Transcriptome Profiling Provides Insights into the Early Development of Tiller Buds in High- and Low-Tillering Orchardgrass Genotypes

Orchardgrass (Dactylis glomerata L.) is among the most economically important perennial cool-season grasses, and is considered an excellent hay, pasture, and silage crop in temperate regions worldwide. Tillering is a vital feature that dominates orchardgrass regeneration and biomass yield. However, transcriptional dynamics underlying early-stage bud development in high- and low-tillering orchardgrass genotypes are unclear. Thus, this study assessed the photosynthetic parameters, the partially essential intermediate biomolecular substances, and the transcriptome to elaborate the early-stage profiles of tiller development. Photosynthetic efficiency and morphological development significantly differed between high- (AKZ-NRGR667) and low-tillering genotypes (D20170203) at the early stage after tiller formation. The 206.41 Gb of high-quality reads revealed stage-specific differentially expressed genes (DEGs), demonstrating that signal transduction and energy-related metabolism pathways, especially photosynthetic-related processes, influence tiller induction and development. Moreover, weighted correlation network analysis (WGCNA) and functional enrichment identified distinctively co-expressed gene clusters and four main regulatory pathways, including chlorophyll, lutein, nitrogen, and gibberellic acid (GA) metabolism pathways. Therefore, photosynthesis, carbohydrate synthesis, nitrogen efficient utilization, and phytohormone signaling pathways are closely and intrinsically linked at the transcriptional level. These findings enhance our understanding of tillering in orchardgrass and perennial grasses, providing a new breeding strategy for improving forage biomass yield.

Transcriptome Analysis Reveals the Potential Molecular Mechanisms of Tiller Bud Development in Orchardgrass

Tillering is a special type of branching and one of the important contributors to the yield of cereal crops. Strigolactone and sucrose play a vital role in controlling tiller formation, but their mechanism has not been elucidated completely in most crops. Orchardgrass (Dactylis glomerata L.) is an important perennial forage with prominent tillering ability among crops. To date, the mechanism of tillering in orchardgrass is still largely unknown. Therefore, we performed a transcriptome and miRNA analysis to reveal the potential RNA mechanism of tiller formation under strigolactone and sucrose treatment in orchardgrass. Our results found that D3, COL5, NCED1, HXK7, miRNA4393-z, and miRNA531-z could be key factors to control tiller bud development in orchardgrass. In addition, strigolactones might affect the ABA biosynthesis pathway to regulate the tiller bud development of orchardgrass, which may be related to the expression changes in miRNA4393-z, NCED1, and D10. miRNA531-z could be involved in the interaction of strigolactones and sucrose in regulating tillering. These results will be further used to clarify the potential mechanism of tillering for breeding new high-tillering and high-production orchardgrass varieties and beneficial to improving the production and reproduction of crops.

Fermentation characteristics and nutritive value of baled grass silages made from meadow fescue, tall fescue, or an orchardgrass cultivar exhibiting a unique nonflowering growth response

Throughout central Wisconsin, many soils are poorly drained, and perennial cool-season grasses are often planted as monocultures or in mixed stands with alfalfa because of the poor persistence of alfalfa under these growing conditions. Our objectives were to compare the fermentation characteristics and nutritive value of perennial cool-season grasses {meadow fescue [Schedonorus pratensis (Huds.) P. Beauv.], orchardgrass (Dactylis glomerata L.), and endophyte-free tall fescue [Schedonorus phoenix (Scop.) Holub]} conserved as baled silages with or without particle-size reduction, and at 2 moisture concentrations. Twenty-four plots (0.23 ha) were arranged in a randomized complete block design with 6 plots/block. Within each of the 4 field blocks, one of the 6 plots was assigned randomly to each of the (3 × 2) factorial combinations of forage type and bale cutting engagement (cut or uncut). The baler cutting mechanism consisted of 15 cutting knives, thereby creating a theoretical length of cut of about 8.1 cm. Generally, sufficient forage was available to produce 2 bales/plot; therefore, one bale was packaged at relatively high moisture (58.3%), whereas the other bale was made at an ideal moisture (44.9%) for this silage preservation method. Theoretically, bale cutting can increase bale weights and densities by reducing particle size, thereby allowing inclusion of additional forage within the same-sized bale. In this experiment, bale-cutting within 1.2 × 1.2 m silage bales (n = 47) increased initial wet and dry bale weights by 4.1 and 4.7%, respectively, but had no practical effect on measures of nutritive value, either on a pre- or postensiled basis. Cutter engagement tended to increase total volatile fatty acids in silages, thereby resulting in a pH reduction of 0.07 pH units (5.54 vs. 5.61). A unique nonflowering growth response by the first-cutting orchardgrass forage resulted in yields of dry matter for orchardgrass (2,977 kg of dry matter/ha) that were only 52 to 53% of those observed for meadow (5,580 kg of dry matter/ha) or tall fescue (5,763 kg of dry matter/ha), which did not differ. Despite the unique vegetative nature of orchardgrass, concentrations of neutral detergent fiber, acid detergent fiber, and acid detergent lignin determined before ensiling exhibited limited variability across forages (60.9 to 62.7%, 35.2 to 36.4%, and 2.75 to 2.99%, respectively). However, a 30-h in vitro incubation determined that orchardgrass exhibited greater neutral detergent fiber digestibility (56.2%) compared with meadow (44.9%) or tall fescue (40.8%), which were also statistically distinct.

