Elymus sibiricus L., a member of the Triticeae tribe, is a grass widely used for forage and restoring degraded grasslands in the Qinghai-Tibetan Plateau (QTP) region. Here, we present a high-quality reference genome assembly of allotetraploid E. sibiricus, consisting of 14 pseudochromosomes. Our findings suggest that large-scale bursts of retrotransposon activity, especially by Gypsy elements and unclassified retrotransposon elements, have played a critical role in the genome expansion of E. sibiricus as compared with other Triticeae. We identified a translocation between chromosomes Es4H and Es6H with a low recombination rate. Population genomic analysis of 90 E. sibiricus accessions and 25 diploid accessions of proposed ancestors from different habitats revealed four distinct groups, although they are of monophyletic origin. Our population analysis supports the idea that the QTP is likely the center of origin and genetic diversity of E. sibiricus. Selective sweep analysis identified significant pathways related to photosynthesis and metabolism, which are likely associated with the multiple environmental adaptations of this species to the climatic conditions of the QTP. Collectively, our study not only provides genomic resources for genetic improvement of the Elymus genus, but also provides important insights on the evolutionary history of E. sibiricus from population genomic analysis and the evolution of the tribe Triticeae.

Elymus nutans Griseb. (Poaceae: Triticeae, 2n=6x=42) is a dominant perennial plant species in the Qinghai-Tibetan Plateau in China, which is an important forage resource in high-altitude and cold regions and is the most popular species used for high yield artificial grassland planting because of its rich nutritional value and good palatability for herbivorous ruminant animals. In this study, using advanced sequencing technology, we generated an allohexaploid reference genome for E. nutans , representing the three sets of chromosomes (subgenomes St, Y, and H). This is the first study to our knowledge to confirm the origin of the Y subgenome, which shares a close relationship with the V subgenome. We predict that E. nutans arose via two-step hybridization and that its speciation occurred ∼3.16 MYA. The whole genome in this study will update the Triticeae family genomics information and provide theoretical basis for the evolutionary of its related speicies. ### Competing Interest Statement The authors have declared no competing interest.

Machine learning (ML) has garnered significant attention for its potential to enhance the accuracy of genomic predictions (GPs) in various economic crops with the use of complete genomic information. Genome-wide association studies (GWAS) are widely used to pinpoint trait-related causal variant loci in genomes. However, the simultaneous integration of both methods for crop genome prediction necessitates further research. In this study, we integrated ML and GWAS to assess the efficiency of GP for seven key agronomic traits in 195 oat (Avena sativa) cultivars from major oat-growing regions around the world. A total of 94 trait-associated single nucleotide polymorphisms were identified through the GWAS study. GP studies were conducted using the classical model genomic best linear unbiased prediction (GBLUP) and six ML models. GBLUP performed poorly in predicting all traits except flag leaf width, while none of the ML models consistently provided the best prediction accuracy across all traits. The prediction accuracy of the GWAS-derived markers was better than that of the use of genome-wide markers, and plant height had the highest prediction rate at 100 GWAS-derived markers, and the rest of the traits for which more markers were required. These results play an important role in advancing the use of GP in small oat breeding programs by optimizing the prediction rate of GP and reducing the number of markers, confirming that high prediction rates can be achieved with smaller datasets.

Drought and cold crucially affect plant growth and distribution. Plants have evolved complex molecular mechanisms to adapt to such adverse environmental conditions. This study examines two Elymus sibiricus (Es) germplasms differing in resilience to these stresses. Analyzing physiological responses and gene expression changes under drought and cold, it reveals the similarities and differences in their molecular mechanisms that underlie these responses. The results indicate that both drought stress and cold stress severely damage the integrity of the cell membrane in Es. Notably, under cold stress, the accumulation of osmotic regulation substances in Es is more significant, which may be related to the regulation of carbohydrate metabolism (CM)-related genes in cold environments. Furthermore, the response to oxidative stress triggered by cold stress in Es is partially inhibited. The enrichment analysis showed that the DEGs responsive to drought stress in Es were mainly related to the pathway of photosynthesis, whereas the DEGs responsive to cold stress were more associated with the protein processing in endoplasmic reticulum (PPER), highlighting distinct molecular responses. In addition, we discovered that the abscisic acid (ABA) signaling transduction plays a dominant role in mediating the drought resistance mechanism of Es. We have identified 86 key candidate genes related to photosynthesis, Phst, CM, and PPER, including 5 genes that can respond to both drought and cold stress. This study provides a foundation for the molecular mechanisms underlying cold and drought resistance in Es, with insight into its future genetic improvement for stress resistance.

