Studies on the temporal,structural,and interacting features of the clubroot resistance gene Rcr1 using CRISPR/Cas9-based systems

Clubroot disease is a severe threat to Brassica crops globally,particularly in western Canada.Genetic resistance,achieved through pyramiding clubroot resistance(CR)genes with different modes of action,is the most important strategy for managing the disease.However,studies on the CR gene functions are quite limited.In this study,we have conducted investigations into the temporal,structural,and interacting features of a newly cloned CR gene,Rcr1,using CRISPR/Cas9 technology.For temporal functionality,we developed a novel CRISPR/Cas9-based binary vector,pHHIGR-Hsp18.2,to deliver Rcr1 into a susceptible canola line(DH12075)and observed that early expression of Rcr1 is critical for conferring resistance.For structural functionality,several independent mutations in specific domains of Rcr1 resulted in loss-offunction,highlighting their importance for CR phenotype.In the study of the interacting features of Rcr1,a cysteine protease gene and its homologous allele in canola were successfully disrupted via CRISPR/Cas9 as an interacting component with Rcr1 protein,resulting in the conversion from clubroot resistant to susceptible in plants carrying intact Rcr1.These results indicated an indispensable role of these two cysteine proteases in Rcr1-mediated resistance response.This study,the first of its kind,provides valuable insights into the functionality of Rcr1.Further,the new vector p HHIGR-Hsp18.2 demonstrated an inducible feature on the removal of add-on traits,which should be useful for functional genomics and other similar research in brassica crops.

Effects of dietary Clostridium butyricum and rumen protected fat on meat quality,oxidative stability,and chemical composition of finishing goats

Background Clostridium butyricum(CB)is a probiotic that can regulate intestinal microbial composition and improve meat quality.Rumen protected fat(RPF)has been shown to increase the dietary energy density and provide essential fatty acids.However,it is still unknown whether dietary supplementation with CB and RPF exerts beneficial effects on growth performance and nutritional value of goat meat.This study aimed to investigate the effects of dietary CB and RPF supplementation on growth performance,meat quality,oxidative stability,and meat nutritional value of finishing goats.Thirty-two goats(initial body weight,20.5±0.82 kg)were used in a completely randomized block design with a 2 RPF supplementation(0 vs.30 g/d)×2 CB supplementation(0 vs.1.0 g/d)factorial treatment arrangement.The experiment included a 14-d adaptation and 70-d data and sample collection period.The goats were fed a diet consisted of 400 g/kg peanut seedling and 600 g/kg corn-based concentrate(dry matter basis).Result Interaction between CB and RPF was rarely observed on the variables measured,except that shear force was reduced(P<0.05)by adding CB or RPF alone or their combination;the increased intramuscular fat(IMF)content with adding RPF was more pronounced(P<0.05)with CB than without CB addition.The pH24h(P=0.009),a*values(P=0.007),total antioxidant capacity(P=0.050),glutathione peroxidase activities(P=0.006),concentrations of 18:3(P<0.001),20:5(P=0.003)and total polyunsaturated fatty acids(P=0.048)were increased,whereas the L*values(P<0.001),shear force(P=0.050)and malondialdehyde content(P=0.044)were decreased by adding CB.Furthermore,CB supplementation increased essential amino acid(P=0.027),flavor amino acid(P=0.010)and total amino acid contents(P=0.024)as well as upregulated the expression of lipoprotein lipase(P=0.034)and peroxisome proliferator-activated receptorγ(PPARγ)(P=0.012),and downregulated the expression of stearoyl-CoA desaturase(SCD)(P=0.034).The RPF supplementation increased dry matter intake(P=0.005),averaged daily gain(trend,P=0.058),hot carcass weight(P=0.046),backfat thickness(P=0.006),concentrations of 16:0(P<0.001)and c9-18:1(P=0.002),and decreased the shear force(P<0.001),isoleucine(P=0.049)and lysine content(P=0.003)of meat.In addition,the expressions of acetyl-CoA carboxylase(P=0.003),fatty acid synthase(P=0.038),SCD(P<0.001)and PPARγ(P=0.022)were upregulated due to RPF supplementation,resulting in higher(P<0.001)content of IMF.Conclusions CB and RPF could be fed to goats for improving the growth performance,carcass traits and meat quality,and promote fat deposition by upregulating the expression of lipogenic genes of Longissimus thoracis muscle.

