Transcriptome-based discovery of EST-SSR markers in Cephalostachyum pingbianense rhizome buds

Cephalostachyum pingbianense is a woody bamboo species endemic to Yunnan, China, with ecological significance and potential for forest restoration. However, limited genomic resources have constrained its molecular study and breeding efforts. In this study, we utilized RNA-Seq data from rhizome buds to identify and characterize expressed sequence tag-simple sequence repeats (EST-SSRs), providing the first transcriptome-based SSR marker development for this species. A total of 28,918 perfect EST-SSRs were identified from the assembled transcriptome, with mononucleotide, dinucleotide, and trinucleotide motifs being the most prevalent. A/T-rich mononucleotides and functionally relevant trinucleotides such as CCG and AGG were dominant, reflecting common SSR patterns in coding regions. The average SSR length was 15.03 bp, with a relative abundance of 192.16 loci/Mb. From these, ten representative primer pairs were designed based on diverse motif types, optimal melting temperatures (58-62 °C), balanced GC content (40-60%), and suitable product sizes (100-300 bp). Therefore, the aim of this study was to conduct a de novo transcriptome assembly of Cephalostachyum pingbianense rhizome buds and mine the resulting data for EST-SSR markers. These newly developed EST-SSR markers provide valuable tools for future studies on genetic diversity, population structure, and breeding applications in Cephalostachyum pingbianense and related bamboo species. © Published under licence by IOP Publishing Ltd.