作者机构:
[Wu, Ya; Zeng, Zaohai; Xia, Rui; Liu, Yuanlong; He, Yehua; Chen, Chengjie; Xu, Jing; Chen, CJ] South China Agr Univ, Coll Hort, State Key Lab Conservat & Utilizat Subtrop Agrobio, Guangzhou 510640, Guangdong, Peoples R China.;[Zeng, Zaohai; Xia, Rui; Liu, Yuanlong; Chen, Chengjie; Xu, Jing; Chen, CJ] South China Agr Univ, Key Lab Biol & Germplasm Enhancement Hort Crops So, Minist Agr & Rural Affair, Guangzhou 510640, Guangdong, Peoples R China.;[Zeng, Zaohai; Xia, Rui; Liu, Yuanlong; Chen, Chengjie; Xu, Jing; Chen, CJ] South China Agr Univ, Guangdong Lab Lingnan Modern Agr, Guangzhou 510640, Guangdong, Peoples R China.;[Li, Jiawei] Jinan Univ, Guangdong Hongkong Macau Inst CNS Regenerat, Guangdong Key Lab Nonhuman Primate Res, Guangzhou 510632, Guangdong, Peoples R China.;[Wang, Xiao] Henan Univ, Sch Life Sci, State Key Lab Crop Stress Adaptat & Improvement, Henan Joint Int Lab Crop MultiOm Res, Kaifeng 475004, Peoples R China.
通讯机构:
[Chen, CJ; Xia, R ] S;South China Agr Univ, Coll Hort, State Key Lab Conservat & Utilizat Subtrop Agrobio, Guangzhou 510640, Guangdong, Peoples R China.;South China Agr Univ, Key Lab Biol & Germplasm Enhancement Hort Crops So, Minist Agr & Rural Affair, Guangzhou 510640, Guangdong, Peoples R China.;South China Agr Univ, Guangdong Lab Lingnan Modern Agr, Guangzhou 510640, Guangdong, Peoples R China.
关键词:
TBtools-II;plugin;biological big data;BSA-seq
摘要:
Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020, its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and references in more than 5000 academic articles. Now, TBtools is a commonly used tool in biological laboratories. Over the past 3 years, thanks to invaluable feedback and suggestions from numerous users, we have optimized and expanded the functionality of the toolkit, leading to the development of an upgraded version-TBtools-II. In this upgrade, we have incorporated over 100 new features, such as those for comparative genomics analysis, phylogenetic analysis, and data visualization. Meanwhile, to better meet the increasing needs of personalized data analysis, we have launched the plugin mode, which enables users to develop their own plugins and manage their selection, installation, and removal according to individual needs. To date, the plugin store has amassed over 50 plugins, with more than half of them being independently developed and contributed by TBtools users. These plugins offer a range of data analysis options including co-expression network analysis, single-cell data analysis, and bulked segregant analysis sequencing data analysis. Overall, TBtools is now transforming from a stand-alone software to a comprehensive bioinformatics platform of a vibrant and cooperative community in which users are also developers and contributors. By promoting the theme"one for all, all for one", we believe that TBtools-II will greatly benefit more biological researchers in this big-data era.
关键词:
gut microbiota;dietary diet;metabolites;short-chain fatty acids;bile acids
摘要:
Type 2 diabetes (T2D) is a commonly diagnosed condition that has been extensively studied. The composition and activity of gut microbes, as well as the metabolites they produce (such as short-chain fatty acids, lipopolysaccharides, trimethylamine N-oxide, and bile acids) can significantly impact diabetes development. Treatment options, including medication, can enhance the gut microbiome and its metabolites, and even reverse intestinal epithelial dysfunction. Both animal and human studies have demonstrated the role of microbiota metabolites in influencing diabetes, as well as their complex chemical interactions with signaling molecules. This article focuses on the importance of microbiota metabolites in type 2 diabetes and provides an overview of various pharmacological and dietary components that can serve as therapeutic tools for reducing the risk of developing diabetes. A deeper understanding of the link between gut microbial metabolites and T2D will enhance our knowledge of the disease and may offer new treatment approaches. Although many animal studies have investigated the palliative and attenuating effects of gut microbial metabolites on T2D, few have established a complete cure. Therefore, conducting more systematic studies in the future is necessary.