Fine mapping of two recessive genes TaFLA1 and TaSPL8 controlling flag leaf angle in bread wheat

Flag leaf angle is one of the key target traits in high yield wheat breeding.A smaller flag leaf angle reduces shading and enables plants to grow at a higher density,which increases yield.Here we identified a mutant,je0407,with an 84.34%-89.35%smaller flag leaf angle compared with the wild type.The mutant also had an abnormal lamina joint and no ligule or auricle.Genetic analysis indicated that the ligule was controlled by two recessive genes,which were mapped to chromosomes 2AS and 2DL.The mutant allele on chromosome 2AS was named Tafla1b,and it was fine mapped to a 1 Mb physical interval.The mutant allele on chr.2DL was identified as Taspl8b,a novel allele of TaSPL8 with a missense mutation in the second exon,which was used to develop a cleaved amplified polymorphic sequence marker.F3 and F4 lines derived from crosses between Jing411 and je0407 were genotyped to investigate interactions between the Tafla1b and Taspl8b alleles.Plants with the Tafla1b/Taspl8a genotype had 58.41%-82.76%smaller flag leaf angles,6.4%-24.9%shorter spikes,and a greater spikelet density(0.382 more spikelets per cm)compared with the wild type.Plants with the Tafla1a/Taspl8b genotype had 52.62%-82.24%smaller flag leaf angles and no differences in plant height or spikelet density compared with the wild type.Tafla1b/Taspl8b plants produced erect leaves with an abnormal lamina joint.The two alleles had dosage effects on ligule formation and flag leaf angle,but no significant effect on thousand-grain weight.The mutant alleles provide novel resources for improvement of wheat plant architecture.

Emerging technological developments to address pest resistance in Bt cotton

Cotton plays a crucial role in shaping Indian economy and rural livelihoods.The cotton crop is prone to numerous insect pests,necessitating insecticidal application,which increases production costs.The advent of the expression of Bacillus thuringiensis(Bt)insecticidal protein in cotton has significantly reduced the burden of pest without compromising environmental or human health.After the introduction of transgenic cotton,the cultivated area expanded to 22 million hectares,with a 64% increase in adoption by farmers worldwide.Currently,Bt cotton accounts for 93% of the cultivated cotton area in India.However,extensive use of Bt cotton has accelerated resistance development in pests like the pink bollworm.Furthermore,the overreliance on Bt cotton has reduced the use of broad-spectrum pesticides,favouring the emergence of secondary pests with significant challenges.This emphasizes the urgent necessity for developing novel pest management strategies.The high-dose and refuge strategy was initially effective for managing pest resistance in Bt cotton,but its implementation in India faced challenges due to misunderstandings about the use of non-Bt refuge crops.Although gene pyramiding was introduced as a solution,combining mono toxin also led to instances of cross-resistance.Therefore,there is a need for further exploration of biotechnological approaches to manage insect resistance in Bt cotton.Advanced biotechnological strategies,such as sterile insect release,RNA interference(RNAi)-mediated gene silencing,stacking Bt with RNAi,and genome editing using clustered regularly interspaced short palindromic repeats/CRISPR-associated protein(CRISPR-Cas),offer promising tools for identifying and managing resistance genes in insects.Additionally,CRISPR-mediated gene drives and the development of novel biopesticides present potential avenues for effective pest management in cotton cultivation.These innovative approaches could significantly enhance the sustainability and efficacy of pest resistance management in Bt cotton.

