Genome-wide transcriptome analysis reveals small RNA profiles involved in early stages of stolon-to- tuber transitions in potato under photoperiodic conditions

Small RNAs (sRNAs), especially miRNAs, act as crucial regulators of plant growth and development. Two other sRNA groups, phased (phasiRNAs) or trans-acting short interfering RNAs (tasiRNAs), are also emerging as potential regulators of plant development. Stolon-to- tuber transition in potato is an important developmental phase governed by many environmental, biochemical and hormonal cues. Photoperiod has a major influence on tuberization. Our knowledge is lacking in understanding the dynamics of early stages of stolon-to- tuber development. We performed sRNA profiling of early stolon stages (4, 7 and 10 d) under Short-Day (SD) and Long-Day (LD) conditions. Altogether, 7 (off 324) conserved and 11 (off 311) novel miRNAs showed differential expression in early stolon stages under SD/LD conditions. Differential expression of important target genes (StGAMYB, StGRAS, StTCP2/4, StPTB6) in early stolon stages indicated their potential role in this process. Off 830 TAS-like loci identified, 24 found to generate 194 phasiRNAs. Our analysis revealed several tuberization genes (StPTB1, POTH1, StCDPKs) as phasiRNA targets. One TAS-like locus (StTm2) was validated for phasiRNA generation and one of its phasiRNA was predicted to cleave StGA2ox1, suggesting its potential role in tuber development. Overall, our study suggests that sRNAs might be involved in regulating early stolon-to- tuber transitions in potato.