期刊:
International Journal of Molecular Sciences,2023年24(3) ISSN:1422-0067
通讯作者:
Jianhua Zhang<&wdkj&>Nenghui Ye
作者机构:
[Chen, Yinke; Teng, Zhenning; Duan, Meijuan; Meng, Shuan; Ye, Nenghui] Hunan Agr Univ, Coll Agr, Changsha 410128, Peoples R China.;[Teng, Zhenning] Chinese Univ Hong Kong, Shenzhen Res Inst, Shenzhen 518057, Peoples R China.;[Duan, Meijuan; Ye, Nenghui] Hunan Agr Univ, Hunan Prov Key Lab Rice Stress Biol, Changsha 410128, Peoples R China.;[Zhang, Jianhua] Hong Kong Baptist Univ, Dept Biol, Hong Kong 999077, Peoples R China.
通讯机构:
[Jianhua Zhang] D;[Nenghui Ye] C;College of Agriculture, Hunan Agricultural University, Changsha 410128, China<&wdkj&>Hunan Provincial Key Laboratory of Rice Stress Biology, Hunan Agricultural University, Changsha 410128, China<&wdkj&>Department of Biology, Hong Kong Baptist University, Hong Kong 999077, China
摘要:
Abstract: Light, temperature, water, and fertilizer are arguably the most important environmental factors regulating crop growth and productivity. Environmental stimuli, including low light, extreme temperatures, and water stresses caused by climate change, affect crop growth and production and pose a growing threat to sustainable agriculture. Furthermore, soil salinity is another major environmental constraint affecting crop growth and threatening global food security. The grain filling stage is the final stage of growth and is also the most important stage in cereals, directly determining the grain weight and final yield. However, the grain filling process is extremely vulnerable to different environmental stimuli, especially for inferior spikelets. Given the importance of grain filling in cereals and the deterioration of environmental problems, understanding environmental stimuli and their effects on grain filling constitutes a major focus of crop research. In recent years, significant advances made in this field have led to a good description of the intricate mechanisms by which different environmental stimuli regulate grain filling, as well as approaches to adapt cereals to changing climate conditions and to give them better grain filling. In this review, the current environmental stimuli, their dose–response effect on grain filling, and the physiological and molecular mechanisms involved are discussed. Furthermore, what we can do to help cereal crops adapt to environmental stimuli is elaborated. Overall, we call for future research to delve deeper into the gene function-related research and the commercialization of gene-edited crops. Meanwhile, smart agriculture is the development trend of the future agriculture under environmental stimuli. Keywords: light; temperature; water; fertilizer; saline–alkali stress; cereal crops; grain filling
通讯机构:
[Tongcheng Fu] C;College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China<&wdkj&>Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, China<&wdkj&>National Energy R&D Center for Non-Food Biomass, Hunan Agricultural University, Changsha, China
关键词:
marginal land;soil aggregate;soil carbon sequestration;soil ecology;soil iron and aluminum oxide;soil microbe
摘要:
Long‐term cultivation of Miscanthus and Saccharum arundinaceum increased soil organic carbon stock in infertile red soils. Soil pH is the main factor affecting soil carbon stock in red soils. Soil copiotrophic and oligotrophic microbes significantly shaped by the cultivation of perennial grasses. Abstract Determining the effect of perennial energy crop (PEC) cultivation on soil organic carbon (SOC) in marginal land soil is vital for carbon neutrality and bioeconomy development. However, a comprehensive and systematic evaluation of the response of SOC content to different PECs and its underlying drivers is still lacking. We used soil data collected from infertile red topsoil (0–20 cm) after 10 years of cultivation with Miscanthus (MS), Panicum virgatum (SG), and Saccharum arundinaceum (SA) to explore the changes in SOC stock induced by PEC. The roles of physical, chemical, and microbiological factors driving the increase in the SOC stock were investigated. Results revealed that SA and MS enhanced SOC stock by 87.97% and 27.52% relative to the uncultivated control. Conversely, PEC increased the percentage of soil mega‐aggregates, geometric mean diameters, soil chelate iron (Fe), and aluminum (Al) oxides, and reduced soil acidity for the infertile red soils. In addition, fungal richness and diversity for PEC soils were enhanced compared to the unplanted soil. It is possible that PEC cultivation reduced the relative abundance of copiotrophic fungi but increased the relative abundance of oligotrophic fungi. Furthermore, variance partitioning analysis revealed that chemical and microbiological factors accounted for 80.54% of the total variation for the SOC stock. The partial least squares path model showed that PEC cultivation enhanced soil carbon (C) stock via soil deacidification and increased soil bacterial function. In conclusion, this study confirms the SOC sequestration potential of PEC cultivation in marginal land and the underlying mechanism driving SOC stock. The main positive factors controlling soil C sequestration included “pH,” while the negative factors were “bacterial community,” “fungal community,” and “bacterial function.” Our research may help encourage and support decision‐makers of wasted marginal land conversion to PEC cultivation.
