Betalain,an economically valuable water-soluble natural plant pigment,is prized for its strong antioxidant activity,making it popular as a dietary supplement and a visual marker for plant transformation.However,market...Betalain,an economically valuable water-soluble natural plant pigment,is prized for its strong antioxidant activity,making it popular as a dietary supplement and a visual marker for plant transformation.However,market demand significantly outstrips current production capacity.This study reports the development of an efficient push-and-pull multigene strategy based on polycistronic expression and metabolic flux regulation to enhance betalain biosynthesis in transgenic maize(Zea mays L.)endosperm.We engineered a novel enhanced RUBY(eRUBY)system derived from the original polycistronic RUBY construct(CYP76AD1P2ADODA1P2ADOPA5GT unit,abbreviated CDG)by introducing arogenate dehydrogenase(ADHα)to increase the L-tyrosine substrate supply.All the genes were driven by the endosperm-specific promoter.Fusion of ADHαinto a single polycistronic eRUBY construct(CDGA)produced significantly higher betanin(6.88 mg g−1 dry weight)and isobetanin(1.81 mg g−1 dry weight)levels than in CDG+A,which stacked the ADHαcassette independently with CDG.The high betalain accumulation in CDGA lines(which also exhibited higher transgene copy number)resulted in a 2.85–7.58-fold improvement in endosperm antioxidant capacity compared to WT(versus 2.48–2.80-fold in CDG+A).Importantly,transgenic plants maintained a normal phenotype.Transcriptome and metabolome analyses further indicated that metabolism of phenylalanine,alanine,aspartate,and glutamate contributes to betalain production.Hybridization with sweet corn successfully created a high-sugar eRUBY maize variety.Collectively,these results demonstrate the successful development of a novel maize germplasm with significantly enhanced nutritional value through high betalain accumulation.展开更多
Leaf thickness in rice critically influences photosynthetic efficiency and yield,yet its genetic basis remains poorly understood,with few functional genes previously characterized.In this study,we employ a pangenome-w...Leaf thickness in rice critically influences photosynthetic efficiency and yield,yet its genetic basis remains poorly understood,with few functional genes previously characterized.In this study,we employ a pangenome-wide association study(Pan-GWAS)on 302 diverse rice accessions from southern China,identifying 49 quantitative trait loci(QTLs)associated with leaf thickness.The most significant locus,qLT9,is fine-mapped to a 79-kb region on chromosome 9.Transcriptomic and genomic sequence analyses identify LOC_Os09g33480,which encodes a protein belonging to Multiple Organellar RNA Editing Factor family,as the key candidate gene.Overexpression and complementation transgenic experiments confirm LOC_Os09g33480(OsLT9)as the functional gene underlying qLT9,demonstrating a 24-bp Indel in its promoter correlates with the expression levels and leaf thickness.Notably,OsLT9 overexpression lines show not only thicker leaf,but also significantly enhanced photosynthetic efficiency and grain yield,establishing a link between leaf thickness modulation and yield enhancement.Population genomic analyses indicate strong selection for OsLT9 during domestication and breeding,with modern cultivars favoring thick leaf haplotype of OsLT9.This study establishes OsLT9 as a key regulator controlling leaf thickness in rice,and provides a valuable genetic resource for molecular breeding of high-yielding rice through optimization of plant architecture.展开更多
The presence of a leafy head is a vital agronomic trait that facilitates the evaluation of the yield and quality of Chinese cabbage.A non-heading mutant(nhm1)was identified in an ethyl methanesulfonate mutagenesis pop...The presence of a leafy head is a vital agronomic trait that facilitates the evaluation of the yield and quality of Chinese cabbage.A non-heading mutant(nhm1)was identified in an ethyl methanesulfonate mutagenesis population of the heading Chinese cabbage double haploid line FT.Segregation analysis revealed that a single recessive gene,Brnhm1,controlled the mutant phenotype.Using MutMap,Kompetitive allele-specific PCR,and cloning analyses,we demonstrated that BraA07g042410.3C,which encodes an ent-kaurene synthase involved in the gibberellin biosynthesis pathway,is the nhm1 mutant candidate gene.A single-nucleotide mutation(C to T)in the fourth exon of BraA07g042410.3C caused an amino acid substitution from histidine to tyrosine.Compared to that of the wild-type FT,BraA07g042410.3C in the leaves of the nhm1 mutant had lower levels of expression.In addition,gibberellin contents were lower in the mutant than in the wild type,and the mutant plant phenotype could be restored to that of the wild type after exogenous GA3 treatment.These results indicate that BraA07g042410.3C caused the non-heading mutation.This is the first study to demonstrate a relationship between gibberellin content in the leaves and leafy head formation in Chinese cabbage.These findings facilitate the understanding of the mechanisms underlying leafy head development in Chinese cabbage.展开更多
