Bread wheat (Triticum aestivum L.), which provides about 20% of daily calorie intake, is the most widely cultivated crop in the world, in terms of total area devoted to its cultivation. Therefore, even small increases in wheat yield can translate into large gains. Reducing the gap between actual and potential grain yield in wheat is a crucial task to feed the increasing world population. Fusarium head blight (FHB) caused by the pathogenic fungus Fusarium graminearum and related Fusarium species is one of the most devastating wheat diseases throughout the world. This disease reduces not only the yield but also the quality by contaminating the grain with mycotoxins harmful for humans, animals and the environment. In recent years, remarkable achievements attained in “omics” technologies have not only provided new insights into understanding of processes involved in pathogenesis but also helped develop effective new tools for practical plant breeding. Sequencing of the genomes of various wheat pathogens, including F. graminearum, as well as those of bread and durum wheat and their wild relatives, together with advances made in transcriptomics and bioinformatics, has allowed the identification of candidate pathogen effectors and corresponding host resistance (R) and susceptibility (S) genes. However, so far, FHB effectors and wheat susceptibility genes/factors have been poorly studied. In this paper, we first briefly highlighted recent examples of improving resistance against pathogens via new techniques in different host species. We then propose effective strategies towards developing wheat cultivars with improved resistance to FHB. We hope that the article will spur discussions and interest among researchers about novel approaches with great potential for improving wheat against FHB.

Elaborate regulation of gene expression is required for plants to maintain normal growth, development, and reproduction. MicroRNAs (miRNAs) and transcription factors are key players that control gene expression in plant regulatory networks. The TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) family comprises plant-specific transcription factors that contain a conserved TCP domain of 59 amino acids. Some members of this family are targeted by miR319, one of the most ancient and evolutionarily conserved miRNAs in plants. Accumulating evidence has revealed that miR319-regulated TCP (MRTCP) genes participate extensively in plant development and responses to environmental stress. In this review, the structural characteristics and classifications of TCP transcription factors and the regulatory relationships between TCP transcription factors and miRNAs are introduced. Current knowledge of the regulatory functions of MRTCP genes in multiple biological pathways including leaf development, vascular formation, flowering, hormone signaling, and response to environmental stresses such as cold, salt, and drought is summarized. This review will be beneficial for understanding the roles of the MRTCP-mediated regulatory network and its molecular mechanisms in plant development and stress response, and provides a theoretical basis for plant genetic improvement.

Common wheat (Triticum aestivum L.) is one of the most important crops because it provides about 20% of the total calories for humans. T. aestivum is an excellent modern species for studying concerted evolution of sub-genomes in polyploid species, because of its large chromosome size and three well-known genome donors. Establishment of common wheat genome reference sequence and development of high-density SNP chips provide an excellent foundation to answer questions of wheat evolution and breeding at the genomic level. By genotyping more than 600 accessions of common wheat and their diploid and tetraploid ancestors using a Wheat660K SNP array, we found dramatic genome changes due to tetraploidization and hexaploidization, in contrast to weaker influences of domestication and breeding on them. Further, since common wheat was introduced in China in 1500 BCE, Chinese landraces formed two subgroups (T. aestivum-L1 and T. aestivum-L2) with considerably diverse geographic distributions and agronomic traits. T. aestivum-L2, mainly distributed in central and east China is found to have more but smaller oval grains with early maturity characteristics. We found that variation and selection in intergenic regions of the A and B sub-genomes dominated this differentiation, in which chromosomes 7A and 3B took the leading roles due to the existence of putative genes related to defense responses and environmental adaption in the highly differentiated regions. Large haplotype blocks were detected on 3B (232.6-398.3 Mb) and 7A (211.7-272.9 Mb) in the landraces, forming two distinct haplotypes, respectively. We discovered that artificial crosses in breeding promoted recombination in the whole genome, however, this recombination and differentiation was highly asymmetric among the three sub-genomes in homoeologous regions. In addition, we found that the wide use of European and northern American cultivars in breeding at early era, led dramatic changes in Chinese wheat genome, whereas, the recent breeding functioned to optimize it. This study will provide the insight for reconsideration of wheat evolution and breeding, and a new strategy for parent selection in breeding.

