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

Our study focused on identifying key genes regulating flowering time and photoperiod response in quinoa. We examined the timing of photoperiod-induced floral transition and analyzed transcriptomes in photoperiod-sensitive and -insensitive quinoa accessions' leaf and shoot apical meristems. Histological analysis showed that floral transition in quinoa initiates two to three weeks after sowing. We found four groups of differentially expressed genes annotated in the QQ74-V2 reference genome that responded to plant development and floral transition, (i) 222 genes responsive to photoperiod in leaves, (ii) 1,812 genes differentially expressed between accessions under long-day conditions in leaves, (iii) 57 genes responding to developmental changes between weeks under short-day conditions in leaves, and (iv) 911 genes responding to floral transition within the shoot apical meristem. Interestingly, among numerous candidate genes, two putative FT orthologues and others (e.g., SOC1, COL, AP1) hav..., We analyzed the development of the Shoot Apical Meristem (SAM) in two quinoa accessions differentially responding to day length. Studying leaf and SAM transcriptomes from plants grown under Short Days (SD) and Long Days (LD) conditions resulted in thousands of differentially expressed genes. Our study provides new insight into quinoa’s flowering time and photoperiod regulation., , # Leaf and shoot apical meristem transcriptomes of quinoa (Chenopodium quinoa Willd.) in response to photoperiod and plant development

Here we release the raw read count data allowing the reproduction of the transcriptomic analysis performed in the linked study. This is a matrix of CPM (count per million mapped reads) resulting from the mapping of 72 RNA-seq samples of quinoa against a transcriptome of 132,965 gene models (including previously annotated genes from the reference genome, and newly annotated transcripts supported by the current RNA-seq dataset). The RNA-seq samples correspond to the transcriptome sequencing of 48 leaf and 24 SAM cDNA libraries from two quinoa cultivars contrasting by their daylength sensitivity grown under short- and long-days conditions. This dataset allows to explore the mechanisms of quinoa’s flowering time and photoperiod regulation at the transcriptomic level.

## Description of the data and file structure

\##List of files for Statistical analyses...