Genome-wide simple sequence repeat analysis and specific molecular marker development of rye.

BACKGROUND: Rye (Secale cereale L.) is the most widely used related species in wheat genetic breeding, and the introduction of its chromosome fragments into the wheat genome through distant hybridization is essential for enriching the genetic diversity of wheat. Rapid and accurate detection of rye chromatin in the wheat genome is important for distant hybridization. Simple sequence repeats (SSRs) are widely distributed in the genome, and SSRs of different species often exhibit species-specific characteristics. RESULTS: In this study, genome-wide SSRs in rye were identified, and their characteristics were outlined. A total of 997,027 SSRs were selected, with a density of 115.97 SSRs/Mb on average. There was no significant difference in the number of SSRs on each chromosome. The number of SSRs on 2R was the highest (15.29%), and the number of SSRs on 1R was the lowest (13.02%). The number of SSRs on each chromosome is significantly correlated with chromosome length. The types of SSR motifs were abundant, and each type of SSR was distributed on 7 chromosomes of rye. The numbers of mononucleotide simple sequence repeats (MNRs), dinucleotide simple sequence repeats (DNRs), and trinucleotide simple sequence repeats (TNRs) were the greatest, accounting for 46.90%, 18.37%, and 22.64% of the total number, respectively. Among the MNRs, the number of G/C repeats and the number of 10 bp motifs were the greatest, accounting for 26.24% and 31.32% of the MNRs, respectively. Based on the SSR sequences, a total of 657 pairs of primers were designed. The PCR results showed that 119 pairs of these primers were rye-specific and could effectively detect rye chromatin in the wheat genome. Moreover, 86 pairs of the primers could also detect one or more specific rye chromosomes. CONCLUSION: These results lay a foundation for both genomic evolution studies of rye and molecular breeding in wheat.

Basic helix-loop-helix (bHLH) gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses.

BACKGROUND: Rye (Secale cereale), one of the drought and cold-tolerant crops, is an important component of the Triticae Dumortier family of Gramineae plants. Basic helix-loop-helix (bHLH), an important family of transcription factors, has played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. However, no systemic analysis of the bHLH transcription factor family has yet been reported in rye. RESULTS: In this study, 220 bHLH genes in S. cereale (ScbHLHs) were identified and named based on the chromosomal location. The evolutionary relationships, classifications, gene structures, motif compositions, chromosome localization, and gene replication events in these ScbHLH genes are systematically analyzed. These 220 ScbHLH members are divided into 21 subfamilies and one unclassified gene. Throughout evolution, the subfamilies 5, 9, and 18 may have experienced stronger expansion. The segmental duplications may have contributed significantly to the expansion of the bHLH family. To systematically analyze the evolutionary relationships of the bHLH family in different plants, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. Finally, the gene expression response characteristics of 22 ScbHLH genes in various biological processes and stress responses were analyzed. Some candidate genes, such as ScbHLH11, ScbHLH48, and ScbHLH172, related to tissue developments and environmental stresses were screened. CONCLUSIONS: The results indicate that these ScbHLH genes exhibit characteristic expression in different tissues, grain development stages, and stress treatments. These findings provided a basis for a comprehensive understanding of the bHLH family in rye.

Genome-wide identification and phylogenetic and expression pattern analyses of EPF/EPFL family genes in the Rye (Secale cereale L.).

Rye (Secale cereale L.) is one of the major cereal crop species in the Triticeae family and is known to be most tolerant to diverse abiotic stresses, such as cold, heat, osmotic, and salt stress. The EPIDERMAL PATTERNING FACTOR (EPF) and EPF-LIKE (EPFL) families of small secreted peptides act to regulate many aspects of plant growth and development; however, their functions are not widely characterized in rye. In this study, we identified 12 ScEPF/EPFL genes, which can be divided into six groups and are evenly distributed on six rye chromosomes. Further examination of the gene structure and protein conservation motifs of EPF/EPFL family members demonstrated the high conservation of the ScEPF/EPFL sequence. Interactions between ScEPF/EPFL proteins and promoters containing hormone- and stress-responsive cis-acting elements suggest that the regulation of ScEPF/EPFL expression is complex. Expression profiling analyses revealed that ScEPF/EPFL genes exhibited tissue-specific expression patterns. Notably, ScEPFL1,ScEPFL7, ScEPFL9, and ScEPFL10 displayed significantly higher expression levels in spikelets compared to other tissues. Moreover, fluorescence quantification experiments demonstrated that these genes exhibited distinct expression patterns in response to various stress conditions, suggesting that each gene plays a unique role in stress signaling pathways. Our research findings provide a solid basis for further investigation into the functions of ScEPF/EPFLs. Furthermore, these genes can serve as potential candidates for breeding stress-resistant rye varieties and improving production yields.

