Understanding water chemistry in karst regions is crucial for improving global water resource management and deepening our knowledge of the biogeochemical cycles shaping these sensitive environments.Despite advance-me...Understanding water chemistry in karst regions is crucial for improving global water resource management and deepening our knowledge of the biogeochemical cycles shaping these sensitive environments.Despite advance-ments in karst hydrology,significant gaps remain in long-term trends,underlying processes,and quantitative effects of environmental changes.This is especially true in areas like the Wujiang River(WJ)in China,where human activities such as reservoir construction and land use/cover changes have accelerated hydrochemical changes.We combined recent and historical monitoring data to provide a detailed analysis of the spatial and temporal characteristics,evolution,and controlling factors of major ions in WJ.These findings are important for local water management and contribute to global efforts to manage similar karst systems facing human-induced pressures.Our research shows clear seasonal differences in solute concentrations,with higher levels during the dry season.WJ’s water is rich in calcium,with Ca-HCO_(3) ion pairs being the most common.Reservoir monitor-ing stations show much higher levels of NO_(3)^(−)and SO_(4)^(2−)compared to river-type stations,likely due to longer hydraulic retention time and increased acid deposition.The study confirms the significant role of pH and water temperature in rock weathering processes.Land use/cover changes were identified as the primary drivers of solute variations(46.37%),followed by lithology(13.92%)and temperature(8.35%).Over the past two decades,in-tense carbonate weathering has been observed,especially during wet seasons.Among karstic provinces,Guizhou Province stands out with the highest ion concentrations,indicative of its extensive karst coverage and heightened weathering processes.展开更多
Coconut(Cocos nucifera L.),a major oil and fruit crop of the Arecaceae family,is extensively cultivated across the Asia—Pacific region.Despite its agricultural importance,genome assembly in coconut remains challengin...Coconut(Cocos nucifera L.),a major oil and fruit crop of the Arecaceae family,is extensively cultivated across the Asia—Pacific region.Despite its agricultural importance,genome assembly in coconut remains challenging due to its large genome size and high proportion of repetitive sequences.Allele-specific expression(ASE)plays a key role in regulating plant development and evolution,yet research on ASE in coconut is limited(Shao et al.,2019;Li et al.,2021;Zhang et al.,2021;Hu et al.,2022).Among phenotypic traits,fruit color is especially important as an indicator of maturity,guiding harvest timing and post-harvest processes(Kapoor et al.,2022).While prior studies have explored various coconut traits such as salt tolerance,fiber content,and plant height(Wang et al.,2021;Yang et al.,2021),investigations into ASE and fruit color remain scarce.展开更多
Highlights OsCAX2 is localized to tonoplast,and cadmium induces its expression.OsCAX2 overexpression reduces cadmium concentration in indica rice grains by 49.1%.Cadmium(Cd)exposure poses significant health risks to h...Highlights OsCAX2 is localized to tonoplast,and cadmium induces its expression.OsCAX2 overexpression reduces cadmium concentration in indica rice grains by 49.1%.Cadmium(Cd)exposure poses significant health risks to humans,and the International Agency for Research on Cancer has classified it as a Group I carcinogen.Cadmium undergoes minimal metabolism in the human body;consequently,prolonged Cd^(2+)exposure can cause severe damage to multiple organs including the liver,kidneys,lungs,bones,and immune system(Shao et al.2024).Rice,one of the three global staple crops,and Cd exposure in humans primarily occurs the consumption of contaminated rice grains.The contribution of rice to the total dietary Cd intake is over 50% for non-smoking Asian populations(Chen et al.2018;Shi et al.2020).展开更多
Nondestructive measurement technology of phenotype can provide substantial phenotypic data support for applications such as seedling breeding,management,and quality testing.The current method of measuring seedling phe...Nondestructive measurement technology of phenotype can provide substantial phenotypic data support for applications such as seedling breeding,management,and quality testing.The current method of measuring seedling phenotypes mainly relies on manual measurement which is inefficient,subjective and destroys samples.Therefore,the paper proposes a nondestructive measurement method for the canopy phenotype of the watermelon plug seedlings based on deep learning.The Azure Kinect was used to shoot canopy color images,depth images,and RGB-D images of the watermelon plug seedlings.The Mask-RCNN network was used to classify,segment,and count the canopy leaves of the watermelon plug seedlings.To reduce the error of leaf area measurement caused by mutual occlusion of leaves,the leaves were repaired by CycleGAN,and the depth images were restored by image processing.Then,the Delaunay triangulation was adopted to measure the leaf area in the leaf point cloud.The YOLOX target detection network was used to identify the growing point position of each seedling on the plug tray.Then the depth differences between the growing point and the upper surface of the plug tray were calculated to obtain plant height.The experiment results show that the nondestructive measurement algorithm proposed in this paper achieves good measurement performance for the watermelon plug seedlings from the 1 true-leaf to 3 true-leaf stages.The average relative error of measurement is 2.33%for the number of true leaves,4.59%for the number of cotyledons,8.37%for the leaf area,and 3.27%for the plant height.The experiment results demonstrate that the proposed algorithm in this paper provides an effective solution for the nondestructive measurement of the canopy phenotype of the plug seedlings.展开更多
Structural variants(SVs)are a type of genetic variation that contribute substantially to phenotypic diversity and evolution.Further study of SVs will help us understand the influence of SVs associated with tea quality...Structural variants(SVs)are a type of genetic variation that contribute substantially to phenotypic diversity and evolution.Further study of SVs will help us understand the influence of SVs associated with tea quality and stress resistance and provide new insight into tea plant breeding improvement and genetic research.However,SVs have not been thoroughly discovered in the tea plant genomes.Herein,we constructed a large-scale SV map across a population of 107 resequenced genomes,including both ancient and cultivated tea plants.A total of 44,240 highconfident SVs were identified,including 34,124 DEL(deletions),4,448 DUP(duplications),2,503 INV(inversions),544 INS(insertions)and 2,621 TRA(translocations).In total,12,400 protein-coding genes were overlapped with SVs,of which 49.5%were expressed in all five tea tissues.SVbased analysis of phylogenetic relationships and population structure in tea plants showed a consistent evolutionary history with the SNP-based results.We also identified SVs subject to artificial selection and found that genes under domestication were enriched in metabolic pathways involving theanine and purine alkaloids,biosynthesis of monoterpenoid,phenylpropanoid,fatty acid,and isoflavonoid,contributing to traits of agronomic interest in tea plants.In addition,a total of 27 terpene synthase(TPS)family genes were selected during domestication.These results indicate that these SVs could provide extensive genomic information for tea quality improvement.展开更多
