title: Metabolomics of forage plants: a review.
abstract: BACKGROUND
  Forage plant breeding is under increasing pressure to deliver new cultivars with improved yield, quality and persistence to the pastoral industry. New innovations in DNA sequencing technologies mean that quantitative trait loci analysis and marker-assisted selection approaches are becoming faster and cheaper, and are increasingly used in the breeding process with the aim to speed it up and improve its precision. High-throughput phenotyping is currently a major bottle neck and emerging technologies such as metabolomics are being developed to bridge the gap between genotype and phenotype; metabolomics studies on forages are reviewed in this article.
  
  
  METHODS
  Major challenges for pasture production arise from the reduced availability of resources, mainly water, nitrogen and phosphorus, and metabolomics studies on metabolic responses to these abiotic stresses in Lolium perenne and Lotus species will be discussed here. Many forage plants can be associated with symbiotic microorganisms such as legumes with nitrogen fixing rhizobia, grasses and legumes with phosphorus-solubilizing arbuscular mycorrhizal fungi, and cool temperate grasses with fungal anti-herbivorous alkaloid-producing Neotyphodium endophytes and metabolomics studies have shown that these associations can significantly affect the metabolic composition of forage plants. The combination of genetics and metabolomics, also known as genetical metabolomics can be a powerful tool to identify genetic regions related to specific metabolites or metabolic profiles, but this approach has not been widely adopted for forages yet, and we argue here that more studies are needed to improve our chances of success in forage breeding.
  
  
  CONCLUSIONS
  Metabolomics combined with other '-omics' technologies and genome sequencing can be invaluable tools for large-scale geno- and phenotyping of breeding populations, although the implementation of these approaches in forage breeding programmes still lags behind. The majority of studies using metabolomics approaches have been performed with model species or cereals and findings from these studies are not easily translated to forage species. To be most effective these approaches should be accompanied by whole-plant physiology and proof of concept (modelling) studies. Wider considerations of possible consequences of novel traits on the fitness of new cultivars and symbiotic associations need also to be taken into account.
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Tennent Drive, Palmerston North 4442, New Zealand. Susanne.rasmussen@agresearch.co.nz
authors.forename: Susanne
authors.initials: S
authors.lastname: Rasmussen
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Parsons
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Jones
mesh_terms: D000383:Agriculture; D018533:Biomass; D001947:Breeding; D060026:Endophytes; D005658:Fungi / Q000378:metabolism* / Q000502:physiology; D023281:Genomics; D005838:Genotype; D019684:Magnoliopsida / Q000378:metabolism* / Q000502:physiology; D055432:Metabolomics; D038821:Mycorrhizae / Q000378:metabolism* / Q000502:physiology; D010641:Phenotype; D012230:Rhizobiaceae / Q000378:metabolism* / Q000502:physiology; D012641:Selection, Genetic; D013312:Stress, Physiological; D013559:Symbiosis