Combining metabolomic and transcriptomic approaches to assess and improve crop quality traits

Abstract

Plant quality trait improvement has become a global necessity due to the world overpopulation. In particular, producing crop species with enhanced nutrients and health-promoting compounds is one of the main aims of current breeding programs. However, breeders traditionally focused on characteristics such as yield or pest resistance, while breeding for crop quality, which largely depends on the presence and accumulation of highly valuable metabolites in the plant edible parts, was left out due to the complexity of plant metabolome and the impossibility to properly phenotype it. Recent technical advances in high throughput metabolomic, transcriptomic and genomic platforms have provided efficient approaches to identify new genes and pathways responsible for the extremely diverse plant metabolome. In addition, they allow to establish correlation between genotype and metabolite composition, and to clarify the genetic architecture of complex biochemical pathways, such as the accumulation of secondary metabolites in plants, many of them being highly valuable for the human diet. In this review, we focus on how the combination of metabolomic, transcriptomic and genomic approaches is a useful tool for the selection of crop varieties with improved nutritional value and quality traits.

Effects of Genotype and Climatic Conditions on the Oil Content and Its Fatty Acids Composition of Carthamus tinctorius L. Seeds

“…Plant quality trait improvement has become a global necessity due to global overpopulation [52]. The study of plant metabolomics is important to improve crop yields and quality, and ensure nutritional and health factors that provide the opportunity to produce functional food [53].…”

Exploring Genotype-by-Environment Interactions of Chemical Composition of Raspberry by Using a Metabolomics Approach

“…Raspberry fruit metabolic composition and quality traits are influenced both by genetic and environmental factors, as observed in this and previous analyses [ 25 , 27 , 39 ]. While the present knowledge about the complex genetic architecture of fruit quality attributes has been extensively improved since the development of QTL mapping and GWAS approaches, combined with high throughput metabolomic platforms [ 40 ], the impact of the environment on fruit metabolite composition is still poorly understood, its analysis being additionally hampered by current unstable climatic conditions triggered by climate change [ 41 , 42 , 43 , 44 , 45 ]. Furthermore, the metabolic characterization of raspberry genotypes for sensory and nutritional qualities remains essential for fruit breeding strategies.…”

Breeding for Nutritional and Organoleptic Quality in Vegetable Crops: The Case of Tomato and Cauliflower

“…Modern breeding needs to address global challenges including climate change, increasing yield and quality to secure a global food supply for a growing world population and participate in maximising the resources of farming systems [1,6]. Current tools in multiomic approaches are a fundamental support for plant breeding to match crop metabolism genetics and further improve organoleptic and nutraceutical quality in new varieties [1].…”

“…Vegetable quality improvement is a global requirement due to current evolution of consumers' demands. In particular, producing vegetables with enhanced nutritional and organoleptic quality is one of the most challenging targets for breeding, facing with climatic changes and the needs for a more efficient production system [1]. High throughput metabolomic, transcriptomic and genomic advances represent useful tools to identify genetic architecture and biochemical pathways and also to predict breeding values for selection and deployment [2].…”