Rice panicle phenotyping is required in rice breeding for high yield and grain quality. To fully evaluate spikelet and kernel traits without threshing and hulling, using X-ray and RGB scanning, we developed an integrated rice panicle phenotyping system and a corresponding image analysis pipeline. We compared five methods of counting spikelets and found that Faster R-CNN achieved high accuracy (R² of 0.99) and speed. Faster R-CNN was also applied to indica and japonica classification and achieved 91% accuracy. The proposed integrated panicle phenotyping method offers benefit for rice functional genetics and breeding.

The yield of rice is mostly affected by three factors, namely, panicle number, grain number and grain weight. Variation in panicle and grain numbers is mainly caused by tiller and panicle branches generated from axillary meristems (AMs). MOC1 encodes a putative GRAS family nuclear protein that regulates AM formation. Although several alleles of MOC1 have been identified, its variation in germplasm resources remains unclear. In the present study we characterized a novel moc1 allele named gnp6 which has a thymine insertion in the coding sequence of the SAW motif in the GRAS domain. This mutation causes arrested branch formation. The SAW motif is necessary for nuclear localization of GNP6/MOC1 where it functions as a transcription factor or co-regulator. Haplotype analysis showed that the coding region of GNP6/MOC1 was conserved without any non-synonymous mutations in 240 rice accessions. However, variation in the promoter region might affect the expression of it and its downstream genes. Joint haplotype analysis of GNP6/MOC1 and MOC3 showed that haplotype combinations H9, H10 and H11, namely MOC1-Hap1 in combination with MOC3-Hap3, MOC3-Hap4 or MOC3-Hap5 could be bred to promote branch formation. These findings will enrich the genetic resources available for rice breeders.

Pre-harvest sprouting (PHS) is a disadvantageous trait in cereal production worldwide, causing large economic losses each year. Its regulation mechanism is still unclear. We generated the Oryza sativa Viviparous1 (OsVP1) mutant using gene editing technique, which shows increased PHS compared with that of the wild type Nipponbare. OsVP1 is localized mainly in the nucleus and expressed in various tissues and organs. Expression of Seed dormancy 4 (Sdr4), a key gene controlling PHS, was sharply reduced in OsVP1 mutants. OsVP1 bound to the specific motif CACCTG in the promoter of Sdr4 and activated its expression in rice protoplasts. Overexpression of Sdr4 reduced the high seed germination rate of OsVP1 mutant cr-osvp1-1, showing that Sdr4 acts as a downstream target of OsVP1. Both OsVP1 and Sdr4 loss-of-function mutants were insensitive to exogenous ABA and employed the ABA signaling pathway in regulating seed dormancy. These findings shed light on the control of seed dormancy aimed at preventing PHS in rice.

In plants, glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the interconversion of glycerol-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP) coupled to the reduction/oxidation of the nicotinamide adenine dinucleotide (NADH) pool, and plays a central role in glycerolipid metabolism and stress response. Previous studies have focused mainly on the NAD⁺-dependent GPDH isoforms, neglecting the role of flavin adenine dinucleotide (FAD)-dependent GPDHs. We isolated and characterized three mitochondrial-targeted FAD-GPDHs in soybean, of which one isoform (GmGPDH12) showed a significant transcriptional response to NaCl and mannitol treatments, suggesting the existence of a major FAD-GPDH isoform acting in soybean responses to salt and osmotic stress. An enzyme kinetic assay showed that the purified GmGPDH12 protein possessed the capacity to oxidize G3P to DHAP in the presence of FAD. Overexpression and RNA interference of GmGPDH12 in soybean hairy roots resulted in elevated tolerance and sensitivity to salt and osmotic stress, respectively. G3P contents were significantly lower in GmGPDH12-overexpressing hair roots and higher in knockdown hair roots, indicating that GmGPDH12 was essential for G3P catabolism. A significant perturbation in redox status of NADH, ascorbic acid (ASA) and glutathione (GSH) pools was observed in GmGPDH12-knockdown plants under stress conditions. The impaired redox balance was manifested by higher reactive oxygen species generation and consequent cell damage or death; however, overexpressing plants showed the opposite results for these traits. GmGPDH12 overexpression contributed to maintaining constant respiration rates under salt or osmotic stress by regulating mRNA levels of key mitochondrial respiratory enzymes. This study provides new evidence for the roles of mitochondria-localized GmGPDH12 in conferring resistance to salt or osmotic stress by maintaining cellular redox homeostasis, protecting cells and respiration from oxidative injury.

