Quinoa (Chenopodium quinoa Willd.) is an herb of the genus Chenopodiaceae that is native to the Andes Mountains of South America. To understand the metabolic differences between various quinoa strains, we selected quinoa strains of four colors (black, red, yellow, and white) and we subjected seeds to extensive targeted metabolomics analysis using liquid chromatography-tandem mass spectrometry and transcriptomics analysis. In total, 90 flavonoid-related metabolites were detected in quinoa seeds of the four colors. We elucida ted the regulatory mechanisms of flavonoid biosynthesis in the different quinoa varieties, and thus identified key genes for flavonoid biosynthesis. The results showed that 18 flavone metabolites and 25 flavonoid-related genes were key contributors to flavonoid biosynthesis in quinoa seeds. The results of this study may provide a basis for the breeding and identification of new quinoa strains and for the screening of potential target genes in flavonoid biosynthesis regulation in quinoa.

Background: Quinoa (Chenopodium quinoa Willd.) originates in high altitude areas, such as the Andes, and has some inherent characteristics of cold, drought, and salinity tolerance, but is sensitive to high temperature. Results: To gain insight into the response mechanism of quinoa to high temperature stress, we conducted an extensive targeted metabolomic study of two cultivars, Dianli-3101 and Dianli-3051, along with a combined transcriptome analysis. A total of 794 metabolites and 54,200 genes were detected, in which the genes related to photosynthesis were found down-regulated at high temperatures, and two metabolites, lipids and flavonoids, showed the largest changes in differential accumulation. Further analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and transcription factors revealed that quinoa inhibits photosynthesis at high temperatures, and the possible strategies being used for high temperature stress management are regulation of heat stress transcription factors (HSFs) to obtain heat tolerance, and regulation of purine metabolism to enhance stress signals for rapid response to high temperature stress. The tolerant genotype could have an enhanced response through lower purine levels. The induction of the stress response could be mediated by HSF transcription factors. The results of this study may provide theoretical references for understanding the response mechanism of quinoa to high temperature stress, and for screening potential high temperature tolerant target genes and high temperature tolerant strains. Conclusions: These findings reveal the regulation of the transcription factor family HSF and the purinergic pathway in response to high temperature stress to improve quinoa varieties with high temperature tolerance.

Quinoa, a cool-weather high-altitude crop, is susceptible to low-temperature stress throughout its reproductive phase. Herein, we performed broadly targeted metabolic profiling of quinoa seedlings to explore the metabolites’ dynamics in response to low-temperature stress and transcriptome analysis to determine the underlying genetic mechanisms. Two variants, namely, Dian Quinoa 2324 and Dian Quinoa 281, were exposed to temperatures of −2, 5, and 22 °C. A total of 794 metabolites were detected; 52,845 genes, including 6628 novel genes, were annotated using UPLC-MS/MS analysis and the Illumina HiSeq system. Combined with morphological indicators to resolve the mechanism underlying quinoa seedling response to low-temperature stress, the molecular mechanisms of quinoa changed considerably based on temperature exposure. Soluble sugars heavily accumulated in plants with cold damage and changes in regulatory networks under freeze damage, such as the upregulation of α-linolenic acid metabolism and a reduction in energy substrates, may explain the spatial patterns of biosynthesis and accumulation of these metabolites. Genes that are actively expressed during cold responses, as revealed by co-expression analyses, may be involved in the regulation thereof. These results provide insights into the metabolic factors in quinoa under low-temperature stress and provide a reference for the screening of quinoa varieties resistant to low temperature.

Colored wheat has been recognized broadly for its nutritional value because of its natural content of the colorant anthocyanin. To investigate the reasons for the formation of the wheat grain color at maturity, metabolomic and transcriptomic analyses were performed on three different grain colors of wheat. Through metabolome analysis, 628 metabolites were identified. Of the 102 flavonoids, there are 9 kinds of anthocyanins related to color formation, mainly cyanidin and peonidin, and their metabolite content was the lowest in white-grain wheat. Among the genes associated with color formation, the structural gene TraesCS2D02G392900 in F3H with the bHLH transcription factor could elucidate the origin of wheat coloration. Multi-omics analysis showed that color formation is mainly influenced by the regulation of genes affecting anthocyanin and related synthesis. The results of this study may provide a theoretical basis for grain color formation at maturity and the nutritional and product development potential of colored wheat lines.

Spot blotch (SB) is a fungal disease that threatens wheat yield and quality. Presently, the molecular mechanism against SB is unclear. In this study, the resistant variety Zhenkang iron shell wheat (Yunmai 0030) and susceptible variety Lincang iron shell wheat (Yunmai 0608) were selected by identifying SB of Yunnan iron shell wheat. The metabolome and transcriptome of leaves of two varieties at different positions were detected using the systemic acquired resistance theory to investigate the molecular and physiological changes in Yunnan iron shell wheat under SB stress. We found that the genes and metabolites related to benzoxazinoid biosynthesis and arginine and proline metabolism were highly enriched after infection with leaf blight. The enriched differential metabolites mainly included phenolic acids, alkaloids, and flavonoids. We further observed that DIBOA- and DIMBOA-glucoside positively affected iron shell wheat resistance to leaf blight and proline and its derivatives were important for plant self-defense. Furthermore, we confirmed that the related metabolites in benzoxazinoid biosynthesis and arginine and proline metabolism positively affected Triticum aestivum ssp. resistance to SB. This study provides new insights into the dynamic physiological changes of wheat in response to SB, helps us better understand the mechanism of resistance to SB, and contributes to the breeding and utilization of resistant varieties.

Quinoa (Chenopodium quinoa Willd.) is a dicotyledonous annual herb of Family Amaranthaceae and Subfamily Chenopodiaceae. It has high nutritional and economic value. Phosphorus (P) is an essential plant macronutrient, a component of many biomolecules, and vital to growth, development, and metabolism. We analyzed the transcriptomes and metabolomes of Dianli–1299 and Dianli–71 quinoa seedlings, compared their phenotypes, and elucidated the mechanisms of their responses to the phosphorus treatments. Phenotypes significantly varied with phosphorus level. The plants responded to changes in available phosphorus by modulating metabolites and genes implicated in glycerophospholipid, glycerolipid and glycolysis, and glyconeogenesis metabolism. We detected 1057 metabolites, of which 149 were differentially expressed (DEMs) and common to the control (CK) vs. the low-phosphorus (LP) treatment samples, while two DEMs were common to CK vs. the high-phosphorus (HP) treatment samples. The Kyoto Encyclopedia of genes and genomes (KEGG) annotated 29,232 genes, of which 231 were differentially expressed (DEGs) and common to CK vs. LP, while one was common to CK vs. HP. A total of 15 DEMs and 11 DEGs might account for the observed differences in the responses of the quinoa seedlings to the various phosphorus levels. The foregoing results may provide a theoretical basis for improving the phosphorus utilization efficiency in quinoa.