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Ninety-seven percent of yam ( Dioscorea  spp.) production takes place in low income food deficit countries (LIFDCs) and the crop provides 200 calories a day to approximately 300 million people. Therefore, yams are vital for food security. Yams have high-yield potential and high market value potential yet current breeding of yam is hindered by a lack of genomic information and genetic resources. New tools are needed to modernise breeding strategies and unlock the potential of yam to improve livelihood in LIFDCs.    Objectives  Metabolomic screening has been undertaken on a diverse panel of  Dioscorea  accessions to assess the utility of the approach for advancing breeding strategies in this understudied crop.    Methods  Polar and lipophilic extracts from tubers of accessions from the global yam breeding program have been comprehensively profiled via gas chromatography-mass spectrometry.    Results  A visual pathway representation of the measured yam tuber metabolome has been delivered as a resource for biochemical evaluation of yam germplasm. Over 200 compounds were routinely measured in tubers, providing a major advance for the chemo-typing of this crop. Core biochemical redundancy concealed trends that were only elucidated following detailed mining of global metabolomics data. Combined analysis on leaf and tuber material identified a subset of metabolites which allow accurate species classification and highlighted the potential of predicting tuber composition from leaf profiles. Metabolic variation was accession-specific and often localised to compound classes, which will aid trait-targeting for metabolite markers.    Conclusions  Metabolomics provides a standalone platform with potential to deliver near-future crop gains for yam. The approach compliments the genetic advancements currently underway and integration with other ‘–omics’ studies will deliver a significant advancement to yam breeding strategies.    Electronic supplementary material  The online version of this article (doi:10.1007/s11306-017-1279-7) contains supplementary material, which is available to authorized users.

Metabolite profiling of yam (Dioscorea spp.) accessions for use in crop improvement programmes