The FW2.2-like(FWL)gene family has been extensively studied across multiple species,demonstrating conserved functions among specific members in organ development,particularly in fruit size regulation.For species with ...The FW2.2-like(FWL)gene family has been extensively studied across multiple species,demonstrating conserved functions among specific members in organ development,particularly in fruit size regulation.For species with limited research foundations,such as Chinese jujube,analyzing this gene family is an effective approach to identify candidate genes for fruit size.This study identified twenty ZjFWL genes and comprehensively analyzed their chromosomal distribution,phylogenetic relationships,gene structure,evolutionary dynamics,expression patterns,and cis-acting elements in their promoters.Natural variation analysis of the ZjFWL10 sequence identified a significant correlation between a seven-base pair deletion in the conserved domain and jujube fruit size.To validate the functional implications of the seven-base pair deletion genotype,heterologous overexpression experiments were conducted in tomatoes,generating three overexpression lines.Comparative analysis with the wild-type demonstrated a significant reduction in fruit size and a notable increase in plant height in the overexpressed lines.This gene may play a critical role in regulating nutrient partitioning in jujube,ultimately affecting fruit size.These findings advance our understanding of fruit size regulation mechanisms and offer valuable insights for genetic improvement strategies targeting jujube fruit size.展开更多
Nuclear magnetic resonance(NMR)spectroscopy is an excellent tool for simultaneous identification and quantification of metabolites(metabolomics).NMR quantification of human lipoprotein subfractions and their component...Nuclear magnetic resonance(NMR)spectroscopy is an excellent tool for simultaneous identification and quantification of metabolites(metabolomics).NMR quantification of human lipoprotein subfractions and their components has proven to be a powerful approach to reveal pathophysiological insights in numerous diseases[1,2].This method has now been standardized with excellent inter-laboratory reproducibility within 10 days for simultaneous quantification of 105 lipoprotein components and 24 low-molecular weight(LMW)metabolites[3];close clustering was also shown for 12 quality-control(QC)samples measured in 3 months although without statistical details[2].However,these reports[[1],[2],[3]]did not cover many vital parameters for lipoprotein components(e.g.,cholesterol-esters and total-lipids),fatty acids,and N-acetyl-glycoproteins(NAGs).展开更多
Eucalyptus urophylla×E.grandis is a major hybrid species of timber plantations.However,our under-standing of Eucalyptus mitochondrial genome,especially within the Myrtaceae family,is limited.In this study,we empl...Eucalyptus urophylla×E.grandis is a major hybrid species of timber plantations.However,our under-standing of Eucalyptus mitochondrial genome,especially within the Myrtaceae family,is limited.In this study,we employed hybrid sequencing combining the Illumina and Oxford Nanopore sequencing to assemble and annotate the mitogenome(mtDNA)of E.urophylla×E.grandis.Our results reveal a structure characterized by one circular mol-ecule,with a cumulative length of 483,907 base pairs(bp)and a GC content of 44.96%.The circular molecule collec-tively harbored 59 annotated genes.Among these,38 were unique protein-coding genes(PCGs),accompanied by 18 transfer RNA(tRNA)genes and 3 ribosomal RNA(rRNA)genes.Our study also examined repetitive sequences,RNA editing sites,and intracellular sequence transfers within the mtDNA.Furthermore,we conducted a phylogenetic analy-sis between E.urophylla×E.grandis and 30 closely related species based on genetic affinities.The outcomes furnish a high-quality organelle genome for E.urophylla×E.grandis,thereby explaining basic insights into organelle genome evo-lution and phylogenetic relationships.展开更多
The canonical CRISPR/Cas editors are constrained by the requirement for specific PAMs,which substantially limits their editable target range.Rice(particularly indica rice)is sensitive to low temperature,which impacts ...The canonical CRISPR/Cas editors are constrained by the requirement for specific PAMs,which substantially limits their editable target range.Rice(particularly indica rice)is sensitive to low temperature,which impacts the yield and restricts the geographic distribution of rice.In this study,we developed PAM-flexible multiplex genome editing tools based on Sp G(recognising NGN-PAMs)and Sp RY(recognising NNN-PAMs)variants.We then tested the feasibility of using a sweet potato leaf curl virus(SPLCV)replicon-based expression vector and single-stranded DNA-binding domain(DBD)to improve the editing efficiency of these PAM-flexible editors.Furthermore,we used Sp G-mediated multiplex genome editing to achieve comprehensive improvement in cold tolerance in indica rice by editing WRKY transcription factors Os WRKY53 and Os WRKY63,to generate high cold-resistant indica rice lines.We concluded that these PAM-flexible multiplex genome editors are powerful tools for multi-gene editing for crop genetic improvement.展开更多
