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Large-scale development, characterization, and cross-amplification of EST–SSR markers in Chinese chive

Author(s): Qingming Tang, Langbo Yi, Xianglin Yuan, Fu Li

Chinese chive (Allium tuberosum Rottler ex Spr.) is an important vegetable crop. However, genetic and breeding studies of the species have been restricted by the lack of simple sequence repeat markers (SSRs). In the present study, a total of 2553 Chinese chive SSRs were developed from the species’ transcriptome, with 626, 643, and 536 of the makers located in coding sequences, 5' untranslated regions and 3' untranslated region, respectively. The annotation of SSR-containing expressed sequence tags revealed that the transcripts were enriched for several Gene Ontology (GO) categories, including ‘protein binding’, ‘regulation of transcription’, and ‘integral to membrane’. Among the 2,553 SSRs, di- and tri-nucleotide repeat motifs were the most abundant (52.3 and 45.6%, respectively), and AC/GT and GAA/TTC were the most frequent di- and tri-nucleotide motifs, respectively. PCR amplification, using 100 SSR primer pairs, revealed that 94% of the markers were of good quality and that 83-88 of the makers could be amplified in six other Allium species. This suggests that the markers had high cross-species transferability. The substantial number of SSRs developed will provide a valuable resource for future genetic and breeding studies in Chinese chive