Hybrid rice achievements, development and prospect in China

This article reviews the history and progress of hybrid rice development. Hybrid rice research was initiated back in 1964, and commercialized in 1976. Three-line and two-line system hybrid rice were developed in 1974 and 1995, respectively. Research on super hybrid rice, which was first launched by Ministry of Agriculture, China in 1996, is discussed, and the great progress of super hybrid rice had been achieved with a new yield record by 15.4 t ha^-1 in the 6.84 ha demonstration location in Xupu, Hunan Province, China in 2014. And the mechanism of heterosis, the techniques of hybrid seed production and the modern field managements in hybrid rice over the past decades are also discussed. Additionally, this article dealt with the intellectual property protection（IPR） and development of hybrid rice seed industry in China. Major factors that constrain hybrid rice development are analyzed and possible solutions to this problems are proposed. Finally, the authors present methods to further increase production yield, and propose an improvement for breeding super high-yielding hybrid rice based on these methods.

Methylome and transcriptome data integration reveals potential roles of DNA methylation and candidate biomarkers of cow Streptococcus uberis subclinical mastitis

Background:Mastitis caused by different pathogens including Streptococcus uberis(S.uberis)is responsible for huge economic losses to the dairy industry.In order to investigate the potential genetic and epigenetic regulatory mecha‑nisms of subclinical mastitis due to S.uberis,the DNA methylome(whole genome DNA methylation sequencing)and transcriptome(RNA sequencing)of milk somatic cells from cows with naturally occurring S.uberis subclinical mastitis and healthy control cows(n=3/group)were studied.Results:Globally,the DNA methylation levels of CpG sites were low in the promoters and first exons but high in inner exons and introns.The DNA methylation levels at the promoter,first exon and first intron regions were nega‑tively correlated with the expression level of genes at a whole‑genome‑wide scale.In general,DNA methylation level was lower in S.uberis‑positive group(SUG)than in the control group(CTG).A total of 174,342 differentially methylated cytosines(DMCs)(FDR<0.05)were identified between SUG and CTG,including 132,237,7412 and 34,693 DMCs in the context of CpG,CHG and CHH(H=A or T or C),respectively.Besides,101,612 methylation haplotype blocks(MHBs)were identified,including 451 MHBs that were significantly different(dMHB)between the two groups.A total of 2130 differentially expressed(DE)genes(1378 with up‑regulated and 752 with down‑regulated expression)were found in SUG.Integration of methylome and transcriptome data with MethGET program revealed 1623 genes with signifi‑cant changes in their methylation levels and/or gene expression changes(MetGDE genes,MethGET P‑value<0.001).Functional enrichment of genes harboring≥15 DMCs,DE genes and MetGDE genes suggest significant involvement of DNA methylation changes in the regulation of the host immune response to S.uberis infection,especially cytokine activities.Furthermore,discriminant correlation analysis with DIABLO method identified 26 candidate biomarkers,including 6 DE genes,15 CpG‑DMCs and 5 dMHBs that discriminated between SUG and CTG.Conclusion:The integration of methylome and transcriptome of milk somatic cells suggests the possible involve‑ment of DNA methylation changes in the regulation of the host immune response to subclinical mastitis due to S.uberis.The presented genetic and epigenetic biomarkers could contribute to the design of management strategies of subclinical mastitis and breeding for mastitis resistance.

Modeling water resources under competing demands for sustainable development: A case study of Kaligandaki Gorge Hydropower Project in Nepal

The challenges posed by climate change require that the quantity and quality of water resources in Nepal be managed with sustainable development practices. The communities around the Kaligandaki Gorge Hydropower Project in the Myagdi District of Nepal depend on river flow for most of their rural and agricultural needs. Without a sustainable development plan, the growing population of the region, confined in an area with declining water resources, will face serious challenges to economic growth. Meteorological data show increasing annual average rainfall at a slight rate of about 0.284 mm/year, with erratic annual percentage change in rainfall in the area. The mean and minimum temperatures show decreasing trends at the rates of 0.05-C and 0.14-C per year, respectively. An assessment of the impacts on water availability for domestic and irrigation usage in the face of competing demands caused by the hydropower development project in the Kaligandaki Gorge was undertaken. The water demand and supply modeling were conducted using the water evaluation and planning (WEAP) model, based on discharge data from the Kaligandaki River, which were obtained from the Department of Hydrology and Meteorology, Nepal. The available data from 2001 to 2003 were used to estimate the model parameters while the stability of these parameters was tested with a validation period from 2004 to 2007. The performance of the model was assessed through statistical measures of calibration with the root mean square error and coefficient of determination, whose values were 0.046% and 0.79, respectively. Two scenarios were created in addition to the base case scenario: the discharge decrement scenario and new irrigation technology scenario. Analysis showed that a prioritization of demands will be necessary in the area in the near future for the purpose of sustainability of water resources, due to climate change impacts.