Transcriptomic analysis reveals the regulatory mechanisms of messenger RNA (mRNA) and long non-coding RNA (lncRNA) in response to waterlogging stress in rye (Secale cereale L.).

BACKGROUND: Waterlogging stress (WS) negatively impacts crop growth and productivity, making it important to understand crop resistance processes and discover useful WS resistance genes. In this study, rye cultivars and wild rye species were subjected to 12-day WS treatment, and the cultivar Secale cereale L. Imperil showed higher tolerance. Whole transcriptome sequencing was performed on this cultivar to identify differentially expressed (DE) messenger RNAs (DE-mRNAs) and long non-coding RNAs (DE-lncRNAs) involved in WS response. RESULTS: Among the 6 species, Secale cereale L. Imperil showed higher tolerance than wild rye species against WS. The cultivar effectively mitigated oxidative stress, and regulated hydrogen peroxide and superoxide anion. A total of 728 DE-mRNAs and 60 DE-lncRNAs were discovered. Among these, 318 DE-mRNAs and 32 DE-lncRNAs were upregulated, and 410 DE-mRNAs and 28 DE-lncRNAs were downregulated. GO enrichment analysis discovered metabolic processes, cellular processes, and single-organism processes as enriched biological processes (BP). For cellular components (CC), the enriched terms were membrane, membrane part, cell, and cell part. Enriched molecular functions (MF) terms were catalytic activity, binding, and transporter activity. LncRNA and mRNA regulatory processes were mainly related to MAPK signaling pathway-plant, plant hormone signal transduction, phenylpropanoid biosynthesis, anthocyanin biosynthesis, glutathione metabolism, ubiquitin-mediated proteolysis, ABC transporter, Cytochrome b6/f complex, secondary metabolite biosynthesis, and carotenoid biosynthesis pathways. The signalling of ethylene-related pathways was not mainly dependent on AP2/ERF and WRKY transcription factors (TF), but on other factors. Photosynthetic activity was active, and carotenoid levels increased in rye under WS. Sphingolipids, the cytochrome b6/f complex, and glutamate are involved in rye WS response. Sucrose transportation was not significantly inhibited, and sucrose breakdown occurs in rye under WS. CONCLUSIONS: This study investigated the expression levels and regulatory functions of mRNAs and lncRNAs in 12-day waterlogged rye seedlings. The findings shed light on the genes that play a significant role in rye ability to withstand WS. The findings from this study will serve as a foundation for further investigations into the mRNA and lncRNA WS responses in rye.

Two functional CC-NBS-LRR proteins from rye chromosome 6RS confer differential age-related powdery mildew resistance to wheat.

Rye (Secale cereale), a valuable relative of wheat, contains abundant powdery mildew resistance (Pm) genes. Using physical mapping, transcriptome sequencing, barley stripe mosaic virus-induced gene silencing, ethyl methane sulfonate mutagenesis, and stable transformation, we isolated and validated two coiled-coil, nucleotide-binding site and leucine-rich repeat (CC-NBS-LRR) alleles, PmTR1 and PmTR3, located on rye chromosome 6RS from different triticale lines. PmTR1 confers age-related resistance starting from the three-leaf stage, whereas its allele, PmTR3, confers typical all-stage resistance, which may be associated with their differential gene expression patterns. Overexpression in Nicotiana benthamiana showed that the CC, CC-NBS, and CC-LRR fragments of PMTR1 induce cell death, whereas in PMTR3 the CC and full-length fragments perform this function. Luciferase complementation imaging and pull-down assays revealed distinct interaction activities between the CC and NBS fragments. Our study elucidates two novel rye-derived Pm genes and their derivative germplasm resources and provides novel insights into the mechanism of age-related resistance, which can aid the improvement of resistance against wheat powdery mildew.

