Correlation between the gut microbiome and neurodegenerative diseases:a review of metagenomics evidence

A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis.As a contributing factor,microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases,such as Alzheimer’s disease,Parkinson’s disease,and amyotrophic lateral sclerosis.High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota’s diverse microorganisms,and for both neuroimmune and neuroendocrine systems.Here,we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases,with an emphasis on multi-omics studies and the gut virome.The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated.Finally,we discuss the role of diet,prebiotics,probiotics,postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.

The chromosome-level genome of double-petal phenotype jasmine provides insights into the biosynthesis of floral scent

Jasmine(Jasminum sambac Aiton)is a well-known cultivated plant species for its fragrant flowers used in the perfume industry and cosmetics.However,the genetic basis of its floral scent is largely unknown.In this study,using PacBio,Illumina,10×Genomics and highthroughput chromosome conformation capture(Hi-C)sequencing technologies,a high-quality chromosome-level reference genome for J.sambac was obtained,exploiting a double-petal phenotype cultivar‘Shuangbanmoli’(JSSB).The results showed that the final assembled genome of JSSB is 580.33 Mb in size(contig N50=1.05 Mb;scaffold N50=45.07 Mb)with a total of 39618 predicted protein-coding genes.Our analyses revealed that the JSSB genome has undergone an ancient whole-genome duplication(WGD)event at 91.68 million years ago(Mya).It was estimated that J.sambac diverged from the lineage leading to Olea europaea and Osmanthus fragrans about 28.8 Mya.On the basis of a combination of genomic,transcriptomic and metabolomic analyses,a range of floral scent volatiles and genes were identified involved in the benzenoid/phenylpropanoid and terpenoid biosynthesis pathways.The results provide new insights into the molecular mechanism of its fragrance biosynthesis in jasmine.

5-Aminolevulinic acid against strawberry Fusarium wilt:Bidirectional regulation of biocontrol agents and pathogens

Strawberry Fusarium wilt (SFW) is a systematic soil-borne disease caused by Fusarium oxysporum f.sp.fragaria (Fof),which infects the vascular bundles,blocking water and nutrient transport from roots to the aboveground.It is a severe pathogen which spreads rapidly and destroys strawberry production.Finding a way to control this disease is of great scientific value and practical importance.In this study,three fungi were isolated from the vascular tissues of sick strawberries in the field.After DNA sequencing,they were identified as Fof,Aspergillus fumigatus and Trichoderma harzianum,respectively,among which the first two are pathogens and the third is a probiotic.All fungi were controlled by thiophanate-methyl (TM),a commercial fungicide.On PDA medium,20 mg·L^(-1)5-aminolevulinic acid (ALA),a natural non-protein amino acid,promoted T.harzianum proliferation,but inhibited Fof and A.fumigatus.In confrontation test,the growth of Fof or A.fumigatus was inhibited by T.harzianum and exogenous ALA promoted T.harzianum growth but significantly inhibited the pathogen growth.When three species of fungi were separately or combinedly inoculated on healthy strawberry plants,T.harzianum promoted plant growth and development while Fof or A.fumigatus caused growth retardation,where Fof directly caused leaf yellowing and plant wilting.When the plants inoculated with different fungus were treated with ALA,the results turned out that ALA alleviated SFW symptoms by bidirectionally promoting T.harzianum proliferation and inhibiting Fof and A.fumigatus.Thus,ALA might be used in comprehensively controlling SFW in strawberry industry.