Analysis of postoperative ocular surface changes and intervention effect after pars plana vitrectomy in meibomian gland dysfunction dry eye patients

AIM:To observe ocular surface changes after phacovitrectomy in patients with mild to moderate meibomian gland dysfunction(MGD)-type dry eye and track clinical treatment response using a Keratograph 5M and a Lipi View interferometer.METHODS:Forty cases were randomized into control group A and treatment group B;the latter received meibomian gland treatment 3d before phacovitrectomy and sodium hyaluronate before and after surgery.The average non-invasive tear film break-up time(NITBUTav),first noninvasive tear film break-up time(NITBUTf),non-invasive measured tear meniscus height(NTMH),meibomian gland loss(MGL),lipid layer thickness(LLT)and partial blink rate(PBR)were measured preoperatively and 1wk,1 and 3mo postoperatively.RESULTS:The NITBUTav values of group A at 1wk(4.38±0.47),1mo(6.76±0.70),and 3mo(7.25±0.68)were significantly lower than those of group B(7.45±0.78,10.46±0.97,and 11.31±0.89;P=0.002,0.004,and 0.001,respectively).The NTMH values of group B at 1wk(0.20±0.01)and 1mo(0.22±0.01)were markedly higher than those of group A(0.15±0.01 and 0.15±0.01;P=0.008 and P<0.001,respectively);however,there was no difference at 3mo.The LLT of group B at 3mo[91.5(76.25-100.00)]significantly exceeded that of group A[65.00(54.50-91.25),P=0.017].No obvious intergroup difference was found in MGL or PBR(P>0.05).CONCLUSION:Mild to moderate MGD dry eye worsens in the short term after phacovitrectomy.Preoperative cleaning,hot compresses,and meibomian gland massage as well as preoperative and postoperative sodium hyaluronate promote the rapid recovery of tear film stability.

Background and Research Prospect of Geo-ecological Survey and Monitor in the Critical Zone of Black Soil

The American Science journal,on the occasion of its 125 publication anniversary,in 2016,released 125 of the most challenging scientific issues(Kennedy et al.,2005)to the world.According to the basics,breadth and the influence,25 of the issues which considered to be the most important were screened,including"How many people can the Earth carry?"(Stokstad,2005;Dailyg et al.,1992;Cohen,1995)and"How high will the greenhouse effect make the earth temperature?

Production systems and important antimicrobial resistant-pathogenic bacteria in poultry:a review

Economic losses and market constraints caused by bacterial diseases such as colibacillosis due to avian pathogenic Escherichia coli and necrotic enteritis due to Clostridium perfringens remain major problems for poultry producers,despite substantial efforts in prevention and control.Antibiotics have been used not only for the treatment and prevention of such diseases,but also for growth promotion.Consequently,these practices have been linked to the selection and spread of antimicrobial resistant bacteria which constitute a significant global threat to humans,ani-mals,and the environment.To break down the antimicrobial resistance(AMR),poultry producers are restricting the antimicrobial use(AMU)while adopting the antibiotic-free(ABF)and organic production practices to satisfy consum-ers’demands.However,it is not well understood how ABF and organic poultry production practices influence AMR profiles in the poultry gut microbiome.Various Gram-negative(Salmonella enterica serovars,Campylobacter jejuni/coli,E.coli)and Gram-positive(Enterococcus spp.,Staphylococcus spp.and C.perfringens)bacteria harboring multiple AMR determinants have been reported in poultry including organically-and ABF-raised chickens.In this review,we discussed major poultry production systems(conventional,ABF and organic)and their impacts on AMR in some potential pathogenic Gram-negative and Gram-positive bacteria which could allow identifying issues and opportuni-ties to develop efficient and safe production practices in controlling pathogens.