Siberian wildrye (Elymus sibiricus L.), a model Elymus Gramineae plant, has high eco-economic value but limited seed and forage yield. TCP transcription factors are widely regarded as influencing yield and quality and being crucial for growth and development; still, this gene family in Siberian wildrye remains unexplored. Therefore, this study looked at the Siberian wildrye TCP gene family’s reaction to several abiotic stresses, its expression pattern, and its potential evolutionary path. Fifty-four members of the EsTCP gene family were discovered. There are two major subfamilies based on the phylogenetic tree: 27 of Class I (PCF) and 27 of Class II (12 CIN-type and 15 TB1/CYC-type). Gene structure, conserved motif, and sequence alignment analyses further validated this classification. Cis-elements found in the promoter region of EsTCPs are associated with lots of plant hormones and stress-related reactions, covering drought induction and cold tolerance. EsCYC5, EsCYC6, and EsCYC7 may regulate tillering and lateral branch development. EsPCF10’s relative expression was significant under five stresses. Additionally, eight EsTCP genes are potential miR319 targets. These findings highlight the critical significance of the TCP gene family in Siberian wildrye, laying the groundwork for understanding the function of the EsTCP protein in abiotic stress studies and high-yield breeding.

Carex capillifolia is an ecologically and economically important fodder grass widely distributed across the Northern Hemisphere, particularly in the Qinghai-Xizang Plateau. Research into its genetic diversity and genomic architecture has been limited. In this study, we present a high-quality genome assembly for C. capillifolia, spanning 386.65 Mb (contig N50 = 14.66 Mb) and comprising 29 chromosomes. Phylogenetic analysis reveals a close evolutionary relationship with C. littledalei, with divergence estimated at 2.19-6.1 million years ago. Comparative genomics analyses identify 26 shared chromosome fusion events specifically between these two species, highlighting a pattern of recent, lineage-specific karyotype reshuffling that contributes to the remarkable karyotypic diversity within Cyperaceae. Using population genomics, genome-environment association (GEA), and transcriptome analysis, we identify multiple climate-associated genetic variants and drought-tolerance genes. Notably, we identify an auxin response factor (ARF) gene and verify its role in enhancing drought tolerance through transgenic experiments. Furthermore, we pinpoint the Ruoergai (RRG) geo-group as possessing the highest adaptability to future climates, which harbors superior adaptive genetic variation and candidate genes that could be targeted in breeding closely related species.

The objective of this experiment was to determine whether compound microbial inoculants could enhance the fermentation of oat and common vetch silage that were stored in the Northwest Sichuan Plateau for 60 days under extremely low temperatures. Oat and common vetch harvested from single and mixed artificially planted grassland of oat and common vetch were chopped into 2–3 cm (oat, S1; common vetch, S2; oat–common vetch = 2:1, S3), then sterile water (T1), Zhuang Lemei IV silage additive (T2), and Fu Zhengxing silage additive (T3) were added to the feed and ensiled at the local outdoor environment for 60 days. Data were analyzed as a 3 × 3 factorial arrangement of treatments with the main effects of the materials, additives, and their interaction. Interactions between the materials and additives significantly affected the fermentation quality and the content of DM, WSC, and NDF and the number of yeasts in forages. Treatments with S3 have significantly higher contents of lactic acid, acetic acid, and lactic acid bacteria in the feed than those in the S1 and S2 treatments, while the contents of AN/TN and propionic acid were significantly lower compared with the S1 and S2 treatments (p < 0.05). Concentrations of lactic acid, acetic acid, and propionic acid were significantly increased and the content of neutral detergent fiber in the T2-treated silage decreased compared with the T1 treatment (p < 0.05). The T3 treatment significantly reduced the number of yeasts in the silage but the compound lactic acid bacteria additive treatment (T1, T2) significantly decreased the butyric acid content and pH of the feed and increased the acid detergent fiber content and the number of lactic acid bacteria in the feed compared with the T1 treatment. Among them, the butyric acid content of the T3 treatment decreased by 63.64–86.05%, while that of the T2 treatment decreased by 36.36–83.33% (p < 0.05). The comprehensive analysis of the membership function revealed that the silage quality was the best after the S3T2 treatment, so the implementation of the S3T2 combination in the Northwest Sichuan Plateau can provide guarantees for the production of local high-quality forage grass and alleviate the shortage of forage grass.

