Abstract: Based on 49 876 transcripts（> 500 bp，89.44 Mb）obtained by full-length transcriptome sequencing of Allium tuberosum，13 111 SSR loci distributed in 10 332 transcripts were detected by MISA software. The frequency of these SSR loci was 26.29% and the average distribution distance was 6.82 kb. Among the six types of SSR loci searched，1–3 nucleotide repeats were dominant and accounted for 98.74% of the total SSR loci，of which mono-，di- and tri-nucleotide repeats were 66.55%，12.52%，and 19.67%，respectively. There are 103 detected repeat motifs，of which AC/GT（2.54%），CA/TG（2.29%），GAA/TTC（1.85%）and AAG/CTT（1.60%）were high frequency repeat motifs in dinucleotide and trinucleotide repeats. The lengths of repeat nucleotide sequences for all SSR loci ranged from 10 bp to 289 bp，of which 11 128（84.88%）were less than 20 bp，and 1 983（15.12%）were larger than 20 bp.According to these SSR loci，a total of 3 311 pairs of SSR primers were designed. Two hundred and eight pairs of primers were randomly selected for amplification tests，164 pairs of primers（78.85%）could amplify clear band effectively，and 39 pairs of primers showed polymorphism in 24 Allium tuberosum germplasm resources. Using the polymorphism primer SSR41，six sexual reproductive progenies from‘Malinjiu’ב791’were successfully identified. These results indicated that the SSR markers developed from the full-length transcriptome sequencing of Allium tuberosum could provide sufficient and reliable markers for analysis of genetic diversity，identification of germplasm resources and screening of sexual reproduction progeny of Allium tuberosum.

Key words: Allium tuberosum, full-length transcriptome, SSR, apomixis