Mixing trait-based corn(Zea mays L.)cultivars increases yield through pollination synchronization and increased cross-fertilization

Abiotic stress such as high temperature at flowering is one of many conditions reducing yield of corn(Zea mays L.).Mixing corn cultivars with diverse functional traits increases within-crop diversity and provides a potential means of mitigating yield losses under stress conditions.We conducted a three-year field study to investigate the effects of cultivar mixtures on kernel setting rate,pollen sources,and yield.This study consisted of six treatments,including two high temperature-tolerant(HTT)monocrops of WK702 and DH701,two high temperature-sensitive(HTS)monocrops of DH605 and DH662,and two HTT–HTS mixtures of WK702-DH605 and DH701-DH662.The anthesis–silking interval(ASI)was 0.9–1.6 days shorter in mixtures than in monocrops.Kernel setting rate was increased in mixtures(86.4%–88.7%)compared with those in monocrops(74.7%–84.1%)as a result of synchrony and complementarity of pollination.Grain yields of the HTT–HTS mixtures increased by 13.3%–18.7%,equivalent to 1169 to1605 kg ha^(-1),in comparison with HTS corn monocrops.The results of SSR markers showed that crossfertilization percentage in corn cultivar mixtures ranged from 29.3%to 47.8%,partially explaining yield improvement.Land equivalent ratio(LER)was 1.12 for corn mixtures and the partial land equivalent ratio(e.g.,>0.5)showed the complementary benefits in corn mixtures.The results indicated that mixing corn cultivars with diverse flowering and drought-tolerance traits increased yields via pollination synchrony.

Residue Return Effects Outweigh Tillage Effects on Soil Microbial Communities and Functional Genes in Black Soil Region of Northeast China

Conservation tillage as an effective alternative to mitigate soil degradation has attracted worldwide attention,but the influences of conservation tillage on soil microbial community and especially function remain unclear.Shotgun metagenomics sequencing was performed to examine the taxonomic and functional community variations of black soils under three tillage regimes,namely no-tillage with residue(maize straw)return(NTS),moldboard plow with residue return(MPS),and moldboard plow without residue return(MPN)in Northeast China.The results revealed:1)Soil bacterial and archaeal communities differed significantly under different tillage regimes in contrast to soil fungal community.2)The overlay of less tillage and residues return under NTS led to unique soil microbial community composition and functional composition.Specifically,in contrast to other treatments,NTS increased the relative abundances of some taxa such as Bradyrhizobium,Candidatus Solibacter,and Reyranella,along with the relative abundances of some taxa such as Sphingomonas,Unclassified Chloroflexi and Nitrososphaera decreased;NTS had a unique advantage of increasing the relative abundances of genes involved in‘ATP-binding cassette(ABC)transporters’and‘quorum sensing(QS)’pathways,while MPN favored the genes involved in‘flagellar assembly’pathway and some metabolic pathways such as‘carbon’and‘glyoxylate and dicarboxylate’and‘selenocompound’metabolisms.3)Significantly different soil bacterial phyla(Acidobacteria,Gemmatimonadetes,and Chloroflexi)and metabolic pathways existed between MPN and another two treatments(NTS and MPS),while did not exist between NTS and MPS.4)Dissolved organic carbon(DOC)and soil bulk density were significantly affected(P<0.05)by tillage and accounted for the variance both in microbial(bacterial)community structure and functional composition.These results indicated that a change in tillage regime from conventional to conservation tillage results in a shift of microbial community and functional genes,and we inferred that residue return played a more prominent role than less tillage in functional shifts in the microbial community of black soils.

