Network analysis identifies QTLs and relationships between seed protein and free amino acids in soybean

The seasonal and daily dynamics of the content of nitrogen-containing compounds in the leaves of Hylotelephium triphyllum plants was studied. The maximum content of total nitrogen, soluble protein and free amino acids in the leaves was observed in the regrowth phase, followed by their reduction towards the end of the growing season. The daily dynamics was characterized by a high content of free amino acids and a low content of soluble protein in the morning hours. In the leaves of H. triphyllum , 23 free amino acids and 2 amides were found. The seasonal and daily dynamics of free amino acids was determined by the content of glutamine and glutamic acid. 4 non-proteinogenic amino acids were found: -aminobutyric, -alanine, ornithine, citrulline. The total proportion of non-theeinogenic amino acids increased with the aging of the leaves from 0,6% of the sum of amino acids during regrowth to 5,8%, in the fruiting phase, which corresponded to a decrease in the content of soluble protein in them. Seasonal and daily dynamics of non-theeinogenic amino acids was determined mainly by -aminobutyric acid. Alanine and -aminobutyric acid were predominated among the amino acids as an indicator of stress. It is assumed that -aminobutyric acid contributes to the regulation of acidity of cell sap in the leaves of H. triphyllum . At low air and soil humidity (flowering phase), the acidity of the cell sap significantly correlates with the content of free amino acids in the leaves.

Free amino acid concentrations and nitrogen isotope signatures in Pinus massoniana (Lamb.) needles of different ages for indicating atmospheric nitrogen deposition

Key messageWe mapped the QTLs for FAAs in edamame seeds and identifiedTOF11 as the causal gene. TOF11 loss-of-function accelerates flowering/maturation and increases FAAs during the edamame stage.The free amino acid (FAA) content in edamame seeds is a determinant of sweetness and umami taste; however, its genetic regulation remains unclear. Therefore, in this study, to elucidate the genetic basis of FAA accumulation, we identified major QTLs and causal genes. We developed a recombinant inbred line population derived from a cross between the Japanese cultivar Enrei (low FAA) and the Japanese landrace edamame Shirayama (high FAA). Using this population, we identified three quantitative trait loci (QTLs) associated with FAA accumulation (qAAD6, qAAD11_1, and qAAD11_2). qAAD11_1 co-localised with qDFD11, a QTL for flowering time. Whole-genome resequencing-based polymorphism analysis revealed five strong candidates within the qDFD11 interval, among which PRR3a/TOF11 was identified as the causal gene for qDFD11. Compared with the wild-type allele, loss-of-function alleles of TOF11 and its homologue TOF12, derived from a mutant and a near-isogenic line with an Enrei background, respectively, both resulted in earlier flowering and maturation, as well as higher FAA accumulation in edamame seeds. These results demonstrated that TOF11 is the causal gene of qAAD11_1. We performed QTL analysis after fixing the qAAD11_1 genotype and identified qAAD11_2, which is tightly linked to qAAD11_1. Because the Shirayama allele at TOF11 and the Enrei allele at qAAD11_2 promote FAA accumulation, breaking their linkage through marker-assisted selection is essential for high-FAA edamame breeding. This study demonstrated that TOF11 regulates not only flowering and maturation but also FAA content at the edamame stage. These findings provide important insights for high-quality edamame breeding.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00122-026-05205-w.

BackgroundAdditional to total protein content, the amino acid (AA) profile is important to the nutritional value of soybean seed. The AA profile in soybean seed is a complex quantitative trait controlled by multiple interconnected genes and pathways controlling the accumulation of each AA. With a total of 621 soybean germplasm, we used three genome-wide association study (GWAS)-based approaches to investigate the genomic regions controlling the AA content and profile in soybean. Among those approaches, the GWAS network analysis we implemented takes advantage of the relationships between specific AAs to identify the genetic control of AA profile.ResultsFor Approach I, GWAS were performed for the content of 24 single AAs under all environments combined. Significant SNPs grouping into 16 linkage disequilibrium (LD) blocks from 18 traits were identified. For Approach II, the individual AAs were grouped by five families according to their metabolic pathways and were examined based on the sum, ratios, and interactions of AAs within the same biochemical family. Significant SNPs grouping into 35 LD blocks were identified, with SNPs associated with traits from the same biochemical family often positioned on the same LD blocks. Approach III, a correlation-based network analysis, was performed to assess the empirical relationships among AAs. Two groups were described by the network topology, Group 1: Ala, Gly, Lys, available Lys (Alys), and Thr and Group 2: Ile and Tyr. Significant SNPs associated with a ratio of connected AAs or a ratio of a single AA to its fully or partially connected metabolic groups were identified within 9 LD blocks for Group 1 and 2 LD blocks for Group 2. Among 40 identified QTL for AA or AA-derived traits, three genomic regions were novel in terms of seed composition traits (oil, protein, and AA content). An additional 24 regions had previously not been specifically associated with the AA content.ConclusionsOur results confirmed loci identified from previous studies but also suggested that network approaches for studying AA contents in soybean seed are valuable. Three genomic regions (Chr 5: 41,754,397–41,893,109 bp, Chr 9: 1,537,829–1,806,586 bp, and Chr 20: 31,554,795–33,678,257 bp) were significantly identified by all three approaches. Yet, the majority of associations between a genomic region and an AA trait were approach- and/or environment-specific. Using a combination of approaches provides insights into the genetic control and pleiotropy among AA contents, which can be applied to mechanistic understanding of variation in AA content as well as tailored nutrition in cultivars developed from soybean breeding programs.

