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Soybean [Glycine max (L.) Merr.] is the most important oilseed crop for animal industry due to its high protein concentration and high relative abundance of essential and non-essential amino acids (AAs). However, the selection for high-yielding genotypes has reduced seed protein concentration over time, and little is known about its impact on AAs. The aim of this research was to determine the genetic shifts of seed composition for 18 AAs in 13 soybean genotypes released between 1980 and 2014. Additionally, we tested the effect of nitrogen (N) fertilization on protein and AAs trends. Soybean genotypes were grown in field conditions during two seasons under a control (0 N) and a N-fertilized treatment receiving 670 kg N ha−1. Seed yield increased 50% and protein decreased 1.2% comparing the oldest and newest genotypes. The application of N fertilizer did not significantly affect protein and AAs concentrations. Leucine, proline, cysteine, and tryptophan concentrations were not influenced by genotype. The other AAs concentrations showed linear rates of decrease over time ranging from − 0.021 to − 0.001 g kg−1 year−1. The shifts of 11 AAs (some essentials such as lysine, tryptophan, and threonine) displayed a relative-to-protein increasing concentration. These results provide a quantitative assessment of the trade-off between yield improvement and seed AAs concentrations and will enable future genetic yield gain without overlooking seed nutritional value. [ABSTRACT FROM AUTHOR]

• Harvest index is inconsistent across literature to describe genetic gain in reproductive allocation at maturity. • Allometric analysis was used to characterize genetic gain in reproductive allocation in R5 in seven soybean varieties. • Allometric analysis at the end of the seed set revealed an increase in relative allocation into pods. • Allocation to seed must have increased, but HI did not capture this necessary change in allocation. Seed yield is commonly expressed as the product of shoot biomass and harvest index (HI) at physiological maturity. However, HI is a size-dependent ratio unsuitable to describe shifts in reproductive partitioning in historical soybean [ Glycine max (L.) Merr.] studies where selection has enhanced shoot biomass. The aim of this work was to analyze allocation of biomass to reproductive organs in the onset of seed filling (R5) using allometric analysis in a set of historical soybean varieties. Seven varieties released between 1980 and 2013 were evaluated in field trials in Rossville (Kansas, United States) under two N fertilizer rates (0 and 670 kg N ha−1) in 2016 and 2017. Seed yield increased at a rate of 0.74 % yr−1 (p < 0.001); while the shoot biomass increased at a rate of 0.41 % yr−1 (p < 0.001), suggesting an increase in allocation to reproduction. However, the rate of increase in HI at maturity was not different from zero highlighting the inadequacy of this trait. Allometric exponents (slopes of the log-log relationships) relating pod and shoot biomass, pod and leaf, and pod and stem plant fractions increased linearly with the year of release (p < 0.05). Allometric analyses thus revealed genetic gains in reproductive allocation not detected by HI at maturity. The latter outcome highlights the contribution of improved reproductive partitioning to soybean yield gains, and the need for allometric analyses to account for size-dependence in allocation of shoot biomass. [ABSTRACT FROM AUTHOR]