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Background  Alfalfa ( Medicago sativa  L.) is one of the most important forage resources in the world due to its high nutritive value. However, its nutritional quality decreases during the transition from budding to flowering. Previous research revealed a decreased crude protein content and increased fibre content in alfalfa forage harvested at later maturity stages, leading to a reduction in nutritional quality. However, the reasons for this phenomenon have not been explained at the molecular level.    Results  In this study, leaves from the WL319HQ alfalfa cultivar were harvested at two developmental stages (budding and mid-flowering). The leaves were used to test the variable expression of proteins and metabolites during these stages. TMT-based quantitative proteomics and LC-MS/MS-based untargeted metabolomics methods were employed in this study. A total of 415 proteins and 49 metabolites showed at least a 1.2-fold difference in abundance during these stages. Most of the differentially expressed proteins and metabolites were involved in metabolic processes, including carbohydrate metabolism, starch and sucrose metabolism, phenylpropanoid biosynthesis, and biosynthesis of amino acids. Alfalfa leaves in mid-flowering contain less crude protein due to the decrease in L-glutamic acid content. Carbohydrate metabolism provides the raw material for the synthesis of hemicellulose, resulting in an increase in the hemicellulose content of the alfalfa leaves, leading to an increase in the NDF content. In addition, the increase in L-phenylalanine content could have provided the conditions necessary for lignin synthesis. These are the main factors leading to reductions in alfalfa relative feed value (RFV) and quality.    Conclusions  This study used joint proteomic and metabolomic analyses to elucidate the relationship between the reduction in the nutritional value of alfalfa and complex biological processes. This provides a theoretical basis for producing high-quality alfalfa hay and sets the stage for further research.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1291-8) contains supplementary material, which is available to authorized users.

Proteomics integrated with metabolomics: analysis of the internal causes of nutrient changes in alfalfa at different growth stages