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) 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.