通讯机构:
[Li, YL ] H;Hunan Agr Univ, Coll Hort, Changsha 410128, Peoples R China.;Hunan Acad Agr Sci, Hunan Hort Res Inst, Changsha 410125, Peoples R China.;Kunpeng Inst Modern Agr, Foshan 528226, Peoples R China.
关键词:
anthocyanins;flavonoid biosynthesis;flower coloring;Loropetalum chinense var. rubrum;metabolomic;transcriptomic
摘要:
Abstract: The Loropetalum chinense and Loropetalum chinense var. rubrum are typical as well as traditional ornamental and Chinese herbal medicines in Asia; however, more information is needed on the mechanisms underlying their flower coloring. Here, we profiled the flavonoid metabolome and carried out full-length sequencing in addition to transcriptome analyses to investigate the flavonoid biosynthesis and global transcriptome changes among different petal coloring cultivars of L. chinense and L. chinense var. rubrum. The total anthocyanins in addition to the RHSCC values and CIE 1976 L*a*b* values of petals were highly consistent with petal color. Moreover, a total of 207 flavonoid components were identified. Of these, 13 flavonoid compounds were considered significantly different expression compounds highly consistent with color information in the 4 samples. Meanwhile, the first reference full-length transcriptome of L. chinense var. rubrum was built, which had 171,783 high-quality nonredundant transcripts with correcting with next-generation sequencing (NGS). Among them, 52,851 transcripts were annotated in the seven databases of NR, KOG, GO, NT, Pfam, Swiss-Port, and KEGG. Combined with NGS analyses, the DETs involved in flavonoids and anthocyanins contributed greatest to the flower coloring. Additionally, the different expressions of eight LcDFRs and four LcANS genes were positively correlated with flavonoid biosynthesis, and the four LcBZ1 as well as one Lc3Mat1 were positively correlated with the content of seven anthocyanins revealed by coupling with metabolomics and transcriptomics analyses. Together, these results were used to mine candidate genes by analyzing flower coloring changes at comprehensive metabolic and transcriptomic levels in L. chinense and L. chinense var. rubrum. Keywords: Loropetalum chinense var. rubrum; flavonoid biosynthesis; anthocyanins; flower coloring; metabolomic; transcriptomic
通讯机构:
[Maoliang Ran; Bin Chen] C;College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha 410128, China
摘要:
Abstract: The regulatory role of non-CpG methylation in mammals has been important in whole-genome bisulfite sequencing. It has also been suggested that non-CpG methylation regulates gene expression to affect the development and health of mammals. However, the dynamic regulatory mechanisms of genome-wide, non-CpG methylation during testicular development still require intensive study. In this study, we analyzed the dataset from the whole-genome bisulfite sequencing (WGBS) and the RNA-seq of precocious porcine testicular tissues across two developmental stages (1 and 75 days old) in order to explore the regulatory roles of non-CpG methylation. Our results showed that genes regulated by non-CpG methylation affect the development of testes in multiple pathways. Furthermore, several hub genes that are regulated by non-CpG methylation during testicular development—such as VEGFA, PECAM1, and FZD7—were also identified. We also found that the relative expression of FZD7 was downregulated by the zebularine-induced demethylation of the first exon of FZD7. This regulatory relationship was consistent with the results of the WGBS and RNA-seq analysis. The immature porcine Sertoli cells were transfected with RNAi to mimic the expression patterns of FZD7 during testicular development. The results of the simulation test showed that cell proliferation was significantly impeded and that cell cycle arrest at the G2 phase was caused by the siRNA-induced FZD7 inhibition. We also