A Spider Monkey Optimization Algorithm Combining Opposition-Based Learning and Orthogonal Experimental Design

As a new bionic algorithm,Spider Monkey Optimization(SMO)has been widely used in various complex optimization problems in recent years.However,the new space exploration power of SMO is limited and the diversity of the population in SMO is not abundant.Thus,this paper focuses on how to reconstruct SMO to improve its performance,and a novel spider monkey optimization algorithm with opposition-based learning and orthogonal experimental design(SMO^(3))is developed.A position updatingmethod based on the historical optimal domain and particle swarmfor Local Leader Phase(LLP)andGlobal Leader Phase(GLP)is presented to improve the diversity of the population of SMO.Moreover,an opposition-based learning strategy based on self-extremum is proposed to avoid suffering from premature convergence and getting stuck at locally optimal values.Also,a local worst individual elimination method based on orthogonal experimental design is used for helping the SMO algorithm eliminate the poor individuals in time.Furthermore,an extended SMO^(3)named CSMO^(3)is investigated to deal with constrained optimization problems.The proposed algorithm is applied to both unconstrained and constrained functions which include the CEC2006 benchmark set and three engineering problems.Experimental results show that the performance of the proposed algorithm is better than three well-known SMO algorithms and other evolutionary algorithms in unconstrained and constrained problems.

Heat-tolerant maize for rainfed hot,dry environments in the lowland tropics:From breeding to improved seed delivery

Climate change-induced heat stress combines two challenges:high day-and nighttime temperatures,and physiological water deficit due to demand-side drought caused by increase in vapor-pressure deficit.It is one of the major factors in low productivity of maize in rainfed stress-prone environments in South Asia,affecting a large population of smallholder farmers who depend on maize for their sustenance and livelihoods.The International Maize and Wheat Improvement Center(CIMMYT)maize program in Asia,in partnership with public-sector maize research institutes and private-sector seed companies in South Asian countries,is implementing an intensive initiative for developing and deploying heat-tolerant maize that combines high yield potential with resilience to heat and drought stresses.With the integration of novel breeding tools and methods,including genomics-assisted breeding,doubled haploidy,fieldbased precision phenotyping,and trait-based selection,new maize germplasm with increased tolerance to heat stress is being developed for the South Asian tropics.Over a decade of concerted effort has resulted in the successful development and release of 20 high-yielding heat-tolerant maize hybrids in CIMMYT genetic backgrounds.Via public–private partnerships,eight hybrids are presently being deployed on over 50,000 ha in South Asian countries,including Bangladesh,Bhutan,India,Nepal,and Pakistan.

Research on arbuscular mycorrhizae in Cuba:a historical review and future perspectives

This review presents the development of researches on arbuscular mycorrhizae(AM)conducted in Cuba,a tropical Caribbean island rich in biodiversity.The key findings from this work are highlighted and presented as a stepping stone for future research.Cuban research has contributed to understand the diversity and functionality of AM in several tropical ecosystems,mainly evergreen forests,agroecosystems,sand dunes and pasturelands.Inventories were conducted in 10 out of 16 provinces reported 79 AM species,representing 25%of the known species worldwide.Cuban researchers have a great deal of expertise in Glomeromycota taxonomy and have described 11 new species,of which six were not reported elsewhere in the world.Furthermore,important studies conducted in Cuba have shed light on the mycotrophic plants,the role of AM in forest ecosystems,and their use in crop production.The contribution of AM to ecosystem processes is a priority line of research.Interdisciplinary and multidisciplinary researches are necessary to define the role of AM symbioses and improve biogeochemical models.Recently created Cuban Mycorrhizal Research Network will help to coordinate validation campaigns for various biofertilizers with training courses for Cuban farmers to disseminate the key results on AM.Despite the challenges for Cuban mycorrhizologists,molecular(genomic)techniques,stable isotopes and nuclear magnetic resonance should also be included as priority lines of research in the future.