Phosphate deficiency is one of the leading causes of crop productivity loss. Phospholipid degradation liberates phosphate to cope with phosphate deficiency. Glycerophosphodiester phosphodiesterases (GPX-PDEs) hydrolyse the intermediate products of phospholipid catabolism glycerophosphodiesters into glycerol-3-phosphate, a precursor of phosphate. However, the function of GPX-PDEs in phosphate remobilization in maize remains unclear. In the present study, we characterized two phosphate deficiency-inducible GPX-PDE genes, ZmGPX-PDE1 and ZmGPX-PDE5, in maize leaves. ZmGPX-PDE1 and ZmGPX-PDE5 were transcriptionally regulated by ZmPHR1, a well-described phosphate starvation-responsive transcription factor of the MYB family. Complementation of the yeast GPX-PDE mutant gde1∆ indicated that ZmGPX-PDE1 and ZmGPX-PDE5 functioned as GPX-PDEs, suggesting their roles in phosphate recycling from glycerophosphodiesters. In vitro enzyme assays showed that ZmGPX-PDE1 and ZmGPX-PDE5 catalysed glycerophosphodiester degradation with different substrate preferences for glycerophosphoinositol and glycerophosphocholine, respectively. ZmGPX-PDE1 was upregulated during leaf senescence, and more remarkably, loss of ZmGPX-PDE1 in maize compromised the remobilization of phosphorus from senescing leaves to young leaves, resulting in a stay-green phenotype under phosphate starvation. These results suggest that ZmGPX-PDE1 catalyses the degradation of glycerophosphodiesters in maize, promoting phosphate recycling from senescing leaves to new leaves. This mechanism is crucial for improving phosphorus utilization efficiency in crops.

Brassinosteroids (BRs) play critical roles in a wide range of plant developmental processes. However, it is unknown whether and how BRs mediate the effect of high temperature (HT) stress during anthesis on the pistil activity of photo-thermosensitive genetic male-sterile (PTSGMS) rice (Oryza sativa L.) lines. This study investigated the question. Three pot-grown PTSGMS rice lines were subjected to HT stress during anthesis. The contents of 24-epibrassinolide (24-EBL) and 28-homobrassinolide (28-HBL), the major forms of BR in rice plants, and levels of reactive oxygen species (ROS) or antioxidants (AOS), hydrogen peroxide (H₂O₂), 1-aminocylopropane-1-carboxylic acid (ACC), ascorbic acid (AsA), and catalase activity in pistils, were determined. HT stress significantly reduced the contents of both 24-EBL and 28-EBL relative to those under normal temperatures, but the reduction varied by PTSGMS line. A line with higher BR contents under HT stress showed lower contents of ACC and H₂O₂, higher catalase activity and AsA content in pistils, and higher fertilization rate, seed-setting rate, and seed yield when the line was crossed with a restorer line, indicating that higher levels of BRs increase HT stress resistance. Applying 24-EBL, 28-HBL or an inhibitor of BR biosynthesis confirmed the roles of BRs in response to HT stress. The results suggest that BRs mediate the effect of HT stress on pistil activity during anthesis and alleviate the harm of HT stress by increasing AOS and suppressing ROS generation.

Drought stress is a limiting factor for wheat production and food security. Drought priming has been shown to increase drought tolerance in wheat. However, the underlying mechanisms are unknown. In the present study, the genes encoding the biosynthesis and metabolism of abscisic acid (ABA) and jasmonic acid (JA), as well as genes involved in the ABA and JA signaling pathways were up-regulated by drought priming. Endogenous concentrations of JA and ABA increased following drought priming. The interplay between JA and ABA in plant responses to drought priming was further investigated using inhibitors of ABA and JA biosynthesis. Application of fluridone (FLU) or nordihydroguaiaretic acid (NDGA) to primed plants resulted in lower chlorophyll-fluorescence parameters and activities of superoxide dismutase and glutathione reductase, and higher cell membrane damage, compared to primed plants (PD) under drought stress. NDGA + ABA, but not FLU + JA, restored priming-induced tolerance, as indicated by a finding of no significant difference from PD under drought stress. Under drought priming, NDGA induced the suppression of ABA accumulation, while FLU did not affect JA accumulation. These results were consistent with the expression of genes involved in the biosynthesis of ABA and JA. They suggest that ABA and JA are required for priming-induced drought tolerance in wheat, with JA acting upstream of ABA.

