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.

The Effect of Technological Conditions on ABE Fermentation and Butanol Production of Rye Straw and the Composition of Volatile Compounds.

The objective of this study was to evaluate the effect of pretreatment and different technological conditions on the course of ABE fermentation of rye straw (RS) and the composition of volatile compounds in the distillates obtained. The highest concentration of ABE and butanol was obtained from the fermentation of pretreated rye straw by alkaline hydrolysis followed by detoxification and enzymatic hydrolysis. After 72 h of fermentation, the maximum butanol concentration, productivity, and yield from RS were 16.11 g/L, 0.224 g/L/h, and 0.402 g/g, respectively. Three different methods to produce butanol were tested: the two-step process (SHF), the simultaneous process (SSF), and simultaneous saccharification with ABE fermentation (consolidation SHF/SSF). The SHF/SSF process observed that ABE concentration (21.28 g/L) was higher than in the SSF (20.03 g/L) and lower compared with the SHF (22.21 g/L). The effect of the detoxification process and various ABE fermentation technologies on the composition of volatile compounds formed during fermentation and distillation were analyzed.

Human Oral Phase Coupled with In Vitro Dynamic Gastrointestinal Digestion for Assessment of Plant Sterol Bioaccessibility from Wholemeal Rye Bread.

A dynamic gastrointestinal digestion system (simgi) after a human oral phase was used, for the first time, to assess the bioaccessibility of plant sterols (PS) from wholemeal rye bread (74.8 ± 2.2 mg of PS/100 g d.m.) and PS-enriched wholemeal rye bread (PS-WRB) (1.6 ± 0.04 g of PS/100 g of fresh bread). The use of these solid food matrices requires a novel adaptation of the gastric phase of the system. The PS identified in the breads are campesterol, campestanol, stigmasterol, ß-sitosterol, sitostanol, Δ5-avenasterol, Δ5,24-stigmastadienol, Δ7-stigmastenol, and Δ7-avenasterol. The bioaccessibility of the total PS, only quantifiable in PS-WRB, is 19.9%, with Δ7-avenasterol being the most bioaccessible and Δ5-avenasterol being the least (p < 0.05). As shown in this study, PS-WRB can be considered to be a good choice to include in the daily diet. Furthermore, although the use of dynamic digestion methods for evaluating bioaccessibility implies high costs and technical complexity, their application means a closer approximation to in vivo scenarios.

Cadmium Maximum Levels and Residue Situation in the German Wheat and Rye Harvest from 1975 to 2021.

For a better understanding of cadmium (Cd) accumulation over long time periods in cereals, Cd levels of the German wheat and rye harvest from 1975 to 2021 were analyzed. Overall, wheat had higher grain Cd concentrations than rye. Comparing mean values from different time periods showed that Cd levels in winter rye have stabilized, while Cd concentrations in winter wheat have decreased. Furthermore, Cd concentrations in almost all samples were below the newly introduced European Commission limits specifying the maximum permissible contaminant levels in foodstuffs (Cd in grains: rye 50 µg/kg FW; wheat 100 µg/kg FW). However, it is important to note that Cd is still ubiquitous in the German wheat and rye harvest. Although there has been a significant reduction in emissions and imissions for around 30 years, the extraordinarily long biological half-life and carcinogenicity of Cd still make it a relevant substance to food safety and human health.

Urinary alkylresorcinol metabolites, biomarkers of whole grain wheat and rye intake, are beneficially associated with liver fat and other fat measures.

