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MMP-9 belongs to the Matrix Metalloprotease family, which is mainly involved in the protein hydrolysis process of extracellular matrix and plays important roles in many biological processes, such as embryogenesis, tissue remodeling, angiogenesis, inflammatory processes and wound healing. In this study, we described the sequence characteristics of the MMP-9 gene in flounder (PoMMP-9). PoMMP-9 was highly homologous to MMP-9 from turbot, medaka, and Fugu rubripes. The mRNA of PoMMP-9 was constitutively expressed in all tested tissues of healthy flounder with the highest expression levels in the head kidney and spleen. A time-dependent expression pattern of PoMMP-9 in the head kidney and spleen was found after the bacterial and virus challenge. This indicates that PoMMP-9 is inducible and involved in immune responses. Indirect immunofluorescence assay showed that the PoMMP-9 was co-localization in the extracellular traps (ETs) released by the leukocytes. After overexpression, PoMMP-9 can recruit more inflammatory cells and play a broad immune process from pathogen elimination to wound healing at the inflammatory site through ETs. In summary, this study provided new insights into the biological function of MMP-9 in teleost.
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Armadilhas Extracelulares , Linguado , Metaloproteinase 9 da Matriz , Animais , Edwardsiella tarda/fisiologia , Doenças dos Peixes , Proteínas de Peixes , Regulação da Expressão Gênica , Imunidade Inata/genética , Metaloproteinase 9 da Matriz/genética , Metaloproteinase 9 da Matriz/metabolismo , FilogeniaRESUMO
The primary approach for variety distinction in Italian ryegrass is currently the DUS (distinctness, uniformity and stability) test based on phenotypic traits. Considering the diverse genetic background within the population and the complexity of the environment, however, it is challenging to accurately distinguish varieties based on DUS criteria alone. In this study, we proposed the application of high-throughput RAD-seq to distinguish 11 Italian ryegrass varieties with three bulks of 50 individuals per variety. Our findings revealed significant differences among the 11 tested varieties. The PCA, DAPC and STRUCTURE analysis indicated a heterogeneous genetic background for all of them, and the AMOVA analysis also showed large genetic variance among these varieties (ΦST = 0.373), which were clearly distinguished based on phylogenetic analysis. Further nucleotide diversity (Pi) analysis showed that the variety 'Changjiang No.2' had the best intra-variety consistency among 11 tested varieties. Our findings suggest that the RAD-seq could be an effectively alternative method for the variety distinction of Italian ryegrass, as well as a potential tool for open-pollinated varieties (OPVs) of other allogamous species.
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Lolium , Itália , Lolium/genética , Fenótipo , FilogeniaRESUMO
Drought is one of the most important factors affecting plant growth and production due to ongoing global climate change. Elymus sibiricus has been widely applied for ecological restoration and reseeding of degraded grassland in the Qinghai-Tibetan Plateau (QTP) because of its strong adaptability to barren, salted, and drought soils. To explore the mechanism of drought resistance in E. sibiricus, drought-tolerant and drought-sensitive genotypes of E. sibiricus were used in metabolomic studies under simulated long-term and short-term drought stress. A total of 1091 metabolites were detected, among which, 27 DMs were considered to be the key metabolites for drought resistance of E. sibiricus in weighted gene co-expression network analysis (WGCNA). Ten metabolites, including 3-amino-2-methylpropanoic acid, coniferin, R-aminobutyrate, and so on, and 12 metabolites, including L-Proline, L-histidine, N-acetylglycine, and so on, showed differential accumulation patterns under short-term and long-term drought stress, respectively, and thus, could be used as biomarkers for drought-tolerant and drought-sensitive E. sibiricus. In addition, different metabolic accumulation patterns and different drought response mechanisms were also found in drought-tolerant and drought-sensitive genotypes of E. sibiricus. Finally, we constructed metabolic pathways and metabolic patterns for the two genotypes. This metabolomic study on the drought stress response of E. sibiricus can provide resources and a reference for the breeding of new drought-tolerant cultivars of E. sibiricus.