Changes in the amino acid profiles during embryonic development of the blacklip abalone ( Haliotis rubra)

Concentrations and nitrogen isotope compositions of free amino acids in Pinus massoniana (Lamb.) needles of different ages as indicators of atmospheric nitrogen pollution

Changes in the concentrations of free and total amino acids of several commercial <i>Vitis labruscana</i> musts during fermentation were examined by automated ion-exchange analysis. Except for proline, lysine, and glycine, there was a dramatic reduction in free amino acid content by the sixth day after yeast inoculation. At the end of the fermentation the concentration of the free amino acids had increased through yeast cellular autolysis but were still only between 2 and 30% of the initial must values. Proline was apparently not utilized by the yeast during fermentation. Except for proline, which averaged 16.4 mg/100 ml wine, all the free amino acids were less than 3 mg/100 ml in the final wine samples. Small amounts of β-alanine, ornithine, and citrulline were found, and cystathionine was detected at the end of the fermentations. Total amino acid concentrations determined from hydrolyzed wine samples showed trends similar to those of the free amino acids during fermentation. Next to proline, the most abundant of the total amino acids were glutamic acid, aspartic acid, lysine, and glycine. In contrast to proline, which existed mostly in the free form, those four amino acids were present primarily in protein and polypeptide form. Levels of protein and total nitrogen decreased initially and then increased during the later stages of the fermentation. An average of 26.1% of the total nitrogen in the wine at the end of fermentation was due to free amino acid nitrogen. Ammonia, apparently readily utilized by the yeast, decreased rapidly during fermentation. The patterns of change in amino acid composition observed during fermentation were similar to those found with vinifera varieties. The differences were primarily quantitative.

Changes in the concentrations of free and total amino acids of several commercial <i>Vitis labruscana</i> musts during fermentation were examined by automated ion-exchange analysis. Except for proline, lysine, and glycine, there was a dramatic reduction in free amino acid content by the sixth day after yeast inoculation. At the end of the fermentation the concentration of the free amino acids had increased through yeast cellular autolysis but were still only between 2 and 30% of the initial must values. Proline was apparently not utilized by the yeast during fermentation. Except for proline, which averaged 16.4 mg/100 ml wine, all the free amino acids were less than 3 mg/100 ml in the final wine samples. Small amounts of β-alanine, ornithine, and citrulline were found, and cystathionine was detected at the end of the fermentations. Total amino acid concentrations determined from hydrolyzed wine samples showed trends similar to those of the free amino acids during fermentation. Next to proline, the most abundant of the total amino acids were glutamic acid, aspartic acid, lysine, and glycine. In contrast to proline, which existed mostly in the free form, those four amino acids were present primarily in protein and polypeptide form. Levels of protein and total nitrogen decreased initially and then increased during the later stages of the fermentation. An average of 26.1% of the total nitrogen in the wine at the end of fermentation was due to free amino acid nitrogen. Ammonia, apparently readily utilized by the yeast, decreased rapidly during fermentation. The patterns of change in amino acid composition observed during fermentation were similar to those found with vinifera varieties. The differences were primarily quantitative.

Content of total and free amino acids in zooplanktonic food of fish larvae

Influence of milk source and ripening time on free amino acid profile of Picante cheese

Free amino acids of sunflower hypocotyl tissue during crown gall tumor development

Abstract. The paper provides an overview of results obtained in the study of variation in free amino acid levels in the blood plasma of breeding roosters (RIR 05 line) during sexual maturation (in the 10th, 15th, 20th and 25th weeks of age). The results prove that dynamic changes in free amino acid concentrations in blood plasma are connected with the sexual maturation of breeding roosters. During this period the concentrations of each particular free amino acid varied at a significance level of P ≤ 0.05 and P ≤ 0.01. Furthermore, in most cases the plasma concentrations of free amino acids in the 10th and 15th week were higher in comparison with those in the 20th and 25th week. Interestingly, the concentrations of individual free amino acids ranged over a wide interval (units, tens and hundreds of μmol/l). In this respect the free amino acids in plasma can be divided into three groups. The first group consisted of amino acids that occurred at low molar concentration (up to 100 μmol/l): cysteic acid, aspartic acid, α-aminoadipic acid, methionine, isoleucine, γ-aminobutyric acid, 3-methylhistidine, tryptophan and ornitine. The second group included amino acids occurring at medium to high molar concentration (100–300 μmol/l): taurine, glutamine, 1/2 cystine, valine, leucine, tyrosine, phenylalanine, histidine, lysine and arginine. Finally, the third group contained threonine, serine, glutamic acid, proline, glycine and alanine that were present at high molar concentrations (above 300 μmol/l). Analyses of plasma in the period from the 10th to 25th week detected dynamic changes in levels of individual free amino acids and showed that the total content of these amino acids gradually decreased to the following mean values: 5 685.00 μmol/l in the 10th week, 5 076.21 μmol/l in the 15th week, 4 384.78 μmol/l in the 20th week and 4 793.30 μmol/l in the 25th week.

