Widely targeted metabolome and transcriptome landscapes of Allium fistulosum–A. cepa chromosome addition lines revealed a flavonoid hot spot on chromosome 5A

Abstract

Here, we report a comprehensive analysis of the widely targeted metabolome and transcriptome profiles of Allium fistulosum L. (FF) with the single extra chromosome of shallot [ A . cepa L. Aggregatum group (AA)] to clarify the novel gene functions in flavonoid biosynthesis. An exhaustive metabolome analysis was performed using the selected reaction monitoring mode of liquid chromatography–tandem quadrupole mass spectrometry, revealing a specific accumulation of quercetin, anthocyanin and flavone glucosides in AA and FF5A. The addition of chromosome 5A from the shallot to A . fistulosum induced flavonoid accumulation in the recipient species, which was associated with the upregulation of several genes including the dihydroflavonol 4-reductase , chalcone synthase , flavanone 3-hydroxylase , UDP-glucose flavonoid-3-O-glucosyltransferase , anthocyanin 5-aromatic acyltransferase-like , pleiotropic drug resistance-like ATP binding cassette transporter , and MYB14 transcriptional factor. Additionally, an open access Allium Transcript Database ( Allium TDB, http://alliumtdb.kazusa.or.jp ) was generated by using RNA-Seq data from different genetic stocks including the A . fistulosum–A . cepa monosomic addition lines. The functional genomic approach presented here provides an innovative means of targeting the gene responsible for flavonoid biosynthesis in A . cepa . The understanding of flavonoid compounds and biosynthesis-related genes would facilitate the development of noble Allium varieties with unique chemical constituents and, subsequently, improved plant stress tolerance and human health benefits.

Metabolome-Based Discrimination Analysis of Shallot Landraces and Bulb Onion Cultivars Associated with Differences in the Amino Acid and Flavonoid Profiles

“…Therefore, shallot landraces with high flavonol and anthocyanin contents can be used for Allium breeding to improve the flavonoid contents in bulb onions and increase their tolerance against abiotic and biotic stresses. Consistently, A. fistulosum with an extra chromosome 5A (FF5A) from shallots exhibited high flavonol and anthocyanin contents, and this was attributed to the upregulation of several flavonoid biosynthesis and regulatory genes in FF5A as compared with the FF genotype [17].…”

“…Our recent studies [7,13,16,17] showed that shallot landraces are crucial genetic resources for Allium breeding due to their high contents of variable bioactive metabolites, including oligosaccharides, flavonoids, saponins, and ACSO compounds. For example, the introgression of chromosome 2A from the shallot (AA) to the Japanese bunching onion (A. fistulosum, FF) improved A. fistulosum (FF2A) disease resistance against Fusarium pathogens, which was attributed to induced-alliospiroside A saponin biosynthesis in the roots of FF2A as compared with the FF genotype [16].…”

Effects of nitrogen application on phytochemical component levels and anticancer and antioxidant activities of Allium fistulosum

“…The antioxidant activity of Allium species has been attributed to a variety of compounds, among which polyphenols are the most important (Nencini et al, 2007). To date, various studies have investigated the total phenolic content and relative activities of these compounds in different plant species (Kujala et al, 2000;Abdelrahman et al, 2019;Assefa et al, 2019). Studies have analyzed the phenolic content of onions among different cultivars (Yang et al, 2004;Chang et al, 2016;Metrani et al, 2020); however, information on how nitrogen fertilizers affect the phenolic content is scarce.…”

Omics approaches inAlliumresearch: Progress and way ahead

“…Among alliums, metabolic profiling is so far performed in onion bulbs, considering cultivars and cultivation year ( Böttcher et al, 2018 ) ; change in organosulfur metabolites after heat treatment in onion ( Kim et al, 2016 ); differentiation profiling of black and fresh garlics ( Molina-Calle et al, 2017 ) ; low-temperature conditioning of “seed” cloves ( Dufoo-Hurtado et al, 2013 ) ; volatile profiling of onion and garlic after subjecting to different drying methods ( Farag et al, 2017 ) ; metabolic profiling of leaves, bulbs, roots, and basal stems in A. roylei and A. porrum L. ( Abdelrahman et al, 2014 ; Soininen et al, 2014a ; Soininen et al, 2012 ); authentication of the geographic origin of garlic ( Hrbek et al, 2018 ) ; bulb color and flavonoids ( Zhang et al, 2018 ; Abdelrahman et al, 2019 ) ; and metabolic profiling of fresh and stored onion bulbs ( Saviano et al, 2019 ) . Metabolomics, along with the artificial neural network, was used for sensory evaluation of garlic and garlic products by using 89 quality indicators ( Liu et al, 2019 ) .…”

“…Similarly, RNA-seq and metabolomics have been integrated into the study of the abiotic stress response ( Abdelrahman et al, 2015 ) , onion bulb color ( Zhang et al, 2018 ), and flavonoids ( Abdelrahman et al, 2019 ) . From these studies, authors have suggested that separate omics analyses by using any single approach can be insufficient for the precise elucidation of various traits and their molecular mechanisms.…”