Rye: genetic ancestry inference at biobank scale.

Biobank projects are generating genomic data for many thousands of individuals. Computational methods are needed to handle these massive data sets, including genetic ancestry (GA) inference tools. Current methods for GA inference do not scale to biobank-size genomic datasets. We present Rye-a new algorithm for GA inference at biobank scale. We compared the accuracy and runtime performance of Rye to the widely used RFMix, ADMIXTURE and iAdmix programs and applied it to a dataset of 488221 genome-wide variant samples from the UK Biobank. Rye infers GA based on principal component analysis of genomic variant samples from ancestral reference populations and query individuals. The algorithm's accuracy is powered by Metropolis-Hastings optimization and its speed is provided by non-negative least squares regression. Rye produces highly accurate GA estimates for three-way admixed populations-African, European and Native American-compared to RFMix and ADMIXTURE (${R}^2 = \ 0.998 - 1.00$), and shows 50× runtime improvement compared to ADMIXTURE on the UK Biobank dataset. Rye analysis of UK Biobank samples demonstrates how it can be used to infer GA at both continental and subcontinental levels. We discuss user consideration and options for the use of Rye; the program and its documentation are distributed on the GitHub repository: https://github.com/healthdisparities/rye.

Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat.

Introgressions of chromosomal segments from related species into wheat are important sources of resistance against fungal diseases. The durability and effectiveness of introgressed resistance genes upon agricultural deployment is highly variable-a phenomenon that remains poorly understood, as the corresponding fungal avirulence genes are largely unknown. Until its breakdown, the Pm17 resistance gene introgressed from rye to wheat provided broad resistance against powdery mildew (Blumeria graminis). Here, we used quantitative trait locus (QTL) mapping to identify the corresponding wheat mildew avirulence effector AvrPm17. It is encoded by two paralogous genes that exhibit signatures of reoccurring gene conversion events and are members of a mildew sublineage specific effector cluster. Extensive haplovariant mining in wheat mildew and related sublineages identified several ancient virulent AvrPm17 variants that were present as standing genetic variation in wheat powdery mildew prior to the Pm17 introgression, thereby paving the way for the rapid breakdown of the Pm17 resistance. QTL mapping in mildew identified a second genetic component likely corresponding to an additional resistance gene present on the 1AL.1RS translocation carrying Pm17. This gene remained previously undetected due to suppressed recombination within the introgressed rye chromosomal segment. We conclude that the initial effectiveness of 1AL.1RS was based on simultaneous introgression of two genetically linked resistance genes. Our results demonstrate the relevance of pathogen-based genetic approaches to disentangling complex resistance loci in wheat. We propose that identification and monitoring of avirulence gene diversity in pathogen populations become an integral part of introgression breeding to ensure effective and durable resistance 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 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.

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.

Leaf rust (Puccinia recondita f. sp. secalis) triggers substantial changes in rye (Secale cereale L.) at the transcriptome and metabolome levels.

BACKGROUND: Rye (Secale cereale L.) is a cereal crop highly tolerant to environmental stresses, including abiotic and biotic stresses (e.g., fungal diseases). Among these fungal diseases, leaf rust (LR) is a major threat to rye production. Despite extensive research, the genetic basis of the rye immune response to LR remains unclear. RESULTS: An RNA-seq analysis was conducted to examine the immune response of three unrelated rye inbred lines (D33, D39, and L318) infected with compatible and incompatible Puccinia recondita f. sp. secalis (Prs) isolates. In total, 877 unique differentially expressed genes (DEGs) were identified at 20 and 36 h post-treatment (hpt). Most of the DEGs were up-regulated. Two lines (D39 and L318) had more up-regulated genes than down-regulated genes, whereas the opposite trend was observed for line D33. The functional classification of the DEGs helped identify the largest gene groups regulated by LR. Notably, these groups included several DEGs encoding cytochrome P450, receptor-like kinases, methylesterases, pathogenesis-related protein-1, xyloglucan endotransglucosylases/hydrolases, and peroxidases. The metabolomic response was highly conserved among the genotypes, with line D33 displaying the most genotype-specific changes in secondary metabolites. The effect of pathogen compatibility on metabolomic changes was less than the effects of the time-points and genotypes. Accordingly, the secondary metabolome of rye is altered by the recognition of the pathogen rather than by a successful infection. The results of the enrichment analysis of the DEGs and differentially accumulated metabolites (DAMs) reflected the involvement of phenylpropanoid and diterpenoid biosynthesis as well as thiamine metabolism in the rye immune response. CONCLUSION: Our work provides novel insights into the genetic and metabolic responses of rye to LR. Numerous immune response-related DEGs and DAMs were identified, thereby clarifying the mechanisms underlying the rye response to compatible and incompatible Prs isolates during the early stages of LR development. The integration of transcriptomic and metabolomic analyses elucidated the contributions of phenylpropanoid biosynthesis and flavonoid pathways to the rye immune response to Prs. This combined analysis of omics data provides valuable insights relevant for future research conducted to enhance rye resistance to LR.