Molecular Cytogenetic Characterization of Novel Wheat-Rye T1RS.1AL Translocation Lines with Resistance to Powdery Mildew and Stripe Rust Derived from the Chinese Rye Landrace Qinling.

Stripe rust and powdery mildew are serious diseases that severely decrease the yield of wheat. Planting wheat cultivars with powdery mildew and stripe rust resistance genes is the most effective way to control these two diseases. Introducing disease resistance genes from related species into the wheat genome via chromosome translocation is an important way to improve wheat disease resistance. In this study, nine novel T1RS.1AL translocation lines were developed from the cross of wheat cultivar Chuannong25 (CN25) and a Chinese rye Qinling. The results of non-denaturing fluorescence in situ hybridization and PCR showed that all new lines were homozygous for the T1RS.1AL translocation. These new T1RS.1AL translocation lines exhibited strong resistance to stripe rust and powdery mildew. The cytogenetics results indicated that the resistance of the new lines was conferred by the 1RS chromosome arms, which came from Qinling rye. The genetic analysis indicated that there were new dominant resistance genes on the 1RS chromosome arm resistant to stripe rust and powdery mildew, and their resistance patterns were different from those of Yr9, Pm8, and Pm17 genes. In addition, the T1RS.1AL translocation lines generally exhibited better agronomic traits in the field relative to CN25. These T1RS.1AL translocations have great potential in wheat-breeding programs in the future.

Genome-wide identification of the plant homeodomain-finger family in rye and ScPHD5 functions in cold tolerance and flowering time.

KEY MESSAGE: 111 PHD genes were newly identified in rye genome and ScPHD5's role in regulating cold tolerance and flowering time was suggested. Plant homeodomain (PHD)-finger proteins regulate the physical properties of chromatin and control plant development and stress tolerance. Although rye (Secale cereale L.) is a major winter crop, PHD-finger proteins in rye have not been studied. Here, we identified 111 PHD genes in the rye genome that exhibited diverse gene and protein sequence structures. Phylogenetic tree analysis revealed that PHDs were genetically close in monocots and diverged from those in dicots. Duplication and synteny analyses demonstrated that ScPHDs have undergone several duplications during evolution and that high synteny is conserved among the Triticeae species. Tissue-specific and abiotic stress-responsive gene expression analyses indicated that ScPHDs were highly expressed in spikelets and developing seeds and were responsive to cold and drought stress. One of these genes, ScPHD5, was selected for further functional characterization. ScPHD5 was highly expressed in the spike tissues and was localized in the nuclei of rye protoplasts and tobacco leaves. ScPHD5-overexpressing Brachypodium was more tolerant to freezing stress than wild-type (WT), with increased CBF and COR gene expression. Additionally, these transgenic plants displayed an extremely early flowering phenotype that flowered more than two weeks earlier than the WT, and vernalization genes, rather than photoperiod genes, were increased in the WT. RNA-seq analysis revealed that diverse stress response genes, including HSPs, HSFs, LEAs, and MADS-box genes, were also upregulated in transgenic plants. Our study will help elucidate the roles of PHD genes in plant development and abiotic stress tolerance in rye.

Detection of Sensitization Profiles with Cellular In Vitro Tests in Wheat Allergy Dependent on Augmentation Factors (WALDA).

