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.

Leaf and shoot apical meristem transcriptomes of quinoa (Chenopodium quinoaWilld.) in response to photoperiod and plant development

“…None of the genes found to be down-or up-regulated after NB by Wu et al (2021) (LHY, ELF3, HY5, PHYA , and CRY1) were differentially regulated in our study. However, CqFT2B and CqZTL, identified by Wu et al (2023) in a transcriptome study of diurnally collected samples under SD and LD, were also found in our study, which supports their role as flowering time regulators. Moreover, Patiranage et al (2021) provided additional evidence that CqFT2B's temporal and diurnal expression in early-and late-flowering quinoa accessions underpins its function as a flowering time regulator.…”

“…(2021) ( LHY, ELF3 , HY5 , PHYA , and CRY1 ) were differentially regulated in our study. However, CqFT2B and CqZTL , identified by Wu et al . (2023) in a transcriptome study of diurnally collected samples under SD and LD, were also found in our study, which supports their role as flowering time regulators.…”

“…Other possible experimental designs include studying diurnal expression patterns and/or switching between photoperiod regimes. Such experimental settings allowed Wu et al (2023) to identify CO-like transcription factors sensitive to the quinoa switch from LD to SD. Moreover, introducing a night break and studying lncRNA instead of mRNA in quinoa, as done by Wu et al (2021), would represent another experimental design that would unveil novel candidate genes putatively involved in photoperiod response.…”

“…Other possible experimental designs include studying diurnal expression patterns and/or switching between photoperiod regimes. Such experimental settings allowed Wu et al . (2023) to identify CO-like transcription factors sensitive to the quinoa switch from LD to SD.…”

“…As a result, CqFT1A, CqCOL2B, CqCOL4A-1, and CqCOL5B were associated with flowering time variation under LD but not under SD conditions. Recently, a transcriptome study of diurnally collected quinoa samples unveiled CO-like transcription factors among the diurnally regulated genes sensitive to the switch from LD to SD (Wu et al, 2023).The regulation of flowering time has also been studied in quinoa-closely-related species. In Chenopodium rubrum, FLOWERING LOCUS T-LIKE 1 (CrFTL1) change of expression was associated with experimental conditions which led to flowering, whereas CrFTL2 was constitutively expressed (Cháb et al, 2008).…”