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Elymus , Elymus/genética , Resistência à Seca , Melhoramento Vegetal , Perfilação da Expressão Gênica , SecasRESUMO
BACKGROUND: Prairie grass (Bromus catharticus) is a typical cool-season forage crop with high biomass production and fast growth rate during winter and spring. However, its genetic research and breeding has remained stagnant due to limited available genomic resources. The aim of this study was to generate large-scale genomic data using high-throughput transcriptome sequencing, and perform a preliminary validation of EST-SSR markers of B. catharticus. RESULTS: Eleven tissue samples including seeds, leaves, and stems were collected from a new high-yield strain of prairie grass BCS1103. A total of 257,773 unigenes were obtained, of which 193,082 (74.90%) were annotated. Comparison analysis between tissues identified 1803, 3030, and 1570 genes specifically and highly expressed in seed, leaf, and stem, respectively. A total of 37,288 EST-SSRs were identified from unigene sequences, and more than 80,000 primer pairs were designed. We synthesized 420 primer pairs and selected 52 ones with high polymorphisms to estimate genetic diversity and population structure in 24 B. catharticus accessions worldwide. Despite low diversity indicated by an average genetic distance of 0.364, the accessions from South America and Asia and wild accessions showed higher genetic diversity. Moreover, South American accessions showed a pure ancestry, while Asian accessions demonstrated mixed internal relationships, which indicated a different probability of gene flow. Phylogenetic analysis clustered the studied accessions into four clades, being consistent with phenotypic clustering results. Finally, Mantel analysis suggested the total phenotypic variation was mostly contributed by genetic component. Stem diameter, plant height, leaf width, and biomass yield were significantly correlated with genetic data (r > 0.6, P < 0.001), and might be used in the future selection and breeding. CONCLUSION: A genomic resource was generated that could benefit genetic and taxonomic studies, as well as molecular breeding for B. catharticus and its relatives in the future.
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Bromus/genética , Perfilação da Expressão Gênica , Genes de Plantas , Proteínas de Plantas/genética , Transcrição Gênica , Etiquetas de Sequências Expressas , Marcadores Genéticos , Repetições de Microssatélites , Proteínas de Plantas/metabolismoRESUMO
BACKGROUND: Siberian wildrye (Elymus sibiricus L.) attracts considerable interest for grassland establishment and pasture recovery in the Qinghai-Tibet Plateau (QTP) due to its excellence in strong stress tolerance, high nutritional value and ease to cultivate. However, the lack of genomic information of E. sibiricus hampers its genetics study and breeding process. RESULTS: In this study, we performed a genome survey and developed a set of SSR markers for E. sibiricus based on Next-generation sequencing (NGS). We generated 469.17 Gb clean sequence which is 58.64× of the 6.86 Gb estimated genome size. We assembled a draft genome of 4.34 Gb which has 73.23% repetitive elements, a heterozygosity ratio of 0.01% and GC content of 45.68%. Based on the gnomic sequences we identified 67,833 SSR loci and from which four hundred were randomly selected to develop markers. Finally, 30 markers exhibited polymorphism between accessions and ten were identified as single-locus SSR. These newly developed markers along with previously reported 30 ones were applied to analyze genetic polymorphism among 27 wild E. sibiricus accessions. We found that single-locus SSRs are superior to multi-loci SSRs in effectiveness. CONCLUSIONS: This study provided insights into further whole genome sequencing of E. sibiricus in strategy selection. The novel developed SSR markers will facilitate genetics study and breeding for Elymus species.