Digestibility and Retention Time of Coastal Bermudagrass (Cynodon dactylon) Hay by Horses

Simple Summary

Longer retention of forages with increased fiber concentrations may be a compensatory digestive strategy in horses. We investigated the digestive characteristics of bermudagrass hay, a prominent warm-season grass in the southeast United States that has greater fiber concentrations than other common forages fed to horses. The morphological structure and photosynthetic pathway of warm-season grasses differ from cool-season grasses and legumes which may have important impacts on equine digestion and digesta transit through the gastrointestinal tract. The retention time of Coastal bermudagrass was longer than alfalfa or orchardgrass hay. The digestibility of Coastal bermudagrass decreased with increasing maturity, but the fiber digestibility of alfalfa and orchardgrass was similar to the earliest maturity of Coastal bermudagrass hay. The chemical composition of the plant cell wall influences diet digestibility and is a major difference between warm-season and cool-season forages. The increased retention time of Coastal bermudagrass allows for microbial fermentation to occur longer, adapting to more difficult-to-digest plant cell walls in warm-season forages. The decrease in diet digestibility when horses consume warm-season forages can be reduced by feeding early maturity forage, by harvesting hay at an earlier stage of growth or managing pastures in a vegetative state.

Abstract

Bermudagrass (Cynodon dactylon) and other warm-season grasses are known for their increased fiber concentrations and reduced digestibility relative to cool-season grasses and legumes. This study investigated the digestive characteristics and passage kinetics of three maturities of Coastal bermudagrass hay. A 5 × 5 Latin square design experiment was used to compare the digestion of five hays: alfalfa (Medicago sativa, ALF), orchardgrass (Dactylis glomerata, ORCH), and Coastal bermudagrass harvested at 4 (CB 4), 6 (CB 6), and 8 weeks of regrowth (CB 8). Horses were fed cobalt-ethylenediaminetetraacetic acid (Co-EDTA) and ytterbium (Yb) labeled neutral detergent fiber (NDF) before an 84-h total fecal collection to determine digesta retention time. Dry matter digestibility was greatest for ALF (62.1%) and least for CB 6 (36.0%) and CB 8 diets (36.8%, SEM = 2.1; p < 0.05). Mean retention time was longer (p < 0.05) for Coastal bermudagrass (particulate 31.3 h, liquid 25.3 h) compared with ORCH and ALF (28.0 h, SEM = 0.88 h; 20.7 h, SEM = 0.70 h). Further evaluation of digesta passage kinetics through mathematical modeling indicated ALF had distinct parameters compared to the other diets. Differences in digestive variables between forage types are likely a consequence of fiber physiochemical properties, warranting further investigation on forage fiber and digestive health.

Transcriptome characterization and differentially expressed genes under flooding and drought stress in the biomass grasses Phalaris arundinacea and Dactylis glomerata

BACKGROUND AND AIMS

Perennial grasses are a global resource as forage, and for alternative uses in bioenergy and as raw materials for the processing industry. Marginal lands can be valuable for perennial biomass grass production, if perennial biomass grasses can cope with adverse abiotic environmental stresses such as drought and waterlogging.

METHODS

In this study, two perennial grass species, reed canary grass (Phalaris arundinacea) and cocksfoot (Dactylis glomerata) were subjected to drought and waterlogging stress to study their responses for insights to improving environmental stress tolerance. Physiological responses were recorded, reference transcriptomes established and differential gene expression investigated between control and stress conditions. We applied a robust non-parametric method, RoDEO, based on rank ordering of transcripts to investigate differential gene expression. Furthermore, we extended and validated vRoDEO for comparing samples with varying sequencing depths.