Tetracentron sinense is a‘living fossil’tree in East Asia.Understanding how this‘living fossil’responds to climate change and adapts to local environments is critical for its conservation.Here,we used resequenced ...Tetracentron sinense is a‘living fossil’tree in East Asia.Understanding how this‘living fossil’responds to climate change and adapts to local environments is critical for its conservation.Here,we used resequenced genomes to clarify the evolutionary history and adaptive potential of T.sinense.We identifiedsix divergent lineages in T.sinense:three lineages from southwestern China(Yunnan Province)and three lineages from the central subtropical region of China.Additionally,we detected hybridization events between some adjacent lineages.Demographic analysis revealed that over the past 10,000 years the effective population size(Ne)of three T.sinense lineages(i.e.,NORTH,SWEST,and YNWEST)increased after their last bottleneck and then remained stable,whereas that of the remaining three lineages(i.e.,YSEAST,YC,and EAST)declined steadily.The decline in effective population size in the Yunnan lineages aligned well with the decrease in genome-wide diversity and a significantincrease in the frequency of runs of homozygosity.Deleterious variants and positively selected sites were involved in the evolution of different lineages.Further,genotype–environment association(GEA)analyses indicated adaptation to temperature-and precipitation-related factors.Genomic offset analyses found the most vulnerable populations,while SC and SC-yad were predicted to better handle extreme changes.Our findingsprovide insights into the evolutionary history and conservation of T.sinense and enhance our understanding of the evolution of living fossil species.展开更多
Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,199...Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,1999;One Thousand Plant Transcriptomes Initiative,2019).Due to its unique phylogenetic status,it holds tremendous interest for botanists.The nuclear and mitochondrial genomes of Amborella were first published in 2013,providing valuable resources for studies on genome and gene family evolution,phylogenomics,and flower development,despite the fact that the assembly is heavily fragmented(Amborella Genome Project,2013;Rice et al.,2013).In 2024,a haplotype-resolved Amborella genome assembly was published,showing significant improvement in quality and completeness(Carey et al.,2024).展开更多
Recent advancements in genome sequencing have enabled the estimation of genetic load through deleterious mutation profiling.However,Chinese populations remain underexplored in this context.We analyze whole-exome seque...Recent advancements in genome sequencing have enabled the estimation of genetic load through deleterious mutation profiling.However,Chinese populations remain underexplored in this context.We analyze whole-exome sequencing data from 5002 individuals,encompassing major Han subgroups―North Han(NHan),South Han(S-Han),and Guangxi Han(G-Han)―as well as 13 ethnic minorities.Notably,G-Han exhibits significant genetic affinity with the Zhuang population.Systematic curation of 2110 ClinVar pathogenic or likely pathogenic variants reveals 93.4%are ultra-rare.Exceptions include GJB2 rs72474224-A(hearing loss),which shows higher frequencies in Zhuang and G-Han,and β-thalassemia-associated HBB variants(rs33986703-A and rs33950507-T),which are elevated in G-Han compared to other Han subgroups.Among 96 autosomal dominant mutation carriers,LDLR variants are predominant(~25%),with comparable frequencies across Han subgroups.Adaptive signatures highlight gene-environment interactions:MTHFR rs1801133-A(UV adaptation)declines southward,while ALDH2 rs671-A(alcohol metabolism)displays the opposite trend.ABCC11 rs17822931-A,associated with cold adaptation,is particularly low frequency in G-Han.Gene-based rare-variant collapsing analyses identify an elevated risk of retinitis pigmentosa in S-Han(PRPF4,TUB).Our findings demonstrate that genetic load in Chinese populations is influenced by demographic history,population structure,and regional adaptation,emphasizing the importance of population-specific frameworks in precision medicine.展开更多
CBF/DREB proteins play a critical role in abiotic stress-mediated gene expression and represent attractive regulons for plant breeding programs.However,no study has been conducted for CBF/DREB protein-related genes in...CBF/DREB proteins play a critical role in abiotic stress-mediated gene expression and represent attractive regulons for plant breeding programs.However,no study has been conducted for CBF/DREB protein-related genes in jujube(Ziziphus jujuba Mill.).In this study,twenty-five ZjDREB genes were identified and annotated from the jujube(Z.jujuba‘Dongzao’)genome.Detailed analysis,including gene classification,annotation,phylogenetic evaluation,conserved motif determination and expression profiling were performed on all genes.Phylogenetic analysis showed that ZjDREB proteins were divided into five subgroups(A1–A5),but lacking a subgroup A6 corresponding to AtDREBs.The ZjDREB genes were distributed in nine of twelve chromosomes in the genome.Additionally,the expression patterns of the DREB genes under different abiotic stresses were investigated using q RT-PCR.Nineteen ZjDREB genes were down-regulated under low temperature,in contrast six ZjDREB genes(01,03,05,11,23 and 24)were up-regulated.Under drought,salinity and high temperature conditions,expression of ZjDREB03,09,10,14,15,17 and 20 genes were induced and showed similar expression patterns,suggesting that various stress conditions share common elements in the signaling pathway.The results suggest that the family of DREB genes play an important role in abiotic stresses in jujube,and provide a foundation for further functional studies of this important class of transcriptional regulators.展开更多
