A cost-effective chloroplast InDel marker panel for tea germplasm discrimination and maternal lineage tracing

Efficient genetic tools are critical for tea germplasm management, a foundation for conservation and breeding, yet practical and cost-effective marker panels for routine maternal lineage analysis remain lacking. We developed a chloroplast Insertion/Deletion (InDel) marker panel for tea by sequencing 18 representative chloroplast genomes and identified genome-wide InDel variations. Twenty-five polymorphic markers with fragment length variations > 4 bp were developed, which can be genotyped via standard PCR and agarose gel electrophoresis. Phylogenetic analysis of 100 tea accessions using the InDel markers produced a tree broadly consistent with that inferred from whole chloroplast genome sequences. Using Core Hunter 3, we optimized a 15-core marker subset, with Mantel test confirming its representativeness ( r = 0.94). In an authenticity test, seven Longjing 43 seedlings from different sources were analyzed; only two samples matched the reference fingerprint, demonstrating the marker system’s practical utility. This study provides the first systematic chloroplast InDel marker panel for tea, with the entire workflow standardized and transferable to other species. The 25-marker panel offers a reliable tool for maternal genetic analysis, while the 15-core subset provides a cost-effective solution for large-scale germplasm authentication, filling a critical gap in the tea molecular breeding toolkit.