Wheat allergy dependent on augmentation factors (WALDA) is the most common gluten allergy in adults. IgE-mediated sensitizations are directed towards ω5-gliadin but also to other wheat allergens. The value of the different in vitro cellular tests, namely the basophil activation test (BAT) and the active (aBHRA) and passive basophil histamine-release assays (pBHRA), in the detection of sensitization profiles beyond ω5-gliadin has not been compared. Therefore, 13 patients with challenge-confirmed, ω5-gliadin-positive WALDA and 11 healthy controls were enrolled. Specific IgE (sIgE), skin prick tests, BATs, aBHRA, and pBHRA were performed with allergen test solutions derived from wheat and other cereals, and results were analyzed and compared. This study reveals a distinct and highly individual reactivity of ω5-gliadin-positive WALDA patients to a range of wheat allergens beyond ω5-gliadin in cellular in vitro tests and SPT. In the BAT, for all tested allergens (gluten, high-molecular-weight glutenin subunits, α-amylase/trypsin inhibitors (ATIs), alcohol-free wheat beer, hydrolyzed wheat proteins (HWPs), rye gluten and secalins), basophil activation in patients was significantly higher than in controls (p = 0.004-p < 0.001). Similarly, significant histamine release was detected in the aBHRA for all test substances, exceeding the cut-off of 10 ng/mL in all tested allergens in 50% of patients. The dependency of tests on sIgE levels against ω5-gliadin differed; in the pBHRA, histamine release to any test substances could only be detected in patients with sIgE against ω5-gliadin ≥ 7.7 kU/L, whereas aBHRA also showed high reactivity in less sensitized patients. In most patients, reactivity to HWPs, ATIs, and rye allergens was observed. Additionally, alcohol-free wheat beer was first described as a promising test substance in ω5-gliadin-positive WALDA. Thus, BAT and aBHRA are valuable tools for the identification of sensitization profiles in WALDA.

Impacts of material characteristics on the anaerobic digestion kinetics and biomethane potential of American bourbon and whiskey stillage.

Stillage of American whiskey (e.g., bourbon) manufacturing is an abundant byproduct that is distinguished from fuel ethanol and malt whisky stillage materials by its highly inconsistent nature due to variability in mash bill composition. The impact of stillage physicochemical characteristics on biomethane production through anaerobic digestion was assessed by characterizing American whiskey stillage samples before batch biochemical methane potential tests of whole stillage. A maximum methane yield of 419 Nml CH4/g VS was obtained under food to microbe ratio (F: M) of 0.5 and organic loading rate (OLR) of 10 g VS/L while digester instability was noted under F: M ratios exceeding 0.5 under batch production. Methane production was significantly influenced by the mash bill composition with lowest methane yields obtained with higher rye content (rye whiskey) and highest methane yields obtained with higher corn content (bourbon or corn whiskey). A multiple linear regression model including C, P, N, and Na was able to accurately describe the methane yield (R2 = 0.93). This study provides valuable insights to aid the design of anaerobic digesters generating renewable natural gas from heterogeneous American whiskey stillage.

The different subtelomeric structure among 1RS arms in wheat-rye 1BL.1RS translocations affecting their meiotic recombination and inducing their structural variation.

BACKGROUND: The 1RS arm of wheat-rye 1BL.1RS translocations contains several subtelomeric tandem repeat families. To study the effect of the difference in the composition of these tandem repeats on the meiotic recombination of 1RS arms can help to enrich the genetic diversity of 1BL.1RS translocation chromosomes. RESULTS: Five wheat-rye 1BL.1RS translocation cultivars/lines were used to build two cross combinations including group 1 (20T401 × Zhou 8425B, 20T401 × Lovrin 10 and 20T401 × Chuannong 17) and group 2 (20T360-2 × Zhou 8425B, 20T360-2 × Lovrin 10 and 20T360-2 × Chuannong 17). Oligonucleotide (oligo) probes Oligo-s120.3, Oligo-TR72, and Oligo-119.2-2 produced the same signal pattern on the 1RS arms in lines 20T401 and 20T360-2, and another signal pattern in the three cultivars Zhou 8425B, Lovrin 10 and Chuannong 17. The Oligo-pSc200 signal disappeared from the 1RS arms of the line 20T401, and the signal intensity of this probe on the 1RS arms of the line 20T360-2 was weaker than that of the three cultivars. The five cultivars/lines had the same signal pattern of the probe Oligo-pSc250. The recombination rate of 1RS arms in group 1 was significantly lower than that in group 2. In the progenies from group 1, unequal meiotic recombination in the subtelomeric pSc119.2 and pSc250 tandem repeat regions, and a 1BL.1RS with inversion of 1RS segment between the pSc200 and the nucleolar organizer region were found. CONCLUSIONS: This study provides a visual tool to detect the meiotic recombination of 1RS arms. The meiotic recombination rate of 1RS arms was affected by the variation of pSc200 tandem repeat, indicating the similar composition of subtelomeric tandem repeats on these arms could increase their recombination rate. These results indicate that the 1RS subtelomeric structure will affect its recombination, and thus the localization of genes on 1RS by means of meiotic recombination might also be affected.