Double Deep Q-Network Method for Energy Efficiency and Throughput in a UAV-Assisted Terrestrial Network

Increasing the coverage and capacity of cellular networks by deploying additional base stations is one of the fundamental objectives of fifth-generation(5G)networks.However,it leads to performance degradation and huge spectral consumption due to the massive densification of connected devices and simultaneous access demand.To meet these access conditions and improve Quality of Service,resource allocation(RA)should be carefully optimized.Traditionally,RA problems are nonconvex optimizations,which are performed using heuristic methods,such as genetic algorithm,particle swarm optimization,and simulated annealing.However,the application of these approaches remains computationally expensive and unattractive for dense cellular networks.Therefore,artificial intelligence algorithms are used to improve traditional RA mechanisms.Deep learning is a promising tool for addressing resource management problems in wireless communication.In this study,we investigate a double deep Q-network-based RA framework that maximizes energy efficiency(EE)and total network throughput in unmanned aerial vehicle(UAV)-assisted terrestrial networks.Specifically,the system is studied under the constraints of interference.However,the optimization problem is formulated as a mixed integer nonlinear program.Within this framework,we evaluated the effect of height and the number of UAVs on EE and throughput.Then,in accordance with the experimental results,we compare the proposed algorithm with several artificial intelligence methods.Simulation results indicate that the proposed approach can increase EE with a considerable throughput.

Short-Term Impact of Elemental Sulfur on Cranberry Nutrition and Crop Performance

Cranberry (Vaccinium macrocarpon Ait.) is an ammophilous plant grown on acid soils (pH 4.0 - 5.5). Elemental sulfur is commonly applied at a recommended rate of 1120 kg S ha−1 per pH unit to acidify cranberry soils, potentially impacting the plant mineral nutrition. The general recommendation may not fit all conditions encountered in the field. Our objective was to develop an equation to predict the sulfur requirement to reach pHwater of 4.2 to tackle nitrification in acidic cranberry soils varying in initial pH values, and to measure the effect of elemental sulfur on the mineral nutrition and the performance of cranberry crops. A 3-yr experiment was designed to test the effect of elemental sulfur on soil and tissue tests and on berry yield and quality. Four S treatments (0, 250, 500 and 1000 kg S ha−1) were established on three duplicated sites during two consecutive years. We ran soil, foliar tissue, berry tissue tests, and measured berry yield, size, anthocyanin content (TAcy), Brix, and firmness. Nutrients were expressed as centered log ratios to reflect nutrient interactions. Results were analyzed using a mixed model. Soil Ca decreased while soil Mn and S increased significantly (p ≤ 0.05). Sulfur showed no significant effects on nutrient balances in uprights. The S impacted negatively berry B balance, and positively berry Mn and S balances. A linear regression model relating pH change to S dosage and elapsed time (R2 = 0.53) showed that to reach pHwater of 4.2 two years after S application, 250 - 1000 kg S ha−1 could be applied depending on initial soil pH value. The stratification of surface-applied elemental S in the soil profile should be further examined in relation to plant rooting and nutrient leaching.

Multi‑omics integration identifies regulatory factors underlying bovine subclinical mastitis

Background Mastitis caused by multiple factors remains one of the most common and costly disease of the dairy industry.Multi-omics approaches enable the comprehensive investigation of the complex interactions between mul-tiple layers of information to provide a more holistic view of disease pathogenesis.Therefore,this study investigated the genomic and epigenomic signatures and the possible regulatory mechanisms underlying subclinical mastitis by integrating RNA sequencing data(mRNA and lncRNA),small RNA sequencing data(miRNA)and DNA methylation sequencing data of milk somatic cells from 10 healthy cows and 20 cows with naturally occurring subclinical mastitis caused by Staphylococcus aureus or Staphylococcus chromogenes.Results Functional investigation of the data sets through gene set analysis uncovered 3458 biological process GO terms and 170 KEGG pathways with altered activities during subclinical mastitis,provided further insights into subclin-ical mastitis and revealed the involvement of multi-omics signatures in the altered immune responses and impaired mammary gland productivity during subclinical mastitis.The abundant genomic and epigenomic signatures with sig-nificant alterations related to subclinical mastitis were observed,including 30,846,2552,1276 and 57 differential methylation haplotype blocks(dMHBs),differentially expressed genes(DEGs),lncRNAs(DELs)and miRNAs(DEMs),respectively.Next,5 factors presenting the principal variation of differential multi-omics signatures were identified.The important roles of Factor 1(DEG,DEM and DEL)and Factor 2(dMHB and DEM),in the regulation of immune defense and impaired mammary gland functions during subclinical mastitis were revealed.Each of the omics within Factors 1 and 2 explained about 20%of the source of variation in subclinical mastitis.Also,networks of impor-tant functional gene sets with the involvement of multi-omics signatures were demonstrated,which contributed to a comprehensive view of the possible regulatory mechanisms underlying subclinical mastitis.Furthermore,multi-omics integration enabled the association of the epigenomic regulatory factors(dMHBs,DELs and DEMs)of altered genes in important pathways,such as‘Staphylococcus aureus infection pathway’and‘natural killer cell mediated cyto-toxicity pathway’,etc.,which provides further insights into mastitis regulatory mechanisms.Moreover,few multi-omics signatures(14 dMHBs,25 DEGs,18 DELs and 5 DEMs)were identified as candidate discriminant signatures with capac-ity of distinguishing subclinical mastitis cows from healthy cows.Conclusion The integration of genomic and epigenomic data by multi-omics approaches in this study provided a better understanding of the molecular mechanisms underlying subclinical mastitis and identified multi-omics candidate discriminant signatures for subclinical mastitis,which may ultimately lead to the development of more effective mastitis control and management strategies.

