Genome-Wide Identification, Evolution, and Stress-Responsive Expression of GRF and GIF Genes in Allotetraploid Quinoa (Chenopodium quinoa)
Abstract
Growth-regulating factors (GRFs) and GRF-interacting factors (GIFs) form a conserved transcriptional module that coordinates meristem activity, organ growth, and regeneration. Quinoa (Chenopodium quinoa Willd.) is an allotetraploid crop with notable stress tolerance, but its GRF/GIF complement has not been systematically characterized. Domain-HMM and homology searches of the QQ74/PI 614886 genome identified 11 CqGRF and 5 CqGIF genes. Phylogenetic, structural, and synteny analyses indicated family conservation accompanied by duplication and divergence; all duplicated pairs showed Ka/Ks < 1, consistent with purifying selection. Subgenome assignment showed balanced retention (8 genes in subgenome A and 8 in subgenome B), and four low-Ks cross-subgenome syntenic pairs were identified as putative retained homeolog-like pairs. Seven CqGRFs retained conserved or near-conserved miR396-like recognition motifs. Promoter analysis identified abundant predicted light-responsive elements together with hormone-, stress-, and development-related elements. Reanalysis of public tissue datasets and the previously published CRA028609 stress RNA-seq dataset showed descriptive tissue-associated expression patterns and gene-specific transcriptional responses to abiotic stress. CqGRF4 and CqGRF10 were significantly induced by cold, whereas CqGRF3 and CqGIF2/4 responded to salinity. qRT-PCR analysis of six selected CqGRF/CqGIF genes during callus formation revealed contrasting explant-dependent expression: all six candidates increased in hypocotyl-derived callus, whereas five decreased significantly in cotyledonary-node-derived callus. A STRING-derived network provided a hypothesis-generating view of potential GRF-GIF associations. Together, these results define the quinoa GRF/GIF repertoire, add polyploid and miR396-regulatory context, and prioritize experimentally supported expression candidates for future functional studies of development, regeneration, and stress responses.