found that the percentage of early apoptotic Sertoli cells was decreased by transfecting them with the RNAi for FZD7. This indicates that FZD7 is an important factor in linking the proliferation and apoptosis of Sertoli cells. We further demonstrated that Sertoli cells that were treated with the medium collected from apoptotic cells could stimulate proliferation. These findings will contribute to the exploration of the regulatory mechanisms of non-CpG methylation in testicular development and of the relationship between the proliferation and apoptosis of normal somatic cells. Keywords: FZD7; non-CpG methylation; Sertoli cells; testes; proliferation; apoptosis
摘要:
Abstract: WRKY transcription factors, as the largest gene family in higher plants, play an important role in various biological processes including growth and development, regulation of secondary metabolites, and stress response. In this study, we performed genome-wide identification and analysis of WRKY transcription factors in S. siamensis. A total of 59 SsWRKY genes were identified that were distributed on all 14 chromosomes, and these were classified into three major groups based on phylogenetic relationships. Each of these groups had similar conserved motifs and gene structures. We compared all the S. siamensis SsWRKY genes with WRKY genes identified from three diverse plant species, and the results implied that segmental duplication and tandem duplication play an important roles in the evolution processes of the WRKY gene family. Promoter region analysis revealed that SsWRKY genes included many cis-acting elements related to plant growth and development, phytohormone response, and both abiotic and biotic stress. Expression profiles originating from the transcriptome database showed expression patterns of these SsWRKY genes in four different tissues and revealed that most genes are expressed in plant roots. Fifteen SsWRKY genes with low-temperature response motifs were surveyed for their gene expression under cold stress, showing that most genes displayed continuous up-regulation during cold treatment. Our study provides a foundation for further study on the function and regulatory mechanism of the SsWRKY gene family. Keywords: Siraitia siamensis; WRKY transcription factor; bioinformatics analysis; expression pattern; cold stress
摘要:
WUSCHEL (WUS) is a crucial transcription factor in regulating plant stem cell development, and its expression can also improve genetic transformation. However, the ectopic expression of WUS always causes pleiotropic effects during genetic transformation, making it important to understand the regulatory mechanisms underlying these phenomena. In our study, we found that the transient expression of the maize WUS ortholog ZmWus2 caused severe leaf necrosis in Nicotiana benthamiana. We performed transcriptomic and non-target metabolomic analyses on tobacco leaves during healthy to wilted states after ZmWus2 transient overexpression. Transcriptomic analysis revealed that ZmWus2 transformation caused active metabolism of inositol trisphosphate and glycerol-3-phosphate, while also upregulating plant hormone signaling and downregulating photosystem and protein folding pathways. Metabolomic analysis mainly identified changes in the synthesis of phenylpropanoid compounds and various lipid classes, including steroid synthesis. In addition, transcription factors such as ethylene-responsive factors (ERFs), the basic helix-loop-helix (bHLH) factors, and MYBs were found to be regulated by ZmWus2. By integrating these findings, we developed a WUS regulatory model that includes plant hormone accumulation, stress responses, lipid remodeling, and leaf necrosis. Our study sheds light on the mechanisms underlying WUS ectopic expression causing leaf necrosis and may inform the development of future genetic transformation strategies.
