Identification of key genes and metabolites involved in meat quality performance in Qinchuan cattle by WGCNA

Understanding the genetic and metabolic elements that impact meat quality is crucial to improving production and meeting consumer demands in the beef sector.Differences in meat quality among various muscle areas in beef cattle can impact pricing in the market.Despite progress in genomics,the specific genes and metabolites that affect meat quality characteristics in Qinchuan cattle remain inadequately understood.Therefore,this study aims to evaluate the meat quality characteristics of four specific muscle locations(tenderloin,striploin,high rib,and ribeye muscles)in Qinchuan bulls,including 10 traits(total protein content(TPC),intramuscular fat(IMF),non-esterified fatty acid(NEFA),meat color(L*,a*,and b*),shear force(SF),cooking loss(CL),pH0,and pH24).This experiment uses transcriptome,metabolome sequencing,and sophisticated analytical methodologies such as weighted gene co-expression network analysis(WGCNA)and protein–protein interaction networks(PPI)to identify the key genes and metabolites associated with specific traits.The findings highlight three notable genes(NDUFAB1,NDUFA12,and NDUFB7)linked to intramuscular fat(IMF),three key genes(CSRP3,ACAA3,and ACADVL)correlated with non-esterified fatty acids(NEFA),and one crucial gene(CREBBP)influencing meat color.In conclusion,this investigation offers a new perspective on the differences in bovine muscle locations and contributes to the molecular understanding of bovine meat quality.Future research endeavors could delve deeper into the identified genes and pathways to enhance beef cattle’s quality and yield.

Extreme drought with seasonal timing consistently promotes CH_(4) uptake through inconsistent pathways in a temperate grassland, China

Methane(CH_(4))is a potent greenhouse gas that has a substantial impact on global warming due to its substantial influence on the greenhouse effect.Increasing extreme precipitation events,such as drought,attributable to global warming that caused by greenhouse gases,exert a profound impact on the intricate biological processes associated with CH_(4) uptake.Notably,the timing of extreme drought occurrence emerges as a pivotal factor influencing CH_(4) uptake,even when the degree of drought remains constant.However,it is still unclear how the growing season regulates the response of CH_(4) uptake to extreme drought.In an effort to bridge this knowledge gap,we conducted a field manipulative experiment to evaluate the impact of extreme drought on CH_(4) uptake during early,middle,and late growing stages in a temperate steppe of Inner Mongolia Autonomous Region,China.The result showed that all extreme drought consistently exerted positive effects on CH_(4) uptake regardless of seasonal timing.However,the magnitude of this effect varied depending on the timing of season,as evidenced by a stronger effect in early growing stage than in middle and late growing stages.Besides,the pathways of CH_(4) uptake were different from seasonal timing.Extreme drought affected soil physical-chemical properties and aboveground biomass(AGB),consequently leading to changes in CH_(4) uptake.The structural equation model showed that drought both in the early and middle growing stages enhanced CH_(4) uptake due to reduced soil water content(SWC),leading to a decrease in NO_(3)–-N and an increase in pmoA abundance.However,drought in late growing stage primarily enhanced CH_(4) uptake only by decreasing SWC.Our results suggested that seasonal timing significantly contributed to regulate the impacts of extreme drought pathways and magnitudes on CH_(4) uptake.The findings can provide substantial implications for understanding how extreme droughts affect CH_(4) uptake and improve the prediction of potential ecological consequence under future climate change.

Effect of soil archaea on N_(2)O emission in alpine permafrost

Soil microbial communities are pivotal in permafrost biogeochemical cycles,yet the variations of abundant and rare microbial taxa and their impacts on greenhouse gas emissions in different seasons,remain elusive,especially in the case of soil archaea.Here,we conducted a study on soil abundant and rare archaeal taxa during the growing and non-growing seasons in the active layer of alpine permafrost in the Qinghai-Tibetan Plateau.The results suggested that,for the archaeal communities in the sub-layer,abundant taxa exhibited higher diversity,while rare taxa maintained a more stable composition from the growing to non-growing season.Water soluble organic carbon and soil porosity were the most significant environmental variables affecting the compositions of abundant and rare taxa,respectively.Stochastic and deterministic processes dominated the assemblies of rare and abundant taxa,respectively.The archaeal ecological network influenced N_(2)O flux through different modules.Rare taxa performed an essential role in stabilizing the network and exerting important effects on N_(2)O flux.Our study provides a pioneering and comprehensive investigation aimed at unravelling the mechanisms by which archaea or other microorganisms influence greenhouse gas emissions in the alpine permafrost.

