Development of <scp>SSR</scp> Markers and Genetic Diversity Analysis of <i>Musa basjoo</i> Using Transcriptome Sequencing

<i>Rhizoma Musae</i>, the underground rhizome of <i>Musa basjoo</i> Siebold et Zucc., serves as a traditional medicinal resource among the Miao ethnic group in Guizhou, China. This study aimed to develop SSR molecular markers from the <i>M. basjoo</i> transcriptome to assess the genetic diversity of its germplasm across diverse regions. A <i>M. basjoo</i> transcriptome database was constructed using high-throughput sequencing, followed by the extraction of SSR loci with MISA software. Polymorphic SSR markers were identified and utilized to evaluate the genetic diversity of 45 <i>M. basjoo</i> germplasm resources. In total, 38,806 <i>M. basjoo</i> Unigenes were obtained, with an average length of 993.00 bp. Comparative annotation against the GO, KEGG, EggNOG, NR, Swiss-prot, and Pfam databases yielded 23,558, 12,412, 25,448, 28,101, 20,056, and 18,460 annotated Unigenes, respectively. A total of 7501 SSR loci were identified, with trinucleotide repeats constituting the predominant class (44.03%), and ACC/GGT being the most frequent motif. Ten pairs of polymorphic primers were developed, all exhibiting a PIC value greater than 0.5. The 45 <i>Musa</i> spp. accessions were classified into three distinct groups using the UPGMA method. The <i>M. basjoo</i> transcriptome harbors abundant polymorphic SSRs. The developed primers enable rapid molecular identification of <i>M. basjoo</i> germplasm and provide insights into its genetic diversity, which may underlie variations in medicinal properties and environmental adaptation. These findings support applications in germplasm conservation, marker-assisted breeding, and quality control of <i>Rhizoma Musae</i> medicinal resources.