通讯机构:
[Fang Wang] K;Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Xiangtan 411105, China<&wdkj&>College of Information and Intelligence, Hunan Agricultural University, Changsha 410128, China
摘要:
Abstract: In recent years, air pollution has become one of the main factors harming the livable environment for human beings. Governments have recognized the importance of controlling air pollution and reached a consensus that regional joint control of air pollution is an effective means of dealing with environmental degradation. In this work, we focus on the impact of fine particulate matter and nitrogen compounds on the air quality of 14 prefecture-level cities in China’s Hunan Province using the insights of complex networks, and further propose a joint treatment scheme for these two pollutants. Multiscale temporal networks are constructed based on the height cross-correlation coefficient, which allows us to assess the variable network structures concerning different time scales. We use four network properties to assess the network structures for the pollutants. Through the Jensen-Shannon divergence of the probability distribution of these network attributes, it is found that NO2 affects AQI more in a short time interval than in a longer time interval. The correlation of both NO2 and PM2.5 among the 14 cities in about 15 days can best reflect the air quality in Hunan Province. In addition, instead of NO2, PM2.5 has become the culprit of air pollution in Hunan Province. The co-movement of the pollutants among the 14 cities is significant. The co-movement of the PM2.5 pollutants can last 45 days, while that of NO2 pollutants will gradually decrease over time. Furthermore, by using spectral clustering based on the network node correlation, we classify the 14 cities into five regions and two regions for PM2.5 and NO2, respectively. It provides a feasible implementation guide for the environmental governance of regional cooperation. Keywords: pollution co-movement; height cross-correlation coefficient; multiscale networks; Jensen-Shannon divergence; spectral clustering
摘要:
The beef cattle industry in China has advanced remarkably since its reform and opening up; consequently, China has become the world's third-largest beef cattle producer. China is also one of the countries with the most substantial research input and output in the field of beef cattle feed and nutrition. The progress and innovation by China in the research field of beef cattle feed and nutrition have undoubtedly promoted the development of the domestic beef cattle industry. This review summarizes recent advances in feed resource development, nutrient requirements, and nutritional regulation of beef cattle in China. Limitations in current research and perspectives on future work are also discussed.
作者机构:
[Sun, Wei; Gao, Shuai; Li, Shuzhen; Su, Guirong; He, Zhiguo] Cent South Univ, Sch Minerals Proc & Bioengn, Changsha 410083, Peoples R China.;[Su, Guirong] Hunan Agr Univ, Sch Biosci & Biotechnol, Changsha 410128, Peoples R China.;[He, ZG; He, Zhiguo] Aerosp Kaitian Environm Technol Co Ltd, Changsha 410100, Peoples R China.;[Zhong, Hui; Zhong, H] Cent South Univ, Sch Life Sci, Changsha 410083, Peoples R China.
通讯机构:
[He, ZG ] A;[Zhong, H ] C;Aerosp Kaitian Environm Technol Co Ltd, Changsha 410100, Peoples R China.;Cent South Univ, Sch Life Sci, Changsha 410083, Peoples R China.
摘要:
Pine oil, commonly used as a flotation frother, could affect the bioleaching process. The attachment and biofilm development of acidophiles on metal sulfides were essential for bioleaching. This study focused on the role of pine oil in the early adhesion and biofilm development by Acidianus manzaensis YN-25 on the chalcopyrite surface. It was revealed that pine oil had a negative effect on the adhesion amount of A. manzaensis on the chalcopyrite surface. After having reached adhesion equilibrium, the percentage of attached cells decreased as the concentration of pine oil increased. The addition of pine oil was found to decrease the negative charge of chalcopyrite and cells, resulting in a higher attraction of acid-base interaction energy and total interaction force. This ultimately led to a stronger adhesion force between chalcopyrite and A. manzaensis. While the addition of pine oil initially delayed the formation of cell microcolonies during the first stage of biofilm formation, which ultimately resulted in larger biofilm coverage compared with the control group. The microcolonies on the mineral surface were also larger and the corrosion pits were bigger with the addition of pine oil. Furthermore, the addition of pine oil weakened the passivation effect and promoted the biological dissolution of chalcopyrite. This study offers a better understanding of the effect of pine oil on the bioleaching of chalcopyrite.
