Transcriptome Analysis Reveals Molecular Signatures Associated with Apical Rooted Cutting (ARC) Technology in Seed Potato Production

Rapid multiplication of quality seed tubers is one of the important factors in sustainable potato production. In this study, we aimed to compare tissue culture-based a novel apical rooted cutting (ARC) technology with conventional tuber system for seed size tuber production. We observed a higher tuber multiplication rate in ARC technology than in conventional tuber system. Further, we performed transcriptome analysis in leaf and tuber tissues of different ARC planting materials (i.e. ARC mother plant, ARC apical, ARC lateral) as well as direct microplant versus conventional tuber (control). The Illumina-based transcriptiome analysis exhibited a high-quality paired-end data and good mapping results with the reference potato genome sequence. Statistically significant ( p < 0.05) differentially expressed genes (DEGs) were identified and categorised into up-regulated and down-regulated genes. Common DEGs were identified by the Venn diagram analysis and gene expression markers (real-time qPCR) were developed for the genes viz . , glucose-6-phosphate/phosphate translocator 2 and homeobox protein knotted-1-like LET6 genes for tuber tissues, and LRR receptor-like serine/threonine-protein kinase, and VQ motif-containing protein TF for leaf tissues of AR0C planting materials. DEGs were functionally annotated with the Gene Ontology terms and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Strikingly, genes associated with sugar/starch metabolism, regulatory elements like TFs (BHLH, MYB21, and WRKY), phytohormones (ABA, GA and auxin), stress-responsive genes (heat shock proteins and serine/threonine protein kinase), kinases and other associated were identified in this study. A few selected genes were validated by real-time quantitative PCR analysis. Altogether, our study provides insights on genes involved in leaf and tuber tissues for successful seed potato production through ARC technology. This study paves a novel path for devising strategies on gene manipulation through genome editing in future.