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DNA de Plantas/genética , Elymus/genética , Etiquetas de Sequências Expressas , Loci Gênicos , Genoma de Planta , Genômica , Repetições de Microssatélites/genética , Mapeamento Cromossômico , Biblioteca Gênica , Marcadores Genéticos , Variação Genética , Sequenciamento de Nucleotídeos em Larga EscalaRESUMO
Galectin-8 gene belongs to the agglutinin family, which can specifically recognize ß-galactoside bonds and play essential roles in many biological processes. In this study, we researched the sequence characteristics and immune-related function of Galectin-8 gene in Japanese flounder Paralichthys olivaceus, named PoGalectin-8. The results showed that the open reading frame of PoGalectin-8 was 891 bp, which encoding a protein with 296 amino acid residues and containing typical HXNPR and WGXEE motifs in the N-terminal and C-terminal CRD domains. Sequence alignment showed that PoGalectin-8 was conserved in different aquatic animals and exhibited the highest similarity (95.27%) with Seriola dumerili. PoGalectin-8 expressed in all detected tissues and exhibited the highest expression level in spleen, followed by skin and kidney. After infected by Edwardsiella tarda, the expression of PoGalectin-8 was down-regulated in the spleen and skin tissues of P. olivaceus. Further to study its immune-related functions, the recombinant PoGalectin-8 (rPoGalectin-8) was expressed and purified. The rPoGalectin-8 can specifically bind to lipopolysaccharide and peptidoglycan, the main components of cell walls from Gram-negative and Gram-positive bacteria. Bacteria binding and the microbial agglutinating experiments showed that the rPoGalectin-8 could bind and agglutinate all examined Gram-positive and Gram-negative bacteria. This study implied that PoGalectin-8, as a pattern recognition receptor, may play important roles during immune responses against bacterial infection, which laid a foundation for further functional identification of Galectin-8 in aquatic animal immunity.
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Doenças dos Peixes/imunologia , Linguados/genética , Linguados/imunologia , Galectinas/genética , Galectinas/imunologia , Regulação da Expressão Gênica/imunologia , Imunidade Inata/genética , Imunidade Adaptativa/genética , Sequência de Aminoácidos , Animais , Sequência de Bases , Edwardsiella tarda/fisiologia , Infecções por Enterobacteriaceae/imunologia , Proteínas de Peixes/química , Proteínas de Peixes/genética , Proteínas de Peixes/imunologia , Galectinas/química , Perfilação da Expressão Gênica/veterinária , Filogenia , Alinhamento de Sequência/veterináriaRESUMO
Centipedegrass (Eremochloa ophiuroides (Munro) Hack.) is commonly used as a low-maintenance warm-season turfgrass owing to its excellent adaptation to various soil types. A better understanding of the genetic diversity pattern of centipedegrass is essential for the efficient development and utilization of accessions. This study used fifty-five pairs of primers to detect the genetic variation and genetic structure of twenty-three wild centipedegrass accessions by Sequence-related amplified polymorphism (SRAP) markers. A total of 919 reliable bands were amplified, among which 606 (65.80%) were polymorphic and 160 (2.91%) were the monomorphic loci. The average polymorphic information content (PIC) value was 0.228. The unweighted pair group method with arithmetic mean (UPGMA) clustering analysis grouped the twenty-three accessions into two clusters. Meanwhile, the structure analysis showed that the tested accessions possessed two main genetic memberships (K = 2). The Mantel test significantly correlated the genetic and geographic distance matrices (r = 0.3854, p = 0.000140). Furthermore, geographical groups showed moderate genetic differentiation, and the highest intragroup genetic diversity was found in the Sichuan group (He = 0.201). Overall, the present research findings could promote the protection and collection of centipedegrass and provide comprehensive information to develop novel breeding strategies.
