香薷EST-SSR位点特征分析及两种柠檬醛型品种鉴定OA

Based on the high-throughput sequencing transcriptome data of 36 Elsholtzia ciliata leaves and stems,SSR loci were retrieved and primers were designed using MISA and Primer3,and their distribution patterns,sequence characteristics,and primer effectiveness were analyzed.Using the developed EST-SSR primers,the 2 lemonal type Elsholtzia ciliata varieties selected by the research group were identified.The results showed that 30 531 SSR loci were identified in the Elsholtzia cilia-ta transcriptome,distributed in 24 509 Unigenes,with an occurrence frequency of 23.86％,including 292 types of repeat motifs,with an average motif length of 13.57 bp.The number of SSRs with a length ranging from 12 to 20 bp was the largest,reaching 17 658(56.84％).A total of 25 615 loci were successfully designed with primers for the Elsholtzia ciliata transcriptome.Among the 80 pairs of randomly selected primers,the effective amplification rate in the 3 Elsholtzia ciliata species was 96.25％.There were 64 pairs of primers that produced a single band,accounting for 80.0％of the primer quantity;9 pairs produced double bands.Only 4 pairs produced multiple bands,accounting for 5％of the primer quantity.The combination of primers SSR1,SSR20 or SSR29 could distinguish the 3 Elsholtzia ciliata species based on agarose gel electrophoresis.Some fragments with the same length were found in the EST-SSR product sequencing results,indicating single nucleotide polymor-phisms(SNP)in addition to size differences.The study showed that the SSR loci in the Elsholtzia ciliata transcriptome presented a high-density feature and contained abundant repeat motifs.The developed EST-SSR molecular markers could provide molecular identification basis for the subsequent variety declaration of lemonal type Elsholtzia ciliata.