Additional far-red light promotes adventitious rooting of doubleroot-cutting grafted watermelon seedlings

Root regeneration is an important factor influencing the healing rate of graft union and the survival of double-root-cutting grafting.To date,little information is available on how to enhance root regeneration of rootstock in grafted watermelon(Citrullus lanatus)seedlings.In this study,the effects of different light treatments on root regeneration were determined.This revealed that addition of far-red light(Fr)could significantly expedite root formation in the rootstock.Moreover,the results of transcriptome analysis revealed that plant hormone pathway and auxinrelated genes were greatly induced by Fr,especially for auxin-response proteins(including CmIAA11,CmIAA17,and CmAUX28),Small auxinup RNA genes(including CmSAUR20 and CmSAUR50)and the auxin efflux transporter(CmPIN3).In addition,the expression of Phytochrome Interacting Factor(PIFs),such as CmPIF1,CmPIF3 and CmPIF7,was remarkably increased by Fr.These genes may act together to activate auxinrelated pathways under Fr treatment.Based on the results of HPLC-MS/MS analysis,the concentrations of different auxin-types in adventitious root were significantly influenced by Fr.Furthermore,the better growth of rootstock root displayed superior vasculature transport activity of the graft union with Fr treatment,which was determined by the acid magenta dyeing experiment.Therefore,all the results suggested that Fr could induce AR formation in rootstocks,which may be associated with the auxin accumulation by regulating the transcriptional level of auxinrelated and PIF genes.The findings of this study demonstrated a practicable way to shorten the healing period of graftings and improve the quality of grafted watermelon seedlings,which will provide a theoretical basis for the speeding development of industrialized seedlings production.

The response of roots and the rhizosphere environment to integrative cultivation practices in paddy rice

Integrative cultivation practices(ICPs)are essential for enhancing cereal yield and resource use efficiency.However,the effects of ICP on the rhizosphere environment and roots of paddy rice are still poorly understood.In this study,four rice varieties were produced in the field.Each variety was treated with six different cultivation techniques,including zero nitrogen application(0 N),local farmers’practice(LFP),nitrogen reduction(NR),and three progressive ICP techniques comprised of enhanced fertilizer N practice and increased plant density(ICP1),a treatment similar to ICP1 but with alternate wetting and moderate drying instead of continuous flooding(ICP2),and the same practices as ICP2 with the application of organic fertilizer(ICP3).The ICPs had greater grain production and nitrogen use efficiency than the other three methods.Root length,dry weight,root diameter,activity of root oxidation,root bleeding rate,zeatin and zeatin riboside compositions,and total organic acids in root exudates were elevated with the introduction of the successive cultivation practices.ICPs enhanced nitrate nitrogen,the activities of urease and invertase,and the diversity of microbes(bacteria)in rhizosphere and non-rhizosphere soil,while reducing the ammonium nitrogen content.The nutrient contents(ammonium nitrogen,total nitrogen,total potassium,total phosphorus,nitrate,and available phosphorus)and urease activity in rhizosphere soil were reduced in all treatments in comparison with the non-rhizosphere soil,but the invertase activity and bacterial diversity were greater.The main root morphology and physiology,and the ammonium nitrogen contents in rhizosphere soil at the primary stages were closely correlated with grain yield and internal nitrogen use efficiency.These findings suggest that the coordinated enhancement of the root system and the environment of the rhizosphere under integrative cultivation approaches may lead to higher rice production.

Analysis of Intraspecies Diversity of Rice Reveals Variation Patterns of Oryza sativa Basic Leucine Zippers

The basic leucine zipper(bZIP)is an important class of transcription factors in plants,playing a critical role in plant growth and development and responses to biotic and abiotic stress.Due to gene presence/absence variations,it is limited to identify bZIP genes based on the reference genome.Therefore,we performed the bZIP gene family analysis in the rice pan-genome.By employing a rice pan-genome,ninety-four OsbZIPs(72 core genes and 22 variable genes)were identified and divided into 11 groups in a phylogenetic tree.Based upon Ka/Ks values in 33 accessions,OsbZIPs were subjected to different selection pressures during domestication.The analysis of the effects of structural variations(SVs)on gene expression,gene structure,and conserved domains showed that SVs could significantly alter the expression levels of certain OsbZIPs,leading to gene truncation and the emergence of numerous atypical genes.Thirty-four differentially expressed OsbZIPs were identified by analyzing RNA-seq data of the Xanthomonas oryzae pv.oryzae(Xoo)infection susceptible(IR24)and resistant(IRBB67)lines under high temperature,and by counting the number of differentially expressed OsbZIPs in different subgroups.These Osb-ZIPs were found to respond to Xoo infection at an early stage and may not be involved in the mechanism of Xa4 and Xa7 resistance to Xoo.The multiple variation patterns of OsbZIP genes provide new insights into the OsbZIP genes in rice.These results provide new resources and offer new directions for functional studies of OsbZIPs.

