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Prostate cancer (PC) is a common cancer among men, and preventive strategies are warranted. Benzoxazinoids (BXs) in rye have shown potential against PC in vitro but human studies are lacking. The aim was to establish a quantitative method for analysis of BXs and investigate their plasma levels after a whole grain/bran rye vs refined wheat intervention, as well as exploring their association with PSA, in men with PC. A quantitative method for analysis of 22 BXs, including novel metabolites identified by mass spectrometry and NMR, was established, and applied to plasma samples from a randomized crossover study where patients with indolent PC (n = 17) consumed 485 g whole grain rye/rye bran or fiber supplemented refined wheat daily for 6 wk. Most BXs were significantly higher in plasma after rye (0.3–19.4 nmol/L in plasma) vs. refined wheat (0.05–2.9 nmol/L) intake. HBOA-glc, 2-HHPAA, HBOA-glcA, 2-HPAA-glcA were inversely correlated to PSA in plasma ( p  < 0.04). To conclude, BXs in plasma, including metabolites not previously analyzed, were quantified. BX metabolites were significantly higher after rye vs refined wheat consumption. Four BX-related metabolites were inversely associated with PSA, which merits further investigation.

The allelopathic potency of rye ( Secale cereale L.) is due mainly to the presence of phytotoxic benzoxazinones—compounds whose biosynthesis is developmentally regulated, with the highest accumulation in young tissue and a dependency on cultivar and environmental influences. Benzoxazinones can be released from residues of greenhouse-grown rye at levels between 12 and 20 kg/ha, with lower amounts exuded by living plants. In soil, benzoxazinones are subject to a cascade of transformation reactions, and levels in the range 0.5–5 kg/ha have been reported. Starting with the accumulation of less toxic benzoxazolinones, the transformation reactions in soil primarily lead to the production of phenoxazinones, acetamides, and malonamic acids. These reactions are associated with microbial activity in the soil. In addition to benzoxazinones, benzoxazolin-2(3 H )-one (BOA) has been investigated for phytotoxic effects in weeds and crops. Exposure to BOA affects transcriptome, proteome, and metabolome patterns of the seedlings, inhibits germination and growth, and can induce death of sensitive species. Differences in the sensitivity of cultivars and ecotypes are due to different species-dependent strategies that have evolved to cope with BOA. These strategies include the rapid activation of detoxification reactions and extrusion of detoxified compounds. In contrast to sensitive ecotypes, tolerant ecotypes are less affected by exposure to BOA. Like the original compounds BOA and MBOA, all exuded detoxification products are converted to phenoxazinones, which can be degraded by several specialized fungi via the Fenton reaction. Because of their selectivity, specific activity, and presumably limited persistence in the soil, benzoxazinoids or rye residues are suitable means for weed control. In fact, rye is one of the best cool season cover crops and widely used because of its excellent weed suppressive potential. Breeding of benzoxazinoid resistant crops and of rye with high benzoxazinoid contents, as well as a better understanding of the soil persistence of phenoxazinones, of the weed resistance against benzoxazinoids, and of how allelopathic interactions are influenced by cultural practices, would provide the means to include allelopathic rye varieties in organic cropping systems for weed control.

