Melatonin mitigates cold-induced damage to pepper seedlings by promoting redox homeostasis and regulating antioxidant profiling

This study assessed the influence of exogenous ME in the mitigation of cold damage in pepper seedlings. Melatonin(ME) is a dynamic molecule that helps plants cope with stress in several ways. Cold stress(CS) is one of the most important environmental factors that restrict plant growth and yield. Pepper(Capsicum annuum L.) is a valuable commercial crop, highly sensitive to CS. Thus, identifying an efficient strategy to mitigate cold damage is critical for long-term pepper production. For this purpose, the roots of pepper seedlings were pretreated with ME(5 μmol · L^(-1)) and exposed to CS for 7 d. The results indicated that CS suppressed pepper growth, hampered photosynthetic capacity, and damaged root architecture in pepper plants. In contrast, the production of reactive oxygen species(ROS), malondialdehyde(MDA), electrolyte leakage(EL), proline, and soluble sugars were enhanced in plants under CS. ME(5 μmol · L^(-1)) pretreatment reduced the negative effects of CS by recovering plant growth, root traits, gas exchange elements, and pigment molecules compared to CS control treatment. Furthermore, ME application efficiently reduced oxidative stress markers [hydrogen peroxide(H_(2)O_(2)), superoxide ion(O_(2)^(·-)), EL, and MDA] while increasing proline and soluble sugar content in pepper leaves. ME application combined with CS further increased antioxidant enzymes and related gene expression. Collectively, our results confirmed the mitigating potential of ME supplementation for CS by maintaining pepper seedling growth,improving the photosynthesis apparatus, regulating pigments, and osmolyte content.

Targeted approaches to improve tomato fruit taste

Tomato(Solanum lycopersicum)is the most valuable fruit and horticultural crop species worldwide.Compared with the fruits of their progenitors,those of modern tomato cultivars are,however,often described as having unsatisfactory taste or lacking f lavor.The f lavor of a tomato fruit arises from a complex mix of tastes and volatile metabolites,including sugars,acids,amino acids,and various volatiles.However,considerable differences in fruit f lavor occur among tomato varieties,resulting in mixed consumer experiences.While tomato breeding has traditionally been driven by the desire for continual increases in yield and the introduction of traits that provide a long shelf-life,consumers are prepared to pay a reasonable premium for taste.Therefore,it is necessary to characterize preferences of tomato f lavor and to define its underlying genetic basis.Here,we review recent conceptual and technological advances that have rendered this more feasible,including multi-omics-based QTL and association analyses,along with the use of trained testing panels,and machine learning approaches.This review proposes how the comprehensive datasets compiled to date could allow a precise rational design of tomato germplasm resources with improved organoleptic quality for the future.

Lack of fitness cost and inheritance of resistance to abamectin based on the establishment of a near-isogenic strain of Tetranychus urticae

Many populations of the two-spotted spider mite, Tetranychus urticae Koch, have developed high levels of resistance to the pesticide abamectin in China and other countries. This study developed a near-isogenic line to understand better the inheritance, cross-resistance, and fitness costs associated with abamectin resistance in the field population of T. urticae in China. We introduced the trait that confers extremely high abamectin resistance in a field-collected population of T. urticae into a susceptible laboratory strain(IPP-SS) to generate an abamectin-resistant near-isogenic line(NIL-Aba).This process was carried out through multiple backcrossing to IPP-SS and via parthenogenesis and abamectin screening. Compared with IPP-SS, the NIL-Aba strain had a 25 147-fold resistance to abamectin and a high level of cross-resistance to bifenthrin(288.17-fold), an intermediate level to emamectin benzoate(42.57-fold), and low levels to bifenazate, chlorfenapyr, cyflumetofen, cyenopyrafen, and cyetpyrafen with resistance ranging from 3.18-to 9.31-fold.But it had no cross-resistance to profenofos. The resistance to abamectin in NIL-Aba was autosomal, incompletely dominant, and polygenic. Based on two sex life table parameters, no fitness cost was found in NIL-Aba. Establishing the NIL-Aba strain provides a reliable basis for an in-depth study of abamectin resistance in T. urticae. New information on toxicological characteristics and fitness cost should facilitate the management of abamectin resistance in field populations of T. urticae.