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

BACKGROUND: The GRAS transcription factor family plays a crucial role in various biological processes in different plants, such as tissue development, fruit maturation, and environmental stress. However, the GRAS family in rye has not been systematically analyzed yet. RESULTS: In this study, 67 GRAS genes in S. cereale were identified and named based on the chromosomal location. The gene structures, conserved motifs, cis-acting elements, gene replications, and expression patterns were further analyzed. These 67 ScGRAS members are divided into 13 subfamilies. All members include the LHR I, VHIID, LHR II, PFYRE, and SAW domains, and some nonpolar hydrophobic amino acid residues may undergo cross-substitution in the VHIID region. Interested, tandem duplications may have a more important contribution, which distinguishes them from other monocotyledonous plants. To further investigate the evolutionary relationship of the GRAS family, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. The response characteristics of 19 ScGRAS members from different subfamilies to different tissues, grains at filling stages, and different abiotic stresses of rye were systematically analyzed. Paclobutrazol, a triazole-based plant growth regulator, controls plant tissue and grain development by inhibiting gibberellic acid (GA) biosynthesis through the regulation of DELLA proteins. Exogenous spraying of paclobutrazol significantly reduced the plant height but was beneficial for increasing the weight of 1000 grains of rye. Treatment with paclobutrazol, significantly reduced gibberellin levels in grain in the filling period, caused significant alteration in the expression of the DELLA subfamily gene members. Furthermore, our findings with respect to genes, ScGRAS46 and ScGRAS60, suggest that these two family members could be further used for functional characterization studies in basic research and in breeding programmes for crop improvement. CONCLUSIONS: We identified 67 ScGRAS genes in rye and further analysed the evolution and expression patterns of the encoded proteins. This study will be helpful for further analysing the functional characteristics of ScGRAS genes.

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.

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.

Young retrotransposons and non-B DNA structures promote the establishment of dominant rye centromere in the 1RS.1BL fused centromere.

The fine centromere structure in Robertsonian wheat-rye translocation chromosomes exhibits variation among different translocation genotypes. Within extensively employed wheat-rye 1RS.1BL translocation lines in wheat breeding, their translocated chromosomes frequently display fused centromere. Nevertheless, the mechanism governing the functionality of the fused centromere in 1RS.1BL translocated chromosomes remains to be clarified. In this study, we investigated the fine centromere structure of the 1RS.1BL translocated chromosome through a combination of cytological and genomics methods. We found that only the rye-derived centromere exhibits functional activity, whether in breeding applications or artificially synthesized translocation chromosomes. The active rye-derived centromere had higher proportion of young full-length long terminal repeat retrotransposons (flLTR-RTs) and more stable non-B DNA structures, which may be beneficial toward transcription of centromeric repeats and CENH3 loading to maintain the activity of rye centromeres. High levels of DNA methylation and H3K9me2 were found in the inactive wheat-derived centromeres, suggesting that it may play a crucial role in maintaining the inactive status of the wheat centromere. Our works elucidate the fine structure of 1RS.1BL translocations and the potential mechanism of centromere inactivation in the fused centromere, contributing knowledge to the application of fused centromere in wheat breeding formation of new wheat-rye translocation lines.

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.

Winter Rye Cover Crops Shelter Competent Squash Phyllosphere Bacteria to Reduce Pseudomonas syringae pv. lachrymans Growth and Angular Leaf Spot Symptoms.