Cover crops have the potential to be agricultural nitrogen (N) regulators that reduce leaching through soils and then deliver N to subsequent cash crops. Yet, regulating N in this way has proven difficult because the few cover crop species that are well-studied excel at either reducing N leaching or increasing N supply to cash crops, but they fail to excel at both simultaneously. We hypothesized that mixed species cover crop stands might balance the N fixing and N scavenging capabilities of individual species. We tested six cover crop monocultures and four mixtures for their effects on N cycling in an organically managed maize-soybean-wheat feed grain rotation in Pennsylvania, USA. For three years, we used a suite of integrated approaches to quantify N dynamics, including extractable soil inorganic N, buried anion exchange resins, bucket lysimeters, and plant N uptake. All cover crop species, including legume monocultures, reduced N leaching compared to fallow plots. Cereal rye monocultures reduced N leaching to buried resins by 90% relative to fallow; notably, mixtures with just a low seeding rate of rye did almost as well. Austrian winter pea monocultures increased N uptake in maize silage by 40 kg N ha-1 relative to fallow, and conversely rye monocultures decreased N uptake into maize silage by 40 kg N ha-1 relative to fallow. Importantly, cover crop mixtures had larger impacts on leaching reduction than on maize N uptake, when compared to fallow plots. For example, a three-species mixture of pea, red clover, and rye had similar maize N uptake to fallow plots, but leaching rates were 80% lower in this mixture than fallow plots. Our results show clearly that cover crop species selection and mixture design can substantially mitigate tradeoffs between N retention and N supply to cash crops, providing a powerful tool for managing N in temperate cropping systems.

Meiotic recombination is a critical process for plant breeding, as it creates novel allele combinations that can be exploited for crop improvement. In wheat, a complex allohexaploid that has a diploid-like behaviour, meiotic recombination between homoeologous or alien chromosomes is suppressed through the action of several loci. Here, we report positional cloning of Pairing homoeologous 2 (Ph2) and functional validation of the wheat DNA mismatch repair protein MSH7-3D as a key inhibitor of homoeologous recombination, thus solving a half-century-old question. Similar to ph2 mutant phenotype, we show that mutating MSH7-3D induces a substantial increase in homoeologous recombination (up to 5.5 fold) in wheat-wild relative hybrids, which is also associated with a reduction in homologous recombination. These data reveal a role for MSH7-3D in meiotic stabilisation of allopolyploidy and provides an opportunity to improve wheat’s genetic diversity through alien gene introgression, a major bottleneck facing crop improvement. In the allohexaploid genome of wheat, meiotic recombination between homoeologues is suppressed through the action of several loci. Here, the authors report the cloning of the long sought-after gene Ph2 and show its function in reduction of homoeologous recombination.

Background Affected by global warming, freeze-thaw occurs more frequently in Northeast China. Meanwhile, as a major grain-producing area, this region is influenced by the invasive plant Solanum rostratum Dunal. Moreover, due to the long-term application of chemical fertilizers, soil cadmium pollution has been aggravated. Therefore, crops in Northeast China may suffer from compound stress simultaneously. However, the impact of combined stress on plants has not been given enough attention, and the interrelationships between different stresses have not been thoroughly studied. This experiment adopted the indoor simulation method. By determining the changing trends and amplitudes of relative conductivity (RC), soluble protein (SP), chlorophyll (Chl), malondialdehyde (MDA) content, and the activities of superoxide dismutase (SOD) and peroxidase (POD), the influence effects of the combined stress of freeze-thaw, S. rostratum extract, and cadmium chloride on the growth and metabolism of seedlings could be judged. Results Under the combined stress of freeze-thaw, cadmium chloride, and S. rostratum extract, the growth of rye seedlings was inhibited; The relative conductivity (RC) increased by 1.92–71.07%, and the content of malondialdehyde (MDA) increased by 17.34–28.11%; The soluble protein (SP) content decreased by 17.82–22.14%; The activities of superoxide dismutase (SOD) and peroxidase (POD) both increased, but POD activity was inhibited at the lowest point of freeze-thaw (-5℃); The chlorophyll (Chl) content decreased by 9.68–19.67%. Conclusion Stress affects osmotic pressure, and seedlings need to accumulate osmoregulatory substances to maintain cell osmotic balance. Compared to a single stress factor, the combined stress of freeze-thaw, cadmium chloride, and S. rostratum extract further enhanced the physiological damage to plants. This compound stress leads to electrolyte leakage, intensified membrane lipid peroxidation, inhibition of protein synthesis, increased osmotic pressure, and disruption of cell osmotic balance. Combined stress further promotes the accumulation of reactive oxygen species (ROS) in the seedlings, leading to oxidative damage and inhibiting photosynthesis.