Pyramiding of multiple genes generates rapeseed introgression lines with clubroot and herbicide resistance, high oleic acid content, and early maturity

Clubroot and herbicide resistance,high oleic acid(OA)content,and early maturity are targets of rapeseed(Brassica napus L.)breeding.The objective of this study was to develop new male-fertility restorer lines by pyramiding favorable genes to improve these traits simultaneously.Seven elite alleles for the four traits were introduced into the restorer line 621R by speed breeding with marker-assisted and phenotypic selection.Six introgression lines(ILs)were developed with four-to seven-gene combinations and crossed with two elite parents to develop hybrids.All ILs and their corresponding hybrids displayed high resistance to both clubroot pathotype 4 and sulfonylurea herbicides.Three ILs and their hybrids showed large increases in OA contents and four showed earlier maturity.These new ILs may be useful in rapeseed hybrid breeding for the target traits.

Comprehensive regulatory networks for tomato organ development based on the genome and RNAome of MicroTom tomato

MicroTom has a short growth cycle and high transformation efficiency,and is a prospective model plant for studying organ development,metabolism,and plant–microbe interactions.Here,with a newly assembled reference genome for this tomato cultivar and abundant RNA-seq data derived from tissues of different organs/developmental stages/treatments,we constructed multiple gene co-expression networks,which will provide valuable clues for the identification of important genes involved in diverse regulatory pathways during plant growth,e.g.arbuscular mycorrhizal symbiosis and fruit development.Additionally,non-coding RNAs,including miRNAs,lncRNAs,and circRNAs were also identified,together with their potential targets.Interacting networks between different types of non-coding RNAs(miRNA-lncRNA),and non-coding RNAs and genes(miRNA-mRNA and lncRNA-mRNA)were constructed as well.Our results and data will provide valuable information for the study of organ differentiation and development of this important fruit.Lastly,we established a database(http://eplant.njau.edu.cn/microTomBase/)with genomic and transcriptomic data,as well as details of gene co-expression and interacting networks on MicroTom,and this database should be of great value to those who want to adopt MicroTom as a model plant for research.

Chromosomal-level genome of macadamia(Macadamia integrifolia)

Macadamia from the family Proteaceae is a plant native to Australia and has long been favoured by people for its crispy and high nutritional and medicinal value.Here,the genome of GUIRE 1(GR1),a highly heterozygous superior cultivar of macadamia nut,was sequenced and assembled using nanopore sequencing,and a 807-Mb genome(contig N50,1.9 Mb;scaffold N50,54.70 Mb)and 14 chromosomes were obtained.A total of 453 Mb(about 55.95%)repetitive sequences and 37,657 protein-coding genes were obtained by gene annotation and homologous protein comparison.Proteaceae diverged from Nelumbonaceae nearly 115.37 million years ago and from Rubiaceae about 140 million years ago.A genome-wide duplication(WGD)event occurred in macadamia 41 million years ago based on the WGD analysis.The functional enrichment analysis of M.integrifolia-specific gene families revealed their roles in signal transduction,protein phosphorylation,protein binding,and defense response.Here,a highly heterozygous genome of M.integrifolia was unlocked to provide a database for breeding and molecular mechanism research.