Sugarcane is a prominent source of sugar and ethanol production. Genetic analysis for trait improvement of sugarcane is greatly hindered by its complex genome, long breeding cycle, and recalcitrance to genetic transformation. The protoplast-based transient transformation system is a versatile and convenient tool for in vivo functional gene analysis; however, quick and effective transformation systems are still lacking for sugarcane. Here, we developed an efficient protoplast-based transformation system by optimizing conditions of protoplasts isolation and PEG-mediated transformation in S. spontaneum. The yield of viable protoplasts was approximately 1.26 × 10⁷ per gram of leaf material, and the transformation efficiency of 80.19% could be achieved under the optimized condition. Furthermore, using this approach, the nuclear localization of an ABI5-like bZIPs transcription factor was validated, and the promoter activity of several putative DNase I hypersensitive sites (DHSs) was assessed. The results indicated this system can be conveniently applied to protein subcellular localization and promoter activity assays. A highly efficient S. spontaneum mesophyll cell protoplast isolation and transient transformation method was developed, and it shall be suitable for in vivo functional gene analysis in sugarcane.

Fusarium head blight (FHB) is one of the prevalent fungal diseases of wheat worldwide. Exploring new FHB resistance quantitative trait loci (QTL) in adapted wheat cultivars is a critical step for breeding new FHB-resistant cultivars. In this study, we developed a population of 236 F_5:7 recombinant inbred lines (RILs) using two popular Chinese wheat cultivars, Yangmai 158 and Zhengmai 9023, with moderate FHB resistance to identify the QTL for FHB type II resistance. This population was evaluated for percentage of symptomatic spikelets per spike (PSS) using single floret injection in repeated greenhouse experiments. Mean PSSs were 33.2% for Yangmai 158 and 30.3% for Zhengmai 9023. A genetic linkage map of 1002 single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) was constructed for the RIL population. Six QTL were identified for FHB resistance, and three of them were repeatable in the both experiments. Zhengmai 9023 contributed the resistance allele at one repeatable QTL, designated as Qfhb.7D, whereas Yangmai 158 contributed the resistance alleles at the other two repeatable QTL, Qfhb.3AL and Qfhb.2DS. The additional QTL, Qfhb.4AS was significant in the mean PSS, and Qfhb.2DL and Qfhb.7AS were significant in only one experiment. Replacement of each allele individually at the three repeatable QTL significantly changed PSSs. Qfhb.3AL, Qfhb.2DS, and Qfhb.7D explained 8.35% to 9.89%, 5.13% to 7.43%, and 6.15% to 9.32% of the phenotypic variations, respectively. The three repeatable QTL contributed by the two parents were additive and stacking the resistance alleles from all the three repeatable QTL showed the highest level of resistance in the current RIL population. Ten SNPs in the QTL regions of Qfhb.3AL, Qfhb.2DS, and Qfhb.7D were converted into KBioscience competitive allele-specific PCR (KASP) assays. One KASP marker for Qfhb.3AL was validated in a panel of wheat cultivars from China. Some of these KASP markers could be useful for marker-assisted selection to stack these QTL.

Grain kernel discoloration (KD) in cereal crops leads to down-grading grain quality and substantial economic losses worldwide. Breeding KD tolerant varieties requires a clear understanding of the genetic basis underlying this trait. Here, we generated a high-density single nucleotide polymorphisms (SNPs) map for a diverse barley germplasm and collected trait data from two independent field trials for five KD related traits: grain brightness (TL), redness (Ta), yellowness (Tb), black point impact (Tbpi), and total black point in percentage (Tbpt). Although grain brightness and black point is genetically correlated, the grain brightness traits (TL, Ta, and Tb) have significantly higher heritability than that of the black point traits (Tbpt and Tbpi), suggesting black point traits may be more susceptible to environmental influence. Using genome-wide association studies (GWAS), we identified a total of 37 quantitative trait loci (QTL), including two major QTL hotspots on chromosomes 4H and 7H, respectively. The two QTL hotspots are associated with all five KD traits. Further genetic linkage and gene transcription analyses identified candidate genes for the grain KD, including several genes in the flavonoid pathway and plant peroxidase. Our study provides valuable insights into the genetic basis for the grain KD in barley and would greatly facilitate future breeding programs for improving grain KD resistance.