Anaerobic fermentation is a critical approach for the efficient recycling of herbal medicinal waste. During fermentation, micro aeration, feedstock properties, and additives significantly influence performance. This study investigated strategies to enhance lactic acid production during the anaerobic fermentation of red clover by incorporating herbal waste Anisodus tanguticus (AT) and Rhodiola rosea (RS) and Lactiplantibacillus plantarum (LP), combined with micro aeration during the bottleneck phase of fermentation. Results showed that LP and AT exhibited a synergistic effect, increasing lactic acid content by 14.35%. Conversely, RS promoted the growth of lactic acid-consuming bacteria (e.g., Hafnia alvei), reducing lactic acid production, although this inhibitory effect was alleviated by LP inoculation, resulting in an 11.11% increase in lactic acid yield. Targeted micro aeration significantly enhanced carbohydrate metabolism increased the abundance of polysaccharide-degrading enzyme genes and boosted lactic acid content by 38.49%-74.33%. However, prolonged aeration activated aerobic bacteria, leading to decreased lactic acid production. These findings highlight the potential of combining targeted micro aeration with herbal waste interventions to overcome fermentation bottlenecks, enhance lactic acid production, and provide innovative solutions for sustainable herbal waste management.

Elymus sibiricus L., an excellent forage and ecological restoration grass, plays a key role in grassland ecological construction and the sustainable development of animal husbandry. In China, the wild germplasm resources of E. sibiricus are abundant, and they are shaped by similar and contrasting climatic conditions to form distinct populations, which enrich the genetic diversity of E. sibiricus. To more comprehensively aggregate E. sibiricus germplasm resources at a lower cost and to more accurately utilize its genetic variation, this study conducted a preliminary exploration of core germplasm collections and fingerprinting of E. sibiricus using single nucleotide polymorphism (SNP) markers. By combining multiple evaluation measures with weighted processing, we successfully identified 36 materials from 90 wild E. sibiricus samples to serve as a core collection. Genetic diversity assessments, allele evaluations, and principal component analyses of the 36 core germplasm samples all indicate that these 36 samples accurately and comprehensively represent the genetic diversity of all 90 E. sibiricus germplasm accessions. Additionally, we identified 290 SNP loci from among the high-quality SNP loci generated by whole-genome sequencing of the 90 E. sibiricus samples as candidate markers. Of these, 52 SNP loci were selected as core markers for DNA fingerprinting of E. sibiricus. Using kompetitive allele-specific PCR (KASP) technology, we also performed population origin identification for 60 wild E. sibiricus germplasm accessions based on these core markers. The core SNP markers screened in this study were able to accurately distinguish between E. sibiricus germplasms from the Qinghai-Tibet Plateau and those from elsewhere. This study not only provides a reference for the continued collection and identification of E. sibiricus germplasm resources but also offers a scientific basis for their conservation and utilization.

