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Background  The BBAA subgenomes of hexaploid common wheat are structurally intact, which makes it possible to extract the BBAA subgenomes to constitute a novel plant type, namely, extracted tetraploid wheat (ETW). ETW displays multiple abnormal phenotypes such as massively reduced biomass and abnormal spike development, compared to extant tetraploid wheat with a BBAA genome. The genetic, biochemical and physiological basis underlying the phenotypic abnormality of ETW remains unknown.    Results  To explore the biochemical basis of these phenotypic abnormalities, we analysed the metabolomic and proteomic profiles and quantified 46 physiological traits of ETW in comparison with its common wheat donor (genome BBAADD), and a  durum  tetraploid wheat cultivar (genome BBAA). Among these three types of wheat, ETW showed a saliently different pattern of nutrient accumulation and seed quality, markedly lower concentrations of many metabolites involved in carbohydrate metabolism, and higher concentrations of many metabolites related to amino acids. Among the metabolites, changes in shikimate and sucrose were the most conspicuous. Higher levels of shikimate and lower levels of sucrose influence many metabolic processes including carbohydrate and amino acid metabolism, which may contribute to the phenotypic abnormalities. Gene expression assay showed downregulation of a shikimate degradation enzyme (5-enolpyruvylshikimate-3-phosphate synthase) coding gene and upregulation of several genes coding for the sucrose hydrolysis enzyme, which could explain the higher levels of shikimate and lower levels of sucrose, respectively.    Conclusions  Our results suggest that significant and irreversible biochemical changes have occurred in the BBAA subgenomes of common wheat during the course of its co-evolution with the DD subgenome at the hexaploid level.    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1796-9) contains supplementary material, which is available to authorized users.

An extracted tetraploid wheat harbouring the BBAA component of common wheat shows anomalous shikimate and sucrose metabolism