Polygalacturonase-inhibiting proteins （PGIPs） are extracellular proteins that belong to the leucine-rich repeat （LRR） protein superfamily. PGIPs inhibit fungal polygalacturonases （PGs） and promote accumulation o...Polygalacturonase-inhibiting proteins （PGIPs） are extracellular proteins that belong to the leucine-rich repeat （LRR） protein superfamily. PGIPs inhibit fungal polygalacturonases （PGs） and promote accumulation of oligogalacturonides, which activate plant defense responses. PGIPs play important roles in resistance to infection of pathogens. In this study, reverse transcriptase-polymerase chain reaction （RT-PCR） and RNA ligase-mediated rapid amplification of cDNA ends （RLM-RACE） were used to isolate the full-length PGIP cDNA from Populus deltoides （GenBank accession no. of PdPGIP2 and PdPGIP4：EF684913 and EF684912）. Domain analysis revealed that the deduced amino acid sequences of PdPGIP2 and PdPGIP4 had a typical PGIP topology. Phylogenetic analysis of known PGIPs indicated that the two PdPGIPs were clustered to the defense-related PGIP clade. Using real-time RT-PCR, the expression patterns of the two PdPGIPs following treatment with a fungal pathogen and defense-related signaling molecules were studied. The expression levels of PdPGIP2 and PdPGIP4 were both up-regulated when inoculated with the phytopathogenic fungus Marssonina brunnea. Therefore, it was proposed that the two PGIPs might be involved in the resistance to Marssonina brunnea in P. deltoides.展开更多
Larix principis-rupprechtii Mayr is a dominant species in coniferous forests of North China.However,early selection of L.principis-rupprechtii for growth traits is poorly characterised.To explore the optimal selection...Larix principis-rupprechtii Mayr is a dominant species in coniferous forests of North China.However,early selection of L.principis-rupprechtii for growth traits is poorly characterised.To explore the optimal selection age for this species,heights(HT)and diameters at breast(DBH)of 40 half-sib families were measured at ages 3,12,22,and 28 years in a progeny test population established in the town of Kangjiahui,Shanxi Province.Age trends in heritability,age–age genetic correlations,and early selection efficiency for height and DBH were analysed.The individual heritability of these growth traits varied over time,and maximized at different ages(0.55 at age 12 for HT and 0.48 at age 28 for DBH).The age–age genetic correlations were always positive,and the majority were high(0.790–0.953)between the juvenile and mature ages for HT and DBH.For the same pairs of measurements,HT demonstrated higher age–age genetic correlations than DBH,and both age–age genetic correlation data sets were described well by the linear relationship with the logarithm of the age ratio(r^(2)>0.90).The regression slope for DBH was lower than that for HT.Based on the early selection efficiency estimates,the optimal selection age could be as early as age 6 for DBH and 8–9 years for HT.The results of this study provide information that can be used to assist early selection practices in L.principis-rupprechtii improvement programs in Shanxi Province.展开更多
As a member of the Frizzled family, Frizzled3 (FZD3) is a receptor of the canonical Wnt signaling pathway and plays a vital role in mammalian hair follicle developmental processes. However, its effects on wool traits ...As a member of the Frizzled family, Frizzled3 (FZD3) is a receptor of the canonical Wnt signaling pathway and plays a vital role in mammalian hair follicle developmental processes. However, its effects on wool traits are not clear. The objectives of this study were to identify the single nucleotide polymorphisms (SNPs) and the expression patterns of FZD3 gene, and then to determine whether it affected wool traits of Chinese Merino sheep (Xinjiang Type) or not. PCR-single stranded conformational polymorphism (PCR-SSCP) and sequencing were used to identify mutation loci, and general linear model (GLM) with SAS 9.1 was used for the association analysis between wool traits and SNPs. Quantitative real-time PCR (qRT-PCR) was used to investigate FZD3 gene expression levels. The results showed that six exons of FZD3 gene were amplified and two mutation loci were identified in exon 1 (NC_019459.2: g.101771685 T>C (SNP1)) and exon 3 (NC_019459.2: g.101810848, A>C (SNP2)), respectively. Association analysis showed that SNP1 was significantly associated with mean fiber diameter (MFD)(P=0.04) and live weight (LW)(P=0.0004), SNP2 was significantly associated with greasy fleece weight (GFW)(P=0.04). The expression level of FZD3 gene in skin tissues of the superfine wool (SF) group was significantly lower (P<0.05) than that of the fine wool (F) group. Moreover, it had a higher expression level (P<0.01) in skin tissues than in other tissues of Chinese Merino ewes. While, its expression level had a fluctuant expression in skin tissues at different developmental stages of embryos and born lambs, with the highest expression levels (P<0.01) at the 65th day of embryos. Our study revealed the genetic relationship between FZD3 variants and wool traits and two identified SNPs might serve as potential and valuable genetic markers for sheep breeding and lay a molecular genetic foundation for sheep marker-assisted selection (MAS).展开更多