Straw return is an effective way to improve crop grain yield and potassium (K) use efficiency by increasing soil K content. However, the effects of straw return on soil K supplying capacity, replacement of K fertilizer, and K-use efficiency under maize (Zea mays L.)-rice (Oryza sativa L.) cropping systems are little studied. A two-year field experiment was conducted to determine the physiological determinants of K-use efficiency under straw return with four K fertilization rates. Sr33 (straw returned plus 33% of K fertilizer applied) and Sr67 (straw returned plus 67% of K fertilizer applied) increased annual crop yields by 1.5% and 3.2% and increased agronomic K-use efficiency by respectively 2.9 and 1.3-fold on average in the two years, compared with the conventional practice S0K100 (no straw returned plus normal amounts of K fertilizer applied). The Sr33 and Sr67 treatments resulted in significantly greater equilibrium K concentration ratios (CR₀^K) and specifically exchangeable K (K_X) values according to quantity/intensity (Q/I) relationship analyses, indicating improvement of the potential soil K supply capacity. However, the Sr67 better maintained the soil exchangeable K level and K balance. The results suggested that K released from maize and rice straw can replace about half of chemical K fertilizer, depending on the available K content in maize-rice cropping system production.

As the end products of cellular regulatory processes, metabolites provide the link between genotypes and phenotypes. Although metabolites have been widely applied for functional gene detection and phenotype prediction in maize, there is little research focusing on the genetic information of metabolites per se. Here, we performed genetic analyses for the kernel metabolites of 11 parental inbred lines of six representative maize varieties, including Zhongdan 2, Danyu 13, Yedan 13, Zhengdan 958, Xianyu 355, and Suyu 16, as well as their 26 reciprocal hybrids. We identified a total of 208 metabolites in maize kernels using untargeted metabolite profiling technology. Both cluster analysis and principal component analysis indicated that kernel metabolites could distinguish hybrids from their parents. Analysis of variance further revealed that 163 metabolites exhibited significant differences between parents and hybrids, and 40 metabolites showed significant differences between reciprocal crosses. We also investigated the genetic effects and heterosis for each metabolite. By taking all hybrids into consideration, about two-thirds of all metabolites displayed overdominant with 36.8% and 31% of them displaying positive overdominant and negative overdominant, respectively. Besides, 27.5% and 20.4% of all hybrid combinations showed significant mid-parent heterosis and over-parent heterosis, respectively. Our findings revealed that kernel metabolites exhibited the diversity of relationship between maize hybrids and their parental lines. Additionally, we identified 25 significant metabolic markers related to 11 agronomic traits using the LASSO method. Seven metabolic markers were associated with more than one trait simultaneously. These results provide a genetic basis for further utilization of metabolites in the genetic improvement of maize.

Maize (Zea mays L.) is one of the most important food crops in the world, and starch is the main component of its endosperm. Transcriptional regulation plays a vital role in starch biosynthesis. However, it is not well understood in maize. We report the identification of the transcription factor ZmNAC126 and its role in regulation of starch synthesis in maize. Transcriptional expression of ZmNAC126 was higher in maize endosperm and kernels than in roots or stems. ZmNAC126 shared a similar expression pattern with starch synthesis genes during seed development, and its expression pattern was also consistent with the accumulation of starch. ZmNAC126 is a typical transcription factor with a transactivation domain between positions 201 and 227 of the amino acid sequence, is located in the nucleus, and binds to CACG repeats in vitro. Yeast one-hybrid assay revealed that ZmNAC126 bound the promoters of ZmGBSSI, ZmSSIIa, ZmSSIV, ZmISA1, and ZmISA2. Transient overexpression of ZmNAC126 in maize endosperm increased the activities of promoters pZmSh2, pZmBt2, pZmGBSSI, pZmSSIIIa, and pZmBT1 but inhibited the activities of pZmISA1 and pZmISA2. ZmNAC126 thus acts in starch synthesis by transcriptionally regulating targeted starch synthesis-related genes in maize kernels.

Sweetpotato [Ipomoea batatas (L.) Lam.], a food crop with both nutritional and medicinal uses, plays essential roles in food security and health-promoting. Chlorogenic acid (CGA), a polyphenol displaying several bioactivities, is distributed in all edible parts of sweetpotato. However, little is known about the specific metabolism of CGA in sweetpotato. In this study, IbPAL1, which encodes an endoplasmic reticulum-localized phenylalanine ammonia lyase (PAL), was isolated and characterized in sweetpotato. CGA accumulation was positively associated with the expression pattern of IbPAL1 in a tissue-specific manner, as further demonstrated by overexpression of IbPAL1. Overexpression of IbPAL1 promoted CGA accumulation and biosynthetic pathway genes expression in leaves, stimulated secondary xylem cell expansion in stems, and inhibited storage root formation. Our results support a potential role for IbPAL1 in sweetpotato CGA biosynthesis and establish a theoretical foundation for detailed mechanism research and nutrient improvement in sweetpotato breeding programs.