Aims: Epidemiological studies that use dietary biomarkers to investigate the association between whole grain intake and the risk of obesity are sparse. We assessed the association between urinary alkylresorcinol metabolites including 3-(3,5-dihydroxyphenyl)-1-propanoic acid (DHPPA) and 3,5-dihydroxybenzoic acid (DHBA), biomarkers of whole grain wheat and rye intake, and body fat measures. Methods: We measured urinary excretion of DHPPA and DHBA, body weight, height, and circumferences of the waist and hip at the baseline and again after 1-year in a representative sample of 306 community-dwelling adults in Huoshan, China. We also measured liver fat accumulation [indicated by the controlled attenuation parameter (CAP)] and other body composition after 1 year. Multivariate-adjusted linear models and linear mixed-effects models were used to analyze single measurement and repeated measurements, respectively. Results: Each 1 µg g-1 creatinine increase in urinary DHPPA levels was associated with 0.21%, 0.23%, 3.64%, and 4.80% decrease in body weight, body mass index (BMI), body fat mass (BFM) and visceral fat level (VFL), respectively (all P < 0.05). Higher DHBA levels were inversely associated with CAP (percentage difference per 1 µg g-1 creatinine increment: -1.98%, P < 0.05). Higher total urinary alkylresorcinol metabolite (DHPPA + DHBA) levels were associated with lower body weight, BMI, BFM, VFL, and CAP, with the percentage differences per 1 µg g-1 creatinine increment of -0.27%, -0.27%, -3.79%, -5.12%, and -2.24%, respectively (all P < 0.05). Conclusions: Our findings suggest that the intake of whole grain wheat and rye, reflected by urinary DHPPA and DHBA, is favorably associated with liver fat and other fat measures.

Lipolysis and Sterol Stability and Bioaccessibility of Wholemeal Rye Bread Enriched with Plant Sterols Subjected to Adult and Elderly Digestion Conditions.

This study evaluated the impact of different digestion conditions (adult and senior) on lipolysis and bioaccessibility of plant sterols (PS) and phytosterol oxidation products (POPs) in PS-enriched wholemeal rye bread. Under adult digestion conditions, the addition of gastric lipase (GL) reduced lipolysis products (by 6.1% for free fatty acids and 11.7% for monoacylglycerols) and the bioaccessibility of PS by 6.7%, compared to the control. In digestion with both GL and cholesterol esterase (CE), these reductions were 12.9, 20.1, and 11.3%, respectively. Both modifications (GL and GL + CE) increased the bioaccessibility of POPs by 4.5-4.0%. When simulating the elderly digestion, the modified gastric and intestinal phases did not alter PS bioaccessibility but decreased POPs bioaccessibility by 21.8% compared to control, along with reduced lipolysis. Incorporating GL and CE thus approached physiological conditions and influenced lipid digestion. Elderly simulated digestion conditions resulted in a positive outcome by maintaining PS bioaccessibility while reducing potentially harmful POPs.

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.

Role of particle size in modulating starch digestibility and textural properties in a rye bread model system.

In cereal products, the use of flour containing clusters of intact cells has been indicated as a potential strategy to decrease starch digestion. Rye possesses more uniform and thicker cell walls than wheat but its protective effect against starch digestion has not been elucidated. In this study, rye flours with three different particle sizes, large (LF) (∼1700 µm), medium (MF) (∼1200 µm), and small (SF) (∼350 µm), were used to produce model bread. The textural properties of these breads were analysed using Textural Profile Analysis (TPA). The starch digestibility of both the flour and the bread was measured using Englyst's method, while the presence of intact cell clusters was examined using Confocal Laser Scanning Microscopy (CLSM). Additionally, the disintegration of bread digesta during simulated digestion was assessed through image analysis. CLSM micrographs revealed that bread made with MF and LF retained clusters of intact cells after processing, whereas bread made with SF showed damaged cell walls. Starch digestibility in LF and MF was lower (p ≤ 0.05) than that in SF. Bread produced with MF and LF exhibited the least (p ≤ 0.05) cohesive and resilient texture, disintegrated more during digestion, and exhibited higher starch digestibility (p ≤ 0.05) than bread made with SF. These results highlight the central role of bread texture on in vitro starch digestibility.

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.

Diagnostic Accuracy of Specific IgE Against Wheat and Rye in Flour-Induced Occupational Asthma.

BACKGROUND: Assessment of IgE-mediated sensitization to flour allergens is widely used to investigate flour-induced occupational asthma. The diagnostic efficiency of detecting specific IgE antibodies (sIgEs) against wheat and rye flour, however, has not been thoroughly compared with other diagnostic procedures. OBJECTIVE: We sought to evaluate the diagnostic accuracy of sIgE against wheat and rye compared with specific inhalation challenge (SIC) with flour as the reference standard. METHODS: This retrospective multicenter study included 264 subjects who completed an SIC with flour in eight tertiary centers, of whom 205 subjects showed a positive SIC result. RESULTS: Compared with SIC, sIgE levels of 0.35 kUA/L or greater against wheat and rye provided similar sensitivities (84% to 85%, respectively), specificities (71% to 78%), positive predictive values (91% to 93%), and negative predictive values (56% to 61%). Increasing the threshold sIgE value to 5.10 kUA/L for wheat and to 6.20 kUA/L for rye provided a specificity of 95% or greater and further enhanced the positive predictive value to 98%. Among subjects with a positive SIC, those who failed to demonstrate sIgE against wheat and rye (n = 26) had significantly lower total serum IgE level and blood and sputum eosinophil counts and a lesser increase in postchallenge FeNO compared with subjects with a detectable sIgE. CONCLUSION: High levels of sIgE against wheat and/or rye flour strongly support a diagnosis of flour-induced occupational asthma without the need to perform an SIC. The absence of detectable sIgE against wheat and rye in subjects with a positive SIC seems to be associated with lower levels of TH2 biomarkers.

