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

Rey, Elodie1 ; Maldonado-Taipe, Nathaly2 ; Emrani, Nazgol2 ; Tester, Mark1; Jung, Christian2

Published Feb 15, 2024 on Dryad. https://doi.org/10.5061/dryad.2rbnzs7w3

Data files

Feb 15, 2024 version files 625.88 MB

Bioinformatic_pipeline.docx

14.53 KB
gene_matrix_leaf.txt

22.54 MB
gene_matrix_meristem.txt

12.72 MB
gene2transcript.txt

5.11 MB
merged_assembly.gff

175.41 MB
R_Script_DEG_analysis_and_MDS_plots.R

20.82 KB
README.md

2.37 KB
RNA-seq_Sample-Description.xlsx

11.16 KB
transcripts.fa

345.66 MB
transcripts.fa.tar.gz

64.39 MB

Abstract

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) have been reported as key regulators of flowering time in other species. Additionally, we used co-expression networks to associate novel transcripts to a putative biological process based on the annotated genes within the same co-expression cluster. The candidate genes in this study would benefit quinoa breeding by identifying and integrating their beneficial haplotypes in crossing programs to develop adapted cultivars to diverse environmental conditions.

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 revealed floral transition initiating two to three weeks after sowing. Differentially expressed genes were categorized in the QQ74-V2 reference genome, encompassing 222 genes responsive to photoperiod in leaves, 1,812 genes under long-day conditions, 57 genes during short-day conditions, and 911 genes during floral transition in shoot apical meristems. Notably, among numerous candidates, two putative FT orthologues and others (e.g., SOC1, COL, AP1) implicated in flowering time regulation in various species were identified. Co-expression networks associated novel transcripts with putative biological processes based on annotated genes in the same cluster. The candidate genes identified have potential applications in quinoa breeding, facilitating the incorporation of beneficial haplotypes in crossbreeding programs to develop cultivars adapted to diverse environmental conditions.

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

https://doi.org/10.5061/dryad.2rbnzs7w3

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:

-->RNA-seq_Sample-Description.xlsx : a table describing the name, accession, tissue, condition, developmental stage, and replication of each RNA-seq library sample used in this study.

-->gene_matrix_leaf.txt : gene matrix of 'expected counts' (estimate maximum likelihood expression levels) produced by rsem for the RNA-seq samples from leaf tissue.

-->gene_matrix_meristem.txt : gene matrix of 'expected counts' (estimate maximum likelihood expression levels) produced by rsem for the RNA-seq samples from meristem tissue.

##List of files for Bioinformatics analyses:

-->gene2transcript.txt : table matching gene and transcript IDs

-->merged_assembly.gff : coordinates of each transcript/gene on the reference genome QQ74_V2

-->transcripts.fa.tar : transcripts assembly including known (from QQ74_V2 reference genome annotation) and newly assembled transcripts using the rna-seq dataset generated for this study.

Code/Software

##List of files compiling the codes to reproduce bioinformatics and statistical analyses

-->R_Script_DEG_analysis_and_MDS_plots.R : the R script used to perform the statistical analysis from the matrix of counts.

-->Bioinformatic_pipeline.docx : code for read mapping against the reference genome, transcripts assembly, and mapping of reads against the transcriptome.