Transcriptomic Sequencing Analysis, Development, and Validation of EST-SSR Markers in Reed Canary Grass

Reed canary grass (Phalaris arundinacea L.) is a promising high-yield cool-season forage with significant ecological application potential in wastewater treatment and wetland restoration. Transcriptome sequences can rapidly assay and characterize a few gene-based microsatellites from various plants. Here, the transcriptome of reed canary grass was sequenced, and 50,155 putative EST-SSRs were identified from 272,328 transcripts, with tri-nucleotide being the most abundant type, followed by mono-nucleotide. A total of 300 EST-SSR markers were randomly selected, among which 45 polymorphic EST-SSR markers were used for the genetic diversity study of 17 reed canary grass accessions (P. arundinacea L.) and 2 accessions of related bulbous canary grass (P. aquatica L.). A total of 218 bands were amplified using 45 SSR markers; the reliable polymorphic bands were 118 (54.13%), the average of the polymorphic information content was 0.36, and the RP value was 0.96. In summary, the transcriptome sequences of reed canary grass contribute to gene prediction and promote molecular biology and genomics studies, whereas polymorphic SSR markers promote molecular-assisted breeding and related studies of Phalaris species.