Identification and functional analysis of transcription factors related to coconut(Cocos nucifera L.)endosperm development based on ATAC-seq

Coconut(Cocos nucifera L.)is a member of the palm tree family(Arecaceae)and the only living species of the genus Cocos.In this paper,the regulatory relationship pathways between multiple transcription factors and functional genes were identified by combining ATAC-seq and RNAseq in coconut endosperm at four different developmental stages(fruit after pollination:7 months,8 months,9 months and 10 months,respectively).The results indicated that the peaks detected in the promoter-TSS area accounted for the largest proportion(11.99%)in the third stage.These results suggest that the chromatin open region of cells in this period is more functional and that there are more functional genes with active transcription.In addition,a large number of potential regulatory relationships between transcription factors and functional genes were detected via bioinformatics analysis at the genomic level.Among them,CnGATA20 was predicted to be an important transcription factor with a binding site on the promoter region of the CnOLE18 gene.The regulatory pathway by which CnGATA20 positively regulates the expression of CnOLE18 was further confirmed by yeast one-hybrid,protoplast transient expression and dual-luciferase reporter system experiments.The results provide a new research strategy for exploring the regulation at both the transcriptional and posttranscriptional levels during coconut endosperm growth and development.

Plant genomes: toward goals of decoding both complex and complete sequences

Over the last 20 or so years,since the first release of the Arabidopsis genome in 2000,scientists have accomplished more than 1,000 de novo genome assemblies(https://plabipd.de/portal/plant-genomes)as well as a series of pan-genomes.The real challenges facing us are the decoding at the highly ploidy level and highly heterozygous plant genomes,as well as giga chromosomes and numerous chromosomes within a cell.

Inaugural Editorial

Tropical plants in the world include 2/3 of higher plant species,covering a large number of cash crops and their wild relatives.They have extremely rich genetic diversities and provide humans with food and beverages,energy,medicine,wood,fuel,various industrial raw materials,etc..They also provide necessary oxygen,water,living environment for other animals and plants,having irreplaceable functions on the health of the ecosystem.Due to the fragility of tropical forest ecosystems caused by human activities,it is necessary and urgent to protect the rare and endangered tropical plants and their habitats.

Challenges and opportunities to improve tropical fruits in Hainan,China

Tropical fruits play a major role in the economic and social development of Hainan(China).Despite favorable climatic conditions,the yield of tropical fruits in Hainan remains low,in part due to the low genetic potential of currently grown tropical fruit varieties.Consequently,there is a need to improve yield potential by exploiting the genome and germplasm resources of tropical fruit species,minimizing post-harvest losses,and improving transportation standards.In this study,we intend to collect germplasm resources from a wide range of domestic and exotic sources to evaluate the genetic yield potential and nutritional quality of fruit using plant morphology,taxonomy and physiological parameters.In this review,we aim to identify current bottlenecks in the Hainan tropical fruit industry and propose solutions through the use of conventional breeding and new biotechnological tools,including the use of omics and CRISPR to enhance yield and tackle biotic and abiotic stresses of tropical fruit species.Producing new fruit cultivars in Hainan,either through conventional strategies or the use of genome editing technology such as CRISPR,could help improve the socioeconomic status of this region.Furthermore,increasing the genetic potential and production of new cultivars can help in meeting the demands of new trade agreements with various nations under the'One Belt,One Road'initiative,Boao Forum for Asia,ASEAN agreements,and the Shanghai Cooperation Organization.

Metabolomics-centered mining of plant metabolic diversity and function:Past decade and future perspectives

Plants are natural experts in organic synthesis,being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival challenges.Metabolomics is a research discipline that integrates the capabilities of several types of research including analytical chemistry,statistics,and biochemistry.Its ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of metabolites.Metabolomics is usually performed by targeting either a specific cell,a specific tissue,or the entire organism.Considerable advances in science and technology over the last three decades have propelled us into the era of multi-omics,in which metabolomics,despite at an earlier developmental stage than genomics,transcriptomics,and proteomics,offers the distinct advantage of studying the cellular entities that have the greatest influence on end phenotype.Here,we summarize the state of the art of metabolite detection and identification,and illustrate these techniques with four case study applications:(i)comparing metabolite composition within and between species,(ii)assessing spatio-temporal metabolic changes during plant development,(iii)mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses,and(iv)assessing the performance of metabolomics as a means of functional gene identification,metabolic pathway elucidation,and metabolomics-assisted breeding through analyzing plant populations with diverse genetic variations.In addition,we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets,including those from genomics,transcriptomics,proteomics,epigenomics,phenomics,microbiomes,and ion-omics studies.Finally,we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity.