Melatonin delays leaf senescence in pak choi(Brassica rapa subsp.chinensis)by regulating biosynthesis of the second messenger cGMP

Melatonin(MT)is a low molecular weight compound with multiple biological functions in plants.It is known to delay leaf senescence in various species.However,no data are available on the MT signaling pathway in postharvest vegetables.This study demonstrates that MT increases cGMP concentration and the expression of the cGMP synthesis gene BcGC1 in pak choi.The c GMP inhibitor LY83583 destroys effect of MT delaying the leaf senescence.LY83583 also prevents MT treatment from reducing the expression of chlorophyll metabolism-related genes(BcNYC1,BcNOL,BcPPH1/2,BcSGR1/2,and BcPAO)and senescence genes(BcSAG12 and BcSAG21).It also inhibits MT from reducing the activity of the key chlorophyll catabolism enzymes Mg-dechelatase,pheophytinase,and pheide a oxygenase.Thus,the ability of MT to maintain high levels of chlorophyll metabolites is also destroyed.The Arabidopsis c GMP synthetic gene mutant atgc1 was used to confirm that delayed leaf senescence caused by MT is mediated,at least in part,by the second messenger c GMP.

Research progress on the breeding of japonica super rice varieties in Jiangsu Province,China

In this study we report the results of a decade-long breeding program for japonica super rice made by Nanjing Branch of Chinese National Center for Rice Improvement in Jiangsu Academy of Agricultural Sciences. We concluded that selection of parents with good comprehensive traits and complementary advantages and disadvantages of both parents in the hybrid combination, and early selection of high heritability traits in earlier segregating generations could significantly improve the breeding efficiency. The use of closely-linked functional markers in pyramiding of multiple genes could greatly increase breeding efficiency, avoiding time-consuming and laborious steps that were used in traditional breeding program. It is also important to coordinate the yield components with variety characteristics such as yield stability, wide adaptability, lodging resistance, and an attractive grain appearance during late growth stage of rice.

A new feasible method for yield gap analysis in regions dominanted by smallholder farmers, with a case study of Jiangsu Province, China

In the regions where crops were mostly produced by smallholder farmers, the analysis of yield gap is difficult due to diverse cultivars, crop managements and yield levels. In order to find an effective method that can reasonably verify the yield gap and the limiting cultivation factors in narrowing yield gaps in areas that are dominanted by smallholder farmers, we worked out a method consisting five progressive procedures as follows: questionnaire investigation of farmer cultivation regime, identification of yield levels and yield gaps, generalization of key cultivation measurements, reconstruction of representative maize populations, and process-based analysis of yield gap. A case study was carried out in Jiangsu Province, China, in which maize is mostly produced by smallholder farmers. A questionnaire investigation of 1 023 smallholder farmers was carried out firstly, then the frequency distribution of maize yield was simulated by an normal distribution function, and then the covering range and average value of the basic yield, farmer yield and high-yield farmer yield levels were calculated out from the equation. Hereby, the yield gaps 1, 2 and 3 were calculated along with the record highest yield from literature and experts, which were 2 564, 2 346 and 2 073 kg ha^(–1), respectively. Moreover, with the covering range of each yield level, the suveyed farmers belonging to each yield level were grouped together and then their major cultivation measures were traced and generalized. With the generalized cultivation measures, representative maize populations of the four yield levels were reconstructed, and thereby clarifing lots of characters of the populations or single plant of each population with processbased analysis of the reconstructed populations. In this case, the main factors causing the yield gap were plant density, fertilizer application rate, logging caused by hurricane, and damages caused by pests. The case study primarily indicated that this five-step method is feasible and effective in yield gap study, especially in smallholder farmers dominant regions.