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Melhoramento Vegetal , Polimorfismo Genético , Polimorfismo Genético/genética , Deriva Genética , Aclimatação , Análise por ConglomeradosRESUMO
Drought is one of the most significant limiting factors affecting plant growth and development on the Qinghai-Tibet Plateau (QTP). Mining the drought-tolerant genes of the endemic perennial grass of the QTP, Siberian wildrye (Elymus sibiricus), is of great significance to creating new drought-resistant varieties which can be used in the development of grassland livestock and restoring natural grassland projects in the QTP. To investigate the transcriptomic responsiveness of E. sibiricus to drought stress, PEG-induced short- and long-term drought stress was applied to two Siberian wildrye genotypes (drought-tolerant and drought-sensitive accessions), followed by third- and second-generation transcriptome sequencing analysis. A total of 40,708 isoforms were detected, of which 10,659 differentially expressed genes (DEGs) were common to both genotypes. There were 2107 and 2498 unique DEGs in the drought-tolerant and drought-sensitive genotypes, respectively. Additionally, 2798 and 1850 DEGs were identified in the drought-tolerant genotype only under short- and long-term conditions, respectively. DEGs numbering 1641 and 1330 were identified in the drought-sensitive genotype only under short- and long-term conditions, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that all the DEGs responding to drought stress in E. sibiricus were mainly associated with the mitogen-activated protein kinase (MAKP) signaling pathway, plant hormone signal transduction, the linoleic acid metabolism pathway, the ribosome pathway, and plant circadian rhythms. In addition, Nitrate transporter 1/Peptide transporter family protein 3.1 (NPF3.1) and Auxin/Indole-3-Acetic Acid (Aux/IAA) family protein 31(IAA31) also played an important role in helping E. sibiricus resist drought. This study used transcriptomics to investigate how E. sibiricus responds to drought stress, and may provide genetic resources and references for research into the molecular mechanisms of drought resistance in native perennial grasses and for breeding drought-tolerant varieties.
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Kengyilia is a newly established genus. Most species in this genus survive in hash environment, which might be an indicator of an acquirement of stress resistance genes and the potential for molecular breeding in Triticeae species. Quantitative real-time PCR (qRT-PCR) is a widely used technique with varied sensitivity heavily dependent on the optimal level of the reference genes. K. melanthera is a typical psammophyte species which has high drought resistance. The reference genes of K. melanthera are not yet reported. This study aims to evaluate the expression stability of 14 candidate reference genes (EF1A, GAPDH, ACT1, UBI, TUBB3, TIPRL, CACS, PPP2R1B, TUBA1A, EIF4A1, CYPA3, TCTP, ABCG11L, and FBXO6L) under five treatments (drought, heat, cold, salt, and ABA) and find the most stable and suitable one even upon stressed conditions. The software NormFinder, GeNorm, BestKeeper, and RefFinder were used for data analysis. In general, the genes CACS and PPP2R1B are concluded to have the best overall performance under the various treatments. With the ABA treatment, TCTP and TIPRL show the best stability. CACS and TCTP, as well as TIPRL and CYPA3, were most stable under the treatments of cold and salt, respectively. CACS and FBXO6L were ranked the highest with the heat treatment and drought treatment, respectively. Finally, the Catalase-1 (CAT1) gene was used to verify the reliability of the above reference genes. Accordingly, CAT1's expression pattern remained unchanged after normalization with stable reference genes. This study provides beneficial information about the stability and reliability of potential reference genes for qRT-PCR in K. melanthera.
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Regulação da Expressão Gênica de Plantas , Genes de Plantas , Expressão Gênica , Poaceae/genética , Reação em Cadeia da Polimerase em Tempo Real/métodos , Reprodutibilidade dos Testes , Cloreto de Sódio , Estresse Fisiológico/genéticaRESUMO
Background: There is a growing need to offer appropriate services to persons with mild cognitive impairment (MCI) and dementia who are faced with depression and anxiety distresses beyond traditional pharmacological treatment. Dance-based interventions as multi-dimensional interventions address persons' physical, emotional, social, and spiritual aspects of well-being. However, no meta-analysis of randomized controlled treatment trials (RCTs) has examined the effectiveness of dance-based interventions on depression and anxiety among persons with MCI and dementia, and the results of RCTs are inconsistent. The study aimed to examine the effectiveness of dance-based interventions on depression (a primary outcome) and anxiety (a secondary outcome) among persons