Identifying Candidate Genes for Improved Nutrition in Watercress through RNA-Seq

Watercress (Nasturtium officinale R. Br.; Brassicaceae) is a peppery-flavoured leafy salad crop with a long tradition of cultivation in southern England. It has received much attention in recent years as one of the most nutrient dense foods and is thought to offer antioxidant and chemopreventive benefits to the consumer. These benefits are derived from the high concentrations of secondary metabolites, particularly phenylpropanoid pathway derivatives and glucosinolates that are present in this species. Despite these benefits, watercress remains largely undeveloped with limited breeding resources and no active breeding programmes worldwide. The aim of our work is to understand the genetic bases of important nutritional traits in watercress and use modern molecular tools to develop breeding knowledge and resources for the future. To this end, we have carried out sequencing, de novo assembly and functional annotation of the watercress transcriptome using RNA-Seq. We also performed differential expression analysis for samples with contrasting phenotypes for antioxidants and glucosinolate content, finding expression differences in relevant pathways. Furthermore, we identified orthologous sequences in the watercress transcriptome to those in the Arabidopsis phenylpropanoid and glucosinolate biosynthetic pathways and demonstrate differential flux through relevant pathways in the high and low lines. Our results are a first and important genetic resource for this understudied crop and include a catalogue of genes known to be, or potentially involved in, nutrient status as well as thousands of markers which could be employed for marker assisted selection and/or genetic mapping for nutritional traits in watercress.