Chitin is an abundant aminopolysaccharide found in insect pests and phytopathogenic microorganisms but absent in higher plants and vertebrates. It is crucial for mitigating threats posed by chitin-containing organisms...Chitin is an abundant aminopolysaccharide found in insect pests and phytopathogenic microorganisms but absent in higher plants and vertebrates. It is crucial for mitigating threats posed by chitin-containing organisms to human health, food safety, and agriculture. Therefore, targeting the chitin biosynthesisassociated bioprocess holds a promise for developing human-safe and eco-friendly antifungal agents or pesticides. Chitin biosynthesis requires chitin synthase and associated factors, which are involved in the modification, regulation, organization or turnover of chitin during its biosynthesis. A number of enzymes such as chitinases, hexosaminidases, chitin deacetylases are closely related and therefore are promising targets for designing novel agrochemicals that target at chitin biosynthesis. This review summarizes the advances in understanding chitin biology over the past decade by our research group and collaborates,specifically regarding essential proteins linked to chitin biosynthesis that can be exploited as promising pesticide targets. Examples of small bioactive molecules that against the activity of these targets are given.展开更多
Tomato(Solanum lycopersicum)is an important fruit and vegetable crop in worldwide.The fertility of tomato reproductive organs can be dramatically decreased when ambient temperatures rise above 35°C,reducing tomat...Tomato(Solanum lycopersicum)is an important fruit and vegetable crop in worldwide.The fertility of tomato reproductive organs can be dramatically decreased when ambient temperatures rise above 35°C,reducing tomato fruit yield.It is necessary to identify transcription factors(TFs)and target genes involved in heat stress response(HSR)signaling cascades in tomato flower buds to improve tomato plant thermotolerance.In this study,we profiled genes expressed in three developmental stages of tomato flower buds.Red and turquoise modules for heat stress(HS)were identified through gene co-expression network analysis,and the genes within these modules were enriched in HS-related pathways.By focusing on the TFs in the two modules,we identified several novel HSR-related TFs,including SlWRKY75,SlMYB117,and SlNAM.Furthermore,homology analysis illustrated a conserved signaling cascade in tomato.Lastly,we identified and experimentally validated four HSF-regulated genes,namely SlGrpE,SlERDJ3A,SlTIL,and SlPOM1,that likely modulate thermotolerance in plants.These results provide a high-resolution atlas of gene expression during tomato flower bud development under HS conditions,which is a valuable resource for uncovering potential regulatory networks associated with the HSR in tomato.展开更多
Photosynthesis is one the most important chemical reaction in plants,and it is the ultimate energy source of any living organisms.The light and dark reactions are two essential phases of photosynthesis.Light reaction ...Photosynthesis is one the most important chemical reaction in plants,and it is the ultimate energy source of any living organisms.The light and dark reactions are two essential phases of photosynthesis.Light reaction harvests light energy to synthesize ATP and NADPH through an electron transport chain,and as well as giving out O_(2);dark reaction fixes CO_(2) into six carbon sugars by utilizing NADPH and energy from ATP.Subsequently,plants convert optical energy into chemical energy for maintaining growth and development through absorbing light energy.Here,firstly,we highlighted the biological importance of photosynthesis,and hormones and metabolites,photosynthetic and regulating enzymes,and signaling components that collectively regulate photosynthesis in tomato.Next,we reviewed the advances in tomato photosynthesis,including two aspects of genetic basis and genetic improvement.Numerous genes regulating tomato photosynthesis are gradually uncovered,and the interaction network among those genes remains to be constructed.Finally,the photosynthesis occurring in fruit of tomato and the relationship between photosynthesis in leaf and fruit were discussed.Leaves and fruits are photosynthate sources and sinks of tomato respectively,and interaction between photosynthesis in leaf and fruit exists.Additionally,future perspectives that needs to be addressed on tomato photosynthesis were proposed.展开更多
Juglans sigillata is an economically valuable nut crop renowned for its nutritional richness,including essential nutrients,antioxidants,and healthy fats,which boost human cardial,brain and gut health.Despite its impor...Juglans sigillata is an economically valuable nut crop renowned for its nutritional richness,including essential nutrients,antioxidants,and healthy fats,which boost human cardial,brain and gut health.Despite its importance,the lack of a complete genome assembly has been a stumbling block in its biological breeding process.Therefore,we generated deep coverage ultralong Oxford Nanopore Technology(ONT)and PacBio HiFi reads to construct a telomere-to-telomere(T2T)genome assembly.The final assembly spans 537.27 Mb with no gaps,demonstrating a remarkable completeness of 98.1%.We utilized a combination of transcriptome data and homologous proteins to annotate the genome,identifying 36018 protein-coding genes.Furthermore,we profiled global cytosine DNA methylations using ONT sequencing data.Global methylome analysis revealed high methylation levels in transposable element(TE)-rich chromosomal regions juxtaposed with comparatively lower methylation in gene-rich areas.By integrating a detailed multi-omics data analysis,we obtained valuable insights into the mechanism underlying endopleura coloration.This investigation led to the identification of eight candidate genes(e.g.ANR)involved in anthocyanin biosynthesis pathways,which are crucial for the development of color in plants.The comprehensive genome assembly and the understanding of the genetic basis of important traits like endopleura coloration will open avenues for more efficient breeding programs and improved crop quality.展开更多
A progressive decline in fertility is a well-documented aspect of female aging and is associated with a range of cellular and molecular alterations,including genomic instability and modifications in epigenetic regulat...A progressive decline in fertility is a well-documented aspect of female aging and is associated with a range of cellular and molecular alterations,including genomic instability and modifications in epigenetic regulation.Epigenetic clocks,which estimate biological age based on DNA methylation patterns,have been extensively utilized to evaluate general health status and the risk of various diseases.Despite their broad application,the utility of epigenetic clocks in assessing female reproductive health remains only partially characterized.This minireview consolidates recent advancements in the application of epigenetic clocks to evaluate the functional status of the female reproductive system.The objective is to investigate their potential for quantifying and predicting the biological age of reproductive tissues,thereby establishing a theoretical basis for clinical applications in reproductive medicine.To date,no comprehensive minireview has systematically examined multi-tissue epigenetic clock models in the context of female reproductive aging,positioning this minireview as a novel contribution to the field.展开更多
Abiotic stresses,particularly salinity,pose a major threat to rice productivity,highlighting the need to identify novel genetic resources to improve stress tolerance.Gamma irradiation remains one of the most widely us...Abiotic stresses,particularly salinity,pose a major threat to rice productivity,highlighting the need to identify novel genetic resources to improve stress tolerance.Gamma irradiation remains one of the most widely used tools breeding stress-tolerant plant varieties.In this study,we identified a salt-tolerant rice mutant,salt-insensitive TILLING line 4(sitl4),generated via gamma irradiation and linked its enhanced tolerance to a loss-of-function mutation in Oryza sativa protein acyltransferase for ABA response 1(OsPATA1),which encodes a DHHC-type palmitoyl acyltransferase.Functional analyses using both sitl4 and a CRISPR/Cas9-mediated OsPATA1-knockout line(ospata1)revealed that disruption of OsPATA1 leads to increased abscisic acid(ABA)accumulation and upregulation of ABA-responsive genes under salt stress conditions.We identified OsEULD1b,a previously uncharacterized Euonymus lectin(EUL)domaincontaining protein,as an interactor of OsPATA1.In sitl4 and ospata1,OsEULD1b displayed cytosolic retention,suggesting that its subcellular redistribution enhances its role in ABA-mediated stress signaling.Taken together,our findings demonstrate that OsPATA1 and OsEULD1b form a regulatory module that modulates the ABA-dependent salt stress responses in rice.These results provide new insights into the molecular mechanisms underlying abiotic stress tolerance and will help to identify potential genetic targets for developing stress-tolerant rice cultivars through molecular breeding or genome editing.展开更多