Status and Prospects of Hybrid Rice Breeding in Jiangsu, China

Research on hybrid rice in Jiangsu Province, China began in 1970. Great progress has been made since then, which can be divided into three stages according to the development of hybrid rice breeding and production in Jiangsu Province. The first stage was beginning stage from 1970 to 1980, when progress was mainly made in cytoplasmic male sterile line breeding. The second stage could be described as developing stage, from 1980 to 1995, when indica hybrid rice was rapidly popularized, and japonica hybrid rice became popular later. From 1996, hybrid rice breeding in Jiangsu Province entered the third stage, when both indica and japonica hybrid rice breeding in the three-line system or intersubspecific hybrid rice breeding in the two-line system made a great breakthrough with the successful breeding of the hybrids Feyou 559, 9 You 138 and Liangyoupeijiu. The developing trend of hybrid rice breeding in Jiangsu Province is also discussed.

Cultivar Selection and Test Site Evaluation of Cotton Regional Trials in Jiangsu Province Based on GGE Biplot

This study was to evaluate the high yielding and stability of candidate cultivars, depict the adaptive planting region, analyze trial location discrim-ination ability and representativeness, as wel as identify the ideal cultivar and trial location, with the aim to provide theory background for cultivar selection and rea-sonable scheme of test location in Jiangsu Province. [Method] The GGE biplot method was used to analyze the lint cotton yield of 12 experimental genotypes in the 6 test locations （three replicates in each） of the cotton regional trial in Jiangsu Province in 2013. [Result] The effects of genotype （G）, environment （E）, and geno-type by environment interaction （G＆#215;E） on lint cotton yield were al highly significant （P〈0.01）, which made it necessary to further explore the specific pattern of geno-type by environment interaction. Jinmian118 （G4） and SF3303 （G5） were the best ideal genotypes screened by the ＂ideal cultivar＂ and ＂ideal location＂ view of GGE biplot, and the ordination of test sites based on the ideal index were in the order of Dafeng （DF）, Yanliang （YL）, Liuhe （LH）, Dongtai （DT）, Yancheng （YC）, and Nantong （NT）, among which NT was relatively weak in representing of the whole target cot-ton planting region in Jiangsu Province. The ＂similarity among locations＂ view of GGE biplot clustered al trial locations into one group, showing that the test sites in the cotton planting region in Jiangsu Province were in the same mega-environment. The ＂which-won-where＂ view of GGE biplot indicated that cotton cultivar Jinmian118 （G4） was the most appropriate cultivar in the homogeneous cotton planting region in Jiangsu Province. [Conclusion] Among the candidate cultivars, Jinmian118 and SF3303 were identified as the most ideal cultivars in this set of conventional cotton regional trial in Jiangsu Province; the test site of Dafeng ranked the first out of al locations in terms of discrimination and representativeness, and al test locations were clustered into the same mega-environmet, which indicated the high efficiency of cultivar selection in the cotton regional trial in Jiangsu Province.

Nitrogen Management Evaluated by Models Combined with GIS-A Case Study of Jiangsu Croplands,China,in 2000