Prunus mume is an important woody plant that has high ornamental and economic value, widely distributed and used in landscape architecture in East Asia. In plants, basic(region) leucine zipper(bZIP) transcription fact...Prunus mume is an important woody plant that has high ornamental and economic value, widely distributed and used in landscape architecture in East Asia. In plants, basic(region) leucine zipper(bZIP) transcription factors play important regulatory roles in growth, development,dormancy and abiotic stress. To date, bZIP transcription factors have not been systematically studied in P. mume. In this study, 49 bZIP genes were first identified in P. mume, and the PmbZIP family was divided into 12 groups according to the grouping principles for the Arabidopsis thaliana bZIP family. For the first time, we constructed a detailed model of the PmbZIP domains(R-x_(3)–N-(x)_7-R/K-x_(2)-K-x_(6)-L-x_(6)-L-_(6)-L). Phylogenetic and synteny analyses showed that PmbZIPs duplication events might have occurred during the large-scale genome duplication events. A relatively short time of speciation and the finding that 91.84% of the bZIP genes formed orthologous pairs between P. mume and Prunus armeniaca provided evidence of a close relationship. Gene expression patterns were analysed in different tissues and periods, indicating that PmbZIP genes with the same motifs exhibited similar expression patterns. The gene expression results showed that PmbZIP31/36/41 genes played a more prominent role in the response to freezing stress than cold stress. The expression level of almost all subset Ⅲ genes was upregulated under freezing treatment, especially after cold exposure. We analysed the gene expression patterns of PmbZIP12/31/36/41/48 and their responses to low-temperature stress, which provided useful resources for future studies on the cold/freezing-tolerant molecular breeding of P. mume.展开更多
Rose is a highly significant ornamental plant with substantial edible and medicinal value,cultivated worldwide primarily for perfume production.Recently,Rosa yangii,a new species found in northwestern Yunnan,China,has...Rose is a highly significant ornamental plant with substantial edible and medicinal value,cultivated worldwide primarily for perfume production.Recently,Rosa yangii,a new species found in northwestern Yunnan,China,has drawn attention due to its strong sweet scented flowers.In this study,the floral components of R.yangii were extracted at different flowering stages using solid phase micro extraction(SPME)and analyzed through gas chromatography-mass spectrometry(GC-MS).A total of 131 volatile organic compounds(VOCs)were detected from R.yangii,including 69 odor compounds.The production and release of floral VOCs were the highest during the initial-open stage,making it the most suitable time for harvesting as a significant number of floral components were synthesized and preserved.The analysis of the odor activity values(OAV)highlighted several key aromatic ingredients of R.yangii,such as eugenol,methyleugenol,benzeneacetaldehyde and phenylethylalcohol,heptanal,decanal,(E)-2-hexen-1-yl acetate,caryophyllene,and others.Metabolome and time-order gene co-expression networks(TO-GCN)revealed that VOCs and benzenoids/phenylpropanoids,along with associated genes,played a pivotal role in the overall floral regulatory network of R.yangii.MYB and bHLH were identified as the essential regulatory factors governing the regulation of eugenol synthase(EGS)and isoeugenol synthase(IGS),consequently influencing the sweet scent of R.yangii.The findings of this study provide a scientific foundation for enhancing fragrance through molecular breeding of ornamental plants.Furthermore,the study facilitated the development and utilization of this new plant’s essential oil material in various industries,including food storage,aromatherapy,cosmetic,and perfumery.展开更多
The term‘ornamental plant’refers to all plants with ornamental value,which generally have beautiful flowers or special plant architectures.China is rich in ornamental plant resources and known as the“mother of gard...The term‘ornamental plant’refers to all plants with ornamental value,which generally have beautiful flowers or special plant architectures.China is rich in ornamental plant resources and known as the“mother of gardens”.Genomics is the science of studying genomes and is useful for carrying out research on genome evolution,genomic variations,gene regulation,and important biological mechanisms based on detailed genome sequence information.Due to the diversity of ornamental plants and high sequencing costs,the progress of genome research on ornamental plants has been slow for a long time.With the emergence of new sequencing technologies and a reduction in costs since the whole-genome sequencing of the first ornamental plant(Prunus mume)was completed in 2012,whole-genome sequencing of more than 69 ornamental plants has been completed in<10 years.In this review,whole-genome sequencing and resequencing of ornamental plants will be discussed.We provide analysis with regard to basic data from whole-genome studies of important ornamental plants,the regulation of important ornamental traits,and application prospects.展开更多