The gene encoding flavonol synthase contributes to lesion mimic in wheat

Lesion mimic often exhibits leaf disease-like symptoms even in the absence of pathogen infection,and is characterized by a hypersensitive-response(HR)that closely linked to plant disease resistance.Despite this,only a few lesion mimic genes have been identified in wheat.In this investigation,a lesion mimic wheat mutant named je0297 was discovered,showing no alteration in yield components when compared to the wild type(WT).Segregation ratio analysis of the F_(2)individuals resulting from the cross between the WT and the mutant revealed that the lesion mimic was governed by a single recessive gene in je0297.Using Bulked segregant analysis(BSA)and exome capture sequencing,we mapped the lesion mimic gene designated as lm6 to chromosome 6BL.Further gene fine mapping using 3315 F_(2)individuals delimited the lm6 within a 1.18 Mb region.Within this region,we identified 16 high-confidence genes,with only two displaying mutations in je0297.Notably,one of the two genes,responsible for encoding flavonol synthase,exhibited altered expression levels.Subsequent phenotype analysis of TILLING mutants confirmed that the gene encoding flavonol synthase was indeed the causal gene for lm6.Transcriptome sequencing analysis revealed that the DEGs between the WT and mutant were significantly enriched in KEGG pathways related to flavonoid biosynthesis,including flavone and flavonol biosynthesis,isoflavonoid biosynthesis,and flavonoid biosynthesis pathways.Furthermore,more than 30 pathogen infection-related(PR)genes exhibited upregulation in the mutant.Corresponding to this expression pattern,the flavonoid content in je0297 showed a significant decrease in the 4^(th)leaf,accompanied by a notable accumulation of reactive oxygen,which likely contributed to the development of lesion mimic in the mutant.This investigation enhances our comprehension of cell death signaling pathways and provides a valuable gene resource for the breeding of disease-resistant wheat.

A likely paleo-autotetraploidization event shaped the high conservation of Nyssaceae genome

Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research,including evolution,genetics,genomics,ecology,agriculture,forestry,and global climate.To investigate which plant conserves best the core eudicots common ancestor genome,we compared Arcto-Tertiary relict Nyssaceae and 30 other eudicot plant families.The genomes of Davidia involucrata(a known living fossil),Camptotheca acuminata and Nyssa sinensis,one per existent genus of Nyssaceae,were performed comparative genomic analysis.We found that Nyssaceae originated from a single Nyssaceae common tetraploidization event(NCT)-autotetraploidization 28-31 Mya after the core eudicot common hexaploidization(ECH).We identified Nyssaceae orthologous and paralogous genes,determined its chromosomal evolutionary trajectory,and reconstructed the Nyssaceae most recent ancestor genome.D.involucrata genome contained the entire seven paleochromosomes and 17 ECH-generated eudicot common ancestor chromosomes and was the slowest in mutation among the analyzed 42 species of 31 plant families.Combing both its high retention of paleochromosomes and its low mutation rate,D.involucrata provides the best case in conservation of the core eudicot paleogenome.