The objective of this study is to provide scientific guidance for optimizing agricultural field nitrogen management that is based on the evaluation of current nitrogen application practice in Jiangsu Province, China, in 2000. The agricultural nitrogen models, consist of the soil mineralization model, the organic manure nitrogen releasing model, and the nitrogenous fertilizer use efficiency model. These models combined with the geographic information system technique were used to describe the spatial variability of nitrogen released from soil and organic manure and to identify its contributing factors. The comparison of the nitrogen fertilizer amount required by croplands, which was simulated by the models with the actual nitrogen fertilizer applied rate, was used to evaluate the current nitrogen application. The results showed that nitrogen was excessively applied in 71.8% croplands, given that the actual crop yield was desired. The excessive nitrogen amounted to 760 kiloton, accounting for 41.5% of the total nitrogen applied. Given that the actual highest yield was desired, nitrogen was reduced in 64.3% croplands. The total shortage of nitrogen was about 800 kiloton. Low use efficiency of nitrogen fertilizer was found in Taihu Lake area, Nanjing-Zhenjiang hilly area, and Xuzhou area, whereas the east beach area of Jiangsu showed an obvious deficiency of nitrogen fertilizer inputs. A balance of nitrogen fertilizer in Jiangsu croplands between excessive and deficient application areas would greatly benefit economic and environmental advantages.

Analysis on Present Situation and Countermeasures of Rural Ecotourism in Jiangsu Province

This article briefly outlines the concept, present situation and form of rural ecotourism. It also preliminarily analyses the existing problems of rural ecotourism. Then countermeasures and suggestions related to the further development of rural ecotourism and promotion of new countryside construction are put forward, which can be summarized as follows: carrying out multichannel financing, in order to strengthen the development dynamics of rural ecotourism; focusing on cultivation of ecological quality consciousness, in order to enhance the protection of resources and the environment; innovating development ideas, in order to create muti-function areas; intensifying the efforts on the training for employee, in order to upgrade comprehensive service level; promoting community participation and intensifying the efforts on the training for farmer, in order to raise farmer's consciousness about development of ecotourism; strengthening the fusion of ecology and culture.

Evaluation on Ideal Test Sites and Regional Characteristics of Cotton Fiber Quality in Jiangsu Province

[Objective] The aim of this study was to explore the dominant fiber quality traits of test sites in cotton regional trials, by analyzing the regional characteristics of cotton fiber quality in Jiangsu province, in order to provide the theory background for cotton fiber quality improvement. [Method] The dominant fiber quality traits of test locations were analyzed with eight main fiber quality indexes of hybrid cotton regional trials during 2009-2013 in Jiangsu province by use of the "ideal test site" view of GGE biplot. [Result] The test locations with the best integrative fiber quality were proved to be Yanliang, and followed by Dongxin and Guanyun; The better test locations in terms of the major fiber quality indexes, including fiber strength, fiber Length and micronaire value, were Guanyun, Xinyang and Yanliang; To sum up, the best test location with balanced fiber quality was Yanliang. The test locations with specialties in fiber quality index were listed as bellow: Dafeng, Xinghua and Dongtai performance better in fiber length; Qidong, Liuhe and Yanhai locations were of better fiber length uniformity; Sheyang and Dongxin were better in micronaire value;while Sheyang along was better in fiber elongation and reflectance. Moreover, the correlation between fiber yellowness and other traits was significant(P<0.01). [Conclusion] The regional characteristic of cotton fiber quality index in Jiangsu province was obvious and fiber yellowness was worthy an indicator trait to assist the comprehensive improvement of cotton fiber quality.

Resistance analysis of the rice variety Huaidao 5 against root-knot nematode Meloidogyne graminicola