Backgroud Before fertilization,spermatozoa undergo a crucial maturation step called capacitation,which is a unique event regulates the sperm’s ability for successful fertilization.The capacitation process takes place...Backgroud Before fertilization,spermatozoa undergo a crucial maturation step called capacitation,which is a unique event regulates the sperm’s ability for successful fertilization.The capacitation process takes place as the spermatozoa pass through the female reproductive tract(FRT).Dihydrolipoamide dehydrogenase(DLD)protein is a post-pyruvate metabolic enzyme,exhibiting reactive oxygen species(ROS)production which causes capacitation.Additionally,other vital functions of DLD in buffalo spermatozoa are hyperactivation and acrosome reaction.DLD produces the optimum amount of ROS required to induce capacitation process in FRT.Depending on physiological or patho-physiological conditions,DLD can either enhance or attenuate the production of reactive oxygen species(ROS).Aim of this study was to investigate whether changes in the production of ROS in sperm cells can impact their ability to fertilize by triggering the capacitation and acrosome reaction.Results In this study,abundance of DLD protein was quantified between high(n=5)and low fertile bull(n=5)sper-matozoa.It was found that compared to high-fertile(HF)bulls,low-fertile(LF)bulls exhibited significantly(P<0.05)higher DLD abundances.Herein,we optimised the MICA concentration to inhibit DLD function,spermatozoa were treated with MICA in time(0,1,2,3,4,and 5 h)and concentrations(1,2.5,5,and 10 mmol/L)dependent manner.Maximum DLD inhibition was found to be at 4 h in 10 mmol/L MICA concentration,which was used for further exper-imentation in HF and LF.Based on DLD inhibition it was seen that LF bull spermatozoa exhibited significantly(P<0.05)higher ROS production and acrosome reaction in comparison to the HF bull spermatozoa.The kinematic parameters of the spermatozoa such as percent total motility,velocity parameters(VCL,VSL,and VAP)and other parameters(BCF,STR,and LIN)were also decreased in MICA treated spermatozoa in comparison to the control(capacitated)spermatozoa.Conclusions The present study provides an initial evidence explaining the buffalo bull spermatozoa with higher DLD abundance undergo early capacitation,which subsequently reduces their capacity to fertilize.展开更多
Zinc(Zn)is an essential micronutrient for both plants and humans.Zn deficiency is common in many paddy fields and reduces yield and grain Zn content(GZC).To accelerate breeding for improved GZC and Zn deficiency toler...Zinc(Zn)is an essential micronutrient for both plants and humans.Zn deficiency is common in many paddy fields and reduces yield and grain Zn content(GZC).To accelerate breeding for improved GZC and Zn deficiency tolerance(ZDT)rice varieties,it is important to identify genes regulating Zn homeostasis.In this study,a member of the Ser/Thr protein phosphatase family,LOC_Os07g48840(named as OsGZ7),was found to contributed to ZDT and GZC in rice.The expression of OsGZ7 in roots and shoots was inhibited by Zn deficiency and toxicity,but induced by iron(Fe),manganese(Mn),and copper(Cu)deficiency,as well as chromium toxicity.OsGZ7 localized to the cytoplasm and was expressed in all tissues during the tillering,flowering,and grain-filling stages,particularly in the leaf blade and leaf sheath.At the seedling stage,knockout of OsGZ7 enhanced ZDT and increased Zn accumulation in both roots and shoots.At the maturity stage,knockout of OsGZ7 enhanced GZC,while overexpression of OsGZ7 reduced GZC.RNA-seq analysis suggested that OsGZ7 might regulate Zn homeostasis by affecting metal binding,hormone signal transduction,and oxidoreductase activity.Taken together,our findings indicate that OsGZ7 contributes to ZDT and Zn accumulation in rice.展开更多
This study evaluated the molecular characterization of different ecotypes of B. aegyptiaca populations in the four sites: Koily alpha, Labgar, Ranérou and Ballou according to the environment with the aim of devel...This study evaluated the molecular characterization of different ecotypes of B. aegyptiaca populations in the four sites: Koily alpha, Labgar, Ranérou and Ballou according to the environment with the aim of developing protection strategies. We sampled leaves of B. aegyptiaca in each individual from each site to extract and amplify a fragment of mitochondrial DNA including cytochrome b and then carefully preserved. DNA extraction, polymerase chain amplification and sequencing of MT-CYB were performed in 64 individuals. Genetic diversity and structure of B. aegyptiaca were determined using the MEGA, DNasp and Arlequin software. The results showed a high haplotype diversity and low nucleotide diversity, indicating a population expansion linked to an important gene flow. Genetic distances between populations were positively correlated with geographic distance. The importance of having highlighted this genetic differentiation of the B. aegyptiaca species between these sites is to be able to understand the degree of genetic heterogeneity of each and correlate it with adaptability because genetic diversity influences the adaptation of the species.展开更多
In this review,we explore the application of next-generation sequencing in liver cancer research,highlighting its potential in modern oncology.Liver cancer,particularly hepatocellular carcinoma,is driven by a complex ...In this review,we explore the application of next-generation sequencing in liver cancer research,highlighting its potential in modern oncology.Liver cancer,particularly hepatocellular carcinoma,is driven by a complex interplay of genetic,epigenetic,and environmental factors.Key genetic alterations,such as mutations in TERT,TP53,and CTNNB1,alongside epigenetic modifications such as DNA methylation and histone remodeling,disrupt regulatory pathways and promote tumorigenesis.Environmental factors,including viral infections,alcohol consum-ption,and metabolic disorders such as nonalcoholic fatty liver disease,enhance hepatocarcinogenesis.The tumor microenvironment plays a pivotal role in liver cancer progression and therapy resistance,with immune cell infiltration,fibrosis,and angiogenesis supporting cancer cell survival.Advances in immune check-point inhibitors and chimeric antigen receptor T-cell therapies have shown po-tential,but the unique immunosuppressive milieu in liver cancer presents challenges.Dysregulation in pathways such as Wnt/β-catenin underscores the need for targeted therapeutic strategies.Next-generation sequencing is accele-rating the identification of genetic and epigenetic alterations,enabling more precise diagnosis and personalized treatment plans.A deeper understanding of these molecular mechanisms is essential for advancing early detection and developing effective therapies against liver cancer.展开更多