Leguminosae plants play a key role in affecting soil physical-chemical and biological properties during grassland succession after farmland abandonment in the Loess Plateau,China

Leguminosae are an important part of terrestrial ecosystems and play a key role in promoting soil nutrient cycling and improving soil properties.However,plant composition and species diversity change rapidly during the process of succession,the effect of leguminosae on soil physical-chemical and biological properties is still unclear.This study investigated the changes in the composition of plant community,vegetation characteristics,soil physical-chemical properties,and soil biological properties on five former farmlands in China,which had been abandoned for 0,5,10,18,and 30 a.Results showed that,with successional time,plant community developed from annual plants to perennial plants,the importance of Leguminosae and Asteraceae significantly increased and decreased,respectively,and the importance of grass increased and then decreased,having a maximum value after 5 a of abandonment.Plant diversity indices increased with successional time,and vegetation coverage and above-and below-ground biomass increased significantly with successional time after 5 a of abandonment.Compared with farmland,30 a of abandonment significantly increased soil nutrient content,but total and available phosphorus decreased with successional time.Changes in plant community composition and vegetation characteristics not only change soil properties and improve soil physical-chemical properties,but also regulate soil biological activity,thus affecting soil nutrient cycling.Among these,Leguminosae have the greatest influence on soil properties,and their importance values and community composition are significantly correlated with soil properties.Therefore,this research provides more scientific guidance for selecting plant species to stabilize soil ecosystem of farmland to grassland in the Loess Plateau,China.

Detection of quantitative trait loci(QTL)associated with spring regrowth in alfalfa(Medicago sativa L.)

Spring regrowth is an important trait for perennial plants including alfalfa,the most cultivated forage legume worldwide.However,the genetic and genomic basis of the trait is largely unknown in alfalfa due to its complex genetic background of the tetroploid genome.The objective of this study was to identify quantitative trait loci(QTLs)associated with spring regrowth using high-resolution genetic linkage maps we constructed previously.In total,36 significant additive effect QTLs for the trait were detected.Among them,10 QTLs individually explained more than 10%of the phenotypic variation(PVE)with four in P1 and six in P2.Six overlapped QTLs intervals were detected with two and four intervals distributed in P1 and P2,respectively.In P1,both overlapped genomic regions were located on homolog 7 D.In P2,the four QTLs with PVE>10%were co-localized on homolog 6 D.Meanwhile,six pairs of significant epistatic QTLs were identified in P2.Screening of potential candidate genes associated with four overlapped QTLs(q CP2019-8,q LF2019-5,q LF2020-4,and q BLUP-3)narrowed down one candidate annotated as MAIL1.The Arabidopsis homolog gene has been reported to play an important role in plant growth.Therefore,the detected QTLs are valuable resources for genetic improvement of alfalfa spring vigor using marker-assisted selection(MAS),and further identification of the associated genes would provide insights into genetic control of spring regrowth in alfalfa.

Plant property regulates soil bacterial community structure under altered precipitation regimes in a semi-arid desert grassland, China

Variations of precipitation have great impacts on soil carbon cycle and decomposition of soil organic matter.Soil bacteria are crucial participants in regulating these ecological processes and vulnerable to altered precipitation.Studying the impacts of altered precipitation on soil bacterial community structure can provide a novel insight into the potential impacts of altered precipitation on soil carbon cycle and carbon storage of grassland.Therefore,soil bacterial community structure under a precipitation manipulation experiment was researched in a semi-arid desert grassland in Chinese Loess Plateau.Five precipitation levels,i.e.,control,reduced and increased precipitation by 40%and 20%,respectively(referred here as CK,DP40,DP20,IP40,and IP20)were set.The results showed that soil bacterial alpha diversity and rare bacteria significantly changed with altered precipitation,but the dominant bacteria and soil bacterial beta diversity did not change,which may be ascribed to the ecological strategy of soil bacteria.The linear discriminate analysis(LDA)effect size(LEfSe)method found that major response patterns of soil bacteria to altered precipitation were resource-limited and drought-tolerant populations.In addition,increasing precipitation greatly promoted inter-species competition,while decreasing precipitation highly facilitated inter-species cooperation.These changes in species interaction can promote different distribution ratios of bacterial populations under different precipitation conditions.In structural equation model(SEM)analysis,with changes in precipitation,plant growth characteristics were found to be drivers of soil bacterial community composition,while soil properties were not.In conclusion,our results indicated that in desert grassland ecosystem,the sensitive of soil rare bacteria to altered precipitation was stronger than that of dominant taxa,which may be related to the ecological strategy of bacteria,species interaction,and precipitation-induced variations of plant growth characteristics.

