Comparative Transcriptome Analysis Reveals Key Functions of MiMYB Gene Family in Macadamia Nut Pericarp Formation.

Macadamia nuts are one of the most important economic food items in the world. Pericarp thickness and flavonoid composition are the key quality traits of Macadamia nuts, but the underlying mechanism of pericarp formation is still unknown. In this study, three varieties with significantly different pericarp thicknesses, namely, A38, Guire No.1, and HAES 900, at the same stage of maturity, were used for transcriptome analysis, and the results showed that there were significant differences in their gene expression profile. A total of 3837 new genes were discovered, of which 1532 were functionally annotated. The GO, COG, and KEGG analysis showed that the main categories in which there were significant differences were flavonoid biosynthesis, phenylpropanoid biosynthesis, and the cutin, suberine, and wax biosynthesis pathways. Furthermore, 63 MiMYB transcription factors were identified, and 56 R2R3-MYB transcription factors were clustered into different subgroups compared with those in Arabidopsis R2R3-MYB. Among them, the S4, S6, and S7 subgroups were involved in flavonoid biosynthesis and pericarp formation. A total of 14 MiMYBs' gene expression were verified by RT-qPCR analysis. These results provide fundamental knowledge of the pericarp formation regulatory mechanism in macadamia nuts.

Integrating transcriptomics and metabolomics to analyze quinoa (Chenopodium quinoa Willd.) responses to drought stress and rewatering.

The crop production of quinoa (Chenopodium quinoa Willd.), the only plant meeting basic human nutritional requirements, is affected by drought stress. To better understand the drought tolerance mechanism of quinoa, we screened the drought-tolerant quinoa genotype "Dianli 129" and studied the seedling leaves of the drought-tolerant quinoa genotype after drought and rewatering treatments using transcriptomics and targeted metabolomics. Drought-treatment, drought control, rewatering-treated, and rewatered control were named as DR, DC, RW, and RC, respectively. Among four comparison groups, DC vs. DR, RC vs. RW, RW vs. DR, and RC vs. DC, we identified 10,292, 2,307, 12,368, and 3 differentially expressed genes (DEGs), and 215, 192, 132, and 19 differentially expressed metabolites (DEMs), respectively. A total of 38,670 genes and 142 pathways were annotated. The results of transcriptome and metabolome association analysis showed that gene-LOC110713661 and gene-LOC110738152 may be the key genes for drought tolerance in quinoa. Some metabolites accumulated in quinoa leaves in response to drought stress, and the plants recovered after rewatering. DEGs and DEMs participate in starch and sucrose metabolism and flavonoid biosynthesis, which are vital for improving drought tolerance in quinoa. Drought tolerance of quinoa was correlated with gene expression differences, metabolite accumulation and good recovery after rewatering. These findings improve our understanding of drought and rewatering responses in quinoa and have implications for the breeding of new drought-tolerance varieties while providing a theoretical basis for drought-tolerance varieties identification.

Transcriptomics and metabolomics analyses of the mechanism of flavonoid synthesis in seeds of differently colored quinoa strains.

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.

Transcriptomics Integrated With Widely Targeted Metabolomics Reveals the Mechanism Underlying Grain Color Formation in Wheat at the Grain-Filling Stage.

Colored wheat grains have a unique nutritional value. To elucidate the color formation mechanism in wheat seeds, comprehensive metabolomic and transcriptomic analyses were conducted on purple (Dianmai 20-1), blue (Dianmai 20-8), and white (Dianmai 16) wheat at the grain-filling stage. The results showed that the flavonoid biosynthesis pathway was closely related to grain color formation. Among the 603 metabolites identified in all varieties, there were 98 flavonoids. Forty-six flavonoids were detected in purple and blue wheat, and there were fewer flavonoids in white wheat than in colored wheat. Integrated transcriptomic and metabolomic analyses showed that gene expression modulated the flavonoid composition and content, resulting in different metabolite levels of pelargonidin, cyanidin, and delphinidin, thus affecting the color formation of wheat grains. The present study clarifies the mechanism by which pigmentation develops in wheat grains and provides an empirical reference for colored wheat breeding.

Non-targeted metabolomics of quinoa seed filling period based on liquid chromatography-mass spectrometry.

Quinoa (Chenopodium quinoa Willd.), an herb belonging to the amaranth family, is rich in minerals, amino acids, vitamins, proteins, and flavonoids. Its grain, compared with other major grains, has unique nutritional value with tremendous applications. This study used four independently bred high-generation lines (seed colors) of quinoa as materials to further understand the metabolic differences in the filling periods of quinoa varieties. Additionally, the non-targeted metabolome of quinoa seeds 35 and 42 days after flowering, respectively, were studied via liquid chromatography-mass spectrometry. The two filling periods of yellow, white, black, and red quinoa grains resulted in significant differences in the metabolites, particularly in L-methionine, S-adenosyl-L-homocysteine, S-adenosyl-L-methionine, pyruvate, fumarate, and oxaloacetate. Soluble sugar, amino acid, and fatty acid contents in quinoa increased after 42 days of flowering. There were metabolic differences between the sugar phosphates (L-fucose, D-mannose-6-phosphate, xylulose-5-phosphate, sedoheptulose-7-phosphate), amino acid (alanine), and organic compounds (kynurenate, tryptamine, serotonin, bilirubin) among the four quinoa varieties. The relative difference in the metabolites was largest when the yellow quinoa grain was compared with the other quinoa varieties and smallest when the red and black varieties were compare. The results of this study provide a basis for the reproduction and identification of new quinoa varieties, as well as for screening potential quality control target genes by combining genomics and transcriptomics.