Resilience traits in pig populations allow animals to deal better with infectious disease and suboptimal production environments.The data on daily weight,feed intake and feed behaviors in pigs are collected in test pe...Resilience traits in pig populations allow animals to deal better with infectious disease and suboptimal production environments.The data on daily weight,feed intake and feed behaviors in pigs are collected in test period by automated feeding stations,which facilitate to evaluate the resilience traits.In this study,we adopted the root mean square error(RMSE)of ordinary least squares(OLS)and the negative residuals of quantile regression(QR)to generate four different novel resilience traits using daily records of feed intake and feed duration between 90 and 180 days of age in a population of commercial Duroc pigs.The genome-wide association studies(GWAS)based on single-and two-trait mixed models were carried out on 550 pigs using 48,603 single nucleotide polymorphisms(SNPs)to identify genomic regions associated with resilience traits in growing pigs.We further focused on the GWAS signals to conduct gene annotation,colocalization with multi-tissue eQTL summary statistics of PigGTEx project and identification of enhancers and promoters using the publicly available data.The genomic heritabilities of four novel resilience traits ranged from 0.09 to 0.41.The pairwise genetic and phenotypic correlations ranged from 0.16 to 0.95 and from 0.05 to 0.36,respectively.Twenty-seven SNPs were identified to be significantly associated with these resilience traits.They were distributed on nine chromosomes(SSC1,SSC2,SSC6,SSC7,SSC8,SSC12,SSC14,SSC16 and SSC17).After annotation,39 QTLs and 49 candidate genes were identified.Several of these are functionally relevant candidate genes including OTUD4,TIFA and CARD14,which are involved in the host immune response,disease susceptibility and signal transduction.Eight unique SNPs were found to be causal in both GWAS and eQTL analyses across 15 tissues.Notably,one SNP(rs80794541)was associated with eQTLs identified concurrently across seven tissues/cell types,including the macrophage cell type.Furthermore,four significant SNPs(rs81467127,rs81356029,rs80794541 and rs81305085)were linked to the function of the primed enhancer,active element,and poised promoter in five pig tissues.Using the porcine fibroblast HiC dataset,SNP(rs81356029)on SSC2 regulates the CARNS1 and SSH3,while SNP(rs80794541)on SSC7 regulates the H2AC6.In this study,we generated four novel resilience traits and identified SNPs significantly associated with these resilience traits in a Duroc pig population.GWAS signals were associated with candidate genes involving in the immune traits,and were linked to the crucial regulatory elements as well.Our findings will contribute to elucidating the genetic mechanism that can enhance genome-enabled breeding and inform further research on resilience in domestic pigs.展开更多
Chitin is an abundant natural biopolymer that plays a crucial role in insect growth and development as a fundamental structural component of the exoskeleton.The membrane-integralβ-glycosyltransferase,chitin synthase,...Chitin is an abundant natural biopolymer that plays a crucial role in insect growth and development as a fundamental structural component of the exoskeleton.The membrane-integralβ-glycosyltransferase,chitin synthase,has been identified as the central component in chitin biosynthesis.However,the precise roles of other proteins in facilitating chitin synthase in chitin biosynthesis remain unclear.In this study,we employed split-ubiquitin membrane yeast two-hybrid(MYTH)and pull-down assays to demonstrate the physical interaction between Twinstar(Tsr),a small molecular protein in the actin-depolymerizing factor ADF/Cofilin protein family,and chitin synthase Krotzkopf verkehrt(Kkv)in Drosophila melanogaster in vitro.The RNA interference(RNAi)-mediated global knockdown of Tsr in D.melanogaster resulted in larval lethality.Furthermore,targeted suppression of Tsr in the tracheal and epidermal tissues also led to larval mortality,while knocking down Tsr in the wing tissues led to wrinkled wings.Additionally,silencing Tsr not only reduced the chitin content in the first longitudinal vein of the wings but also led to the absence of the chitin lamellar structure.To validate the functional conservation of Tsr in other insect orders,the two agricultural pests Ostrinia furnacalis and Tribolium castaneum,representing lepidoptera and coleoptera insects,respectively,were investigated.Knockdown experiments targeting the Drosophila Tsr orthologues OfTsr in O.furnacalis and TcTsr in T.castaneum produced abnormal larvae during molting or pupation in O.furnacalis and lethality in T.castaneum.Our findings not only improve ourknowledge of the chitin biosynthesis machinery in insect cuticles but also provide new potential targets for the control of major agricultural pests.展开更多
Potato(Solanum tuberosum)is a globally important staple crop.However,cultivated potato varieties are highly sensitive to low temperatures.The molecular mechanisms underlying freezing resistance in potatoes remain poor...Potato(Solanum tuberosum)is a globally important staple crop.However,cultivated potato varieties are highly sensitive to low temperatures.The molecular mechanisms underlying freezing resistance in potatoes remain poorly understood.Through comparative metabolome and transcriptome analyses of freezing-tolerant(CM,Solanum commersonii)and freezing-sensitive(DM,DM1-3516R44)varieties,we identified a coldinduced UDP-glycosyltransferase gene,ScUGT73B4,which is associated with the accumulation of glycosylated flavonoids in wild CM varieties.Overexpression of ScUGT73B4 led to increased accumulation of glycosylated flavonoids and enhanced antioxidant capacity,resulting in improved freezing tolerance in potato plantlets.These findings reveal a UDP-glycosyltransferase in the flavonoid pathway and offer a potential valuable genetic resource for breeding potatoes with improved freezing tolerance.展开更多
Increasing number of structural variations(SVs)have been identified as causative mutations for diverse agronomic traits.However,the systematic exploration of SVs quantity,distribution,and contribution in wheat was lac...Increasing number of structural variations(SVs)have been identified as causative mutations for diverse agronomic traits.However,the systematic exploration of SVs quantity,distribution,and contribution in wheat was lacking.Here,we report high-quality gene-based and SV-based pangenomes comprising 22 hexaploid wheat assemblies showing a wide range of chromosome size,gene number,and TE component,which indicates their representativeness of wheat genetic diversity.Pan-gene analyses uncover 140,261 distinct gene families,of which only 23.2%are shared in all accessions.Moreover,we build a∼16.15 Gb graph pangenome containing 695,897 bubbles,intersecting 5132 genes and 230,307 cis-regulatory regions.Pairwise genome comparisons identify∼1,978,221 non-redundant SVs and 497 SV hotspots.Notably,the density of bubbles as well as SVs show remarkable aggregation in centromeres,which probably play an important role in chromosome plasticity and stability.As for functional SVs exploration,we identify 2769 SVs with absolute relative frequency differences exceeding 0.7 between spring and winter growth habit groups.Additionally,several reported functional genes in wheat display complex structural graphs,for example,PPD-A1,VRT-A2,and TaNAAT2-A.These findings deepen our understanding of wheat genetic diversity,providing valuable graphical pangenome and variation resources to improve the efficiency of genome-wide association mapping in wheat.展开更多
Tomato,a vegetable of considerable global significance,has been the subject of extensive breeding efforts primarily aimed at achieving high yields and resistance to multiple stressors.However,despite these endeavors,t...Tomato,a vegetable of considerable global significance,has been the subject of extensive breeding efforts primarily aimed at achieving high yields and resistance to multiple stressors.However,despite these endeavors,the quality of fruits still cannot fully satisfy the diverse preferences of the majority of consumers.The elucidation of genetic determinants underlying fruit quality traits,coupled with the advancement of gene editing techniques,has significantly contributed to the enhancement of tomato quality.Combining with gene editing technology to improve tomato fruit quality traits represents a viable approach for maximizing the utilization of essential genes in breeding programs.This review provides a comprehensive summary of the significant genes associated with tomato fruit quality traits,as well as an overview of the current advancements and potential avenues for enhancing tomato quality through gene editing technology.Four important aspects of fruit quality-appearance,flavor,nutritional profiles and postharvest properties form the basis of the review,providing a thorough update on the state of research in tomato fruit quality improvement via new gene editing techniques.展开更多
基金supported by Guangdong Basic and Applied Basic Research Foundation(Nos.2023A1515110824 and 2025A1515011839)Shenzhen Science and Technology Program(No.RCBS20231211090638066).
