Identification of the global diurnal rhythmic transcripts, transcription factors and time-of-day specific cis elements in Chenopodium quinoa

Abstract

Background: Photoperiod is an important environmental cue interacting with circadian clock pathway to optimize the local adaption and yield of crops. Quinoa (Chenopodium quinoa) in family Amaranthaceae has been known as superfood due to the nutritious elements. As quinoa was originated from the low-latitude Andes, most of the quinoa accessions are short-day type. Short-day type quinoa usually displays altered growth and yield status when introduced into higher latitude regions. Thus, deciphering the photoperiodic regulation on circadian clock pathway will help breed adaptable and high yielding quinoa cultivars.

Results: In this study, we conducted RNA-seq analysis of the diurnally collected leaves of quinoa plants treated by short-day (SD) and long-day conditions (LD), respectively. We identified 19,818 (44% of global genes) rhythmic genes in quinoa using HAYSTACK analysis. We identified the putative circadian clock architecture and investigated the photoperiodic regulatory effects on the expression phase and amplitude of global rhythmic genes, core clock components and transcription factors. The global rhythmic transcripts were involved in time-of-day specific biological processes. A higher percentage of rhythmic genes had advanced phases and strengthened amplitudes when switched from LD to SD. The transcription factors of CO-like, DBB, EIL, ERF, NAC, TALE and WRKY families were sensitive to the day length changes. We speculated that those transcription factors may function as key mediators for the circadian clock output in quinoa. Besides, we identified 15 novel time-of-day specific motifs that may be key cis elements for rhythm-keeping in quinoa.

Conclusions: Collectively, this study lays a foundation for understanding the circadian clock pathway and provides useful molecular resources for adaptable elites breeding in quinoa.

Keywords: Chenopodium quinoa; Cis elements; Diurnal rhythmic genes; Phase shift; Photoperiod; Transcription factors.

Fig. 1

44.26% of the global transcripts were identified as diurnal cycling genes in quinoa by using HAYSTACK algorithm. A Venn diagram of the rhythmic genes under SD and LD. 20.39% of the global transcripts displayed rhythmicity under both photoperiods. 19.81% and 4.05% were SD-specific and LD-specific oscillating, respectively. B Statistics of the cycling transcripts classified into different models. Spike model and Asymt1 model harbored the most genes under LD and SD, respectively, and Cos model contained the least cycling genes regardless of light length. C Numbers of cycling transcripts phased to different time points (ZT00 to ZT23). The outer two cycles represent light conditions under SD and LD. Yellow and black stand for day and night time, respectively

Fig. 2

The diurnal rhythmic genes were enriched in time-of-day specific biological processes. Gene ontology analysis of rhythmic genes under LD (A) and SD (B) was performed using AgriGO v2.0 tool with False Discovery Rate (FDR) ≤ 0.05. Red indicates more significant enriched items

Fig. 3

Comparison of the phases of oscillating transcripts between SD and LD. A Numbers of transcripts that phase-shifted to different hours between SD and LD. SD is the reference. B Phase shift topology map of the oscillating transcripts between SD and LD. Only the cycling genes displayed rhythm both under SD and LD were used for phase shift analysis

Fig. 4

Most of the key regulators in circadian clock pathway had advanced phases and strengthened amplitudes under SD than under LD. A Diurnal expression analysis indicated the core circadian clock components CqLHY, CqPRR5/7/9, CqELF4 and CqLUX homologs had advanced phases and strengthened amplitudes under SD. B The clock associated regulators CqGI, CqFKF1, CqZTL and the clock output gene CqCO were advanced, while the clock input gene CqCRY1 and the output gene CqCDF1 were lagged by SD

Fig. 5

Identification of the diurnal rhythmic transcription factors and expression changes under SD and LD. A Percentage of the commonly rhythmic, SD- and LD-specific rhythmic transcription factors in each family. B Comparison of the average phase shift and amplitude change values of in each transcription factors family between under SD and under LD. Only the commonly oscillating transcription factors under both photoperiods were used for analysis

Fig. 6

Frequencies of the cis elements with time-of-day specific enrichment. A Z-score profiles of 5 cis elements with time-of-day specific enrichment under both conditions. B Z-score profiles of 6 and 4 cis elements with time-of-day specific enrichment under LD and SD, respectively