Genome-wide identification, phylogenetic and expression pattern analysis of HSF family genes in the Rye (Secale cereale L.).

BACKGROUND: Heat shock factor (HSF), a typical class of transcription factors in plants, has played an essential role in plant growth and developmental stages, signal transduction, and response to biotic and abiotic stresses. The HSF genes families has been identified and characterized in many species through leveraging whole genome sequencing (WGS). However, the identification and systematic analysis of HSF family genes in Rye is limited. RESULTS: In this study, 31 HSF genes were identified in Rye, which were unevenly distributed on seven chromosomes. Based on the homology of A. thaliana, we analyzed the number of conserved domains and gene structures of ScHSF genes that were classified into seven subfamilies. To better understand the developmental mechanisms of ScHSF family during evolution, we selected one monocotyledon (Arabidopsis thaliana) and five (Triticum aestivum L., Hordeum vulgare L., Oryza sativa L., Zea mays L., and Aegilops tauschii Coss.) specific representative dicotyledons associated with Rye for comparative homology mapping. The results showed that fragment replication events modulated the expansion of the ScHSF genes family. In addition, interactions between ScHSF proteins and promoters containing hormone- and stress-responsive cis-acting elements suggest that the regulation of ScHSF expression was complex. A total of 15 representative genes were targeted from seven subfamilies to characterize their gene expression responses in different tissues, fruit developmental stages, three hormones, and six different abiotic stresses. CONCLUSIONS: This study demonstrated that ScHSF genes, especially ScHSF1 and ScHSF3, played a key role in Rye development and its response to various hormones and abiotic stresses. These results provided new insights into the evolution of HSF genes in Rye, which could help the success of molecular breeding in Rye.

Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement.

BACKGROUND: During domestication and subsequent improvement plants were subjected to intensive positive selection for desirable traits. Identification of selection targets is important with respect to the future targeted broadening of diversity in breeding programmes. Rye (Secale cereale L.) is a cereal that is closely related to wheat, and it is an important crop in Central, Eastern and Northern Europe. The aim of the study was (i) to identify diverse groups of rye accessions based on high-density, genome-wide analysis of genetic diversity within a set of 478 rye accessions, covering a full spectrum of diversity within the genus, from wild accessions to inbred lines used in hybrid breeding, and (ii) to identify selective sweeps in the established groups of cultivated rye germplasm and putative candidate genes targeted by selection. RESULTS: Population structure and genetic diversity analyses based on high-quality SNP (DArTseq) markers revealed the presence of three complexes in the Secale genus: S. sylvestre, S. strictum and S. cereale/vavilovii, a relatively narrow diversity of S. sylvestre, very high diversity of S. strictum, and signatures of strong positive selection in S. vavilovii. Within cultivated ryes we detected the presence of genetic clusters and the influence of improvement status on the clustering. Rye landraces represent a reservoir of variation for breeding, and especially a distinct group of landraces from Turkey should be of special interest as a source of untapped variation. Selective sweep detection in cultivated accessions identified 133 outlier positions within 13 sweep regions and 170 putative candidate genes related, among others, to response to various environmental stimuli (such as pathogens, drought, cold), plant fertility and reproduction (pollen sperm cell differentiation, pollen maturation, pollen tube growth), and plant growth and biomass production. CONCLUSIONS: Our study provides valuable information for efficient management of rye germplasm collections, which can help to ensure proper safeguarding of their genetic potential and provides numerous novel candidate genes targeted by selection in cultivated rye for further functional characterisation and allelic diversity studies.

Cover Crop Amendments and Lettuce Plant Growth Stages Alter Rhizobacterial Properties and Roles in Plant Performance.

