Integrative Omic Dissection of Quinoa Hsp20 Genes: From In Silico Re-Annotation to Transcriptional Profiling Under Heat, Drought, and Salinity Stress

The Hsp20 protein family, recognized in all organisms for its chaperone activity in the heat-stress response, is part of the Heat Shock Protein (Hsp) superfamily, defined by a conserved alpha-crystallin domain (ACD). Hsp20s are the smallest proteins in the superfamily (mostly between 15 and 22 kDa) and assist in protein refolding during stress and developmental processes. In this study, we characterize the Hsp20 gene family in Chenopodium quinoa (2n = 4x = 36) using an integrative omic approach. C. quinoa is well known for its global contributions to food production and tolerance to various abiotic stresses. We identified 69 CqHsp20 genes distributed across the nine chromosomes of each subgenome (A and B), organized mainly into homologous pairs, with paralogs on eight chromosomes, likely from tandem duplications, suggesting a well-conserved evolutionary pattern within the species. The phylogenetic analysis grouped CqHsp20 proteins into two main clusters, split into four sub-clusters based on peptides’ cellular localization, consistent with a characteristic gene structure and conserved motif analysis. The integration of transcriptomic data from published experiments enabled us to detect a cluster of putatively ubiquitously expressed CqHsp20, as well as other groups that showed differential responses across abiotic stress conditions. The pattern shows more genes with transcriptional activity under drought and salinity than under heat, key adaptive traits underlying quinoa’s known ecological versatility. Some of these genes, with null or low transcriptional activity under heat stress, encode organelle-targeting peptides, a phenomenon not reported in other model plant studies. Varying expression within CqHsp20 homologous and paralogs supports the idea that gene duplication creates genomic diversity, facilitating adaptation to variable extreme environments. However, while theoretical and in silico analysis provide valuable insight into quinoa Hsp20 response, empirical data are essential to unequivocally understand how these gene expression variations affect quinoa response to abiotic stressors.