KEY RESULTS

This allowed us to identify expressed genes under drought and waterlogging whilst using only a limited number of RNA sequencing experiments. Validating the methodology, several differentially expressed candidate genes involved in the stage 3 step-wise scheme in detoxification and degradation of xenobiotics were recovered, while several novel stress-related genes classified as of unknown function were discovered.

CONCLUSIONS

Reed canary grass is a species coping particularly well with flooding conditions, but this study adds novel information on how its transcriptome reacts under drought stress. We built extensive transcriptomes for the two investigated C3 species cocksfoot and reed canary grass under both extremes of water stress to provide a clear comparison amongst the two species to broaden our horizon for comparative studies, but further confirmation of the data would be ideal to obtain a more detailed picture.

Combinations of Small RNA, RNA, and Degradome Sequencing Uncovers the Expression Pattern of microRNA⁻mRNA Pairs Adapting to Drought Stress in Leaf and Root of Dactylis glomerata L

Drought stress is a global problem, and the lack of water is a key factor that leads to agricultural shortages. MicroRNAs play a crucial role in the plant drought stress response; however, the microRNAs and their targets involved in drought response have not been well elucidated. In the present study, we used Illumina platform (https://www.illumina.com/) and combined data from miRNA, RNA, and degradome sequencing to explore the drought- and organ-specific miRNAs in orchardgrass (Dactylis glomerata L.) leaf and root. We aimed to find potential miRNA⁻mRNA regulation patterns responding to drought conditions. In total, 519 (486 conserved and 33 novel) miRNAs were identified, of which, 41 miRNAs had significant differential expression among the comparisons (p < 0.05). We also identified 55,366 unigenes by RNA-Seq, where 12,535 unigenes were differently expressed. Finally, our degradome analysis revealed that 5950 transcripts were targeted by 487 miRNAs. A correlation analysis identified that miRNA ata-miR164c-3p and its target heat shock protein family A (HSP70) member 5 gene comp59407_c0 (BIPE3) may be essential in organ-specific plant drought stress response and/or adaptation in orchardgrass. Additionally, Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses found that "antigen processing and presentation" was the most enriched downregulated pathway in adaptation to drought conditions. Taken together, we explored the genes and miRNAs that may be involved in drought adaptation of orchardgrass and identified how they may be regulated. These results serve as a valuable genetic resource for future studies focusing on how plants adapted to drought conditions.

Use of two grasses for the phytoremediation of aqueous solutions polluted with terbuthylazine

The capacity of two grasses, tall fescue (Festuca arundinacea) and orchardgrass (Dactylis glomerata), to remove terbuthylazine (TBA) from polluted solutions has been assessed in hydroponic cultures. Different TBA concentrations (0.06, 0.31, 0.62, and 1.24 mg/L) were chosen to test the capacity of the two grasses to resist the chemical. Aerial biomass, effective concentrations (to cause reductions of 10, 50, and 90% of plant aerial biomass) and chlorophylls contents of orchardgrass were found to be more affected. Tall fescue was found to be more capable of removing the TBA from the growth media. Furthermore, enzymes involved both in the herbicide detoxification and in the response to herbicide-induced oxidative stress were investigated. Glutathione S-transferase (GST, EC. 2.5.1.18) and ascorbate peroxidase (APX, EC. 1.11.1.11) of tall fescue were found to be unaffected by the chemical. GST and APX levels of orchardgrass were decreased by the treatment. These negative modulations exerted by the TBA on the enzyme of orchardgrass explained its lower capacity to cope with the negative effects of the TBA.

Genetic Diversity and Association of EST-SSR and SCoT Markers with Rust Traits in Orchardgrass (Dactylis glomerata L.)

