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

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.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1501-4) contains supplementary material, which is available to authorized users.

Integrated mRNA and miRNA transcriptome analysis reveals a regulatory network for tuber expansion in Chinese yam (Dioscorea opposita)

“…Tuber and root development and environmental responses involve gene regulatory networks [21,24,35,37]. miRNA and target genes have been extensively studied in tuber development [21,28], which significantly advanced our understanding of molecular regulatory networks underlying during yam tuber expansion. In this study, based on our RNA-Seq and small RNA analysis, previous transcriptomics analysis and results of other tuber crops, a putative model of regulatory network associated with yam tuber expansion was proposed (Fig.…”

“…Potato is a tuber crop. Several transcriptome analyses revealed that numerous genes are regulated in early stages of stolon-to-tuber transitions, or tuberization by nutrients, photoperiodic conditions, exogenous hormones, and stress in potato tuber [21][22][23][24]. Former transcriptomic study revealed that some putative genes were involved in dioscin biosynthesis [25], along with this chalcone isomerase (CHS), flavanone 3-hydroxylase (F3H), flavonoid 3′-monooxygenase (F3'H), dihydroflavonol 4-reductase (DFR), leucoanthocyanidin dioxygenase (LDOX), and flavonol 3-O-glucosyltransferase (UF3GT) were significantly expressed in flavonoid biosynthesis [26].…”

Integrated mRNA and miRNA transcriptome analysis reveals regulatory network of yam tuber expansion

“…Tuber development and environmental responses involve gene regulatory networks [21][22][23][24][34][35][36][37].…”

“…miRNA and target genes has been extensively studied in tuber development [21,28], which greatly advanced our understanding of molecular regulatory networks underlying during yam tuber expansion. In this study, based on our transcriptome and small RNA analysis, previous transcriptomics analysis and results of other tuber crops, a putative model of the regulatory network associated with yam tuber expansion was proposed (Fig 13).…”

“…Transcriptome techniques can efficiently find and detect these genes and proteins. Potato is a tuber crop, many transcriptome analyses revealed that many genes are regulated in early stages of stolon-to-tuber transitions, or tuberization by nutrients, photoperiodic conditions, exogenous hormones, and stress [21][22][23][24]. Former transcriptome study revealed that some putative genes were involved in dioscin biosynthesis [25], and chalcone isomerase (CHS), flavanone 3-hydroxylase (F3H), flavonoid 3'-monooxygenase(F3'H), dihydroflavonol 4-reductase(DFR), leucoanthocyanidin dioxygenase(LDOX), and flavonol 3-Oglucosyltransferase(UF3GT) were significantly expressed in flavonoid biosynthesis [26].…”