Cover crops, a soil conservation practice, can contribute to reducing disease pressure caused by Pseudomonas syringae, considered one of the most important bacterial plant pathogens. We recently demonstrated that the phyllosphere (leaf surface) bacterial community structure changed when squash (Cucurbita pepo) was grown with a rye (Secale cereale) cover crop treatment, followed by a decrease of angular leaf spot disease symptoms on squash caused by P. syringae pv. lachrymans. Application of biocontrol agents is a known agricultural practice to mitigate crop losses due to microbial disease. In this study, we tested the hypothesis that some phyllosphere bacteria promoted when squash is grown on cover crops could be isolated and used as a biocontrol agent to decrease angular leaf spot symptoms. We grew squash during a 2-year field experiment using four agricultural practices: bare soil, cover crops, chemically terminated cover crops, and plastic cover. We sampled squash leaves at three different dates each year and constructed a collection of cultivable bacterial strains isolated from squash leaves and rye cover crop material. Each isolated strain was identified by 16S rRNA gene sequencing and used in in vitro (Petri dish) pathogen growth and in vivo (greenhouse) symptom control assays. Four bacterial isolates belonging to the genera Pseudarthrobacter, Pseudomonas, Delftia, and Rhizobium were shown to inhibit P. syringae pv. lachrymans growth and angular leaf spot symptom development. Strikingly, the symptom control efficacy of all strains was stronger on older leaves. This study sheds light on the importance of bacterial isolation from cover crop sources to promote disease control. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

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.

Rye-grass-derived probiotics alleviate heat stress effects on broiler growth, health, and gut microbiota.

The primary aim of this study was to assess the impact of liquid (S-LAB) and lyophilized (L-LAB) probiotics sourced from Rye-Grass Lactic Acid Bacteria on broilers experiencing heat stress. The study involved 240 broiler chicks divided into six groups. These groups included a negative control (Control) with broilers raised at a normal temperature (24 °C) on a basal diet, and positive control groups (S-LAB and L-LAB) with broilers under normal temperature receiving a lactic acid bacteria supplement (0.5 mL/L) from rye-grass in their drinking water. The heat stress group (HS) comprised broilers exposed to cyclic heat stress (5-7 h per day at 34-36 °C) on a basal diet, while the heat stress and probiotic groups (S-LAB/HS and L-LAB/HS) consisted of broilers under heat stress supplemented with the rye-grass-derived lactic acid bacteria. Results indicated that heat stress without supplementation (HS) led to reduced body weight gain, T3 levels, citrulline, and growth hormone levels, along with an increased feed conversion ratio, serum corticosterone, HSP70, ALT, AST, and leptin levels. Heat stress also negatively impacted cecal microbiota, decreasing lactic acid bacteria (LABC) while increasing E. coli and coliform bacteria (CBC) counts. Probiotic supplements (S-LAB/HS and L-LAB/HS) mitigated these effects by enhancing broilers' resilience to heat stress. In conclusion, rye grass-derived S-LAB and L-LAB probiotics can effectively support broiler chickens under heat stress, promoting growth, liver function, hormonal balance, gut health, and cecal microbiome ecology. These benefits are likely mediated through improved gut health.

Spring applied phosphorus loss with cover crops in no-till terraced field.

Cover crops (CC) can improve phosphorus (P) cycling by reducing water related P losses and contributing to P nutrition of a rotational crop. This is particularly important in claypan soils with freeze-thaw cycles in early spring in the Midwest U.S. This 4-year study (2019-2022) examined the impact of CC monoculture and mix of CC species on P losses from a fertilizer application, and determined the P balance in soil compared to no cover crop (noCC). The CC mix consisted of wheat (Triticum aestivum L.), radish (Raphanus raphanistrum subsp. Sativus), and turnip (Brassica rapa subsp. Rapa) (3xCCmix) in 2019 and 2021 before corn, and cereal rye (Secale cereale L.) was planted as monoculture before soybean in 2020 and 2022. The 3xCCmix had no effect on total phosphorus (TP) and dissolved reactive phosphorus (PO4-P) concentration or load in 2019 and 2021. Cereal rye reduced TP and PO4-P load 70% and 73%, respectively, compared to noCC. The variation in soil moisture, temperature, and net precipitation from fertilizer application until CC termination affected available soil P pools due to variability in CC species P uptake, residue decomposition, and P loss in surface water runoff. Overall, the P budget calculations showed cereal rye had 2.4 kg ha-1 greater P uptake compared to the 3xCCmix species which also reduced P loss in water and had greater differences in soil P status compared to noCC. This study highlights the benefit of CCs in reducing P loss in surface runoff and immobilizing P through plant uptake. However, these effects were minimal with 3xCCmix species and variability in crop residue decomposition from different CC species could affect overall P-soil balance.