摘要:
BACKGROUND: Staphylococcus aureus is one of the most important foodborne pathogens in the world and the main cause of dairy cow mastitis. Few studies have investigated the epidemic pedigree of S. aureus of bovine origin in Hunan, China. Therefore, we aimed to analyze the capsular polysaccharides (CP), molecular typing, and antibiotic resistance characteristics of S. aureus isolated from raw milk of dairy farms in Hunan Province. METHODS: Between 2018 and 2022, 681 raw milk samples were collected from dairy cows from farms in Changsha, Changde, Shaoyang, Yongzhou, and Chenzhou in Hunan Province. S. aureus was isolated from these samples, and the isolates were subjected to molecular typing, CP typing, and determination of antibiotic resistance through broth dilution and polymerase chain reaction (PCR). RESULTS: From 681 raw milk samples, 76 strains of S. aureus were isolated. The pathogenicity of 76 isolates was determined preliminarily by detecting cp5 and cp8 CP genes. Eighteen types of antimicrobial resistance phenotypes of 76 S. aureus strains were detected by the broth dilution method, and 11 kinds of related resistance genes were amplified by PCR. The S. aureus isolates had CP5 (42.10%) and CP8 (57.89%). S. aureus had a multiple antimicrobial resistance rate of 26.75%. The isolated strains had the highest resistance rate to penicillin (82.89%) and showed varying degrees of resistance to other drugs, but no isolate showed resistance to doxycycline. The 76 isolates all carried two or more antibiotic resistance genes, with a maximum of eight antibiotics resistance genes. FemB was detected in all isolates, but none of isolates carried vanA, ermA, or glrA. The 76 isolates were divided into 22 sequence types (ST) and 20 spa types by MLST and spa typing, and the number of t796-ST7 (n=15) isolates was the highest, which may be the major epidemic strain of multidrug-resistant S. aureus. CONCLUSION: The present findings indicate the need to increase production of the CP8 S. aureus vaccine in Hunan Province and strengthen resistance monitoring of t796-ST7 isolates with the prevalent molecular type of multi-drug resistant strains. The use of β-lactam, macrolides, and lincosamides should be reduced; doxycycline, sulfonamides, and glycopeptides could be appropriately added to veterinary antibiotics to treat infectious diseases in dairy cows.
通讯机构:
[Yunling Peng] G;Gansu Provincial Key Lab of Arid Land Crop Science, Lanzhou 730070, China
关键词:
GO analysis;maize;GSEA;SNP;PCR;drought tolerant
摘要:
Abstract: Drought stress is a significant abiotic factor influencing maize growth and development. Understanding the molecular mechanism of drought tolerance is critical to develop the drought tolerant genotype. The identification of the stress responsive gene is the first step to developing a drought tolerant genotype. The aim of the current research was to pinpoint the genes that are essential for conserved samples in maize drought tolerance. In the current study, inbred lines of maize, 478 and H21, a drought-tolerant and susceptible line, were cultivated in the field and various treatments were applied. The circumstances during the vegetative stage (severe drought, moderate drought and well-watered environments) and RNA sequencing were used to look into their origins. In 478, 68%, 48% and 32% of drought-responsive genes (DRGs) were found, with 63% of DRGs in moderate drought and severe drought conditions in H21, respectively. Gene ontology (GO) keywords were explicitly enriched in the DRGs of H21, which were considerably over-represented in the two lines. According to the results of the GSEA, “phenylpropanoid biosynthesis” was exclusively enriched in H21, but “starch and sucrose metabolism” and “plant hormone signal transduction” were enhanced in both of the two lines. Further investigation found that the various expression patterns of genes linked to the trehalose biosynthesis pathway, reactive oxygen scavenging, and transcription factors, may have a role in maize’s ability to withstand drought. Our findings illuminate the molecular ways that respond to lack and offer gene resources for maize drought resistance. Similarly, SNP and correlation analysis gave us noticeable results that urged us to do the same kind of analysis on other crops. Additionally, we isolated particular transcription factors that could control the expression of genes associated to photosynthesis and leaf senescence. According to our findings, a key factor in tolerance is the equilibrium between the induction of leaf senescence and the preservation of photosynthesis under drought. Keywords: GO analysis; maize; GSEA; SNP; PCR; drought tolerant