Disease resistance conferred by components of essential chrysanthemum oil and the epigenetic regulation of OsTPS1

The sesquiterpene alpha-bisabolol is the predominant active ingredient in essential oils that are highly valued in the cosmetics industry due to its wound healing,anti-inflammatory,and skin-soothing properties.Alpha-bisabolol was thought to be restricted to Compositae plants.Here we reveal that alpha-bisabolol is also synthesized in rice,a non-Compositae plant,where it acts as a novel sesquiterpene phytoalexin.Overexpressing the gene responsible for the biosynthesis of alpha-bisabolol,Os TPS1,conferred bacterial blight resistance in rice.Phylogenomic analyses revealed that alpha-bisabolol-synthesizing enzymes in rice and Compositae evolved independently.Further experiments demonstrated that the natural variation in the disease resistance level was associated with differential transcription of Os TPS1 due to polymorphisms in its promoter.We demonstrated that Os TPS1 was regulated at the epigenetic level by JMJ705 through the methyl jasmonate pathway.These data reveal the cross-family accumulation and regulatory mechanisms of alpha-bisabolol production.

A novel ambigrammatic mycovirus,PsV5,works hand in glove with wheat stripe rust fungus to facilitate infection

Here we describe a novel narnavirus,Puccinia striiformis virus 5(PsV5),from the devastating wheat stripe rust fungus P.striiformis f.sp.tritici(Pst).The genome of PsV5 contains two predicted open reading frames(ORFs)that largely overlap on reverse strands:an RNA-dependent RNA polymerase(RdRp)and a reverseframe ORF(rORF)with unknown function.Protein translations of both ORFs were demonstrated by immune technology.Transgenic wheat lines overexpressing PsV5(RdRp-rORF),RdRp ORF,or rORF were more susceptible to Pst infection,whereas PsV5-RNA interference(RNAi)lines were more resistant.Overexpression of PsV5(RdRp-rORF),RdRp ORF,or rORF in Fusarium graminearum also boosted fungal virulence.We thus report a novel ambigrammatic mycovirus that promotes the virulence of its fungal host.The results are a significant addition to our understanding of virosphere diversity and offer insights for sustainable wheat rust disease control.

Population analysis reveals the roles of DNA methylation in tomato domestication and metabolic diversity

DNA methylation is an important epigenetic marker,yet its diversity and consequences in tomato breeding at the population level are largely unknown.We performed whole-genome bisulfite sequencing(WGBS),RNA sequencing,and metabolic profiling on a population comprising wild tomatoes,landraces,and cultivars.A total of 8,375 differentially methylated regions(DMRs)were identified,with methylation levels progressively decreasing from domestication to improvement.We found that over 20%of DMRs overlapped with selective sweeps.Moreover,more than 80%of DMRs in tomato were not significantly associated with single-nucleotide polymorphisms(SNPs),and DMRs had strong linkages with adjacent SNPs.We additionally profiled 339 metabolites from 364 diverse accessions and further performed a metabolic association study based on SNPs and DMRs.We detected 971 and 711 large-effect loci via SNP and DMR markers,respectively.Combined with multi-omics,we identified 13 candidate genes and updated the polyphenol biosynthetic pathway.Our results showed that DNA methylation variants could complement SNP profiling of metabolite diversity.Our study thus provides a DNA methylome map across diverse accessions and suggests that DNA methylation variation can be the genetic basis of metabolic diversity in plants.