Assessment of induced allelopathy in crop-weed co-culture with rye-pigweed model.

This study evaluates induced allelopathy in a rye-pigweed model driven by rye's (Secale cereale L.) allelopathic potential as a cover crop and pigweed's (Amaranthus retroflexus L.) notoriety as a weed. The response of rye towards pigweed's presence in terms of benzoxazinoids (BXs) provides valuable insight into induced allelopathy for crop improvement. In the 2 week plant stage, pigweed experiences a significant reduction in growth in rye's presence, implying allelopathic effects. Rye exhibits increased seedling length and BXs upsurge in response to pigweed presence. These trends persist in the 4 week plant stage, emphasizing robust allelopathic effects and the importance of different co-culture arrangements. Germination experiments show rye's ability to germinate in the presence of pigweed, while pigweed exhibits reduced germination with rye. High-performance liquid chromatography with diode-array detection (HPLC-DAD) analysis identifies allelopathic compounds (BXs), 2,4-dihydroxy-1,4-benzoxazin-3-one (DIBOA) and 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) in rye. Rye significantly increases BX production in response to pigweed, age-dependently. Furthermore, pigweed plants are screened for possible BX uptake from the rhizosphere. Results suggest that allelopathy in rye-pigweed co-cultures is influenced by seed timing, and age-dependent dynamics of plants' allelopathic compounds, providing a foundation for further investigations into chemical and ecological processes in crop-weed interactions.

Major chromosome rearrangements in intergeneric wheat × rye hybrids in compatible and incompatible crosses detected by GBS read coverage analysis.

The presence of incompatibility alleles in primary amphidiploids constitutes a reproductive barrier in newly synthesized wheat-rye hybrids. To overcome this barrier, the genome stabilization process includes large-scale chromosome rearrangements. In incompatible crosses resulting in fertile amphidiploids, the elimination of one of the incompatible alleles Eml-A1 or Eml-R1b can occur already in the somatic tissue of the wheat × rye hybrid embryo. We observed that the interaction of incompatible loci Eml-A1 of wheat and Eml-R1b of rye after overcoming embryo lethality leads to hybrid sterility in primary triticale. During subsequent seed reproductions (R1, R2 or R3) most of the chromosomes of A, B, D and R subgenomes undergo rearrangement or eliminations to increase the fertility of the amphidiploid by natural selection. Genotyping-by-sequencing (GBS) coverage analysis showed that improved fertility is associated with the elimination of entire and partial chromosomes carrying factors that either cause the disruption of plant development in hybrid plants or lead to the restoration of the euploid number of chromosomes (2n = 56) in the absence of one of the incompatible alleles. Highly fertile offspring obtained in compatible and incompatible crosses can be successfully adapted for the production of triticale pre-breeding stocks.

The freeze-thaw cycle exacerbates the ecotoxicity of polystyrene nanoplastics to Secale cereale L. seedlings.