Lettuce plants respond differently to cover crop amendments by altering their biomass and nitrogen uptake (Nup) at different plant growth stages. Nonetheless, plant-microbe interactions involved in the alterations are scarcely studied. This study elucidated how the properties of the soil microbial community inhabiting the rhizosphere associated with lettuce (Lactuca sativa L. var. crispa "Red fire") change during plant growth stages. Lettuce plants were cultivated in control soil and soil with rye, hairy vetch (HV), and rye plus HV (rye + HV) cover crop amendments. Rhizosphere soil samples were collected at the mid-growth and mature stages of plant development. DNA was extracted from the soil, and the 16S rRNA region was amplified using polymerase chain reaction to analyze bacterial genes and community structures and functions. Cover crop amendments and plant growth stages increased or decreased the relative abundances of bacterial taxa at the genus level. Plant maturity decreased 16S rRNA gene expression and the number of bacterial operational taxonomic units in all treatments. The unique, core, and shared taxa with low relative abundances may be associated with improved lettuce Nup and lettuce shoot and root biomass at each plant growth stage under different cover crop amendments based on multivariate analysis between plant indicators and bacterial genera groups. This study revealed the importance of bacterial groups with low relative abundance in plant-microbe interactions; such bacteria may promote the cover crop application for high lettuce productivity.

Characteristic of the gene candidate SecARS encoding alkylresorcinol synthase in Secale.

BACKGROUND: Alkylresorcinols (ARs) are compounds belonging to the class of phenolic lipids. A rich source of ARs are cereal grains such as rye, wheat, triticale or barley. ARs found in plants are characterized by a variety of biological properties such as antimicrobial, antifungal and cytotoxic activity. Moreover, they are proven to have a positive influence on human health. Here, we aimed to find and characterize the gene with ARs synthase activity in the species Secale cereale. METHODS AND RESULTS: Using BAC library screening, two BAC clones containing the gene candidate were isolated and sequenced. Bioinformatic analyses of the resulting contigs were used to examine the structure and other features of the gene, including promoter, intron, 3'UTR and 5'UTR. Mapping using the FISH procedure located the gene on the 4R chromosome. Comparative analysis showed that the gene is highly similar to sequences coding for type III polyketide synthase. The level of gene expression in various parts of the plant was investigated, and the biochemical function of the gene was confirmed by heterologous expression in yeast. CONCLUSIONS: The conducted analyses contributed to a better understanding of the processes related to ARs synthesis. Although the research concerned the rye model, the knowledge gained may help in understanding the genetic basis of ARs biosynthesis in other species of the Poaceae family as well.

The relation of whole grain surrogate estimates and food definition to total whole grain intake in the Finnish adult population.

OBJECTIVES: Challenges in estimating total whole grain intake have led to the use of surrogate estimates, of which accuracy has not been assessed. We examined the suitability of five potential surrogates (dietary fiber; bread; rye bread; rye, oat and barley combined; rye) and a whole grain food definition to measure total whole grain intake in the Finnish adult population. METHODS: Our data comprised 5094 Finnish adults participating in the national FinHealth 2017 Study. Dietary intake was assessed by a validated FFQ. Food and nutrient intakes, including total whole grain, were calculated utilizing the Finnish Food Composition Database. The Healthgrain Forum whole grain food definition was applied to examine definition-based whole grain intake. Spearman correlations and quintile cross-classifications were calculated. RESULTS: Definition-based whole grain intake and consumption of rye, oat and barley combined had consistently the strongest correspondence with total whole grain intake. Rye and rye bread consumption also corresponded well with total whole grain intake. The correspondences of dietary fiber and bread with total whole grain were lower and more affected by the exclusion of energy under-reporters. Furthermore, their correlations with total whole grain intake varied the most between population subgroups. CONCLUSIONS: Rye-based estimates, especially rye, oat and barley combined, and definition-based whole grain intake appeared suitable surrogate estimates of total whole grain intake for epidemiological research of Finnish adults. The variation between surrogate estimates in their correspondence with total whole grain intake demonstrated the need for further evaluation of their accuracy in different populations and regarding specific health outcomes.

Sustainability of cover cropping practice with changing climate in Illinois.