Design and experiment of pneumatic seed clearing mechanism for pin-hole tube wheat plot precision sowing device

For the problem that when wheat is sucked up by the air suction method,the seeds are aligned in a small area,making it difficult for the contact seed cleaning mechanism to clean the seeds.The mechanism of seed cleaning airflow on wheat seed was studied,the flow velocity distribution relationship of the jet section was defined,the mathematical model of the jet velocity of circular and plane sections was established,and the key factors that could have a significant influence on seed cleaning effect were explored.A non-contact positive pressure air flow seed cleaning method was proposed.After theoretical calculations,it is concluded that the core section lengths of the circular section jet and the inline jet are 24.8 mm and 28.8 mm,respectively.The clearing distance is set to 20 mm.Through the single-factor test,the best air tube nozzle shape was clarified as a vertical inline nozzle.The angle of seed cleaning,the air velocity of seed cleaning,and the negative supply pressure were selected as influencing factors,and the seed leakage index,seed reabsorption index,and seed qualification index as the evaluation indicators to conduct a 3-factor 5-horizontal rotation test.A mathematical regression model of influencing factors and evaluation indexes was established to analyze the influence of these factors and indexes.The optimal operation parameters were obtained as the seed cleaning Angle of 19°,the seed cleaning air velocity of 58 m/s,and the negative pressure of 8.5 kPa.Under the optimal parameters,the seed leakage suction index is 8.23%,the seed reabsorption index is 0.33%,and the seed qualification index is 91.44%,which meets the design requirements.

Natural variations of OsAUX5,a target gene of OsWRKY78,control the neutral essential amino acid content in rice grains

Grain essential amino acid(EAA)levels contribute to rice nutritional quality.However,the molecular mechanisms underlying EAA accumulation and natural variation in rice grains remain unclear.Here we report the identification of a previously unrecognized auxin influx carrier subfamily gene,OsAUX5,which encodes an amino acid transporter that functions in uptake of multiple amino acids.We identified an elite haplotype of Pro::OsAUX5^(Hap2) that enhances grain EAA accumulation without an apparent negative effect on agronomic traits.Natural variations of OsAUX5 occur in the cis elements of its promoter,which are differentially activated because of the different binding affinity between OsWRKY78 and the W-box,contributing to grain EAA variation among rice varieties.The two distinct haplotypes were shown to have originated from different Oryza rufipogon progenitors,which contributed to the divergence between japonica and indica.Introduction of the indica-type Pro::OsAUX5^(Hap2) genotype into japonica could significantly increase EAA levels,indicating that indica-type Pro::OsAUX5^(Hap2) can be utilized to increase grain EAAs of japonica varieties.Collectively,our study uncovers an WRKY78–OsAUX5-based regulatory mechanism controlling grain EAA accumulation and provides a potential target for breeding EAA-rich rice.

Elucidation of the melitidin biosynthesis pathway in pummelo

Specialized plant metabolism is a rich resource of compounds for drug discovery.The acylated flavonoid glycoside melitidin is being developed as an anti-cholesterol statin drug candidate,but its biosynthetic route in plants has not yet been fully characterized.Here,we describe the gene discovery and functional characterization of a new flavonoid gene cluster(UDP-glucuronosyltransferases(Cg UGTs),1,2rhamnosyltransferase(Cg1,2Rha T),acyltransferases(Cg ATs))that is responsible for melitidin biosynthesis in pummelo(Citrus grandis(L.)Osbeck).Population variation analysis indicated that the tailoring of acyltransferases,specific for bitter substrates,mainly determine the natural abundance of melitidin.Moreover,3-hydroxy-3-methylglutaryl-Co A reductase enzyme inhibition assays showed that the product from this metabolic gene cluster,melitidin,may be an effective anti-cholesterol statin drug candidate.Co-expression of these clustered genes in Nicotiana benthamiana resulted in the formation of melitidin,demonstrating the potential for metabolic engineering of melitidin in a heterologous plant system.This study establishes a biosynthetic pathway for melitidin,which provides genetic resources for the breeding and genetic improvement of pummelo aimed at fortifying the content of biologically active metabolites.