In the context of global climate change, recurrent freeze-thaw cycles (FTC) and concurrent exposure to polystyrene nanoplastics (PSNPs) directly impact crop growth and indirectly affect resilience to abiotic stress. In January 2023, experiments at the Environmental Biology Laboratory, Jilin University, Changchun, China, exposed rye seedlings to 100 nm PSNPs at concentrations of 0, 10, 50, and 100 mg/L for seven days, followed by three FTC. Scanning electron microscopy (SEM) demonstrated that PSNPs migrated from the roots to the leaves, with FTC significantly exacerbating their accumulation within plant tissues. Transmission electron microscopy (TEM) observations showed that FTC disrupted normal cell division, and combined stress from NPs damaged plant organs, particularly chloroplasts, thereby substantially inhibiting photosynthesis. FTC delayed plant phenological stages. Under combined stress, malondialdehyde (MDA) accumulation in plant tissues increased by 15.6%, while hydrogen peroxide (H2O2) content decreased. Simultaneously, the activities of peroxidase (POD) and catalase (CAT) increased by 34.2% and 38.6%, respectively. Molecular docking unveiled that PSNPs could bind to the active center of POD/CAT through hydrogen bonding or hydrophobic interactions. The Integrated Biomarker Response (IBR) index highlighted FTC as a crucial determinant for pronounced effects. Moreover, an apparent dose-dependent effect was observed, with antioxidant enzyme activities in rye seedlings induced by low pollutant concentrations and inhibited by high concentrations. These results indicate that FTC and PSNPs can disrupt plant membrane systems and cause severe oxidative damage. Overall, this study provides compelling scientific evidence of the risks associated with NPs exposure in plants subjected to abiotic stress.

All-in-one 2LabsToGo system for analysis of ergot alkaloids in whole rye.

Ergot alkaloids, naturally occurring mycotoxins of Claviceps fungi, pose health risks. This necessitates accurate analysis methods to ensure food safety. This study explored the open-source miniaturized all-in-one 2LabsToGo system to analyze ergot alkaloids in whole rye samples. It is suited for sustainable atline analysis as it combines all planar chromatography tasks, allowing low-cost quality control in milling plants. The LOD and LOQ of ergocristine were determined to be 0.4 and 1.2 ng/zone, respectively. Detectability of ergot alkaloids was proven to be below the current maximum limit of 500 µg/kg for rye milling products. The repeatability (%RSD) was 4.1 % and the coefficient of determination of the analytical response (R2) was 0.9918 for ergocristine. The mean recovery rate of ergot alkaloids in spiked whole rye grain was close to 100 %. Results of screening whole rye for ergot alkaloids were successfully verified by comparison with those obtained by conventional status quo HPTLC instrumentation.

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.

Biogenic amines as an indicator of rye leaven quality during production and storage.

Rye leaven, the basic constituent of sour rye soup ('zurek' or white borsch), was obtained through three methods of initiating lacto-fermentation of rye flour. Optimal concentrations of NaCl (1.5%) and garlic (0.5%) were selected by utilizing the response surface methodology. During the production and storage of leaven at 10 °C and 20 °C, the secalin proteins of rye flour degraded significantly and the concentration of free amino acids increased, making the rye leaven an environment potentially conducive to the formation of biogenic amines. Putrescine (max. conc: 116.7 mg kg-1) and tyramine (max. conc: 63.4 mg kg-1) were the amines that occurred in the largest amounts in the leavens. The final concentration of histamine (after 150 days of storage) did not exceed 22 mg kg-1. Regardless of the method of initiation of fermentation, the products that contained fewer biogenic amines better retained their sensory characteristics (r ≤ -0.89, p < 0.05) and had a higher number of lactic acid bacteria (r ≤ -0.66, p < 0.05).

3D Porous Edible Scaffolds from Rye Secalin for Cell-Based Pork Fat Tissue Culturing.

Cellular agriculture holds hope for a sustainable alternative to conventional meat, yet multiple technical challenges remain. These include the large-scale production of edible scaffolds and culturing methods for fat tissues, which are key to meat texture, flavor, and nutritional values. Herein. we disclose our method in the facile fabrication of sponge-like plant protein scaffolds by applying commercial sugar cubes as highly permeable templates. The prepared secalin scaffolds feature a high porosity of 85-90%, fully interconnected pores, and high water stability. The mechanical properties of scaffolds could be tuned by varying sugar-to-protein weight ratio and post-water annealing treatment. Moreover, murine preadipocytes (3T3-L1) and porcine adipose-derived stem cells (ADSCs) readily infiltrate, adhere, proliferate, and differentiate on the secalin scaffolds to develop a fat tissue morphology. A cultured fat tissue was produced by culturing porcine ADSCs for 12 days, which remarkably resembles conventional porcine subcutaneous adipose tissue in appearance, texture, flavor, and fatty acid profiles. The research demonstrates the great potential of sponge-like secalin scaffolds for cultured fat tissue production.

