Flavonoids are a class of specialized metabolites found in many different plant species. They protect against UV radiation, scavenge reactive oxygen species, are involved in plant defense responses, and are associated with plant‐microorganism interactions. They have also been reported to possess health‐promoting effects including anti‐inflammatory, antioxidant, anticancer activity, and antihypertensive effects. Flavonoids encompass >10,000 structures where the types and amounts depend on the plant species, developmental stage, organ, and growth conditions. The diversity of flavonoid structures represents a significant challenge in the analysis of plant flavonoids. Many analytical techniques have been developed to detect and quantify flavonoids, and the most productive of these techniques use liquid chromatography (LC) coupled to mass spectrometry (MS) to analyze flavonoids due to the excellent combination of selectivity and sensitivity of MS. In addition, mass spectral libraries have been constructed to further aid flavonoid identification. Here, the use of ultra‐high pressure liquid chromatography coupled to mass spectrometry (UHPLC‐MS) in plant flavonoid analyses, with an emphasis on sample extraction, flavonoid separation, and MS detection, is described. © 2018 by John Wiley & Sons, Inc.

Lignin provides essential mechanical support for plant cell walls but decreases the digestibility of forage crops and increases the recalcitrance of biofuel crops. Attempts to modify lignin content and/or composition by genetic modification often result in negative growth effects. Although several studies have attempted to address the basis for such effects in individual transgenic lines, no common mechanism linking lignin modification with perturbations in plant growth and development has yet been identified. To address whether a common mechanism exists, we have analyzed transposon insertion mutants resulting in independent loss of function of five enzymes of the monolignol pathway, as well as one double mutant, in the model legume Medicago truncatula. These plants exhibit growth phenotypes from essentially wild type to severely retarded. Extensive phenotypic, transcriptomic, and metabolomics analyses, including structural characterization of differentially expressed compounds, revealed diverse phenotypic consequences of lignin pathway perturbation that were perceived early in plant development but were not predicted by lignin content or composition alone. Notable phenotypes among the mutants with severe growth impairment were increased trichome numbers, accumulation of a variety of triterpene saponins, and extensive but differential ectopic expression of defense response genes. No currently proposed model explains the observed phenotypes across all lines. We propose that reallocation of resources into defense pathways is linked to the severity of the final growth phenotype in monolignol pathway mutants of M. truncatula, although it remains unclear whether this is a cause or an effect of the growth impairment.