Species within the genus Chenopodium hold significant research interest due to their nutritional richness and salt tolerance. However, the morphological similarities among closely related species and a dearth of genomic resources have impeded their comprehensive study and utilization. In the present research, we conduct the sequencing and assembly of chloroplast (cp) genomes from six Chenopodium and related species, five of which were sequenced for the first time. These genomes ranged in length from 151,850 to 152,215 base pairs, showcased typical quadripartite structures, and encoded 85 protein-coding genes (PCGs), 1 pseudogene, 37 tRNA genes, and 8 rRNA genes. Compared with the previously published sequences of related species, these cp genomes are relatively conservative, but there are also some interspecific differences, such as inversion and IR region contraction. We discerned 929 simple sequence repeats (SSRs) and a series of highly variable regions across 16 related species, predominantly situated in the intergenic spacer (IGS) region and introns. The phylogenetic evaluations revealed that Chenopodium is more closely related to genera such as Atriplex, Beta, Dysphania, and Oxybase than to other members of the Amaranthaceae family. These lineages shared a common ancestor approximately 60.80 million years ago, after which they diverged into distinct genera. Based on InDels and SNPs between species, we designed 12 pairs of primers for species identification, and experiments confirmed that they could completely distinguish 10 related species.

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.

Heat shock protein 90 (HSP90) is an evolutionarily conserved molecular chaperone. Numerous studies have shown that it is widely involved in protein folding, assembly, stabilization, activation, and degradation in response to various biotic and abiotic stresses in many normal cellular processes and under stress conditions. We identified 11 members of the CqHSP90 gene family in the quinoa (Chenopodium quinoa) genome by bioinformatics analysis. Phylogenetic tree analysis showed that quinoa was more closely related to dicotyledonous plants than to monocotyledonous plants. Quinoa is susceptible to high-temperature stress during its growth and development. We analyzed the cis-acting elements of its promoter, and found that nearly 1/3 of the cis-acting elements were stress-responsive, and 2/3 of them had heat-responsive elements. The results of qRT-PCR showed that heat shock at 40 °C could induce a high expression of CqHSP90.1c and CqHSP90.6a. Subcellular localization indicates that they are all membrane proteins. At the same time, both CqHSP90.1c and CqHSP90.6a overexpression lines improved the tolerance of Arabidopsis thaliana under high temperature, indicating that both of them had a positive regulatory effect under heat stress. Results of this study could provide useful information for further study on the biological role of CqHSP90.1c and CqHSP90.6a, and provide theoretical basis for quinoa resistance breeding.

Quinoa is a high-nutrition crop originating from the Andes Mountains that is tolerant to cold, drought and salt. However, the mechanism of the high-temperature response in quinoa is still unclear. In this study, quinoa line YL-6 was used to analyze the changes in photosynthetic parameters, physiological parameters and the transcriptome after 0, 3, 12 and 24 h of heat stress. Our results showed that photosynthetic parameters, including the maximum quantum yield of PSII (Fv/Fm), steady-state effective quantum yield (ΦPSII_Lss), non-photochemical quenching (NPQ_Lss), and photochemical quenching coefficients (qL_Lss, qP_Lss), decreased significantly under heat stress, whereas the activities of antioxidant enzymes, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), increased significantly at the early stage. The contents of osmotic adjustment substances such as proline, soluble protein and soluble sugar showed a non-single change trend. WGCNA was conducted to group the differentially expressed genes (DEGs) into 12 co-expression modules. Key modules associated with heat perception and signal transduction were identified, and a core regulatory network was subsequently constructed. Hub genes encoding molecular chaperones and transcription factors were screened, among which heat shock proteins (HSPs) were the most prominent. These results could provide a theoretical basis for analyzing the regulatory network of heat stress, exploring heat-resistant genes and introducing and domesticating quinoa.