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.

CRISPR/CasΦ2-mediated gene editing in wheat and rye.

The compact CRISPR/CasΦ2 system provides a complementary genome engineering tool for efficient gene editing including cytosine and adenosine base editing in wheat and rye with high specificity, efficient use of the protospacer-adjacent motif TTN, and an alternative base-editing window.

Inclusion of a Bacillus-based probiotic in non-starch polysaccharides-rich broiler diets.

This study examined the effects of a 3-strain Bacillus-based probiotic (BP; Bacillus amyloliquefaciens and two Bacillus subtilis) in broiler diets with different rye levels on performance, mucus, viscosity, and nutrient digestibility. We distributed 720 one-d-old female broilers into 72 pens and designed nine diets using a 3 × 3 factorial approach, varying BP levels (0, 1.2 × 106, and 1.2 × 107 CFU/g) and rye concentrations (0, 200, 400 g/kg). On d 35, diets with 200 or 400 g/kg rye reduced broiler weight gain (BWG). Diets with 400 g/kg rye had the highest FCR, while rye-free diets had the lowest (p ≤0.05). Adding BP increased feed intake and BWG in weeks two and three (p ≤0.05). It should be noted that the overall performance fell below the goals of the breed. Including rye in diets reduced the coefficient of apparent ileal digestibility (CAID) for protein, ether extract (EE), calcium, phosphorus, and all amino acids (p ≤0.05). Rye-free diets exhibited the highest CAID for all nutrients, except for methionine, EE, and calcium, while diets with 400 g/kg of rye demonstrated the lowest CAID (p ≤0.05). BP in diets decreased phosphorus CAID (p ≤0.05). Diets containing 1.2 × 107 CFU/g (10X) of BP exhibited higher CAID of methionine than the other two diets (p ≤0.05). Diets containing 10X of BP showed higher CAID of cysteine than diets with no BP (p ≤0.05). Ileal viscosity increased as the inclusion level of rye in the diets increased (p ≤0.05). The ileal concentration of glucosamine in chickens fed diets with 400 g/kg of rye was higher than in those fed diets with no rye (p ≤0.05). Furthermore, ileal galactosamine concentrations were elevated in diets with 200 and 400 g/kg of rye when compared to rye-free diets (p ≤0.05). However, BP in diets had no impact on ileal viscosity, galactosamine, or glucosamine (p > 0.05). In conclusion, the applied Bacillus strains appeared to have a limited capacity to produce arabinoxylan-degrading enzymes and were only partially effective in mitigating the negative impacts of rye arabinoxylans on broilers.

Investigation of chromosomal genetic characteristics and identification of structural variation in the offspring of hexaploid triticale×hexaploid wheat.

Hexaploid triticale is an important genetic resource for genetic improvement of common wheat, which can broaden the genetic basis of wheat. In order to lay a foundation for the subsequent research and utilization of triticale germplasm materials, the chromosomal genetic characteristics of cross and backcross offspring of hexaploid triticale×hexaploid wheat were investigated in the process of transferring rye chromatin from hexaploid triticale to hexaploid wheat. Hybrid and backcross combinations were prepared with hexaploid triticale 16yin171 as the maternal parent and hexaploid wheat Chuanmai62 as the paternal parent. The chromosomes in root tip cells of F1, BC1F1 and BC1F2 plants were traced and identified non-denaturing florescence in situ hybridization (ND-FISH). The results indicated that the backcross setting rate of hybrid F1 was 2.61%. The transmission frequency of 2R chromosome was the highest in BC1F1 plants while the transmissibility of rye chromosome in BC1F2 plant was 6R>4R>2R, and the 5B-7B wheat translocation in BC1F2 plants showed severe segregation. A total of 24 structural variant chromosomes were observed both in BC1F1 and BC1F2 plants, including chromosome fragments, isochromosomes, translocations, and dicentric chromosomes. In addition, the seed length and 1000-grain weight of some BC1F2 plants were better than that of the hexaploid wheat parent Chuanmai 62. Therefore, multiple backcrosses should be adopted as far as possible to make the rapid recovery of group D chromosomes, ensuring the recovery of fertility in offspring, when hexaploid tritriale is used as a bridge to introduce rye genetic material into common wheat. At the same time, the potential application value of chromosomal structural variation materials should be also concerned.