Watermelon domestication was shaped by stepwise selection and regulation of the metabolome

Although crop domestication has greatly aided human civilization,the sequential domestication and regulation of most quality traits remain poorly understood.Here,we report the stepwise selection and regulation of major fruit quality traits that occurred during watermelon evolution.The levels of fruit cucurbitacins and flavonoids were negatively selected during speciation,whereas sugar and carotenoid contents were positively selected during domestication.Interestingly,fruit malic acid and citric acid showed the opposite selection trends during the improvement.We identified a novel gene cluster(CGC1,cucurbitacin gene cluster on chromosome 1)containing both regulatory and structural genes involved in cucurbitacin biosynthesis,which revealed a cascade of transcriptional regulation operating mechanisms.In the CGC1,an allele caused a single nucleotide change in Cl ERF1 binding sites(GCC-box)in the promoter of Cl Bh1,which resulted in reduced expression of Cl Bh1 and inhibition of cucurbitacin synthesis in cultivated watermelon.Functional analysis revealed that a rare insertion of 244 amino acids,which arose in C.amarus and became fixed in sweet watermelon,in Cl OSC(oxidosqualene cyclase)was critical for the negative selection of cucurbitacins during watermelon evolution.This research provides an important resource for metabolomics-assisted breeding in watermelon and for exploring metabolic pathway regulation mechanisms.

Single-cell RNA landscape of the special fiber initiation process in Bombax ceiba

As a new source of natural fibers,the Bombax ceiba tree can provide thin,light,extremely soft and warm fiber material for the textile industry.Natural fibers are an ideal model system for studying cell growth and differentiation,but the molecular mechanisms that regulate fiber initiation are not fully understood.In B.ceiba,we found that fiber cells differentiate from the epidermis of the inner ovary wall.Each initiated cell then divides into a cluster of fiber cells that eventually develop into mature fibers,a process very different from the classical fiber initiation process of cotton.We used high-throughput single-cell RNA sequencing(scRNA-seq)to examine the special characteristics of fiber initiation in B.ceiba.A total of 15567 high-quality cells were identified from the inner wall of the B.ceiba ovary,and 347 potential marker genes for fiber initiation cell types were identified.Two major cell types,initiated fiber cells and epidermal cells,were identified and verified by RNA in situ hybridization.A developmental trajectory analysis was used to reconstruct the process of fiber cell differentiation in B.ceiba.Comparative analysis of scRNAseq data from B.ceiba and cotton(Gossypium hirsutum)confirmed that the additional cell division process in B.ceiba is a novel species-specific mechanismfor fiber cell development.Candidate genes and key regulators that may contribute to fiber cell differentiation and division in B.ceiba were identified.This work reveals gene expression signatures during B.ceiba fiber initiation at a single-cell resolution,providing a new strategy and viewpoint for investigation of natural fiber cell differentiation and development.

Development of a widely targeted volatilomics method for profiling volatilomes in plants

Volatile organic compounds play essential roles in plant environment interactions as well as determining the fragrance of plants.Although gas chromatography-mass spectrometry-based untargeted metabolo-mics is commonly used to assess plant volatiles,it suffers from high spectral convolution,low detection sensitivity,a limited number of annotated metabolites,and relatively poor reproducibility.Here,we report a widely targeted volatilomics(WTV)method that involves using a“targeted spectra extraction”algorithm to address spectral convolution,constructing a high-coverage MS2 spectral tag library to expand volatile annotation,adapting a multiple reaction monitoring mode to improve sensitivity,and using regression models to adjust for signal drift.The newly developed method was used to profile the volatilome of rice grains.Compared with the untargeted method,the newly developed WTV method shows higher sensitivity(for example,the signal-to-noise ratio of guaicol increased from 4.1 to 18.8),high annotation coverage(the number of annotated volatiles increased from 43 to 132),and better reproducibility(the number of volatiles in quality control samples with relative standard deviation value below 30.0%increased from 14 to 92 after normalization).Using the WTV method,we studied the metabolic responses of tomato to environmental stimuli and profiled the volatilomes of different rice accessions.The results identified benzothiazole as a potential airborne signal priming tomato plants for enhanced defense and 2-nonanone and 2-heptanone as novel aromatic compounds contributing to rice fragrance.These case studies suggest that the widely targeted volatilomics method is more efficient than those currently used and may considerably promote plant volatilomics studies.