Abstract
BackgroundSmall RNAs (sRNAs), especially miRNAs, act as crucial regulators of plant growth and development. Two other sRNA groups, trans-acting short-interfering RNAs (tasiRNAs) or phased siRNAs (phasiRNAs), 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. Among different environmental factors, photoperiod has a major influence on tuberization. Several mobile signals, mRNAs, proteins and transcription factors have been widely studied for their role in tuber formation in potato, however, no information is yet available that describes the molecular signals governing the early stages of stolon transitions or cell-fate changes at the stolon tip before it matures to potato. Stolon could be an interesting model for studying below ground organ development and we hypothesize that small RNAs might be involved in regulation of stolon-to-tuber transition process in potato. Also, there is no literature that describes the phased siRNAs in potato development.ResultsWe performed sRNA profiling of early stolon stages (4, 7 and 10 d) under long-day (LD; 16 h light, 8 h dark) and short-day (SD; 8 h light, 16 h dark) photoperiodic conditions. Altogether, 7 (out of 324) conserved and 12 (out of 311) novel miRNAs showed differential expression in early stolon stages under SD vs LD photoperiodic conditions. Key target genes (StGRAS, StTCP2/4 and StPTB6) exhibited differential expression in early stolon stages under SD vs LD photoperiodic conditions, indicative of their potential role in tuberization. Out of 830 TAS-like loci identified, 24 were cleaved by miRNAs to generate 190 phased siRNAs. Some of them targeted crucial tuberization genes such as StPTB1, POTH1 and StCDPKs. Two conserved TAS loci, referred as StTAS3 and StTAS5, which share close conservation with members of the Solanaceae family, were identified in our analysis. One TAS-like locus (StTm2) was validated for phased siRNA generation and one of its siRNA was predicted to cleave an important tuber marker gene StGA2ox1.ConclusionOur study suggests that sRNAs and their selective target genes could be associated with the regulation of early stages of stolon-to-tuber transitions in a photoperiod-dependent manner in potato.
Highlights
Small RNAs, especially miRNAs, act as crucial regulators of plant growth and development
Identification of conserved and novel miRNAs Deep-sequencing analyses using miRPRo showed that among total raw reads, on an average 4.6% of final clean reads were counted as conserved mature miRNAs, whereas 0.76% of final clean reads were counted as novel mature miRNAs
In this study, we have identified 7 conserved and 12 novel miRNAs to be differentially expressed in early stages of stolon-to-tuber development in a photoperiod dependent manner
Summary
Small RNAs (sRNAs), especially miRNAs, act as crucial regulators of plant growth and development. Small RNAs (sRNAs) have emerged as crucial regulators of plant growth and development, as well as in different abiotic and biotic stress responses [1,2,3]. Based on their biogenesis and functional modes, sRNAs are classified into two major groups: microRNAs (miRNAs) and short-interfering RNAs (siRNAs) [4]. TAS or PHAS loci encode for respective precursors, which are cleaved by specific miRNAs to form a double stranded RNA through RNA-dependent RNA polymerase 6 These double stranded RNAs are further cleaved by Dicer-like 4 to generate 21–22 nt siRNAs that perform gene silencing similar to miRNAs [13,14,15]. Phased siRNAs producing loci cannot be categorized as TAS loci until the function of siRNAs generated from it has been proven
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