通讯机构:
[He, C.] E;[Song, B.] K;Engineering Research Center for Germplasm Innovation and New Variety Breeding of Horticultural Crops, China;Key Laboratory of Potato Biology and Biotechnology, China
摘要:
Anthocyanin biosynthesis is affected by light, temperature, and other environmental factors. The regulation mode of light on anthocyanin synthesis in apple, pear, tomato and other species has been reported, while not clear in potato. In this study, potato RM-210 tubers whose peel will turn purple gradually after exposure to light were selected. Transcriptome analysis was performed on RM-210 tubers during anthocyanin accumulation. The expression of StMYBA1 gene continued to increase during the anthocyanin accumulation in RM-210 tubers. Moreover, co-expression cluster analysis of differentially expressed genes showed that the expression patterns of StMYBA1 gene were highly correlated with structural genes CHS and CHI. The promoter activity of StMYBA1 was significantly higher in light conditions, and StMYBA1 could activate the promoter activity of structural genes StCHS, StCHI, and StF3H. Further gene function analysis found that overexpression of StMYBA1 gene could promote anthocyanin accumulation and structural gene expression in potato leaves. These results demonstrated that StMYBA1 gene promoted potato anthocyanin biosynthesis by activating the expression of structural genes under light conditions. These findings provide a theoretical basis and genetic resources for the regulatory mechanism of potato anthocyanin synthesis.
摘要:
Ramie (Boehmeria nivea [L.] Gaud.), a nutritious animal feed, is rich in protein and produces a variety of secondary metabolites that increase its palatability and functional composition. Ethylene (ETH) is an important plant hormone that regulates the growth and development of various crops. In this study, we investigated the impact of ETH sprays on the growth and metabolism of forage ramie. We explored the mechanism of ETH regulation on the growth and secondary metabolites of forage ramie using transcriptomic and metabolomic analyses. Spraying ramie with ETH elevated the contents of flavonoids and chlorogenic acid and decreased the lignin content in the leaves and stems. A total of 1076 differentially expressed genes (DEGs) and 51 differentially expressed metabolites (DEMs) were identified in the leaves, and 344 DEGs and 55 DEMs were identified in the stems. The DEGs that affect phenylpropanoid metabolism, including BGLU41, LCT, PER63, PER42, PER12, PER10, POD, BAHD1, SHT, and At4g26220 were significantly upregulated in the leaves. Ethylene sprays downregulated tyrosine and chlorogenic acid (3-O-caffeoylquinic acid) in the leaves, but lignin biosynthesis HCT genes, including ACT, BAHD1, and SHT, were up- and downregulated. These changes in expression may ultimately reduce lignin biosynthesis. In addition, the upregulation of caffeoyl CoA-O-methyltransferase (CCoAOMT) may have increased the abundance of its flavonoids. Ethylene significantly downregulated metabolites, affecting phenylpropanoid metabolism in the stems. The differential 4CL and HCT metabolites were downregulated, namely, phenylalanine and tyrosine. Additionally, ETH upregulated 2-hydroxycinnamic acid and the cinnamyl hydroxyl derivatives (caffeic acid and p-coumaric acid). Cinnamic acid is a crucial intermediate in the shikimic acid pathway, which serves as a precursor for the biosynthesis of flavonoids and lignin. The ETH-decreased gene expression and metabolite alteration reduced the lignin levels in the stem. Moreover, the HCT downregulation may explain the inhibited lignin biosynthesis to promote flavonoid biosynthesis. In conclusion, external ETH application can effectively reduce lignin contents and increase the secondary metabolites of ramie without affecting its growth and development. These results provide candidate genes for improving ramie and offer theoretical and practical guidance for cultivating ramie for forage.