Identification of a Rye Spring Mutant Derived from a Winter Rye Variety by High-Altitude Environment Screening Using RNA Sequencing Technology.

Wintergrazer-70 and Ganyin No1 are high-yield forage varieties suitable for cultivation in high-altitude areas of Tibet (4300 m above sea level). Ganyin No1 was developed from Wintergrazer-70, with the latter serving as its parent variety. Ganyin No1 was identified as a spring variety, and subsequent RNA sequencing was conducted. RNA sequencing analysis identified 4 differentially expressed genes related to vernalization and 28 genes related to photoperiod regulation. The Sc7296g5-i1G3 gene is related to the flowering inhibition of rye, which may be related to the phenotypic difference in the Ganyin No1 variety in winter and spring. This finding provides valuable insights for future research on Ganyin No1, especially in addressing feed shortages in Tibet during winter and spring.

Identification of quantitative trait loci associated with leaf rust resistance in rye by precision mapping.

BACKGROUND: Leaf rust (LR) is among the most destructive fungal diseases of rye (Secale cereale L.). Despite intensive research using various analytical and methodological approaches, such as quantitative trait locus (QTL) mapping, candidate gene expression analysis, and transcriptome sequencing, the genetic basis of the rye immune response to LR remains unclear. RESULTS: A genome-wide association study was employed to detect QTLs controlling the immune response to LR of rye. A mapping population, G38A, was constructed by crossing two inbred lines: 723 (susceptible to LR) and JKI-NIL-Pr3 (a donor of the LR resistance gene Pr3). For genotyping, SNP-DArT and silico-DArT markers were used. Resistance phenotyping was conducted by visual assessment of the infection severity in detached leaf segments inoculated with two isolates of Puccinia recondita f. sp. secalis, namely, 60/17/2.1 (isolate S) in the main experiment and 86/n/2.1_5x (isolate N) in the validation experiment, at 10 and 17 days post-infection (dpi), respectively. In total, 42,773 SNP-DArT and 105,866 silico-DArT markers were included in the main analysis including isolate S, of which 129 and 140 SNP-DArTs and 767 and 776 silico-DArTs were significantly associated (p ≤ 0.001; - log10(p) ≥ 3.0) with the immune response to LR at 10 and 17 dpi, respectively. Most significant markers were mapped to chromosome 1R. The number of common markers from both systems and at both time points occupying common chromosomal positions was 37, of which 21 were positioned in genes, comprising 18 markers located in exons and three in introns. This gene pool included genes encoding proteins with a known function in response to LR (e.g., a NBS-LRR disease resistance protein-like protein and carboxyl-terminal peptidase). CONCLUSION: This study has expanded and supplemented existing knowledge of the genetic basis of rye resistance to LR by (1) detecting two QTLs associated with the LR immune response of rye, of which one located on the long arm of chromosome 1R is newly detected, (2) assigning hundreds of markers significantly associated with the immune response to LR to genes in the 'Lo7' genome, and (3) predicting the potential translational effects of polymorphisms of SNP-DArT markers located within protein-coding genes.

Genotype-Specific Expression of Selected Candidate Genes Conferring Resistance to Leaf Rust of Rye (Secale cereale L.).

Leaf rust (LR) caused by Puccinia recondita f. sp. secalis (Prs) is a highly destructive disease in rye. However, the genetic mechanisms underlying the rye immune response to this disease remain relatively uncharacterised. In this study, we analysed the expression of four genes in 12 rye inbred lines inoculated with Prs at 20 and 36 h post-treatment (hpt): DXS (1-deoxy-D-xylulose 5-phosphate synthase), Glu (ß-1,3-glucanase), GT (UDP-glycosyltransferase) and PR-1 (pathogenesis-related protein 1). The RT-qPCR analysis revealed the upregulated expression of the four genes in response to Prs in all inbred lines and at both time-points. The gene expression data were supported by microscopic and macroscopic examinations, which revealed that eight lines were susceptible to LR and four lines were highly resistant to LR. A relationship between the infection profiles and the expression of the analysed genes was observed: in the resistant lines, the expression level fold changes were usually higher at 20 hpt than at 36 hpt, while the opposite trend was observed in the susceptible lines. The study results indicate that DXS, Glu, GT and PR-1 may encode proteins crucial for the rye defence response to the LR pathogen.