文摘Understanding water chemistry in karst regions is crucial for improving global water resource management and deepening our knowledge of the biogeochemical cycles shaping these sensitive environments.Despite advance-ments in karst hydrology,significant gaps remain in long-term trends,underlying processes,and quantitative effects of environmental changes.This is especially true in areas like the Wujiang River(WJ)in China,where human activities such as reservoir construction and land use/cover changes have accelerated hydrochemical changes.We combined recent and historical monitoring data to provide a detailed analysis of the spatial and temporal characteristics,evolution,and controlling factors of major ions in WJ.These findings are important for local water management and contribute to global efforts to manage similar karst systems facing human-induced pressures.Our research shows clear seasonal differences in solute concentrations,with higher levels during the dry season.WJ’s water is rich in calcium,with Ca-HCO_(3) ion pairs being the most common.Reservoir monitor-ing stations show much higher levels of NO_(3)^(−)and SO_(4)^(2−)compared to river-type stations,likely due to longer hydraulic retention time and increased acid deposition.The study confirms the significant role of pH and water temperature in rock weathering processes.Land use/cover changes were identified as the primary drivers of solute variations(46.37%),followed by lithology(13.92%)and temperature(8.35%).Over the past two decades,in-tense carbonate weathering has been observed,especially during wet seasons.Among karstic provinces,Guizhou Province stands out with the highest ion concentrations,indicative of its extensive karst coverage and heightened weathering processes.
基金supported by Central Public-interest Scientific Institution Basal Research Fund(CATAS-Nos.1630152023007,1630152023011,1630152023012,1630152023013)the National Natural Science Foundation of China(Grant No.32071805).
文摘Coconut(Cocos nucifera L.),a major oil and fruit crop of the Arecaceae family,is extensively cultivated across the Asia—Pacific region.Despite its agricultural importance,genome assembly in coconut remains challenging due to its large genome size and high proportion of repetitive sequences.Allele-specific expression(ASE)plays a key role in regulating plant development and evolution,yet research on ASE in coconut is limited(Shao et al.,2019;Li et al.,2021;Zhang et al.,2021;Hu et al.,2022).Among phenotypic traits,fruit color is especially important as an indicator of maturity,guiding harvest timing and post-harvest processes(Kapoor et al.,2022).While prior studies have explored various coconut traits such as salt tolerance,fiber content,and plant height(Wang et al.,2021;Yang et al.,2021),investigations into ASE and fruit color remain scarce.
基金financially supported by the National Key R&D Program of China(2024YFD1200800)the Guangdong Basic and Applied Basic Research Foundation,China(2024A1515030094)。
文摘Highlights OsCAX2 is localized to tonoplast,and cadmium induces its expression.OsCAX2 overexpression reduces cadmium concentration in indica rice grains by 49.1%.Cadmium(Cd)exposure poses significant health risks to humans,and the International Agency for Research on Cancer has classified it as a Group I carcinogen.Cadmium undergoes minimal metabolism in the human body;consequently,prolonged Cd^(2+)exposure can cause severe damage to multiple organs including the liver,kidneys,lungs,bones,and immune system(Shao et al.2024).Rice,one of the three global staple crops,and Cd exposure in humans primarily occurs the consumption of contaminated rice grains.The contribution of rice to the total dietary Cd intake is over 50% for non-smoking Asian populations(Chen et al.2018;Shi et al.2020).
基金funded by the National Key Research and Development Program of China(Grant No.2019YFD1001900)the HZAU-AGIS Cooperation Fund(Grant No.SZYJY2022006).
文摘Nondestructive measurement technology of phenotype can provide substantial phenotypic data support for applications such as seedling breeding,management,and quality testing.The current method of measuring seedling phenotypes mainly relies on manual measurement which is inefficient,subjective and destroys samples.Therefore,the paper proposes a nondestructive measurement method for the canopy phenotype of the watermelon plug seedlings based on deep learning.The Azure Kinect was used to shoot canopy color images,depth images,and RGB-D images of the watermelon plug seedlings.The Mask-RCNN network was used to classify,segment,and count the canopy leaves of the watermelon plug seedlings.To reduce the error of leaf area measurement caused by mutual occlusion of leaves,the leaves were repaired by CycleGAN,and the depth images were restored by image processing.Then,the Delaunay triangulation was adopted to measure the leaf area in the leaf point cloud.The YOLOX target detection network was used to identify the growing point position of each seedling on the plug tray.Then the depth differences between the growing point and the upper surface of the plug tray were calculated to obtain plant height.The experiment results show that the nondestructive measurement algorithm proposed in this paper achieves good measurement performance for the watermelon plug seedlings from the 1 true-leaf to 3 true-leaf stages.The average relative error of measurement is 2.33%for the number of true leaves,4.59%for the number of cotyledons,8.37%for the leaf area,and 3.27%for the plant height.The experiment results demonstrate that the proposed algorithm in this paper provides an effective solution for the nondestructive measurement of the canopy phenotype of the plug seedlings.
基金supported by Shenzhen Science and Technology Program(Grant No.RCYX20210706092103024)two projects funded by the State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops(No.SKL2018001 to X.Z.and No.SKL20190012 to H.Z.)。
文摘Structural variants(SVs)are a type of genetic variation that contribute substantially to phenotypic diversity and evolution.Further study of SVs will help us understand the influence of SVs associated with tea quality and stress resistance and provide new insight into tea plant breeding improvement and genetic research.However,SVs have not been thoroughly discovered in the tea plant genomes.Herein,we constructed a large-scale SV map across a population of 107 resequenced genomes,including both ancient and cultivated tea plants.A total of 44,240 highconfident SVs were identified,including 34,124 DEL(deletions),4,448 DUP(duplications),2,503 INV(inversions),544 INS(insertions)and 2,621 TRA(translocations).In total,12,400 protein-coding genes were overlapped with SVs,of which 49.5%were expressed in all five tea tissues.SVbased analysis of phylogenetic relationships and population structure in tea plants showed a consistent evolutionary history with the SNP-based results.We also identified SVs subject to artificial selection and found that genes under domestication were enriched in metabolic pathways involving theanine and purine alkaloids,biosynthesis of monoterpenoid,phenylpropanoid,fatty acid,and isoflavonoid,contributing to traits of agronomic interest in tea plants.In addition,a total of 27 terpene synthase(TPS)family genes were selected during domestication.These results indicate that these SVs could provide extensive genomic information for tea quality improvement.
基金supported by the National Key Research and Development Program of China (No. 2022YFD1700200)the National Natural Science Foundation of China (Nos. 32161133010, 3230170969)+1 种基金the Innovation Program of Chinese Academy of Agricultural Sciences, the Shenzhen Science and Technology Program (No. KQTD20180411143628272)the Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District (No. PT202101–02)。
文摘Chitin is an abundant aminopolysaccharide found in insect pests and phytopathogenic microorganisms but absent in higher plants and vertebrates. It is crucial for mitigating threats posed by chitin-containing organisms to human health, food safety, and agriculture. Therefore, targeting the chitin biosynthesisassociated bioprocess holds a promise for developing human-safe and eco-friendly antifungal agents or pesticides. Chitin biosynthesis requires chitin synthase and associated factors, which are involved in the modification, regulation, organization or turnover of chitin during its biosynthesis. A number of enzymes such as chitinases, hexosaminidases, chitin deacetylases are closely related and therefore are promising targets for designing novel agrochemicals that target at chitin biosynthesis. This review summarizes the advances in understanding chitin biology over the past decade by our research group and collaborates,specifically regarding essential proteins linked to chitin biosynthesis that can be exploited as promising pesticide targets. Examples of small bioactive molecules that against the activity of these targets are given.