摘要:
Abstract: Cutleaf groundcherry (Physalis angulata L.), an annual plant containing a variety of active ingredients, has great medicinal value. However, studies on the genetic diversity and population structure of P. angulata are limited. In this study, we developed chloroplast microsatellite (cpSSR) markers and applied them to evaluate the genetic diversity and population structure of P. angulata. A total of 57 cpSSRs were identified from the chloroplast genome of P. angulata. Among all cpSSR loci, mononucleotide markers were the most abundant (68.24%), followed by tetranucleotide (12.28%), dinucleotide (10.53%), and trinucleotide (8.77%) markers. In total, 30 newly developed cpSSR markers with rich polymorphism and good stability were selected for further genetic diversity and population structure analyses. These cpSSRs amplified a total of 156 alleles, 132 (84.62%) of which were polymorphic. The percentage of polymorphic alleles and the average polymorphic information content (PIC) value of the cpSSRs were 81.29% and 0.830, respectively. Population genetic diversity analysis indicated that the average observed number of alleles (Na), number of effective alleles (He), Nei’s gene diversity (h), and Shannon information indices (I) of 16 P. angulata populations were 1.3161, 1.1754, 0.1023, and 0.1538, respectively. Moreover, unweighted group arithmetic mean, neighbor-joining, principal coordinate, and STRUCTURE analyses indicated that 203 P. angulata individuals from 16 populations were grouped into four clusters. A molecular variance analysis (AMOVA) illustrated the considerable genetic variation among populations, while the gene flow (Nm) value (0.2324) indicated a low level of gene flow among populations. Our study not only provided a batch of efficient genetic markers for research on P. angulata but also laid an important foundation for the protection and genetic breeding of P. angulata resources. Keywords: Physalis angulata; Solanaceae; simple sequence repeat; genetic variation; population structure
通讯机构:
[Jin-Song Luo; Zhenhua Zhang] C;College of Resources, Hunan Agricultural University, Changsha 410128, China<&wdkj&>Hunan Provincial Key Laboratory of Farmland Pollution Control and Agricultural Resources Use, Hunan Provincial Key Laboratory of Nutrition in Common University, National Engineering Laboratory on Soil and Fertilizer Resources Efficient Utilization, Changsha 410128, China
摘要:
Abstract: The safe production of food on Cd-polluted land is an urgent problem to be solved in South China. Phytoremediation or cultivation of rice varieties with low Cd are the main strategies to solve this problem. Therefore, it is very important to clarify the regulatory mechanism of Cd accumulation in rice. Here, we identified a rice variety with an unknown genetic background, YSD, with high Cd accumulation in its roots and shoots. The Cd content in the grains and stalks were 4.1 and 2.8 times that of a commonly used japonica rice variety, ZH11, respectively. The Cd accumulation in the shoots and roots of YSD at the seedling stage was higher than that of ZH11, depending on sampling time, and the long-distance transport of Cd in the xylem sap was high. Subcellular component analysis showed that the shoots, the cell wall, organelles, and soluble fractions of YSD, showed higher Cd accumulation than ZH11, while in the roots, only the cell wall pectin showed higher Cd accumulation. Genome-wide resequencing revealed mutations in 22 genes involved in cell wall modification, synthesis, and metabolic pathways. Transcriptome analysis in Cd-treated plants showed that the expression of pectin methylesterase genes was up-regulated and the expression of pectin methylesterase inhibitor genes was down-regulated in YSD roots, but there were no significant changes in the genes related to Cd uptake, translocation, or vacuole sequestration. The yield and tiller number per plant did not differ significantly between YSD and ZH11, but the dry weight and plant height of YSD were significantly higher than that of ZH11. YSD provides an excellent germplasm for the exploration of Cd accumulation genes, and the cell wall modification genes with sequence- and expression-level variations provide potential targets for phytoremediation. Keywords: cadmium accumulation; cell wall; pectin methylesterase; rice; phytoremediation; multi-omics