The Eruca sativa Genome and Transcriptome: A Targeted Analysis of Sulfur Metabolism and Glucosinolate Biosynthesis Pre and Postharvest

Abstract

Rocket (Eruca sativa) is a source of health-related metabolites called glucosinolates (GSLs) and isothiocyanates (ITCs) but little is known of the genetic and transcriptomic mechanisms responsible for regulating pre and postharvest accumulations. We present the first de novo reference genome assembly and annotation, with ontogenic and postharvest transcriptome data relating to sulfur assimilation, transport, and utilization. Diverse gene expression patterns related to sulfur metabolism, GSL biosynthesis, and glutathione biosynthesis are present between inbred lines of rocket. A clear pattern of differential expression determines GSL abundance and the formation of hydrolysis products. One breeding line sustained GSL accumulation and hydrolysis product formation throughout storage. Multiple copies of MYB28, SLIM1, SDI1, and ESM1 have increased and differential expression postharvest, and are associated with GSLs and hydrolysis product formation. Two glucosinolate transporter gene (GTR2) copies were found to be associated with increased GSL accumulations in leaves. Monosaccharides (which are essential for primary metabolism and GSL biosynthesis, and contribute to the taste of rocket) were also quantified in leaves, with glucose concentrations significantly correlated with the expression of numerous GSL-related genes. Significant negative correlations were observed between the expression of glutathione synthetase (GSH) genes and those involved in GSL metabolism. Breeding line "B" showed increased GSH gene expression and low GSL content compared to two other lines where the opposite was observed. Co-expression analysis revealed senescence (SEN1) and oxidative stress-related (OXS3) genes have higher expression in line B, suggesting that postharvest deterioration is associated with low GSL concentrations.

Quantitative trait loci analysis of glucosinolate, sugar, and organic acid concentrations in Eruca vesicaria subsp. sativa

“…Eruca contains 11 pairs of chromosomes (2 n = 22) (Bell and Wagstaff 2019 ) indicating that the distribution and density of selected SNPs was not sufficient to resolve chromosome-equivalent LGs. Several identified LGs may be representative of single chromosomes due to the presence of markers from common reference genome assembly scaffolds (Bell et al 2020a ; Additional File 3 ). LG1 is low density compared to LG3 and LG9, containing only seven markers.…”

“…Where QTL were identified, the underlying genome assembly scaffolds were scrutinized for transcriptional or biosynthetic genes related to the respective metabolites. This was done through utilization of a genome annotation (Bell et al 2020a ) and visualization using Integrated Genomics Viewer (IGV; Robinson et al 2017 ).…”

“… a = Bell et al 2020a Abbreviations : QTL Quantitative trait loci, 4MGB 4-methoxyglucobrassicin, IGMT Indole glucosinolate methyl transferase, CCOAOMT Caffeoyl-CoA O-methyltransferase, JAZ Jasmonate ZIM domain-containing, TSB Tryptophan synthase beta chain …”

“…Breeders aim to improve the environmental stability of phytochemical traits underlying these attributes, but the genetic loci have not been previously identified. The species has comparable genome size to B. oleracea and Raphanus sativus (Bell et al 2020a ) and has many biochemical similarities to the genetically distinct ‘wild’ rocket, Diplotaxis genus. The Eruca genome may therefore prove to be useful in understanding orthologous genetic mechanisms underlying nutritional and organoleptic traits in these related leafy vegetable species.…”

Sustainable Use of Bioactive Compounds from Solanum Tuberosum and Brassicaceae Wastes and by-Products for Crop Protection—A Review

“…Wentzell et al demonstrated that the AOP2 enzyme encoding gene is the major regulator of aliphatic GSL biosynthesis and accumulation; furthermore, its overexpression resulted in upregulation of the entire biosynthetic pathway [ 191 , 192 ]. The recent release of Eruca sativa genome [ 193 ] will represent a valuable resource to identify the gene target for genetic engineering strategies in this species. Elicitation, through diverse approaches both physical and chemical, is an experimental procedure well established to modulate the content of secondary metabolites in plant tissues/organs and examples about GSLs were also recorded.…”