Genome-Wide Identification and Expression Analysis of the β-Amylase Gene Family in Chenopodium quinoa

β-Amylase (BAM) is an important starch hydrolase, playing a role in a variety of plant growth and development processes. In this study, 22 BAM gene family members (GFMs) were identified in quinoa (Chenopodium quinoa), an ancient crop gaining modern consumer acceptance because of its nutritional qualities. The genetic structure, phylogenetic and evolutionary relationships, and expression patterns of CqBAM GFMs in different tissues, were analyzed. Phylogenetic analyses assigned the CqBAMs, AtBAMs, and OsBAMs into four clades. The CqBAM gene family had expanded due to segmental duplication. RNA-seq analysis revealed expression of the duplicated pairs to be similar, with the expression of CqBAM GFM pairs showing a degree of tissue specificity that was confirmed by reverse transcription quantitative PCR (RT-qPCR). Several CqBAM GFMs were also responsive to abiotic stresses in shoots and/or roots. In conclusion, the BAM gene family in quinoa was identified and systematically analyzed using bioinformatics and experimental methods. These results will help to elucidate the evolutionary relationship and biological functions of the BAM gene family in quinoa.

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.

Seed Pretreatment and Foliar Application of Proline Regulate Morphological, Physio-Biochemical Processes and Activity of Antioxidant Enzymes in Plants of Two Cultivars of Quinoa (Chenopodium quinoa Willd.)

In the current study, the effects of exogenously applied proline (25 and 50 mM) and low-temperature treatment were examined on the physiochemical parameters in the plants of two cultivars (V1 and V2) of quinoa (Chenopodium quinoa Willd.). The seeds were also exposed to chilling stress at 4 °C before sowing. Plants raised from the seeds treated with low temperature showed reduced plant growth and contents of chlorophyll and carotenoids, but they had significantly increased contents of malondialdehyde, proline, ascorbic acid, total free amino acids, total soluble sugars, and total phenolics, as well as the activity of the peroxidase (POD) enzyme. Cold stress applied to seeds remained almost ineffective in terms of bringing about changes in plant root, hydrogen peroxide, glycine betaine and activities of superoxide dismutase (SOD), and catalase (CAT) enzymes. The exogenous application of proline significantly increased plant growth, the contents of chlorophyll, carotenoids, proline, ascorbic acid, total free amino acids, phenolics, and total soluble sugars, as well as the activities of SOD, POD, and CAT, but it decreased malondialdehyde content. Overall, foliar application of proline was better than the seed treatment in improving root dry weight, root length, chlorophyll a, carotenoids, glycine betaine, ascorbic acid and superoxide dismutase activity, whereas seed pre-treatment with proline was effective in improving shoot dry weight, shoot length, hydrogen peroxide, malondialdehyde, and peroxidase activity in both quinoa cultivars.