The concentrations of total free amino acids, single free amino acids, urea, and ammonia were determined in plasma of mice during experimental infection with the MHV-3 strain of mouse hepatitis virus. Analysis of free amino acids was done by ion-exchange resin chromatography under conditions that allowed the use of a single chromatographic column, separation of glutamine and asparagine, and an accelerated rate of chromatography. The results showed that as early as 6 hr after infection there was a decrease in the concentration of several free amino acids as well as in the total concentration of free amino acids in plasma. For most of the amino acids the decrease persisted until 48 hr. Only at 72 hr, during severe cytolysis, did the concentration of amino acids increase significantly. It is suggested that the decrease during the initial phases of the infection may be due to a thermolabile factor that is produced by circulating leukocytes and that effects a flow of free amino acids from the plasma toward the liver. The final increase in concentration of several free amino acids reflects the cytolytic damage to the liver caused by the virus.

Concentrations of free amino acids in the hemolymph of uninfected Australorbis glabratus from Surinam, Venezuela, Puerto Rico, and Brazil were determined by automatic recording column chromatography. Additionally, the hemolymphs of normal and of Schistosoma mansoni-infected Puerto Rican A. glabratus were compared with respect to concentration of free amino acids and protein. The concentrations of certain free amino acids varied considerably in the different strains of uninfected snails, but similar variations also occurred in duplicate samples prepared from one of the strains. Total free amino acids of the hemolymph of infected snails varied only slightly. Levels of all free amino acids decreased during the course of infection with S. mansoni. The total free amino acid concentration in the hemolymph of snails with mature infections was approximately one-half that of normal snails. Total hemolymph protein varied among individual uninfected snails and was significantly decreased among infected snails. Several recent studies have dealt with the biochemical nature of snail hemolymph. Qualitative studies of amino acids of Australorbis glabratus hemolymph have been made (Dusanic and Lewert, 1963; Targett, 1962), and the hemolymph proteins have been characterized (Dusanic and Lewert, 1963; Wright and Ross, 1963; Michelson, 1966). This study was designed to determine quantitatively the hemolymph amino acids in four geographic strains of A. glabratus, one of which is highly refractory to infection by Schistosoma mansoni. Additionally, the free amino acid concentrations of the hemolymph of one of the strains were determined during the course of infection by S. mansoni, and the total protein concentrations of the hemolymph of infected and normal A. glabratus were compared. MATERIALS AND METHODS Maintenance and infection of snails A. glabratus from Venezuela (Ag-Ven) and Surinam (Ag-Sur) were obtained from the Tropical Research Medical Laboratory in San Juan, Puerto Rico, in 1962; the Puerto Rican strain of A. glabratus (Ag-PR) was obtained in 1958 from the National Institutes of Health; the Brazilian strain Received for publication 23 December 1966. * This study was supported by a NASA Predoctoral Traineeship to the senior author. t Present address: Department of Tropical Public Health, Harvard School of Public Health, 25 Shattuck Street, Boston, Massachusetts 02115. (Ag-Bah) originated in Bahia and was supplied to us in 1964 by Dr. W. L. Paraense. The Puerto Rican NIH strain of S. mansoni was used to infect Ag-PR. Exposures en masse to 20 to 40 miracidia per snail resulted in infection rates of over 90%. Infected and normal snails were maintained at 27 C in groups of 25 or less in 1-gal glass jars. Water was aerated continuously and changed every 10 to 14 days, leaf lettuce was provided as food, and the snails were fed a supplement once a week (Etges and Gresso, 1965). Collection and preparation of hemolymph Hemolymph for amino acid analysis was obtained from snails 14 to 17 mm in diameter. Snails were starved for 24 hr, rinsed with tap water, and allowed to air-dry. Hemolymph, obtained by puncturing the heart, was collected in 1-ml centrifuge tubes in ice water. Debris was removed by centrifugation (1,000 g/10 min), and the hemolymph was stored in sealed glass vials at -10 C for use within 6 weeks. Samples of 6 ml each, representing the hemolymph pooled from 175 to 225 snails, were used for each analysis. Single pools from uninfected Ag-Bah, Ag-Sur, and Ag-Ven, and duplicate pools from Ag-PR, were analyzed. Hemolymph was drawn from separate groups of snails (Ag-PR) 6, 16, and 32 days postexposure to determine the effect of infection. In addition, fresh hemolymph samples from 50 normal and 20 infected (shedding) Ag-PR, each 15 mm in diameter, were withdrawn for protein determinations. Hemolymph for amino acid analysis was deproteinized by dialysis. Each sample was filtered through a Millipore filter (0.45 J porosity) into a cellophane dialysis bag and allowed to dialyze at 3 to 5 C for 3 days against 50 ml of distilled water, which was changed daily. The total dialysate was

Characterization of free amino acid QTLs in maize opaque2 recombinant inbred lines