Plant dormancy is essential for perennial plant survival.Different genotypes of Prunus mume,including Eumume group and Apricot Mei group,undergo leaf senescence and dormancy at different times.In order to verify the c...Plant dormancy is essential for perennial plant survival.Different genotypes of Prunus mume,including Eumume group and Apricot Mei group,undergo leaf senescence and dormancy at different times.In order to verify the cold resistance of P.mume,freeze resistance evaluation was carried out.Our results showed that Apricot Mei group had a stronger freezing tolerance than Eumume group and that leaf senescence and dormancy of Apricot Mei group occurred at an earlier period before winter.Based on phenotypic data in response to seasonal climate change,the significant candidate regions were selected using GWAS.Furthermore,through KEGG pathway and qRT-PCR analyses,we found that the ethylene-related genes,including PmEIL(Pm002057)and PmERF(Pm004265),were significantly upregulated in‘Songchun’Mei(Apricot Mei group)and downregulated in‘Zaohua Lve’Mei(Eumume group).Ethylene-related genes expression models showed that ethylene may be indirectly involved in the induction of dormancy.The PmEIL and PmERF genes were the core genes of the ethylene signal transduction pathway and were regulated by the exogenous ACC or PZA compounds.For non-dormant or weekly dormant perennial plants,application of ACC was able to induce plant dormancy and thus enhance cold/freeze tolerance.Overall,the expression of the major ethylene genes played a significant role in dormancy induction and freezing tolerance in P.mume;accordingly,application of ACC and PZA compounds were an effective approach for enhancing cold/freeze of tolerance of woody plant.展开更多
Plant architecture includes vital traits that influence and benefit crops,and economically important trees.Different plant architectures provide natural beauty.Weeping ornamental plants are aesthetically appealing to ...Plant architecture includes vital traits that influence and benefit crops,and economically important trees.Different plant architectures provide natural beauty.Weeping ornamental plants are aesthetically appealing to people.The regulatory mechanism controlling the weeping trait is poorly understood in crape myrtle.To investigate the weeping trait mechanism,transcriptional profiling of different organs in weeping and upright crape myrtle was performed based on phenotype.Phenotypic and histological analyses demonstrated that endodermal cells were absent,and that new shoot phenotypes could be rescued by the GA3 treatment of weeping plants.The transcriptional analysis and coexpression network analysis(WGCNA)of differentially expressed genes indicated that GA synthesis and signal transduction pathways play a role in weeping traits.When the expression level of a negative element of GA signaling,LfiGRAS1,was reduced by virus-induced gene silencing(VIGS),new branches grew in infected plants in a negatively geotropic manner.An integrated analysis implied that GA had a strong influence on weeping crape myrtle by interacting with other factors.This study helps to elucidate the mechanism governing the weeping trait and can improve the efficiency of breeding in Lagerstroemia.展开更多
Common carp are among the oldest domesticated fish in the world.As such,there are many food and ornamental carp strains with abundant phenotypic variations due to natural and artificial selection.Hebao red carp(HB,Cyp...Common carp are among the oldest domesticated fish in the world.As such,there are many food and ornamental carp strains with abundant phenotypic variations due to natural and artificial selection.Hebao red carp(HB,Cyprinus carpio wuyuanensis),an indigenous strain in China,is renowned for its unique body morphology and reddish skin.To reveal the genetic basis underlying the distinct skin color of HB,we constructed an improved highfidelity(HiFi) HB genome with good contiguity,completeness,and correctness.Genome structure comparison was conducted between HB and a representative wild strain,Yellow River carp(YR,C.carpio haematopterus),to identify structural variants and genes under positive selection.Signatures of artificial selection during domestication were identified in HB and YR populations,while phenotype mapping was performed in a segregating population generated by HB×YR crosses.Body color in HB was associated with regions with fixed mutations.The simultaneous mutation and superposition of a pair of homologous genes(mitfa) in chromosomes A06 and B06 conferred the reddish color in domesticated HB.Transcriptome analysis of common carp with different alleles of the mitfa mutation confirmed that gene duplication can buffer the deleterious effects of mutation in allotetraploids.This study provides new insights into genotype-phenotype associations in allotetraploid species and lays a foundation for future breeding of common carp.展开更多
基金supported by grants from the Biological Breeding-National Science and Technology Major Project(2024ZD04077)the Invigorate the Seed Industry of Guangdong Province(2024-NPY-00-044)+3 种基金the National Natural Science Foundation of China(32272120)the Guangxi Science and Technology Major Project(GKAA24206023)the National Key Research and Development Program of China(2024YFF1000800)the Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops Major Project(FCBRCE-202502,FCBRCE-202504).