A bibliometric analysis of carbon exchange in global drylands

Drylands refer to regions with an aridity index lower than 0.65,and billions of people depend on services provided by the critically important ecosystems in these areas.How ecosystem carbon exchange in global drylands(CED)occurs and how climate change affects CED are critical to the global carbon cycle.Here,we performed a comprehensive bibliometric study on the fields of annual publications,marked journals,marked institutions,marked countries,popular keywords,and their temporal evolution to understand the temporal trends of CED research over the past 30 a(1991-2020).We found that the annual scientific publications on CED research increased significantly at an average growth rate of 7.93%.Agricultural Water Management ranked first among all journals and had the most citations.The ten most productive institutions were centered on drylands in America,China,and Australia that had the largest number and most citations of publications on CED research."Climate change"and climate-related(such as"drought","precipitation","temperature",and"rainfall")research were found to be the most popular study areas.Keywords were classified into five clusters,indicating the five main research focuses on CED studies:hydrological cycle,effects of climate change,carbon and water balance,productivity,and carbon-nitrogen-phosphorous coupling cycles.The temporal evolution of keywords further showed that the areas of focus on CED studies were transformed from classical pedology and agricultural research to applied ecology and then to global change ecological research over the past 30 a.In future CED studies,basic themes(such as"water","yield",and"salinity")and motor themes(such as"climate change","sustainability",and"remote sensing")will be the focus of research on CED.In particular,multiple integrated methods to understand climate change and ecosystem sustainability are potential new research trends and hotspots.

Using the response-effect trait framework to disentangle the effects of environmental change on the ecosystem services

Functional traits play a vital role in mediating the responses of ecosystem services to environmental changes and in predicting the functioning of the ecosystem.However,the connection between functional traits and ecosystem services has become increasingly intricate due to climate change and human activities for degraded ecosystems.To investigate this relationship,we selected 27 sampling sites in the Yanhe River Basin of the Chinese Loess Plateau,each containing two types of vegetation ecosystems:natural vegetation and artificial vegetation ecosystems.At each sampling site,we measured ecosystem services and calculated the composition index of community traits.We established a response–effect trait framework that included environmental factors such as climate,elevation and human activities.Our results showed that leaf tissue density(LTD)was the overlapping response and effect trait when responding to climate change.LTD is positively correlated with mean annual temperature and negatively correlated with supporting services.Under the influence of human activities,leaf nitrogen content and leaf dry matter content were carriers of environmental change.Comparing the two vegetation ecosystems,the relationship between functional traits and ecosystem services showed divergent patterns,indicating that human activities increased the uncertainty of the relationship between functional traits and ecosystem services.Trait-based ecology holds promise for enhancing predictions of ecosystem services responses to environmental changes.However,the predictive ability is influenced by the complexity of environmental changes.In conclusion,our study highlights the importance of understanding the complex connection between functional traits and ecosystem services in response to climate changes and human activities.

Critical function of DNA methyltransferase 1 in tomato development and regulation of the DNA methylome and transcriptome

DNA methylation confers epigenetic regulation on gene expression and thereby on various biological processes.Tomato has emerged as an excellent system to study the function of DNA methylation in plant development.To date,regulation and function of DNA methylation maintenance remains unclear in tomato plants.Here,we report the critical function of tomato(Solanum lycopersicum)Methyltransferase 1(Sl MET1)in plant development and DNA methylome and transcriptome regulation.Using CRISPR-Cas9 gene editing,we generated slmet1 mutants and observed severe developmental defects with a frame-shift mutation,including small and curly leaves,defective inflorescence,and parthenocarpy.In leaf tissues,mutations in Sl MET1 caused CG hypomethylation and CHH hypermethylationon a whole-genome scale,leading to a disturbed transcriptome including ectopic expression of many RIN target genes such as ACC2 in leaf tissues,which are normally expressed in fruits.Neither the CG hypomethylation nor CHH hypermethylation in the slmet1 mutants is related to tissue culture.Meanwhile,tissue culture induces non-CG hypomethylation,which occurs more frequently at gene regions than at TE regions.Our results depict Sl MET1-and tissue culture-dependent tomato DNA methylomes,and that Sl MET1 is required for maintaining a normal transcriptome and normal development of tomato.

