymorphism. The unweighted pair group method with arithmetic mean clustering results indicated that the thirty pairs of primers could precisely distinguish the germplasms. This study reveals the SSR distribution characteristics of red raspberry and provides a scientific basis for further genetic diversity studies and genetic linkage map construction for this species.

Vitis amurensis grape cultivars and hybrids are mainly used to make wines in Northeast Asia with a cold winter. Anthocyanidin glucosylation at 5-O position catalyzed by 5-O-glucosyltransferase (5GT) in grape skins is crucial for color stability of red wines. To study 5GT functions in anthocyanidin diglucosides synthesis of V. amurensis, 20 5GTs were preliminarily identified from a genome-wide characterization of the UDP-glycosyltransferase family according to the reported 5GTs, which were also performed phylogenetic and bioinformatics analysis. Two important 5GTs, Vitvi0900582.t01 and Vitvi05g01269.t01, were screened through analyses of anthocyanidin diglucosides accumulation and gene expression in berry skins of three representative grape cultivars with significant differences in anthocyanin glycosylation. Fourteen alleles of each of the 5GTs were cloned from 14 V. amurensis cultivars and hybrids as well as from V. vinifera ‘Cabernet Sauvignon’, and sequence analysis and functional prediction were performed. From three perspectives of phenotype, transcriptional level, and genotype, it has been found that the functional allele at the Vitvi0900582.t01 locus of Chr 9 played a decisive role in the synthesis of abundant anthocyanidin diglucosides in V. amurensis. In addition, the trace anthocyanidin diglucosides detected in V. vinifera ‘Cabernet Sauvignon’ were led by the functional allele at the Vitvi05g01269.t01 locus of Chr 5. This study provides preliminary data for further research on the regulatory mechanism of anthocyanidin diglucosides in the grapes with the V. amurensis pedigree to improve their wine quality in future breeding efforts.