Plants cultivated on the Qinghai-Tibet Plateau (QTP) are exposed to high ultraviolet radiation intensities, so they require effective mechanisms to adapt to these stress conditions. UV-B radiation is an abiotic stress factor that affects plant growth, development, and environmental adaptation. Elymus sibiricus is a common species in the alpine meadows of the QTP, with high-stress resistance, large biomass, and high nutritional value. This species plays an important role in establishing artificial grasslands and improving degraded grasslands. In this study, UV-B radiation-tolerant and UV-B radiation-sensitive E. sibiricus genotypes were subjected to simulated short-term (5 days, 10 days) and long-term (15 days, 20 days) UV-B radiation stress and the metabolite profiles evaluated to explore the mechanism underlying UV-B radiation resistance in E. sibiricus. A total of 699 metabolites were identified, including 11 primary metabolites such as lipids and lipid-like molecules, phenylpropanoids and polyketides, organic acids and their derivatives, and organic oxygen compounds. Principal component analysis distinctly clustered the samples according to the cultivar, indicating that the two genotypes exhibit distinct response mechanisms to UV-B radiation stress. The results showed that 14 metabolites, including linoleic acid, LPC 18:2, xanthosine, and 23 metabolites, including 2-one heptamethoxyflavone, glycyrrhizin, and caffeic acid were differentially expressed under short-term and long-term UV-B radiation stress, respectively. Therefore, these compounds are potential biomarkers for evaluating E. sibiricus response to UV-B radiation stress. Allantoin specific and consistent expression was up-regulated in the UV-B radiation-tolerant genotype, thereby it can be used to identify varieties resistant to UV-B radiation. Different metabolic profiles and UV-B radiation response mechanisms were observed between the UV-B radiation-tolerant and UV-B radiation-sensitive E. sibiricus genotypes. A model for the metabolic pathways and metabolic profiles was constructed for the two genotypes. This metabolomic study on the E. sibiricus response to UV-B radiation stress provides a reference for the breeding of new UV-B radiation-tolerant E. sibiricus cultivars.

Oats (Avena sativa) are an important cereal crop and cool-season forage worldwide. Heat shock protein 90 (HSP90) is a protein ubiquitously expressed in response to heat stress in almost all plants. To date, the HSP90 gene family has not been comprehensively reported in oats. Herein, we have identified twenty HSP90 genes in oats and elucidated their evolutionary pathways and responses to five abiotic stresses. The gene structure and motif analyses demonstrated consistency across the phylogenetic tree branches, and the groups exhibited relative structural conservation. Additionally, we identified ten pairs of segmentally duplicated genes in oats. Interspecies synteny analysis and orthologous gene identification indicated that oats share a significant number of orthologous genes with their ancestral species; this implies that the expansion of the oat HSP90 gene family may have occurred through oat polyploidization and large fragment duplication. The analysis of cis-acting elements revealed their influential role in the expression pattern of HSP90 genes under abiotic stresses. Analysis of oat gene expression under high-temperature, salt, cadmium (Cd), polyethylene glycol (PEG), and abscisic acid (ABA) stresses demonstrated that most AsHSP90 genes were significantly up-regulated by heat stress, particularly AsHSP90-7, AsHSP90-8, and AsHSP90-9. This study offers new insights into the amplification and evolutionary processes of the AsHSP90 protein, as well as its potential role in response to abiotic stresses. Furthermore, it lays the groundwork for understanding oat adaptation to abiotic stress, contributing to research and applications in plant breeding.

BACKGROUND:Reed canary grass has been identified as a suitable species for restoring plateau wetlands and understanding plant adaptation mechanisms in wetland environments. In this study, we subjected a reed canary grass cultivar 'Chuanxi' to waterlogging, salt, and combined stresses to investigate its phenotypic characteristics, physiological indices, and transcriptome changes under these conditions. RESULTS:The results revealed that the growth rate was slower under salt stress than under waterlogging stress. The chlorophyll content and energy capture efficiency of the PS II reaction center decreased with prolonged exposure to each stress. Conversely, while the activities of enzymes associated with respiratory metabolism, as well as MDA, PRO, Na+, and K+-ATPase, increased. The formation of distinct aerenchyma was observed under waterlogging stress and combined stress. Transcriptome sequencing analysis identified 5,379, 4,169, and 14,993 DEGs under CK vs. W, CK vs. S, and CK vs. SW conditions, respectively. The WRKY was found to be the most abundant under waterlogging stress, whereas the MYB predominated under salt stress and combined stress. Glutathione metabolic pathways and Plant hormone signal transduction have also been found to play important roles in stress. CONCLUSION:By integrating phenotypic, physiological, anatomical, and transcriptomic, this research provides valuable insights into how reed canary grass responds to salt, waterlogging, and combined stresses. These findings may inform the ecological application of reed canary grass in high-altitude wetlands and for breeding purposes.