LOWER TEMPERATURE 1 Enhances ABA Responses and Plant Drought Tolerance by Modulating the Stability and Localization of C2-Domain ABA-Related Proteins in Arabidopsis

Plasma membrane-associated abscisic acid(ABA)signal transduction is an integral part of ABA signaling.The C2-domain ABA-related(CAR)proteins play important roles in the recruitment of ABA receptors to the plasma membrane to facilitate ABA signaling.However,how CAR proteins are regulated remains unclear.In this study,we conducted a genetic screen for mutants with altered leaf transpiration and identified an uncharacterized protein,LOWER TEMPERATURE 1(LOT1),which regulates the dynamic localization and stability of CAR proteins.The lotimutant had a lower leaf temperature as compared with the wild type due to higher transpiration.We found that LOT1 physically interacts with CAR9,and ABA reduces LOT1-CAR9 interaction in the nucleus,likely via Ca^2+,resulting in increased localization of CAR9 to the plasma membrane.We further found that the stability of CAR9 is affected by LOT1 less CAR9 proteins were accumulated and more were ubiquitinated in lot1.While the lot1 car9 and/of f car9 mutants were hyposerisitive to ABA,the hyposensitive phenotype of loticould be rescued by CAR9 overexpression.Collectively,our study reveals that LOT1 regulates plant tolerance to drought stress by affecting ABA signaling through regulating the stability and dynamic localization of CAR9.

Effects of Robinia pseudoacacia on the undergrowth of herbaceous plants and soil properties in the Loess Plateau of China

Aims The introduction of Robinia pseudoacacia(RP)has some effects on undergrowth herbaceous plants(UH),soil properties and their relationships,which may be related to the vegetation zone.However,few studies have tested effects of RP on UH and soil over a large-scale area of the Loess Plateau.Methods The study area consisted of three vegetation zones(the steppe,forest-steppe and forest zone).Two canopy plant types were selected:RP stands and adjacent native vegetation.We measured five leaf functional traits:leaf carbon content(LC),leaf nitrogen content(LN),leaf phosphorus content(LP),specific leaf area(SLA)and leaf tissue density(LTD).The functional diversity,species diversity and community-weighted mean(CWM)traits were calculated.Important Findings(i)CWM.LN,CWM.LP and CWM.SLA increased significantly,whereas CWM.LC and CWM.LTD decreased significantly in the three vegetation zones,compared with the native communities.(ii)Species diversity,functional diversity and community biomass decreased in the steppe zone,increased in the forest zone,and did not differ significantly in the forest-steppe zone.(iii)We found only soil organic carbon(P<0.05)and soil total nitrogen(P<0.05)in the forest zone decreased significantly compared with the native plots.(iv)The relationship between UH and soil properties was affected by RP and the vegetation zone.Overall,the effect of RP on UH and soil properties was associated with the vegetation zone.This result is of great significance to the planning of restoration and reconstruction of artificial forests in the Loess Plateau.

MDP25 mediates the fine-tuning of microtubule organization in response to salt stress

