Spatial transcriptomics provide insights into the secondary lateral rooting difficulties of tetraploid forsythia cuttings

Polyploidy breeding is an important technique for crop improvement through artificial induction of chromosome doubling. In tetraploid forsythia, we observed a significant reduction in secondary lateral roots of cuttings, leading to low survival rates that severely limit the agricultural application of tetraploid forsythia. In this study, we employed spatial transcriptomics to systematically characterize cell types, spatial gene expression patterns, and dosage effects in lateral roots of diploid and tetraploid forsythia. We further investigated how gene dosage alterations correlate with impaired secondary lateral root formation in tetraploids. Our results demonstrate that positive dosage effects of key synthases for ethylene and methyl jasmonate likely elevate these hormones in tetraploid pericycle cells, subsequently upregulating TIFYs and ERFs to suppress secondary lateral root initiation. Classical arabinogalactan protein 4 may be downregulated in epidermal and cortical sclerenchyma cells (ECSCs) due to modulation by abscisic acid signaling genes, thereby hindering the breakthrough of secondary root primordia through ECSCs. Our study deepens the understanding of gene dosage effects in polyploid plants and provides critical insights into the molecular mechanisms underlying polyploid rooting challenges, offering clues of practical solutions for cultivation. • The first spatial transcriptomic atlas of Forsythia suspensa lateral roots was constructed. • Spatial transcriptomics revealed the gene dosage landscape in Forsythia suspensa lateral roots at single-cell resolution. • Molecular clues were uncovered underlying the reduced secondary lateral roots in tetraploid Forsythia suspensa .