with MCI and dementia. Methods: A systematic review with meta-analysis was conducted. The inclusion criteria were: population: people of all ages with MCI and dementia; intervention: dance-based interventions; control group: no treatment, usual care, or waiting list group; outcome: depression and anxiety; study design: published or unpublished RCTs. Seven electronic databases (Cochrane, PsycINFO, Web of Science, PubMed, EBSCO, CNKI, WanFang) were searched from 1970 to March 2021. Grey literature and reference lists from relevant articles were also searched and reviewed. The Cochrane "Risk of Bias" tool was used to assess study quality. RevMan 5.4 was used for meta-analysis and heterogeneity was investigated by subgroup and sensitivity analysis. GRADE was applied to assess the evidence quality of depression and anxiety outcomes. Results: Five randomized controlled trials were identified. Sample sizes ranged from 21 to 204. The risk of bias was low, except for being rated as high or unclear for most included studies in two domains: allocation concealment, blinding participants and personnel. Meta-analysis of depression outcome showed no heterogeneity (I 2 = 0%), indicating that the variation in study outcomes did not influence the interpretation of results. There were significant differences in decreasing depression in favor of dance-based interventions compared with controls [SMD = -0.42, 95% CI (-0.60, -0.23), p < 0.0001] with a small effect size (Cohen's d = 0.3669); Compared with the post-intervention data, the follow-up data indicated diminishing effects (Cohen's d = 0.1355). Dance-based interventions were more effective in reducing depression for persons with dementia than with those having MCI, and were more effective with the delivery frequency of 1 h twice a week than 35 min 2-3 times a week. Also, one included RCT study showed no significant benefit on anxiety rating scores, which demonstrated small effect sizes at 6 weeks and 12 weeks (Cohen's d = 0.1378, 0.1675, respectively). GRADE analysis indicated the evidence quality of depression was moderate, and the evidence quality of anxiety was low. Conclusions: Dance-based interventions are beneficial to alleviate depression among persons with MCI and dementia. More trials of high quality, large sample sizes are needed to gain more profound insight into dance-based interventions, such as their effects of alleviating anxiety, and the best approaches to perform dance-based interventions.
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Russian wildrye, Psathyrostachys junceus (Fisch.) Nevski, is an important wild steppe perennial grass, which is characterized by longevity and short robust rhizomes. It also has highly resistance in grazing and abiotic stress. In this study, the genetic diversity of eleven P. juncea wild germplasms from north and central Asia was investigated using AFLP markers. The P. juncea populations were divided into three clades in both UPGMA dendrogram and PCoA clustering corresponding to the three genetic memberships in STRUCTURE analysis. The genetic specificity of Xinjiang (XJ) populations was revealed by the highest N e (1.5411) and H j (0.3553) and their dispersion shown in UPGMA. High inbreeding coefficient (Wright's F statistics, f = 0.496, F st = 0.128) was observed although a moderate degree of gene flow (N m = 1.4736) existed, that may ascribe to habitat fragmentation or the low seedling recruitment, which ultimately resulted in decrease of population size and their genetic diversity. The key factors inducing moderate genetic differentiation detected in this study were isolation by distance (IBD), climatic variabilities and geographical barriers. All these results provide insights into the study of genetic status and germplasm collecting of Russian wildrye.
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Trifolium L., which belongs to the IR lacking clade (IRLC), is one of the largest genera in the Leguminosae and contains several economically important fodder species. Here, we present whole chloroplast (cp) genome sequencing and annotation of two important annual grasses, Trifolium alexandrinum (Egyptian clover) and T. resupinatum (Persian clover). Abundant single nucleotide polymorphisms (SNPs) and insertions/deletions (In/Dels) were discovered between those two species. Global alignment of T. alexandrinum and T. resupinatum to a further thirteen Trifolium species revealed a large amount of rearrangement and repetitive events in these fifteen species. As hypothetical cp open reading frame (ORF) and RNA polymerase subunits, ycf1 and rpoC2 in the cp genomes both contain vast repetitive sequences and observed high Pi values (0.7008, 0.3982) between T. alexandrinum and T. resupinatum. Thus they could be considered as the candidate genes for phylogenetic analysis of Trifolium species. In addition, the divergence time of those IR lacking Trifolium species ranged from 84.8505 Mya to 4.7720 Mya. This study will provide insight into the evolution of Trifolium species.