The NAC (NAM, ATAF, and CUC) family is one of the largest families of plant-specific transcription factors. It is involved in many plant growth and development processes, as well as abiotic/biotic stress responses. So far, little is known about the NAC family in Chenopodium quinoa. In the present study, a total of 90 NACs were identified in quinoa (named as CqNAC1-CqNAC90) and phylogenetically divided into 14 distinct subfamilies. Different subfamilies showed diversities in gene proportions, exon–intron structures, and motif compositions. In addition, 28 CqNAC duplication events were investigated, and a strong subfamily preference was found during the NAC expansion in quinoa, indicating that the duplication event was not random across NAC subfamilies during quinoa evolution. Moreover, the analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios suggested that the duplicated CqNACs might have mainly experienced purifying selection pressure with limited functional divergence. Additionally, 11 selected CqNACs showed significant tissue-specific expression patterns, and all the CqNACs were positively regulated in response to salt stress. The result provided evidence for selecting candidate genes for further characterization in tissue/organ specificity and their functional involvement in quinoa’s strong salinity tolerance.

Background: Chenopodium quinoaWilld. (quinoa) is a pseudocereal crop of the Amaranthaceae family and represents a promising species with the nutritional content and high tolerance to stressful environments, such as soils affected by high salinity. The basic leucine zipper (bZIP) transcription factor represents exclusively in eukaryotes and can be related to many biological processes. So far, the genomes of quinoa and 3 other Amaranthaceae crops (Spinacia oleracea,Beta vulgaris, andAmaranthus hypochondriacus) have been fully sequenced. However, information about thebZIPsin these Amaranthaceae species is limited, and genome-wide analysis of thebZIPfamily is lacking in quinoa.Results: We identified 94bZIPsin quinoa (named asCqbZIP1-CqbZIP94). All theCqbZIPswere phylogenetically splitted into 12 distinct subfamilies. The proportion ofCqbZIPswas different in each subfamily, and members within the same subgroup shared conserved exon-intron structures and protein motifs. Besides, 32 duplicatedCqbZIPgene pairs were investigated, and the duplicatedCqbZIPshad mainly undergone purifying selection pressure, which suggested that the functions of the duplicatedCqbZIPsmight not diverge much. Moreover, we identified thebZIPmembers in 3 other Amaranthaceae species, and 41, 32, and 16 orthologous gene pairs were identified between quinoa andS. oleracea,B. vulgaris, andA. hypochondriacus, respectively. Among them, most were a single copy being present inS. oleracea,B. vulgaris, andA. hypochondriacus, and two copies being present in allotetraploid quinoa. The function divergence within thebZIPorthologous genes might be limited. Additionally, 11 selectedCqbZIPshad specific spatial expression patterns, and 6 of 11CqbZIPswere up-regulated in response to salt stress. Among the selectedCqbZIPs, 3 of 4 duplicated gene pairs shared similar expression patterns, suggesting that these duplicated genes might retain some essential functions during subsequent evolution.Conclusions: The present study provided the first systematic analysis for the phylogenetic classification, motif and gene structure, expansion pattern, and expression profile of thebZIPfamily in quinoa. Our results would lay an important foundation for functional and evolutionary analysis of CqbZIPs, and provide promising candidate genes for further investigation in tissue specificity and their functional involvement in quinoa’s resistance to salt stress.