基金supported by grants from the National Natural Science Foundation of China(Grant No.32072571)the 111 Project(Grant No.B17043)the Construction of Beijing Science,and Technology Innovation and Service Capacity in Top Subjects(Grant No.CEFF-PXM2019_014207_000032)。
文摘Tomato(Solanum lycopersicum)is an important fruit and vegetable crop in worldwide.The fertility of tomato reproductive organs can be dramatically decreased when ambient temperatures rise above 35°C,reducing tomato fruit yield.It is necessary to identify transcription factors(TFs)and target genes involved in heat stress response(HSR)signaling cascades in tomato flower buds to improve tomato plant thermotolerance.In this study,we profiled genes expressed in three developmental stages of tomato flower buds.Red and turquoise modules for heat stress(HS)were identified through gene co-expression network analysis,and the genes within these modules were enriched in HS-related pathways.By focusing on the TFs in the two modules,we identified several novel HSR-related TFs,including SlWRKY75,SlMYB117,and SlNAM.Furthermore,homology analysis illustrated a conserved signaling cascade in tomato.Lastly,we identified and experimentally validated four HSF-regulated genes,namely SlGrpE,SlERDJ3A,SlTIL,and SlPOM1,that likely modulate thermotolerance in plants.These results provide a high-resolution atlas of gene expression during tomato flower bud development under HS conditions,which is a valuable resource for uncovering potential regulatory networks associated with the HSR in tomato.
基金supported by grants from the National Key Research&Development Plan(Grants Nos.2022YFF10030022022YFD1200502)+7 种基金National Natural Science Foundation of China(Grant Nos.3237269631991182)Wuhan Biological Breeding Major Project(Grant No.2022021302024852)Key Project of Hubei Hongshan Laboratory(2021hszd007)HZAU-AGIS Cooperation Fund(Grant No.SZYJY2023022)Funds for High Quality Development of Hubei Seed Industry(HBZY2023B004)Hubei Agriculture Research System(2023HBSTX4-06)Hubei Key Research&Development Plan(Grants Nos.2022BBA0066,2022BBA0062)。
文摘Photosynthesis is one the most important chemical reaction in plants,and it is the ultimate energy source of any living organisms.The light and dark reactions are two essential phases of photosynthesis.Light reaction harvests light energy to synthesize ATP and NADPH through an electron transport chain,and as well as giving out O_(2);dark reaction fixes CO_(2) into six carbon sugars by utilizing NADPH and energy from ATP.Subsequently,plants convert optical energy into chemical energy for maintaining growth and development through absorbing light energy.Here,firstly,we highlighted the biological importance of photosynthesis,and hormones and metabolites,photosynthetic and regulating enzymes,and signaling components that collectively regulate photosynthesis in tomato.Next,we reviewed the advances in tomato photosynthesis,including two aspects of genetic basis and genetic improvement.Numerous genes regulating tomato photosynthesis are gradually uncovered,and the interaction network among those genes remains to be constructed.Finally,the photosynthesis occurring in fruit of tomato and the relationship between photosynthesis in leaf and fruit were discussed.Leaves and fruits are photosynthate sources and sinks of tomato respectively,and interaction between photosynthesis in leaf and fruit exists.Additionally,future perspectives that needs to be addressed on tomato photosynthesis were proposed.
基金supported by the Yunnan Seed Laboratory,China(202205AR070001-15)the National Natural Science Foundation of China,China(Grant No.32160697)。
文摘Juglans sigillata is an economically valuable nut crop renowned for its nutritional richness,including essential nutrients,antioxidants,and healthy fats,which boost human cardial,brain and gut health.Despite its importance,the lack of a complete genome assembly has been a stumbling block in its biological breeding process.Therefore,we generated deep coverage ultralong Oxford Nanopore Technology(ONT)and PacBio HiFi reads to construct a telomere-to-telomere(T2T)genome assembly.The final assembly spans 537.27 Mb with no gaps,demonstrating a remarkable completeness of 98.1%.We utilized a combination of transcriptome data and homologous proteins to annotate the genome,identifying 36018 protein-coding genes.Furthermore,we profiled global cytosine DNA methylations using ONT sequencing data.Global methylome analysis revealed high methylation levels in transposable element(TE)-rich chromosomal regions juxtaposed with comparatively lower methylation in gene-rich areas.By integrating a detailed multi-omics data analysis,we obtained valuable insights into the mechanism underlying endopleura coloration.This investigation led to the identification of eight candidate genes(e.g.ANR)involved in anthocyanin biosynthesis pathways,which are crucial for the development of color in plants.The comprehensive genome assembly and the understanding of the genetic basis of important traits like endopleura coloration will open avenues for more efficient breeding programs and improved crop quality.
文摘A progressive decline in fertility is a well-documented aspect of female aging and is associated with a range of cellular and molecular alterations,including genomic instability and modifications in epigenetic regulation.Epigenetic clocks,which estimate biological age based on DNA methylation patterns,have been extensively utilized to evaluate general health status and the risk of various diseases.Despite their broad application,the utility of epigenetic clocks in assessing female reproductive health remains only partially characterized.This minireview consolidates recent advancements in the application of epigenetic clocks to evaluate the functional status of the female reproductive system.The objective is to investigate their potential for quantifying and predicting the biological age of reproductive tissues,thereby establishing a theoretical basis for clinical applications in reproductive medicine.To date,no comprehensive minireview has systematically examined multi-tissue epigenetic clock models in the context of female reproductive aging,positioning this minireview as a novel contribution to the field.
基金supported by the Basic Science Research Program through the National Research Foundation of Korea(NRF)Ministry of Education(RS-2021-NR060130,00355529).
文摘Abiotic stresses,particularly salinity,pose a major threat to rice productivity,highlighting the need to identify novel genetic resources to improve stress tolerance.Gamma irradiation remains one of the most widely used tools breeding stress-tolerant plant varieties.In this study,we identified a salt-tolerant rice mutant,salt-insensitive TILLING line 4(sitl4),generated via gamma irradiation and linked its enhanced tolerance to a loss-of-function mutation in Oryza sativa protein acyltransferase for ABA response 1(OsPATA1),which encodes a DHHC-type palmitoyl acyltransferase.Functional analyses using both sitl4 and a CRISPR/Cas9-mediated OsPATA1-knockout line(ospata1)revealed that disruption of OsPATA1 leads to increased abscisic acid(ABA)accumulation and upregulation of ABA-responsive genes under salt stress conditions.We identified OsEULD1b,a previously uncharacterized Euonymus lectin(EUL)domaincontaining protein,as an interactor of OsPATA1.In sitl4 and ospata1,OsEULD1b displayed cytosolic retention,suggesting that its subcellular redistribution enhances its role in ABA-mediated stress signaling.Taken together,our findings demonstrate that OsPATA1 and OsEULD1b form a regulatory module that modulates the ABA-dependent salt stress responses in rice.These results provide new insights into the molecular mechanisms underlying abiotic stress tolerance and will help to identify potential genetic targets for developing stress-tolerant rice cultivars through molecular breeding or genome editing.
基金Bill&Melinda Gates Foundation(Grant number OPP1154401).
