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.

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.

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.

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.

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.

Co/carbon nanofiber with adjustable size and content of Co nanoparticles for tunable microwave absorption and thermal conductivity

Electromagnetic pollution and heat dissipation problems are becoming increasingly worthy of attention due to the rapid development of electronic devices,which puts forward an urgent demand for microwave absorbers with excellent thermal management performance.Herein,high-performance Co/carbon nanofiber(Co/CNF)microwave absorbers with high thermal conductivity were fabricated by facile step-by-step method.The microwave absorption properties can be readily tuned by adjusting the content and size of Co nanoparticles through concentration gradient adsorption.Benefiting from the formation of dielectric and magnetic coupling network,Co/CNF composites possess intensive dipole polarization,interface polarization,and magnetic loss.The optimal Co/CNF composites exhibit outstanding microwave absorption performance with a minimum reflection loss(RL)of−53.0 dB at 11.44 GHz,and a maximum effective absorption bandwidth(EAB)of 5.5 GHz.In addition,the thermal conductivities of the Co/CNF-natural rubber(Co/CNF-NR)composites are significantly improved.This work may inspire the exploration of high-efficiency heat-conduction microwave absorbers based on CNF.

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.

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.

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.

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.

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.

The pineapple reference genome:Telomere-to-telomere assembly, manually curated annotation, and comparative analysis

Pineapple is the third most crucial tropical fruit worldwide and available in five varieties.Genomes of different pineapple varieties have been released to date;however,none of them are complete,with all exhibiting substantial gaps and representing only two of the five pineapple varieties.This significantly hinders the advancement of pineapple breeding efforts.In this study,we sequenced the genomes of three varieties:a wild pineapple variety,a fiber pineapple variety,and a globally cultivated edible pineapple variety.We constructed the first gap-free reference genome(Ref)for pineapple.By consolidating multiple sources of evidence and manually revising each gene structure annotation,we identified 26,656 proteincoding genes.The BUSCO evaluation indicated a completeness of 99.2%,demonstrating the high quality of the gene structure annotations in this genome.Utilizing these resources,we identified 7,209 structural variations across the three varieties.Approximately 30.8%of pineapple genes were located within±5 kb of structural variations,including 30 genes associated with anthocyanin synthesis.Further analysis and functional experiments demonstrated that the high expression of AcMYB528 aligns with the accumulation of anthocyanins in the leaves,both of which may be affected by a 1.9-kb insertion fragment.In addition,we developed the Ananas Genome Database,which offers data browsing,retrieval,analysis,and download functions.The construction of this database addresses the lack of pineapple genome resource databases.In summary,we acquired a seamless pineapple reference genome with highquality gene structure annotations,providing a solid foundation for pineapple genomics and a valuable reference for pineapple breeding.

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.

The NET locus determines the food taste,cooking and nutrition quality of rice

Rice(Oryza sativa L)is one of the most important crops world-wide,providing much of the calorific needs for half of the global population[1].Due to the development of the global economy and the improvement of living standards,people's demand for rice has gradually changed from"being fll"to"eating well",with tasty and nutritious varieties being essential for the latter.In the past few decades,lots of studies have focused on improving the eating and cooking quality(ECQ)of rice to meet the demand for taste[2].Although metabolic engineering has been applied in rice biofortif-cation in recent years[3.4],efforts on improving comprehensive nutrition in rice remain fragmented[5-7].Thus,characterizing QTLs and genes underlying nutrient abundance will provide new guidance for breeding varieties with health benefits.

Integration of rhythmic metabolome and transcriptome provides insights into the transmission of rhythmic fluctuations and temporal diversity of metabolism in rice

Various aspects of the organisms adapt to cyclically changing environmental conditions via transcriptional regulation.However,the role of rhythmicity in altering the global aspects of metabolism is poorly characterized.Here,we subjected four rice(Oryza sativa)varieties to a range of metabolic profiles and RNA-seq to investigate the temporal relationships of rhythm between transcription and metabolism.More than 40%of the rhythmic genes and a quarter of metabolites conservatively oscillated across four rice accessions.Compared with the metabolome,the transcriptome was more strongly regulated by rhythm;however,the rhythm of metabolites had an obvious opposite trend between day and night.Through association analysis,the time delay of rhythmic transmission from the transcript to the metabolite level was~4 h under long-day conditions,although the transmission was nearly synchronous for carbohydrate and nucleotide metabolism.The rhythmic accumulation of metabolites maintained highly coordinated temporal relationships in the metabolic network,whereas the correlation of some rhythmic metabolites,such as branched-chain amino acids(BCAAs),was significantly different intervariety.We further demonstrated that the cumulative diversity of BCAAs was due to the differential expression of branched-chain aminotransferase 2 at dawn.Our research reveals the flexible pattern of rice metabolic rhythm existing with conservation and diversity.

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.

Rice metabolic regulatory network spanning the entire life cycle

As one of the most important crops in the world,rice(Oryza sativa)is a model plant for metabolome research.Although many studies have focused on the analysis of specific tissues,the changes in metab-olite abundance across the entire life cycle have not yet been determined.In this study,combining both tar-geted and nontargeted metabolite profiling methods,a total of 825 annotated metabolites were quantified in rice samples from different tissues covering the entire life cycle.The contents of metabolites in different tissues of rice were significantly different,with various metabolites accumulating in the plumule and radicle during seed germination.Combining these data with transcriptome data obtained from the same time period,we constructed the Rice Metabolic Regulation Network.The metabolites and co-expressed genes were further divided into 12 clusters according to their accumulation patterns,with members within each cluster displaying a uniform and clear pattern of abundance across development.Using this dataset,we established a comprehensive metabolic profile of the rice life cycle and used two independent strategies to identify novel transcription factors-namely the use of known regulatory genes as bait to screen for new networks underlying lignin metabolism and the unbiased identification of new glycerophospholipid metabolism regulators on the basis of tissue specificity.This study thus demonstrates how guilt-by-association analysis of metabolome and transcriptome data spanning the entire life cycle in cereal crops provides novel resources and tools to aid in understanding the mechanisms underlying important agro-nomic traits.