Faujiah Nurhasanah Ritonga, Runxian Song, Deanova Frestiana Br Pelawi, Arida Susilowati, Triaty Handayani
Bambusa oldhamii Munro is an economically important bamboo species valued for its edible shoots and structural culms, yet genomic resources for molecular breeding remain scarce. This study aimed to mine and characterize expressed sequence tag-simple sequence repeats (EST-SSRs) from the tip shoot transcriptome of Bambusa oldhamii, utilizing publicly available data from the NCBI Transcriptome Shotgun Assembly. Using Krait software, a total of 13,126 perfect SSRs were identified, with trinucleotide motifs being the most abundant (37.16%), followed by mononucleotide (33.89%) and dinucleotide repeats (25.67%). The relative abundance and density of SSRs were calculated as 190.89 loci/Mb and 3,157.64 bp/Mb, respectively. The most dominant motifs included A, AG, and CCG, which are commonly associated with coding regions and functional gene expression. Ten representative EST-SSR primer pairs were developed across six motif types, designed with optimal parameters for downstream molecular applications. The results demonstrate the potential of EST-SSRs from tip shoot transcriptomes as effective tools for functional marker development. This study provides the first comprehensive set of EST-SSR markers for Bambusa oldhamii, contributing valuable resources for genetic diversity assessment, marker-assisted selection, and bamboo breeding programs. © Published under licence by IOP Publishing Ltd.
Faculty of Forestry, Universitas Sumatera Utara, USU 2 Bekala Campus, Deli Serdang, Pancurbatu, 20355, Indonesia; Center of Excellence for Bamboo, Universitas Sumatera Utara, Medan, 20155, Indonesia; Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High-Quality Rice in Southern China, Guangdong, Guangzhou, 510640, China; Forestry Study Program, PSDKU USK Gayo Lues, Faculty of Agriculture, Syiah Kuala University, 24655, Indonesia
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