文摘Backgroud Before fertilization,spermatozoa undergo a crucial maturation step called capacitation,which is a unique event regulates the sperm’s ability for successful fertilization.The capacitation process takes place as the spermatozoa pass through the female reproductive tract(FRT).Dihydrolipoamide dehydrogenase(DLD)protein is a post-pyruvate metabolic enzyme,exhibiting reactive oxygen species(ROS)production which causes capacitation.Additionally,other vital functions of DLD in buffalo spermatozoa are hyperactivation and acrosome reaction.DLD produces the optimum amount of ROS required to induce capacitation process in FRT.Depending on physiological or patho-physiological conditions,DLD can either enhance or attenuate the production of reactive oxygen species(ROS).Aim of this study was to investigate whether changes in the production of ROS in sperm cells can impact their ability to fertilize by triggering the capacitation and acrosome reaction.Results In this study,abundance of DLD protein was quantified between high(n=5)and low fertile bull(n=5)sper-matozoa.It was found that compared to high-fertile(HF)bulls,low-fertile(LF)bulls exhibited significantly(P<0.05)higher DLD abundances.Herein,we optimised the MICA concentration to inhibit DLD function,spermatozoa were treated with MICA in time(0,1,2,3,4,and 5 h)and concentrations(1,2.5,5,and 10 mmol/L)dependent manner.Maximum DLD inhibition was found to be at 4 h in 10 mmol/L MICA concentration,which was used for further exper-imentation in HF and LF.Based on DLD inhibition it was seen that LF bull spermatozoa exhibited significantly(P<0.05)higher ROS production and acrosome reaction in comparison to the HF bull spermatozoa.The kinematic parameters of the spermatozoa such as percent total motility,velocity parameters(VCL,VSL,and VAP)and other parameters(BCF,STR,and LIN)were also decreased in MICA treated spermatozoa in comparison to the control(capacitated)spermatozoa.Conclusions The present study provides an initial evidence explaining the buffalo bull spermatozoa with higher DLD abundance undergo early capacitation,which subsequently reduces their capacity to fertilize.
基金supported by the National Key R&D Program of China(Grant No.2022YFE0139400)the National Natural Science Foundation of China(Grant No.31961143016)the Shenzhen Science and Technology Program,China(Grant No.JCYJ20200109150650397).
文摘Zinc(Zn)is an essential micronutrient for both plants and humans.Zn deficiency is common in many paddy fields and reduces yield and grain Zn content(GZC).To accelerate breeding for improved GZC and Zn deficiency tolerance(ZDT)rice varieties,it is important to identify genes regulating Zn homeostasis.In this study,a member of the Ser/Thr protein phosphatase family,LOC_Os07g48840(named as OsGZ7),was found to contributed to ZDT and GZC in rice.The expression of OsGZ7 in roots and shoots was inhibited by Zn deficiency and toxicity,but induced by iron(Fe),manganese(Mn),and copper(Cu)deficiency,as well as chromium toxicity.OsGZ7 localized to the cytoplasm and was expressed in all tissues during the tillering,flowering,and grain-filling stages,particularly in the leaf blade and leaf sheath.At the seedling stage,knockout of OsGZ7 enhanced ZDT and increased Zn accumulation in both roots and shoots.At the maturity stage,knockout of OsGZ7 enhanced GZC,while overexpression of OsGZ7 reduced GZC.RNA-seq analysis suggested that OsGZ7 might regulate Zn homeostasis by affecting metal binding,hormone signal transduction,and oxidoreductase activity.Taken together,our findings indicate that OsGZ7 contributes to ZDT and Zn accumulation in rice.
文摘This study evaluated the molecular characterization of different ecotypes of B. aegyptiaca populations in the four sites: Koily alpha, Labgar, Ranérou and Ballou according to the environment with the aim of developing protection strategies. We sampled leaves of B. aegyptiaca in each individual from each site to extract and amplify a fragment of mitochondrial DNA including cytochrome b and then carefully preserved. DNA extraction, polymerase chain amplification and sequencing of MT-CYB were performed in 64 individuals. Genetic diversity and structure of B. aegyptiaca were determined using the MEGA, DNasp and Arlequin software. The results showed a high haplotype diversity and low nucleotide diversity, indicating a population expansion linked to an important gene flow. Genetic distances between populations were positively correlated with geographic distance. The importance of having highlighted this genetic differentiation of the B. aegyptiaca species between these sites is to be able to understand the degree of genetic heterogeneity of each and correlate it with adaptability because genetic diversity influences the adaptation of the species.
文摘In this review,we explore the application of next-generation sequencing in liver cancer research,highlighting its potential in modern oncology.Liver cancer,particularly hepatocellular carcinoma,is driven by a complex interplay of genetic,epigenetic,and environmental factors.Key genetic alterations,such as mutations in TERT,TP53,and CTNNB1,alongside epigenetic modifications such as DNA methylation and histone remodeling,disrupt regulatory pathways and promote tumorigenesis.Environmental factors,including viral infections,alcohol consum-ption,and metabolic disorders such as nonalcoholic fatty liver disease,enhance hepatocarcinogenesis.The tumor microenvironment plays a pivotal role in liver cancer progression and therapy resistance,with immune cell infiltration,fibrosis,and angiogenesis supporting cancer cell survival.Advances in immune check-point inhibitors and chimeric antigen receptor T-cell therapies have shown po-tential,but the unique immunosuppressive milieu in liver cancer presents challenges.Dysregulation in pathways such as Wnt/β-catenin underscores the need for targeted therapeutic strategies.Next-generation sequencing is accele-rating the identification of genetic and epigenetic alterations,enabling more precise diagnosis and personalized treatment plans.A deeper understanding of these molecular mechanisms is essential for advancing early detection and developing effective therapies against liver cancer.
基金funded by the National Key Research and Development Program of China(2024YFF1000100 and 2021YFD1301102)the National Natural Science Foundations of China(32172702)the National Agricultural Science and Technology Innovation Program,Chinese Academy of Agricultural Sciences(ASTIP-IAS02).
文摘Resilience traits in pig populations allow animals to deal better with infectious disease and suboptimal production environments.The data on daily weight,feed intake and feed behaviors in pigs are collected in test period by automated feeding stations,which facilitate to evaluate the resilience traits.In this study,we adopted the root mean square error(RMSE)of ordinary least squares(OLS)and the negative residuals of quantile regression(QR)to generate four different novel resilience traits using daily records of feed intake and feed duration between 90 and 180 days of age in a population of commercial Duroc pigs.The genome-wide association studies(GWAS)based on single-and two-trait mixed models were carried out on 550 pigs using 48,603 single nucleotide polymorphisms(SNPs)to identify genomic regions associated with resilience traits in growing pigs.We further focused on the GWAS signals to conduct gene annotation,colocalization with multi-tissue eQTL summary statistics of PigGTEx project and identification of enhancers and promoters using the publicly available data.The genomic heritabilities of four novel resilience traits ranged from 0.09 to 0.41.The pairwise genetic and phenotypic correlations ranged from 0.16 to 0.95 and from 0.05 to 0.36,respectively.Twenty-seven SNPs were identified to be significantly associated with these resilience traits.They were distributed on nine chromosomes(SSC1,SSC2,SSC6,SSC7,SSC8,SSC12,SSC14,SSC16 and SSC17).After annotation,39 QTLs and 49 candidate genes were identified.Several of these are functionally relevant candidate genes including OTUD4,TIFA and CARD14,which are involved in the host immune response,disease susceptibility and signal transduction.Eight unique SNPs were found to be causal in both GWAS and eQTL analyses across 15 tissues.Notably,one SNP(rs80794541)was associated with eQTLs identified concurrently across seven tissues/cell types,including the macrophage cell type.Furthermore,four significant SNPs(rs81467127,rs81356029,rs80794541 and rs81305085)were linked to the function of the primed enhancer,active element,and poised promoter in five pig tissues.Using the porcine fibroblast HiC dataset,SNP(rs81356029)on SSC2 regulates the CARNS1 and SSH3,while SNP(rs80794541)on SSC7 regulates the H2AC6.In this study,we generated four novel resilience traits and identified SNPs significantly associated with these resilience traits in a Duroc pig population.GWAS signals were associated with candidate genes involving in the immune traits,and were linked to the crucial regulatory elements as well.Our findings will contribute to elucidating the genetic mechanism that can enhance genome-enabled breeding and inform further research on resilience in domestic pigs.