文摘Betalain,an economically valuable water-soluble natural plant pigment,is prized for its strong antioxidant activity,making it popular as a dietary supplement and a visual marker for plant transformation.However,market demand significantly outstrips current production capacity.This study reports the development of an efficient push-and-pull multigene strategy based on polycistronic expression and metabolic flux regulation to enhance betalain biosynthesis in transgenic maize(Zea mays L.)endosperm.We engineered a novel enhanced RUBY(eRUBY)system derived from the original polycistronic RUBY construct(CYP76AD1P2ADODA1P2ADOPA5GT unit,abbreviated CDG)by introducing arogenate dehydrogenase(ADHα)to increase the L-tyrosine substrate supply.All the genes were driven by the endosperm-specific promoter.Fusion of ADHαinto a single polycistronic eRUBY construct(CDGA)produced significantly higher betanin(6.88 mg g−1 dry weight)and isobetanin(1.81 mg g−1 dry weight)levels than in CDG+A,which stacked the ADHαcassette independently with CDG.The high betalain accumulation in CDGA lines(which also exhibited higher transgene copy number)resulted in a 2.85–7.58-fold improvement in endosperm antioxidant capacity compared to WT(versus 2.48–2.80-fold in CDG+A).Importantly,transgenic plants maintained a normal phenotype.Transcriptome and metabolome analyses further indicated that metabolism of phenylalanine,alanine,aspartate,and glutamate contributes to betalain production.Hybridization with sweet corn successfully created a high-sugar eRUBY maize variety.Collectively,these results demonstrate the successful development of a novel maize germplasm with significantly enhanced nutritional value through high betalain accumulation.
基金supported by the National Natural Science Foundation of China(32301845)GuangDong Basic and Applied Basic Research Foundation(2022A1515012339)+3 种基金the National Key R&D Program of China(2024YFD1200801)Seed industry revitalization project of special fund for rural revitalization strategy in Guangdong Province(2024-NPY-00-001)Modern Seed Industry Innovation Capacity Enhancement Progject of Guangdong Academy of Agricultural Sciences,Elite Rice Plan of GDRRI(2023YG01)Guangdong Key Laboratory of Rice Science and Technology(2023B1212060042).
文摘Leaf thickness in rice critically influences photosynthetic efficiency and yield,yet its genetic basis remains poorly understood,with few functional genes previously characterized.In this study,we employ a pangenome-wide association study(Pan-GWAS)on 302 diverse rice accessions from southern China,identifying 49 quantitative trait loci(QTLs)associated with leaf thickness.The most significant locus,qLT9,is fine-mapped to a 79-kb region on chromosome 9.Transcriptomic and genomic sequence analyses identify LOC_Os09g33480,which encodes a protein belonging to Multiple Organellar RNA Editing Factor family,as the key candidate gene.Overexpression and complementation transgenic experiments confirm LOC_Os09g33480(OsLT9)as the functional gene underlying qLT9,demonstrating a 24-bp Indel in its promoter correlates with the expression levels and leaf thickness.Notably,OsLT9 overexpression lines show not only thicker leaf,but also significantly enhanced photosynthetic efficiency and grain yield,establishing a link between leaf thickness modulation and yield enhancement.Population genomic analyses indicate strong selection for OsLT9 during domestication and breeding,with modern cultivars favoring thick leaf haplotype of OsLT9.This study establishes OsLT9 as a key regulator controlling leaf thickness in rice,and provides a valuable genetic resource for molecular breeding of high-yielding rice through optimization of plant architecture.
基金supported by the National Key Research and Development Program of China(Grant no.2017YFD0101802).
