Features of Activity of the Phenylpropanoid Biosynthesis Pathway in Melanin-Accumulating Barley Grains

Integrated Metabolomics and Transcriptomics Analysis of Flavonoid Biosynthesis Pathway in Polygonatum cyrtonema Hua

Flavonoids, a class of phenolic compounds, are one of the main functional components and have a wide range of molecular structures and biological activities in Polygonatum. A few of them, including homoisoflavonoids, chalcones, isoflavones, and flavones, were identified in Polygonatum and displayed a wide range of powerful biological activities, such as anti-cancer, anti-viral, and blood sugar regulation. However, few studies have systematically been published on the flavonoid biosynthesis pathway in Polygonatum cyrtonema Hua. Therefore, in the present study, a combined transcriptome and metabolome analysis was performed on the leaf, stem, rhizome, and root tissues of P. cyrtonema to uncover the synthesis pathway of flavonoids and to identify key regulatory genes. Flavonoid-targeted metabolomics detected a total of 65 active substances from four different tissues, among which 49 substances were first study to identify in Polygonatum, and 38 substances were flavonoids. A total of 19 differentially accumulated metabolites (DAMs) (five flavonols, three flavones, two dihydrochalcones, two flavanones, one flavanol, five phenylpropanoids, and one coumarin) were finally screened by KEGG enrichment analysis. Transcriptome analysis indicated that a total of 222 unigenes encoding 28 enzymes were annotated into three flavonoid biosynthesis pathways, which were "phenylpropanoid biosynthesis", "flavonoid biosynthesis", and "flavone and flavonol biosynthesis". The combined analysis of the metabolome and transcriptome revealed that 37 differentially expressed genes (DEGs) encoding 11 enzymes (C4H, PAL, 4CL, CHS, CHI, F3H, DFR, LAR, ANR, FNS, FLS) and 19 DAMs were more likely to be regulated in the flavonoid biosynthesis pathway. The expression of 11 DEGs was validated by qRT-PCR, resulting in good agreement with the RNA-Seq. Our studies provide a theoretical basis for further elucidating the flavonoid biosynthesis pathway in Polygonatum.

Transcriptional convergence after repeated duplication of an amino acid transporter gene leads to the independent emergence of the black husk/pericarp trait in barley and rice

The repeated emergence of the same trait (convergent evolution) in distinct species is an interesting phenomenon and manifests visibly the power of natural selection. The underlying genetic mechanisms have important implications to understand how the genome evolves under environmental challenges. In cereal crops, both rice and barley can develop black-coloured husk/pericarp due to melanin accumulation. However, it is unclear if this trait shares a common origin. Here, we fine-mapped the barley HvBlp gene controlling the black husk/pericarp trait and confirmed its function by gene silencing. The result was further supported by a yellow husk/pericarp mutant with deletion of the HvBlp gene, derived from gamma ray radiation of the wild-type W1. HvBlp encodes a putative tyrosine transporter homologous to the black husk gene OsBh4 in rice. Surprisingly, synteny and phylogenetic analyses showed that HvBlp and OsBh4 belonged to different lineages resulted from dispersed and tandem duplications, respectively, suggesting that the black husk/pericarp trait has emerged independently. The dispersed duplication (dated at 21.23 MYA) yielding HvBlp occurred exclusively in the common ancestor of Triticeae. HvBlp and OsBh4 displayed converged transcription in husk/pericarp tissues, contributing to the black husk/pericarp trait. Further transcriptome and metabolome data identified critical candidate genes and metabolites related to melanin production in barley. Taken together, our study described a compelling case of convergent evolution resulted from transcriptional convergence after repeated gene duplication, providing valuable genetic insights into phenotypic evolution. The identification of the black husk/pericarp genes in barley also has great potential in breeding for stress-resilient varieties with higher nutritional values.

Characterization key genes of Arabidopsis seedlings in response to β-caryophyllene, eugenol using combined transcriptome and WGCN analysis

Weeds present a significant challenge to high crop yield and quality. In our study, we investigated the phytotoxic activity of β-caryophyllene (BCP) and eugenol, which are natural allelopathic chemical compounds, on Arabidopsis seedlings. We found that these compounds inhibited the growth of Arabidopsis thaliana plants. When either BCP or eugenol was applied, it led to decrease in the content of cell wall components such as lignin, cellulose, hemicellulose, and pectin; and increase in the levels of endogenous hormones like ETH, ABA, SA, and JA in the seedlings. Through transcriptome profiling, we identified 7181 differentially expressed genes (DEGs) in the roots and shoots that were induced by BCP or eugenol. The genes involved in the synthesis of lignin, cellulose, hemicellulose, and pectin were down-regulated, whereas genes related to synthesis and signal transduction of ABA, ETH, SA, and JA were up-regulated. However, genes related to IAA synthesis and signal transduction were found to be down-regulated. Furthermore, we characterized 24 hub genes using Weighted Correlation Network Analysis (WGCNA). Among them, the identified 16 genes in response to BCP was primarily associated with hypoxia stress, while 8 genes induced by eugenol were linked to inhibition of cell division. Our results suggested that BCP and eugenol had ability to target multiple genes to inhibit growth and development of Arabidopsis plants. Therefore, they can serve as excellent candidates for natural biological herbicides.

Integrated metabolite analysis and health-relevant in vitro functionality of white, red, and orange maize (Zea mays L.) from the Peruvian Andean race Cabanita at different maturity stages

The high maize (Zea mays L.) diversity in Peru has been recognized worldwide, but the investigation focused on its integral health-relevant and bioactive characterization is limited. Therefore, this research aimed at studying the variability of the primary and the secondary (free and dietary fiber-bound phenolic, and carotenoid compounds) metabolites of three maize types (white, red, and orange) from the Peruvian Andean race Cabanita at different maturity stages (milk-S1, dough-S2, and mature-S3) using targeted and untargeted methods. In addition, their antioxidant potential, and α-amylase and α-glucosidase inhibitory activities relevant for hyperglycemia management were investigated using in vitro models. Results revealed a high effect of the maize type and the maturity stage. All maize types had hydroxybenzoic and hydroxycinnamic acids in their free phenolic fractions, whereas major bound phenolic compounds were ferulic acid, ferulic acid derivatives, and p-coumaric acid. Flavonoids such as luteolin derivatives and anthocyanins were specific in the orange and red maize, respectively. The orange and red groups showed higher phenolic ranges (free + bound) (223.9-274.4 mg/100 g DW, 193.4- 229.8 mg/100 g DW for the orange and red maize, respectively) than the white maize (162.2-225.0 mg/100 g DW). Xanthophylls (lutein, zeaxanthin, neoxanthin, and a lutein isomer) were detected in all maize types. However, the orange maize showed the highest total carotenoid contents (3.19-5.87 μg/g DW). Most phenolic and carotenoid compounds decreased with kernel maturity in all cases. In relation to the primary metabolites, all maize types had similar fatty acid contents (linoleic acid > oleic acid > palmitic acid > α-linolenic acid > stearic acid) which increased with kernel development. Simple sugars, alcohols, amino acids, free fatty acids, organic acids, amines, and phytosterols declined along with grain maturity and were overall more abundant in white maize at S1. The in vitro functionality was similar among Cabanita maize types, but it decreased with the grain development, and showed a high correlation with the hydrophilic free phenolic fraction. Current results suggest that the nutraceutical characteristics of orange and white Cabanita maize are better at S1 and S2 stages while the red maize would be more beneficial at S3.