Jute (Corchorus spp.) is a member of the Malvaceae family, which comprises more than 100 species. The systematic positions of jute species have remained unsettled. Chloroplasts are maternally inherited and their genomes are widely used for plant phylogenetic studies. In the present study, the chloroplast genomes of Corchorus capsularis and C. olitorius were assembled, with sizes of respectively 161,088 and 161,766 bp. Both genomes contained 112 unique genes (78 protein-coding, four rRNA, and 30 tRNA genes). Four regions with high variation between the two species were located in single-copy rather than inverted-repeat regions. A total of 66 simple sequence repeats (SSRs) were identified in the C. capsularis chloroplast genome and 56 in that of C. olitorius. Comparison of the two chloroplast genome sequences permitted the evaluation of nucleotide variation including 2417 single-nucleotide polymorphisms sites and 294 insertion or deletion sites, of which one marker (cpInDel 205) could discriminate the two jute species. Comparison of the C. capsularis and C. olitorius chloroplast genomes with those of other species in the Malvaceae revealed breakpoints in the accD locus, which is involved in fatty acid synthesis, in C. capsularis and C. olitorius. This finding suggests that genes from the chloroplast genome might have been transferred to the nuclear genome in some Corchorus species. This hypothesis was supported by synteny analysis of the accD region among the nuclear, chloroplast, and mitochondrial genomes. To our knowledge, this is the first report of the assembled chloroplast genome sequences of C. capsularis and C. olitorius. C. capsularis and C. olitorius are closely related to Gossypium species and there are abundant microstructure variations between these two genera. These results will expand our understanding of the systematics of species in the Malvaceae.

Astragalus sinicus is a commonly used legume green manure that fixes atmospheric N₂ and accumulates mineral nutrients and organic substances that are beneficial to soils and subsequent crops. However, little is known about genotypic variation in, and molecular mechanisms of, Pi (phosphate) uptake and storage in A. sinicus. We recorded the morphological responses of six A. sinicus cultivars from four regions of China to external Pi application and measured their Pi accumulation. We identified full-length transcripts of Pi-signaling and Pi-homeostasis regulators by sequencing and measured the expression level of these genes by qRT-PCR. The major components in Pi signaling and Pi homeostasis were largely conserved between A. sinicus and the model species rice and Arabidopsis. Different A. sinicus varieties responded differently to low-phosphorus (P) stress, and their Pi accumulation was positively correlated with the expression of vacuolar Pi influx gene (SYG1/PHO81/XPR1-MAJOR FACILITATOR SUPERFAMILY (SPX-MFS)-TYPE PROTEIN) AsSPX-MFS2 and negatively correlated with the expression of the vacuolar Pi efflux gene (VACUOLAR Pi EFFLUX TRANSPORTER) AsVPE1. We identified key Pi-signaling and Pi-homeostasis regulators in A. sinicus. The expression of vacuolar Pi transporter genes could be used as an index to select A. sinicus accessions with high Pi accumulation.

Soybean [Glycine max (L.) Merr.] is a global protein source and is currently expanding in Central and Northern Europe. Protein and oil content are two important quality traits that have been studied in different germplasm, however, their genetic architecture in early-maturing European soybean has not been investigated yet. In this study, we therefore performed QTL mapping for both traits using 944 recombinant inbred lines derived from eight families from a half-diallel crossing design. We identified five QTL for each trait, with the QTL on chromosomes 8, 15, and 20 being identified for both protein content and oil content. The known major QTL on chromosome 20 was detected in four families whereas the other QTL were only found in single families. Further analyses revealed the QTL to have pleiotropic but inverse effects on both traits. The effect of the major QTL was comparable between families, illustrating that it is largely independent from the genetic background. Collectively, our results illustrate the quantitative nature of protein and oil content in early European soybean. Marker-assisted selection for the QTL is possible, but the inverse effect on protein and oil content should be kept in mind.