Meloidogyne graminicola has emerged as one of the most destructive plant-parasitic nematodes affecting rice(Oryza sativa)production worldwide.Resistance to M.graminicola in rice could be the most effective option for its management.However,sources of germplasm with resistance to M.graminicola in rice remain limited.Here,we describe the root attraction,gall formation and genetic analysis of the resistance to M.graminicola in the rice variety Huidao 5.A nematode attraction assay showed that second-stage juveniles(J2s)of M.graminicola were attracted at the root tip of Huaidao 5 within 8 h without a significant reduction in attraction compared to the susceptible rice variety Nanjing 9108.Microscopic observation of the infection revealed that the J2s invaded root tissues 12 h after inoculation,but their subsequent movement to the root tip was hindered in Huaidao 5,resulting in decreased nematode number compared to Nanjing 9108.Additionally,we used the soil and hydroponic culture systems to simulate upland and flooding conditions in the paddy fields respectively,and found that gall number was significantly reduced,and nematode development was clearly suppressed in Huaidao 5.To investigate the genetic basis of this resistance,cross breeding was performed between the Huaidao 5 and Nanjing 9108 varieties.There was no reduction in the resistance of the F_(1) offspring to M.graminicola in the greenhouse or field trials,suggesting that a dominant gene could control resistance in Huaidao 5.In summary,this study provides a detailed characterization of a novel source of resistance to M.graminicola in rice,which is of great potential for use in crop breeding.

The effect of protein oxidation on the formation of advanced glycation end products after chicken myofibrillar protein glycation

Investigation that protein oxidation to the formation of advanced glycation end products(AGEs)after chicken myofibrillar protein glycation is limited.Models of protein oxidation induced by different concentrations of hydroxyl radicals(·OH)were developed after the chicken myofibrillar protein mild glycation(MPG).Results exhibited that levels of AGEs and surface hydrophobicity(H_(0))steadily increased with the a ddition of h ydrogen peroxide(H_(2)O_(2))concentration.However,levels of s ulfhydryl group,free amino group,and particle size gradually decreased with the H_(2)O_(2)concentration.The protein carbonyl value increased in H_(2)O_(2)concentration until 10 mmol/L.Pearson's correlation indicated that MPG structure modification(unfolding and degradation)induced by protein oxidation were significantly positively correlated with AGEs concentration(P<0.05).Finally,a mechanism was proposed to hypothesize t he effect of protein oxidation on the formation of AGEs under MPG conditions.

Effect of sodium alginate-based hydrogel loaded with lutein on gut microbiota and inflammatory response in DSS-induced colitis mice

In order to effectively deliver lutein to the inflamed colon and better exert its pharmacological activity,this paper constructed a sodium alginate hydrogel-based delivery system loaded with lutein nanoparticles,evaluated the regulation on the expression and secretion of related inflammatory factors in mice with colitis,and its impact on intestinal microbial environment.The results showed that comparing lutein crystal and its nanoparticle,lutein hydrogel alleviated dextran sodium sulfate(DSS)-induced colitis in mice more effectively by adjusting fecal heme content,colon tissue damage,and inflammatory factor levels.Moreover,lutein hydrogel increased the expression of intestinal tight junction proteins zonula occluden-1(ZO-1),claudin-1 and occludin to maintain the integrity of the intestinal-barrier,inhibited the nuclear factor-κB(NF-κB)pathway and reduced expression and secretion of inflammatory factors including tumour necrosis factor-α(TNF-α),inducible nitric oxide synthase(iNOS),NOD-like receptors 3(NLRP3)and interleukin(IL)-1β.In addition,the intestinal microbial environment of mice with colitis was improved by down-regulating the relative abundance of Desulfovibrionaceae and up-regulating the relative abundance of Erysipelotrichaceae and Rikenellaceae.As a slow-release carrier to load lutein nanoparticles,sodium alginate-based hydrogel has potential application prospect.

Transcriptome analysis reveals the mechanism of chronic heat stress on meat quality of broilers