The effect of conditions of rye cultivation (conventional and organic) and method of mash preparation and fermentation, as well as supportive enzyme and yeast strains on the alcoholic fermentation efficiency and chemical composition of the obtained distillates was assessed. The conditions of rye cultivation did not affect the chemical composition of the tested rye grain; however the differences in the fermentation efficiency were observed. The supplementation of mashes from both conventional and organic rye grain with protease had a positive effect on ethanol biosynthesis. The rye distillates contained low concentrations of acetaldehyde (from 22.25 to 34.07 mg/L of 100% v/v alcohol and met the recommendations for agricultural distillates (<100 mg acetaldehyde/L of 100% v/v alcohol) in Polish distilleries. The samples obtained from both conventional and organic rye grain, pretreated by the thermal-pressure method, were found to contain higher concentrations of methanol than those obtained by the pressureless method of starch liberation. The concentrations of methanol in all distillates remained below the limit specified in EU Regulation 2019/787 for ethyl alcohol of agricultural origin (i.e., rectified spirit) (≤30 g/hL of 100% v/v alcohol). The distillates from organic rye grain subjected to pressureless pretreatment contained significantly lower concentrations of 2-methylbutanol and 3-methylbutanol than analogous distillates from conventional rye grain. The digestion of mashes with a protease preparation has been shown to increase the concentrations of 3-methyl-butyl acetate and 2-methyl-butyl acetate in distillates, irrespective of the rye grain type, the processing method, and the yeast strain employed for fermentation.

Aluminium (Al) toxicity limits crop productivity, particularly at low soil pH. Proline (Pro) plays a role in protecting plants against various abiotic stresses. Using the relatively Al-tolerant cereal rye ( Secale cereale L.), we evaluated Pro metabolism in roots and shoots of two genotypes differing in Al tolerance, var. RioDeva (sensitive) and var. Beira (tolerant). Most enzyme activities and metabolites of Pro biosynthesis were analysed. Al induced increases in Pro levels in each genotype, but the mechanisms were different and were also different between roots and shoots. The Al-tolerant genotype accumulated highest Pro levels and this stronger increase was ascribed to simultaneous activation of the ornithine (Orn)-biosynthetic pathway and decrease in Pro oxidation. The Orn pathway was particularly enhanced in roots. Nitrate reductase (NR) activity, N levels, and N/C ratios demonstrate that N-metabolism is less inhibited in the Al-tolerant line. The correlation between Pro changes and differences in Al-sensitivity between these two genotypes, supports a role for Pro in Al tolerance. Our results suggest that differential responses in Pro biosynthesis may be linked to N-availability. Understanding the role of Pro in differences between genotypes in stress responses, could be valuable in plant selection and breeding for Al resistance.

Rye regeneration in anther cultures is problematic and affected by albino plants. DNA methylation changes linked to Cu ions in the induction medium affect reprogramming microspores from gametophytic to sporophytic path. Alternations in S-adenosyl-L-methionine (SAM), glutathione (GSH), or β-glucans and changes in DNA methylation in regenerants obtained under different in vitro culture conditions suggest a crucial role of biochemical pathways. Thus, understanding epigenetic and biochemical changes arising from the action of Cu and Zn that participate in enzymatic complexes may stimulate progress in rye doubled haploid plant regeneration. The Methylation-Sensitive Amplified Fragment Length Polymorphism approach was implemented to identify markers related to DNA methylation and sequence changes following the quantification of variation types, including symmetric and asymmetric sequence contexts. Reverse-Phase High-Pressure Liquid Chromatography (RP-HPLC) connected with mass spectrometry was utilized to determine SAM, GSH, and glutathione disulfide, as well as phytohormones, and RP-HPLC with a fluorescence detector to study polyamines changes originating in rye regenerants due to Cu or Zn presence in the induction medium. Multivariate and regression analysis revealed that regenerants derived from two lines treated with Cu and those treated with Zn formed distinct groups based on DNA sequence and methylation markers. Zn treated and control samples formed separate groups. Also, Cu discriminated between controls and treated samples, but the separation was less apparent. Principal coordinate analysis explained 85% of the total variance based on sequence variation and 69% of the variance based on DNA methylation changes. Significant differences in DNA methylation characteristics were confirmed, with demethylation in the CG context explaining up to 89% of the variance across genotypes. Biochemical profiles also demonstrated differences between controls and treated samples. The changes had different effects on green and albino plant regeneration efficiency, with cadaverine (Cad) and SAM affecting regeneration parameters the most. Analyses of the enzymes depend on the Cu or Zn ions and are implemented in the synthesis of Cad, or SAM, which showed that some of them could be candidates for genome editing. Alternatively, manipulating SAM, GSH, and Cad may improve green plant regeneration efficiency in rye.