基金supported by the National Natural Science Foundation of China(32161133010)the National Key Research and Development Program of China(2022YFD1700200)+2 种基金the Innovation Program of Chinese Academy of Agricultural Sciences(CAAS-CSCB-202302)the Shenzhen Science and Technology Program,China(KQTD20180411143628272)the Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District,China(PT202101-02).
文摘Chitin is an abundant natural biopolymer that plays a crucial role in insect growth and development as a fundamental structural component of the exoskeleton.The membrane-integralβ-glycosyltransferase,chitin synthase,has been identified as the central component in chitin biosynthesis.However,the precise roles of other proteins in facilitating chitin synthase in chitin biosynthesis remain unclear.In this study,we employed split-ubiquitin membrane yeast two-hybrid(MYTH)and pull-down assays to demonstrate the physical interaction between Twinstar(Tsr),a small molecular protein in the actin-depolymerizing factor ADF/Cofilin protein family,and chitin synthase Krotzkopf verkehrt(Kkv)in Drosophila melanogaster in vitro.The RNA interference(RNAi)-mediated global knockdown of Tsr in D.melanogaster resulted in larval lethality.Furthermore,targeted suppression of Tsr in the tracheal and epidermal tissues also led to larval mortality,while knocking down Tsr in the wing tissues led to wrinkled wings.Additionally,silencing Tsr not only reduced the chitin content in the first longitudinal vein of the wings but also led to the absence of the chitin lamellar structure.To validate the functional conservation of Tsr in other insect orders,the two agricultural pests Ostrinia furnacalis and Tribolium castaneum,representing lepidoptera and coleoptera insects,respectively,were investigated.Knockdown experiments targeting the Drosophila Tsr orthologues OfTsr in O.furnacalis and TcTsr in T.castaneum produced abnormal larvae during molting or pupation in O.furnacalis and lethality in T.castaneum.Our findings not only improve ourknowledge of the chitin biosynthesis machinery in insect cuticles but also provide new potential targets for the control of major agricultural pests.
基金supported by the National Natural Science Foundation of China(Grant Nos.U2002204 and 32272725)the China National Key Research and Development Program(Grant No.2022YFF1002500)+2 种基金the China Postdoctoral Science Foundation(Grant No.2024M753583)the Guangdong Major Project of Basic and Applied Basic Research(Grant No.2021B0301030004)Natural Science Foundation of Henan(Grant No.222300420109)。
文摘Potato(Solanum tuberosum)is a globally important staple crop.However,cultivated potato varieties are highly sensitive to low temperatures.The molecular mechanisms underlying freezing resistance in potatoes remain poorly understood.Through comparative metabolome and transcriptome analyses of freezing-tolerant(CM,Solanum commersonii)and freezing-sensitive(DM,DM1-3516R44)varieties,we identified a coldinduced UDP-glycosyltransferase gene,ScUGT73B4,which is associated with the accumulation of glycosylated flavonoids in wild CM varieties.Overexpression of ScUGT73B4 led to increased accumulation of glycosylated flavonoids and enhanced antioxidant capacity,resulting in improved freezing tolerance in potato plantlets.These findings reveal a UDP-glycosyltransferase in the flavonoid pathway and offer a potential valuable genetic resource for breeding potatoes with improved freezing tolerance.
基金supported by the National Key Research and Development Program of China(2023YFF1000100 and 2023YFA0914601)the Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District(PT202101-01).
文摘Increasing number of structural variations(SVs)have been identified as causative mutations for diverse agronomic traits.However,the systematic exploration of SVs quantity,distribution,and contribution in wheat was lacking.Here,we report high-quality gene-based and SV-based pangenomes comprising 22 hexaploid wheat assemblies showing a wide range of chromosome size,gene number,and TE component,which indicates their representativeness of wheat genetic diversity.Pan-gene analyses uncover 140,261 distinct gene families,of which only 23.2%are shared in all accessions.Moreover,we build a∼16.15 Gb graph pangenome containing 695,897 bubbles,intersecting 5132 genes and 230,307 cis-regulatory regions.Pairwise genome comparisons identify∼1,978,221 non-redundant SVs and 497 SV hotspots.Notably,the density of bubbles as well as SVs show remarkable aggregation in centromeres,which probably play an important role in chromosome plasticity and stability.As for functional SVs exploration,we identify 2769 SVs with absolute relative frequency differences exceeding 0.7 between spring and winter growth habit groups.Additionally,several reported functional genes in wheat display complex structural graphs,for example,PPD-A1,VRT-A2,and TaNAAT2-A.These findings deepen our understanding of wheat genetic diversity,providing valuable graphical pangenome and variation resources to improve the efficiency of genome-wide association mapping in wheat.
基金supported by grants from the National Key Research&Development Plan(Grant Nos.2022YFD1200502,2021YFD1200201)National Natural Science Foundation of China(Grant Nos.32372696,31991182)+6 种基金Wuhan Biological Breeding Major Project(Grant No.2022021302024852)HZAU-AGIS Cooperation Fund(Grant No.SZYJY2023022)Funds for High Quality Development of Hubei Seed Industry(Grant No.HBZY2023B004)Hubei Agriculture Research System(Grant No.2023HBSTX4-06)Hubei Key Research&Development Plan(Grant Nos.2022BBA0066,2022BBA0062)Funds of National Key Laboratory for Germplasm Innovation&Utilization of Horticultural Crops(Grant No.Horti-3Y-2024-008)Key Project of Hubei Hongshan Laboratory(Grant No.2021hszd007).
文摘Tomato,a vegetable of considerable global significance,has been the subject of extensive breeding efforts primarily aimed at achieving high yields and resistance to multiple stressors.However,despite these endeavors,the quality of fruits still cannot fully satisfy the diverse preferences of the majority of consumers.The elucidation of genetic determinants underlying fruit quality traits,coupled with the advancement of gene editing techniques,has significantly contributed to the enhancement of tomato quality.Combining with gene editing technology to improve tomato fruit quality traits represents a viable approach for maximizing the utilization of essential genes in breeding programs.This review provides a comprehensive summary of the significant genes associated with tomato fruit quality traits,as well as an overview of the current advancements and potential avenues for enhancing tomato quality through gene editing technology.Four important aspects of fruit quality-appearance,flavor,nutritional profiles and postharvest properties form the basis of the review,providing a thorough update on the state of research in tomato fruit quality improvement via new gene editing techniques.