Climate change could adversely impact the best management practices (BMPs) designed to build a sustainable agro-ecological environment. Cover cropping is a conservation practice capable of reducing nitrate-nitrogen (NO3-N) loadings by consuming water and nitrate from the soil. The objective of this study was to investigate how climate change would impact the proven water quality benefits of cereal rye as a winter cover crop (CC) over the climate divisions of Illinois using the DSSAT model. Moreover, this study explores the sustainability of the CC with the changing climate conditions by using five regional climate models (RCMs) projections of two warming scenarios-rcp45 (a medium emission scenario - radiative forcing of 4.5 W/m2) and rcp85 (a high emission scenario - radiative forcing of 8.5 W/m2)). The CC impact simulated in the warming scenarios for the near-term (2021-2040) and the far-term future (2041-2060) were compared with the baseline scenario (2001-2020). Our results conclude that the climate change may negatively impact [average of CC and no CC (NCC)] maize yield (-6.6%) while positively affecting soybean yield (17.6%) and CC biomass (73.0%) by the mid-century. Increased mineralization caused by rising temperature could increase the nitrate loss via tile flow (NLoss) and nitrate leached (NLeached) up to 26.3% and 7.6% on average by the mid-century in Illinois. Increasing CC biomass could reduce the NLoss more considerably in all the scenarios compared to the baselines. Nevertheless, the NLoss level in the CC treatment can increase from the near-term to far-term future and could get closer to the baseline levels in the NCC treatment. These results suggest that CC alone may not address nitrate loss goals via subsurface drainage (caused by increasing N mineralization) in future. Therefore, more robust and cost-effective BMPs are needed to aid the CC benefits in preventing nutrient loss from the agricultural fields.

Rye Dietary Fiber Components upon the Influence of Fermentation Inoculated with Probiotic Microorganisms.

Rye flour is used as the main ingredient of sourdough bread, which has technological and gastronomic benefits and increased nutritional value. The transformations observed during fermentation and baking may enable the conversion or degradation of rye dietary fiber carbohydrates built mainly of arabinoxylans, fructans, and ß-glucans. This study aimed to determine the dynamics of the changes in the contents of complex carbohydrates in sourdoughs inoculated with potential probiotic microorganisms as well as the polysaccharide composition of the resulting bread. Sourdoughs were inoculated with the potential probiotic microorganisms Saccharomyces boulardii, Lactiplantibacillus plantarum, Lacticaseibacillus rhamnosus, and Bacillus coagulans, and spontaneous fermentation was performed as a control. Samples of the sourdoughs after 24 and 48 h of fermentation and of bread obtained with these sourdoughs were analyzed for the content of individual dietary fiber components. The present study demonstrated that the treatments applied contributed to an increased total content of arabinoxylans in the breads, and the inoculation of the sourdoughs with the potential probiotic strains improved their solubility in water. The use of the S.boulardii strain may seem prospective as it allowed for the greatest reduction in fructans in the rye bread. Rye sourdough bread is an attractive source of dietary fiber and can be modified for different nutritional needs.

Production and Characterization of a Novel Symbiotic Plant-based Beverage Rich in Antioxidant Phenolic: Mung Bean and Rye Sprouts.

There is an increasing demand for non-dairy probiotic food due to the constraints associated with dairy probiotics. In this study, a co-culture synbiotic beverage was prepared using a mixture of mung bean and rye sprouts inoculated with Lactobacillus plantarum (B-28) and Lactobacillus casei (B-29), along with inulin and oligofructose as prebiotics. The effects of prebiotic addition and starter culture on the survival of probiotics during cold storage and simulated gastric conditions were examined. Additionally, titratable acidity, pH, phenolic content, antioxidant activity, and sensory characteristics were evaluated over a 28-day period. The resulting product demonstrated good survival for L. casei (107 CFU.ml-1) and L. plantarum (106 CFU.ml-1) after 4 weeks under refrigeration with no significant changes in quality. The samples exhibited significantly high total phenolic content (TPC), ranging from 19.18 to 25.75 mg GAE/100 mL, which L. casei-containing drinks exhibited the highest TPC activity (p < 0.05). All treatments showed a significant reduction in probiotic survival during gastrointestinal digestion in the laboratory conditions (p < 0.05), although more than 50% survival was observed for all strains. The addition of prebiotics to the beverages led to a significant decrease in phenolic content (p < 0.05), but improved sensory scores. The highest turbidity was observed in the sample containing both probiotics and inulin on the 28th day at 38.1 (NTU). In general, the synergistic effect of probiotics was more pronounced when used together with both prebiotics in the beverages compared to their individual use. The results suggest that the production of this beverage could serve as a nutritious alternative to lactose-sensitive dairy beverages and contribute to the development of future probiotic food products.

