Genome-wide survey, characterization, and expression analysis of bZIP transcription factors in Chenopodium quinoa.

BACKGROUND: Chenopodium quinoa Willd. (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, and Amaranthus hypochondriacus) have been fully sequenced. However, information about the bZIPs in these Amaranthaceae species is limited, and genome-wide analysis of the bZIP family is lacking in quinoa. RESULTS: We identified 94 bZIPs in quinoa (named as CqbZIP1-CqbZIP94). All the CqbZIPs were phylogenetically splitted into 12 distinct subfamilies. The proportion of CqbZIPs was different in each subfamily, and members within the same subgroup shared conserved exon-intron structures and protein motifs. Besides, 32 duplicated CqbZIP gene pairs were investigated, and the duplicated CqbZIPs had mainly undergone purifying selection pressure, which suggested that the functions of the duplicated CqbZIPs might not diverge much. Moreover, we identified the bZIP members in 3 other Amaranthaceae species, and 41, 32, and 16 orthologous gene pairs were identified between quinoa and S. oleracea, B. vulgaris, and A. hypochondriacus, respectively. Among them, most were a single copy being present in S. oleracea, B. vulgaris, and A. hypochondriacus, and two copies being present in allotetraploid quinoa. The function divergence within the bZIP orthologous genes might be limited. Additionally, 11 selected CqbZIPs had specific spatial expression patterns, and 6 of 11 CqbZIPs were up-regulated in response to salt stress. Among the selected CqbZIPs, 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 the bZIP family 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.

Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Transcription Factor in Chenopodium quinoa.

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.

Copper-caused oxidative stress triggers the activation of antioxidant enzymes via ZmMPK3 in maize leaves.

Copper (Cu) is a necessary trace element participated in many physiological processes in plants. But excessive Cu2+ is toxic, which can activate intracellular signals that lead to cellular damage. The mitogen-activated protein kinase (MAPK) cascade is at the center of cell signal transduction and has been reported to be involved in stress-related signaling pathways. ZmMPK3, a kind of MAPKs in maize cells, can be activated by diverse abiotic stresses. In the present study, we investigated the effects of Cu2+ on hydrogen peroxide (H2O2) level, ZmMPK3 activity as well as the activities of antioxidant enzymes superoxide dismutase (SOD), catalase (CAT) and ascorbic acid peroxidase (APX) using maize leaf as an experimental model. The results demonstrated that acute Cu2+ exposure for 24 hours led to rapid increases of H2O2 level and the increase in ZmMPK3 activity as well as the total activities of antioxidant enzymes SOD, CAT and APX. H2O2 scavenger, dimethylthiourea (DMTU), effectively inhibited the Cu2+-increased H2O2 level and the activity of ZmMPK3 as well as the activities of the antioxidant enzymes SOD, CAT and APX. Pre-treatment with the MAPK inhibitor, PD98059, significantly blocked the Cu2+-increased activities of ZmMPK3, CAT, APX and SOD, but didn't affect the accumulation of H2O2. Our results suggest that Cu2+ causes oxidative stress to the maize leaves which then activates defense antioxidant enzymes via MAPK pathway. Thus, the signaling pathway is Cu2+-H2O2-ZmMPK3-antioxidant enzymes.

Genome-Wide Characterization of Heat-Shock Protein 70s from Chenopodium quinoa and Expression Analyses of Cqhsp70s in Response to Drought Stress.

Heat-shock proteins (HSPs) are ubiquitous proteins with important roles in response to biotic and abiotic stress. The 70-kDa heat-shock genes (Hsp70s) encode a group of conserved chaperone proteins that play central roles in cellular networks of molecular chaperones and folding catalysts across all the studied organisms including bacteria, plants and animals. Several Hsp70s involved in drought tolerance have been well characterized in various plants, whereas no research on Chenopodium quinoa HSPs has been completed. Here, we analyzed the genome of C. quinoa and identified sixteen Hsp70 members in quinoa genome. Phylogenetic analysis revealed the independent origination of those Hsp70 members, with eight paralogous pairs comprising the Hsp70 family in quinoa. While the gene structure and motif analysis showed high conservation of those paralogous pairs, the synteny analysis of those paralogous pairs provided evidence for expansion coming from the polyploidy event. With several subcellular localization signals detected in CqHSP70 protein paralogous pairs, some of the paralogous proteins lost the localization information, indicating the diversity of both subcellular localizations and potential functionalities of those HSP70s. Further gene expression analyses revealed by quantitative polymerase chain reaction (qPCR) analysis illustrated the significant variations of Cqhsp70s in response to drought stress. In conclusion, the sixteen Cqhsp70s undergo lineage-specific expansions and might play important and varied roles in response to drought stress.