Elymus sibiricus L. (Siberian wildrye, Es ), a species belonging to the wheat tribe, is extensively employed as forage and for the reclamation of degraded grasslands within the Qinghai-Tibet Plateau (QTP). This study provides a high-quality reference genome assembly for the allotetraploid Es , which is composed of 14 pseudomolecules with the total genome size of 6.57 Gb. Our finding suggest that large-scale bursts of retrotransposons are critical for the genome expansion of Es . We discovered a translocation event between the Es 4H and Es 6H chromosomes with a low frequency of combination. Phylogenetic analyses of 90 Es accessions and 25 diploid accessions representing proposed ancestors from various habitats revealed the existence of four distinct populations. We further provided support for the hypothesis that the QTP is the center of origin and genetic diversity for Es . Collectively, our study offers valuable insights into the evolution of Es , as well as providing genomic resources for genetic enhancement in the Elymus genus and wheat tribe.### Competing Interest StatementThe authors have declared no competing interest.

为揭示野生老芒麦形态变异特征和遗传背景,对我国野生老芒麦主要分布区域不同生态类型的104个居群520份野生老芒麦种质进行了23个形态指标测定和遗传多样性分析.结果表明:不同生境老芒麦材料的形态特征存在显著差异,数量性状变异系数为9.49％～49.56％;聚类分析将104个居群分为具有各自明显特征和开发利用潜力的4类;形态特征与地理环境因子的相关性分析发现,野生老芒麦抽穗早晚及茎秆叶鞘基部小刺等特殊性状与其海拔呈显著相关;主成分分析发现,株高、抽穗、茎节数、单株干鲜重、旗叶长宽等指标代表了老芒麦67.79％形态多样性,是造成老芒麦形态特征变异的主要因素,可作为老芒麦形态分化的重要参考指标.

Kengyilia melanthera is one of the most important forages, and has received significant attention as a desirable ecological pioneer grass for conserving grasslands and mitigating degradation pressure in a region. It is widely distributed in the alpine sandy meadow zone of the Eastern Qinghai–Tibet Plateau (QTP). Therefore, determining the optimal harvest time of this species is critical. A two-year field experiment (2016–2017) was utilized in this study to evaluate the impact of eight harvest times on the seed yield and quality of K. melanthera ‘Aba’. The results show that the fresh weight (FW), dry weight (DW), seed yield (SY), thousand-grain weight (TGW), accelerated aging germination percentage (AAGP), and dehydrogenase activity (DA) of seeds increased with the extension of harvest time in two trial years, while the water content (WC) of seeds decreased. In both trial years, the germination percentage (GEP), germination potential (GP), and acid phosphatase activity (APA) of seeds increased initially and then decreased with the extension of harvest time. The comprehensive evaluation of the membership function and hierarchical clustering revealed that the 30th day after peak anthesis was the optimal harvest time for both 2016 and 2017. During this time, FW, DW, SY, TGW, AAGP, DA, WC, GEP, GP, and APA reached their optimal value, with 0.815 g, 0.518 g, 1773.67 kg·hm−2, 143.81%, 66%, 16.23 µg·mL−1, 36.01%, 87%, 85%, and 2.50 nmol·min−1 in 2016 and 0.805 g, 0.515 g, 1847.42 kg·hm−2, 133.96%, 65%, 16.52 µg·mL−1, 36.04%, 86.5%, 83.5%, and 2.55 nmol·min−1 in 2017, respectively. This study uncovers several high-efficiency and long-term technological solutions for cultivating high yields and quality production of K. melanthera in East QTP.