Correlation between leaf epicuticular wax composition and structure, physio-biochemical traits and drought resistance in glaucous and non-glaucous near-isogenic lines of rye.

The objective of this research was to investigate the differences between glaucous and non-glaucous near-isogenic lines (NILs) of winter rye (Secale cereale L.) in terms of epicuticular wax layer properties (weight, composition, and crystal morphology), selected physiological and biochemical responses, yield components, above-ground biomass, and plant height under soil drought stress. An important aspect of this analysis was to examine the correlation between the above characteristics. Two different NIL pairs were tested, each consisting of a typical glaucous line and a non-glaucous line with a recessive mutation. The drought experiment was conducted twice (2015-2016). Our study showed that wax accumulation during drought was not correlated with higher leaf hydration and glaucousness. Environmental factors had a large impact on the response of the lines to drought in individual years, both in terms of physiological and biochemical reactions, and the composition of epicuticular leaf wax. The analysed pairs displayed significantly different responses to drought. Demonstration of the correlation between the components of rye leaf wax and the physiological and biochemical parameters of rye NILs is a significant achievement of this work. Interestingly, the study showed a correlation between the wax components and the content of photosynthetic pigments and tocopherols, whose biosynthesis, similarly to the biosynthesis of wax precursors, is mainly located in chloroplasts. This suggests a relationship between wax biosynthesis and plant response to various environmental conditions and drought stress.

Variations of subtelomeric tandem repeats and rDNA on chromosome 1RS arms in the genus Secale and 1BL.1RS translocations.

BACKGROUND: The wheat-rye 1BL.1RS translocations have played an important role in common wheat breeding programs. Subtelomeric tandem repeats have been often used to investigate polymorphisms of 1RS arms, but further research about their organizations on the 1RS chromosome is needed. RESULTS: 162 1RS arms from a wild rye species (Secale strictum) and six cultivated rye accessions (Secale cereale L.) (81 plants), 102 1BL.1RS and one 1AL.1RS translocations were investigated using oligo probes Oligo-TaiI, Oligo-pSc119.2-1, Oligo-pTa71A-2, Oligo-pSc200 and Oligo-pSc250, which were derived from tandem repeats TaiI, pSc119.2, pTa71, pSc200 and pSc250, respectively. The variations of 1RS arms were revealed by signal intensity of probes Oligo-pSc119.2-1, Oligo-pTa71A-2, Oligo-pSc200 and Oligo-pSc250. Proliferation of rDNA sequences on the 1RS chromosomes was observed. According to the presence of probe signals, 34, 127 and 144 of the 162 1RS arms contained TaiI, pSc200 and pSc250, respectively, and all of them contained pSc119.2 and pTa71. Most of the 1RS arms in rye contained three kinds of subtelomeric tandem repeats, the combination of pSc119.2, pSc200 and pSc250 was most common, and only eight of them contained TaiI, pSc119.2, pSc200 and pSc250. All of the 1RS arms in 1BL.1RS and 1AL.1RS translocations contained pSc119.2, pTa71, pSc200 and pSc250, but the presence of the TaiI family was not observed. CONCLUSION: New organizations of subtelomeric tandem repeats on 1RS were found, and they reflected new genetic variations of 1RS arms. These 1RS arms might contain abundant allelic diversity for agricultural traits. The narrow genetic base of 1RS arms in 1BL.1RS and 1AL.1RS translocations currently used in agriculture is seriously restricting their use in wheat breeding programs. This research has found new 1RS sources for the future restructuring of 1BL.1RS translocations. The allelic variations of these 1RS arms should be studied more intensely as they may enrich the genetic diversity of 1BL.1RS translocations.