Microtubules are dynamic cytoskeleton structures playing fundamental roles in plant responses to salt stress.The precise mechanisms by which microtubule organization is regulated under salt stress are largely unknown.Here,we report that Arabidopsis thaliana MICROTUBULE-DESTABILIZING PROTEIN 25(MDP25;also known as PLASMA MEMBRANEASSOCIATED CATION-BINDING PROTEIN 1(PCaP1))helps regulate microtubule organization.Under salt treatment,elevated cytosolic Ca^(2+) concentration caused MDP25 to partially dissociate from the plasma membrane,promoting microtubule depolymerization.When Ca^(2+) signaling was blocked by BAPTA-AM or LaCl_(3),microtubule depolymerization in wild-type and MDP25-overexpressing cells was slower,while there was no obvious change in mdp25 cells.Knockout of MDP25 improved microtubule reassembly and was conducive to microtubule integrity under long-term salt treatment and microtubule recovery after salt stress.Moreover,mdp25 seedlings exhibited a higher survival rate under salt stress.The presence microtubule-disrupting reagent oryzalin or microtubule-stabilizing reagent paclitaxel differentially affected the survival rates of different genotypes under salt stress.MDP25 promoted microtubule instability by affecting the catastrophe and rescue frequencies,shrinkage rate and time in pause phase at the microtubule plus-end and the depolymerization rate at the microtubule minus-end.These findings reveal a role for MDP25 in regulating microtubule organization under salt treatment by affecting microtubule dynamics.

Erratum to:The fungal endophyte Epichloë gansuensis increases NaCl-tolerance in Achnatherum inebrians through enhancing the activity of plasma membrane H^(+)-ATPase and glucose-6-phosphate dehydrogenase

1.In the results,we mistakenly described the information of Figure 9B.The correct sentence should be“The factor 1 and factor 2 explained 71.30%and 16.68%of the total variance,respectively.The 0 mmol L^(-1) NaCl concentration showed the highest contribution(29.95%)to factor 1 in roots of E+plants,and 200 mmol L^(-1) NaCl concentration was significantly loaded(45.95%)on factor 2 in roots of E+plants(Figure 9B).”

The fungal endophyte Epichloëgansuensis increases NaCltolerance in Achnatherum inebrians through enhancing the activity of plasma membrane H^(+)-ATPase and glucose-6-phosphate dehydrogenase

Salt stress negatively affects plant growth,and the fungal endophyte Epichloëgansuensis increases the tolerance of its host grass species,Achnatherum inebrians,to abiotic stresses.In this work,we first evaluated the effects of E.gansuensis on glucose-6-phosphate dehydrogenase(G6PDH)and plasma membrane(PM)H^(+)-ATPase activity of Achnatherum inebrians plants under varying NaCl concentrations.Our results showed that the presence of E.gansuensis increased G6PDH,PMH^(+)-ATPase,superoxide dismutase and catalase activity to decrease O2•^(–),H_(2)O_(2)and Na^(+)contents in A.inebrians under NaCl stress,resulting in enhanced salt tolerance.In addition,the PM NADPH oxidase activity and NADPH/NADP+ratios were all lower in A.inebrians with E.ganusensis plants than A.inebrians plants without this endophyte under NaCl stress.In conclusion,E.gansuensis has a positive role in improving host grass yield under NaCl stress by enhancing the activity of G6PDH and PM H^(+)-ATPase to decrease ROS content.This provides a new way for the selection of stress-resistant and high-quality forage varieties by the use of systemic fungal endophytes.

Drought stress and plant ecotype drive microbiome recruitment in switchgrass rhizosheath

The rhizosheath,a layer of soil grains that adheres firmly to roots,is beneficial for plant growth and adaptation to drought environments.Switchgrass is a perennial C4 grass which can form contact rhizosheath under drought conditions.In this study,we characterized the microbiomes of four different rhizocompartments of two switchgrass ecotypes(Alamo and Kanlow)grown under drought or well-watered conditions via 16S ribosomal RNA amplicon sequencing.These four rhizocompartments,the bulk soil,rhizosheath soil,rhizoplane,and root endosphere,harbored both distinct and overlapping microbial communities.The root compartments(rhizoplane and root endosphere)displayed low-complexity communities dominated by Proteobacteria and Firmicutes.Compared to bulk soil,Cyanobacteria and Bacteroidetes were selectively enriched,while Proteobacteria and Firmicutes were selectively depleted,in rhizosheath soil.Taxa from Proteobacteria or Firmicutes were specifically selected in Alamo or Kanlow rhizosheath soil.Following drought stress,Citrobacter and Acinetobacter were further enriched in rhizosheath soil,suggesting that rhizosheath microbiome assembly is driven by drought stress.Additionally,the ecotype-specific recruitment of rhizosheath microbiome reveals their differences in drought stress responses.Collectively,these results shed light on rhizosheath microbiome recruitment in switchgrass and lay the foundation for the improvement of drought tolerance in switchgrass by regulating the rhizosheath microbiome.