Analysis of SSR Characterization in Transcriptome for Pampass Grass Cortaderia selloana

Background: The perennial herbaceous pampas grass (Cortaderia selloana: Poaceae) integrates ecological and ornamental functions, serving both environmental rehabilitation and landscape enhancement. Its robust stress tolerance also positions it as a valuable genetic resource for improving resilience in other plant species. The study aimed to analyze characteristics of simple sequence repeats (SSRs) in the transcriptome of pampass grass (Cortaderia selloana) to lay a foundation for developing molecular markers for this species. Methods: Using C. selloana leaves, high-throughput sequencing was performed on the NovaSeq × Plus platform. SSR loci were identified from transcriptome data using MISA software, followed by analysis of their distribution and sequence characteristics. Result: A total of 333.731 reference sequences (unigenes) were obtained, among which 20.684 SSR loci were mined (frequency of occurrence 6.20%, average distribution distance 7.47 kb). SSR repeat motifs were dominated by mononucleotides (7781 SSRs, accounting for 37.62%), trinucleotides (8232 SSRs, 39.80%), and dinucleotides (4064 SSRs, 19.65%). Among 171 repeat motifs, A/T mononucleotide motifs predominated (91.34%), followed by AG/CT dinucleotide motifs (60.58%). SSR repeats were mostly distributed within the 6-15 range, with numbers of all six nucleotide repeat types progressively decreasing as motif repeat count increased. SSR lengths were mostly concentrated in the 12-40 bp range, with SSRs within this length range accounting for 56.90% of all SSR loci. Among these, 3329 SSR loci (16.10%) exhibited higher polymorphism potential (length greater than 20 bp). SSR loci in C. selloana exhibit high frequency, diverse repeat motifs, high polymorphism potential and considerable potential for research on genetic diversity, molecular identification of cultivars, and development of novel molecular markers in this species.