Background:Chronic heat stress has a negative impact on poultry meat quality.Although this has been extensively investigated,previous studies have primarily focused on metabolic alterations and oxidative stress in the pectoralis major(PM)muscle under chronic heat stress,and not all of the underlying molecular mechanisms are completely understood.Methods:A total of 144 male Arbor Acres broilers(28 d old)were randomly allocated into 3 treatment groups:(1)the normal control(NC)group,with broilers raised at 22℃and fed a basal diet;(2)the heat stress(HS)group,with birds raised at 32℃and fed a basal diet;and(3)the pair-fed(PF)group,with birds raised at 22℃and fed the amount of feed equal to the feed consumed on the previous day by the HS group.The experiment lasted for 14 d.Results:Chronic heat stress decreased the average daily feed intake and average daily gain,increased feed:gain ratio(P<0.05);and increased drip loss,cooking loss,shear force,hardness,and decreased p H,redness(a*);and springiness of PM muscle(P<0.05).Furthermore,chronic heat stress decreased muscle fiber density,increased connective tissue,and led to intracellular vacuolation.The transcriptome analyses indicated that the effect of chronic heat stress on meat quality was not only related to metabolism and oxidative stress,but also to signal transduction,immune system,transport and catabolism,cell growth and death,and muscle structure.Conclusions:Chronic heat stress has a negative impact on the growth performance,meat quality,and the PM muscle structure of broilers.Transcriptome analysis revealed a comprehensive understanding of the mechanism of the chronic heat stress-induced deterioration of broiler meat quality at the transcriptional level.

Introgression of sharp eyespot resistance from Dasypyrum villosum chromosome 2VL into bread wheat

Wheat sharp eyespot, a stem disease caused by the soilborne fungus Rhizoctonia cerealis van der Hoeven,has become a threat to wheat production worldwide. Exploiting resistance resources from wild relatives of wheat is a promising strategy for controlling this disease. In this study, a new wheat–Dasypyrum villosum T2DS·2V#4L translocation line in the background of Chinese Spring(CS) showed stable resistance to R. cerealis. Introgression of the T2DS·2V#4L chromosome into wheat cultivar Aikang 58 by backcrossing produced a marked increase in sharp eyespot resistance in NIL-T2DS·2V#4L in comparison with NILT2DS·2DL, and no detrimental effects of 2V#4L on agronomic traits were observed in the BC2F2, BC2F2:3,and BC2F2:4generations. Flow-sorted sequencing of 2V#4L yielded 384.3 Mb of assembled sequence, and8836 genes were predicted of which 6154 had orthologs in at least one of the 2AL, 2BL, and 2DL arms of CS, whereas 1549 genes were unique to 2V#4L. About 100,000 SNPs were detected in genes of 2V#4L and2DL in 10 sequenced bread wheat cultivars. A Kompetitive Allele Specific Polymerase chain reaction and30 conserved ortholog sequence markers were developed to trace the 2V#4L chromatin in wheat backgrounds. T2DS·2V#4L compensating translocation lines represent novel germplasm with sharp eyespot resistance and the markers will allow rapid detection in breeding programs.

Low light intensity elongates period and defers peak time of photosynthesis: a computational approach to circadian-clock-controlled photosynthesis in tomato

Photosynthesis is involved in the essential process of transforming light energy into chemical energy.Although the interaction between photosynthesis and the circadian clock has been confirmed,the mechanism of how light intensity affects photosynthesis through the circadian clock remains unclear.Here,we propose a first computational model for circadian-clock-controlled photosynthesis,which consists of the light-sensitive protein P,the core oscillator,photosynthetic genes,and parameters involved in the process of photosynthesis.The model parameters were determined by minimizing the cost function(δ=8.56),which is defined by the errors of expression levels,periods,and phases of the clock genes(CCA1,PRR9,TOC1,ELF4,GI,and RVE8).The model recapitulates the expression pattern of the core oscillator under moderate light intensity(100μmol m^(-2) s^(-1)).Further simulation validated the dynamic behaviors of the circadian clock and photosynthetic outputs under low(62.5μmol m^(-2) s^(-1))and normal(187.5μmol m^(-2) s^(-1))intensities.When exposed to low light intensity,the peak times of clock and photosynthetic genes were shifted backward by 1–2 hours,the period was elongated by approximately the same length,and the photosynthetic parameters attained low values and showed delayed peak times,which confirmed our model predictions.Our study reveals a potential mechanism underlying the circadian regulation of photosynthesis by the clock under different light intensities in tomato.