Orchardgrass (Dactylis glomerata L.), is a well-known perennial forage species; however, rust diseases have caused a noticeable reduction in the quality and production of orchardgrass. In this study, genetic diversity was assessed and the marker-trait associations for rust were examined using 18 EST-SSR and 21 SCoT markers in 75 orchardgrass accessions. A high level of genetic diversity was detected in orchardgrass with an average genetic diversity index of 0.369. For the EST-SSR and SCoT markers, 164 and 289 total bands were obtained, of which 148 (90.24%) and 272 (94.12%) were polymorphic, respectively. Results from an AMOVA analysis showed that more genetic variance existed within populations (87.57%) than among populations (12.43%). Using a parameter marker index, the efficiencies of the EST-SSR and SCoT markers were compared to show that SCoTs have higher marker efficiency (8.07) than EST-SSRs (4.82). The results of a UPGMA cluster analysis and a STRUCTURE analysis were both correlated with the geographic distribution of the orchardgrass accessions. Linkage disequilibrium analysis revealed an average r² of 0.1627 across all band pairs, indicating a high extent of linkage disequilibrium in the material. An association analysis between the rust trait and 410 bands from the EST-SSR and SCoT markers using TASSEL software revealed 20 band panels were associated with the rust trait in both 2011 and 2012. The 20 bands obtained from association analysis could be used in breeding programs for lineage selection to prevent great losses of orchardgrass caused by rust, and provide valuable information for further association mapping using this collection of orchardgrass.

Effect of water-soluble carbohydrate content in orchardgrass pasture on grazing time and rumen fermentation in dairy cows

Two experiments were conducted to clarify the effect of water-soluble carbohydrate (WSC) content in orchardgrass pasture on the diurnal distribution of grazing time. Six ruminally cannulated, non-lactating dairy cows were grazed on either of two pastures with different orchardgrass cultivars containing low WSC (LWSC; cultivar: 'Hokkai 28') or high WSC (HWSC; cultivar: 'Harunemidori'). The cows were grazed in morning and evening sessions in experiment 1, whereas the cows were grazed throughout the day in experiment 2. In experiment 1, grazing time of the cows on HWSC was longer than that of the cows on LWSC (P < 0.01). This difference was larger in the morning session than in the evening session (pasture × grazing session: P < 0.05). Effects on herbage intake were similar to those on grazing time. In experiment 2, daily total grazing time was longer for the cows on HWSC than for those on LWSC (P < 0.05). The cows on HWSC spent a longer time grazing than those on LWSC in the morning between 03.00 and 09.00 hours (P < 0.01). The results indicated that prolonged grazing time in the period between dawn and early morning could increase daily herbage intake in cows grazed on pastures of orchardgrass cultivars with high-WSC content.

Characterization of orchardgrass p23, a flowering plant Hsp90 cohort protein

p23 is a heat shock protein 90 (Hsp90) co-chaperone and stabilizes the Hsp90 heterocomplex in mammals and yeast. In this study, we isolated a complementary DNA (cDNA) encoding p23 from orchardgrass (Dgp23) and characterized its functional roles under conditions of thermal stress. Dgp23 is a 911 bp cDNA with an open reading frame predicted to encode a 180 amino acid protein. Northern analysis showed that expression of Dgp23 transcripts was heat inducible. Dgp23 has a well-conserved p23 domain and interacted with an orchardgrass Hsp90 homolog in vivo, like mammalian and yeast p23 homologs. Recombinant Dgp23 is a small acidic protein with a molecular mass of approximately 27 kDa and pI 4.3. Dgp23 was also shown to function as a chaperone protein by suppression of malate dehydrogenase thermal aggregation. Differential scanning calorimetry thermograms indicated that Dgp23 is a heat-stable protein, capable of increasing the T (m) of lysozyme. Moreover, overexpression of Dgp23 in a yeast p23 homolog deletion strain, Deltasba1, increased cell viability. These results suggest that Dgp23 plays a role in thermal stress-tolerance and functions as a co-chaperone of Hsp90 and as a chaperone.

A Comparative Analysis of Extraction Methods for the Recovery of Anguina sp. from Grass Seed Samples

Four procedures were compared in their efficacy to extract juveniles of Anguina agrostis from commercial grass seed. The procedures included those currently used by the state regulatory laboratories of Oregon and California, as well as new tests developed to determine juvenile viability for the phytosanitary certification of fumigated grass seed. Eleven seed lots of Agrostis tenuis (bentgrass) and Dactylis glomerata (orchardgrass) naturally infested with varying levels of juveniles of Anguina were individually analyzed. Only one procedure, a new live recovery test, yielded nematodes in all 11 samples and is recommended as the best method for use by regulatory agencies. In comparison, although the other three extraction procedures resulted in greater numbers of Anguina agrostis juveniles per gram of seed, they failed to yield any nematodes in as many as four seed lots with low infection levels.