Reed canary grass ( Phalaris arundinacea L.) is a promising high-yield cool-season forage with significant ecological application potential in wastewater treatment and wetland restoration. Transcriptome sequences can rapidly assay and characterize a few gene-based microsatellites from various plants. Here, the transcriptome of reed canary grass was sequenced, and 50,155 putative EST-SSRs were identified from 272,328 transcripts, with tri-nucleotide being the most abundant type, followed by mono-nucleotide. A total of 300 EST-SSR markers were randomly selected, among which 45 polymorphic EST-SSR markers were used for the genetic diversity study of 17 reed canary grass accessions (P. arundinacea L.) and two accessions of related bulbous canary grass (P. aquatica L.). A total of 218 bands were amplified using 45 SSR markers; the reliable polymorphic bands were 118 (54.13%), the average of the polymorphic information content was 0.36, and the RP value was 0.96. In summary, the transcriptome sequences of reed canary grass contribute to gene prediction and promote molecular biology and genomics studies, whereas polymorphic SSR markers promote molecular-assisted breeding and related studies of Phalaris species.

为进一步评价川西短芒披碱草在大田生产条件下的生产性能,课题组于2015～2018 年,以国审品种同德短芒披碱草为对照,分别在四川红原县、道孚县和青海海晏县开展了川西短芒披碱草多年多点的大田生产试验.连续 3 年的生产试验结果表明,川西短芒披碱草在各试验点生长良好,生产性能表现优良,综合评价优于对照品种同德短芒披碱草.川西短芒披碱平均鲜草产量为17760kg/hm2,较对照增产 14.7％,增产显著;干草产量平均为 6469kg/hm2,较对照增产 13.2％,增产极显著.川西短芒披碱草较对照同德短芒披碱草具有突出的丰产性和一定的稳定性,在四川省阿坝州红原县、甘孜州道孚县和青海省海北州海晏县均能很好的适应,适宜在类似生态区推广种植.

In order to make better use of the wild resources of Elymus sibiricus germplasm, in this study the 1 723 materials of wild Elymus species resources from the Qinghai-Tibet Plateau, Northwest of China, North China and Northeast of China and some foreign regions were collected, from which, total of 990 wild E. sibiricus germplasm were identified by phenotypic characteristics and the Flow Cytometry detection. The results showed that the DNA content of E. sibiricus was between 5.86～7.30 Gb with average of 6.66Gb. The DNA content of Elymus nutans Griseb was between 9.50～10.36 Gb with average of 9.97Gb. It was found out that dorsal hair appeared in the basal leaf sheath of some wild E. sibiricus materials from Northwest of China, North China and Northeast of China, which was different from the description of the morphological characteristics of E. sibiricus in Chinese Flora,which was positively correlated with longitude and latitude（P ＜ 0.01）,and negatively correlated with altitude, annual mean temperature and annual mean rainfall（P＜0.01）,indicating that there was an inevitable relationship between the existence of the dorsal hair in the basal leaf sheath of E. sibiricus and its environmental factors and which possibly was one of the adaptive mechanisms of E. sibiricus germplasm to its environment. The results of this study provided a new basis for the morphological identification of E. sibiricus,and for the exploring E. sibiricus germplasm resources and breeding application.

To explore the effects of crop rotation combined with reduced fertilization on crop yield and soil nutrients in the rotation system, and to optimize fertilizer application in rotation system of burclover（Medicago polymorpha）-rice（Oryza sativa）,this study adopted the double-factor completely randomized design, and set up five treatments, including "continuous cropping rice（high fertilizer）" "burclover（no fertilizer） + rice（middle fertilizer）" "burclover（fertilizer） + rice（middle fertilizer）" "burclover（no fertilizer） + rice（low fertilizer）",and "burclover（fertilizer） + rice（low fertilizer）". The results showed that there were significant differences in yield and soil nutrients with the reduced fertilizer in rotation system. The highest rice yield in the treatment of “burclover（fertilizer） + rice（low fertilizer）” was higher than the other treatments in the same year, with organic matter significantly increased by 14.81%～38.13%,soil pH reduced by 2.34%～5.03%,and soil nitrogen content significantly increased by 0.80%～35.66%（P＜0.05）. Thus, reducing fertilizer application in crop rotation can effectively improve yield and soil nutrients in crop rotation systems.