N6-methyladenine (6 mA) has emerged as a potential epigenetic marker in eukaryotic genomes, yet its precise distribution patterns and biological functions in plant genomes are still not fully understood. In this study, we investigated the occurrence, global levels, and distribution patterns of 6 mA in four rye species: Secale cereale , S. strictum , S. sylvestre , and S. vavilovii . Using multiple complementary approaches, i.e., ELISA, ultra-performance liquid chromatography tandem mass-spectrometry (UPLC-MS/MS), immunofluorescence, and high-throughput sequencing (PacBio and MeDIP-seq), 6 mA was detected in all the examined species. The level of 6 mA in the genomic DNA of the rye species, depending on the species and organ, ranged from approximately 1 to 10 per million nucleotides. Immunofluorescence revealed specific chromosomal distribution patterns of 6 mA. The 6 mA signal in the rye chromosomes was dispersed along all chromosome arms, while no 6 mA signals were detected in the centromeric and telomeric regions, indicating that large blocks of constitutive subtelomeric and pericentromeric heterochromatin along with functional telomeric and centromeric regions do not contain 6 mA residues. To precisely map the genomic distribution of 6 mA, a machine learning approach combining PacBio methylation calls with MeDIP-seq data was developed, which enabled the identification of 6 mA-enriched regions across the genomes of all the four rye species. The findings provide comprehensive insights into the presence and distribution of 6 mA in the rye genomes, contributing to the growing understanding of this modification’s potential role in the plant epigenetic regulation.

Background Gluten proteins from wheat, rye, and barley play a substantial role in human nutrition. At the same time, they can trigger several different immune reactions. This, together with their influence on the quality of grain products and their emerging role as biomaterials, makes them an interesting target for further study. The proteins’ propensity for aggregation challenges heterologous eukaryotic production systems. The yeast Komagataella phaffii has demonstrated excellent qualities as a production host for heterologous proteins and was therefore investigated as a platform strain. Results A gene coding for the rye ( Secale cereale ) prolamin 75k γ-secalin was cloned and inserted into K. phaffii ; protein expression was verified via mass spectrometry and immunoblotting and quantified via ELISA. Different parameters were investigated regarding their effect on target protein production and endoplasmic reticulum (ER) homeostasis, including the induction temperature and co- and post-translational import into the ER. At 28°C, the cells produced 1.69-fold more 75k γ-secalin than at 20°C. The introduction of the MATα-pro-region, in conjunction with either the MATα-pre- or OST1-pre-signal, led to significantly lower 75k γ-secalin accumulation, 0.20- and 0.18-fold, respectively. No mutant showed significant changes in the unfolded protein response compared to a non-producing strain. Conclusions K. phaffii is a suitable host for prolamin production. The absence of a significant unfolded protein response during 75k γ-secalin expression indicates little challenge of ER-homeostasis by the aggregation-prone protein. It underscores K. phaffii’ s imminent role in protein production. The significantly decreased protein yield through the common protein secretion leader component MATα-pro demonstrates the need for further investigation into the role of secretion signals in optimizing K. phaffii as a production platform for repetitive, aggregation-prone proteins.