文摘The presence of a leafy head is a vital agronomic trait that facilitates the evaluation of the yield and quality of Chinese cabbage.A non-heading mutant(nhm1)was identified in an ethyl methanesulfonate mutagenesis population of the heading Chinese cabbage double haploid line FT.Segregation analysis revealed that a single recessive gene,Brnhm1,controlled the mutant phenotype.Using MutMap,Kompetitive allele-specific PCR,and cloning analyses,we demonstrated that BraA07g042410.3C,which encodes an ent-kaurene synthase involved in the gibberellin biosynthesis pathway,is the nhm1 mutant candidate gene.A single-nucleotide mutation(C to T)in the fourth exon of BraA07g042410.3C caused an amino acid substitution from histidine to tyrosine.Compared to that of the wild-type FT,BraA07g042410.3C in the leaves of the nhm1 mutant had lower levels of expression.In addition,gibberellin contents were lower in the mutant than in the wild type,and the mutant plant phenotype could be restored to that of the wild type after exogenous GA3 treatment.These results indicate that BraA07g042410.3C caused the non-heading mutation.This is the first study to demonstrate a relationship between gibberellin content in the leaves and leafy head formation in Chinese cabbage.These findings facilitate the understanding of the mechanisms underlying leafy head development in Chinese cabbage.
基金supported by the National Natural Science Foundation of China(31800559)the National Key Research and Development Program of China(2022YFD2200404)+2 种基金the National XA Science and Technology Innovation Project,China(2022XACX1100)the Science and Technology Major Project of Guangxi,China(‘Guike’AB16380060)the central government guides local science and technology development project“Germplasm Innovation of Xinjiang Characteristic Fruit Tree”,and partly supported by the open funds of the National Key Laboratory for Germplasm Innovation&Utilization of Horticultural Crops,China.
文摘The FW2.2-like(FWL)gene family has been extensively studied across multiple species,demonstrating conserved functions among specific members in organ development,particularly in fruit size regulation.For species with limited research foundations,such as Chinese jujube,analyzing this gene family is an effective approach to identify candidate genes for fruit size.This study identified twenty ZjFWL genes and comprehensively analyzed their chromosomal distribution,phylogenetic relationships,gene structure,evolutionary dynamics,expression patterns,and cis-acting elements in their promoters.Natural variation analysis of the ZjFWL10 sequence identified a significant correlation between a seven-base pair deletion in the conserved domain and jujube fruit size.To validate the functional implications of the seven-base pair deletion genotype,heterologous overexpression experiments were conducted in tomatoes,generating three overexpression lines.Comparative analysis with the wild-type demonstrated a significant reduction in fruit size and a notable increase in plant height in the overexpressed lines.This gene may play a critical role in regulating nutrient partitioning in jujube,ultimately affecting fruit size.These findings advance our understanding of fruit size regulation mechanisms and offer valuable insights for genetic improvement strategies targeting jujube fruit size.
基金financial supports from the National Key R&D Program of China(Grant Nos.:2022YFC3400700 and 2022YFA0806400)the Shanghai Municipal Science and Technology Major Project,China(Grant No.:2017SHZDZX01)the National Natural Science Foundation of China(Grant No.:31821002).
文摘Nuclear magnetic resonance(NMR)spectroscopy is an excellent tool for simultaneous identification and quantification of metabolites(metabolomics).NMR quantification of human lipoprotein subfractions and their components has proven to be a powerful approach to reveal pathophysiological insights in numerous diseases[1,2].This method has now been standardized with excellent inter-laboratory reproducibility within 10 days for simultaneous quantification of 105 lipoprotein components and 24 low-molecular weight(LMW)metabolites[3];close clustering was also shown for 12 quality-control(QC)samples measured in 3 months although without statistical details[2].However,these reports[[1],[2],[3]]did not cover many vital parameters for lipoprotein components(e.g.,cholesterol-esters and total-lipids),fatty acids,and N-acetyl-glycoproteins(NAGs).
基金supported by the Fundamental Research Funds for the Central Universities(2021ZY62)the National Natural ScienceFoundation of China(31901337)the 5·5 Engineering Research&Innovation Team Project of Beijing Forestry University(BLRC2023C06).
文摘Eucalyptus urophylla×E.grandis is a major hybrid species of timber plantations.However,our under-standing of Eucalyptus mitochondrial genome,especially within the Myrtaceae family,is limited.In this study,we employed hybrid sequencing combining the Illumina and Oxford Nanopore sequencing to assemble and annotate the mitogenome(mtDNA)of E.urophylla×E.grandis.Our results reveal a structure characterized by one circular mol-ecule,with a cumulative length of 483,907 base pairs(bp)and a GC content of 44.96%.The circular molecule collec-tively harbored 59 annotated genes.Among these,38 were unique protein-coding genes(PCGs),accompanied by 18 transfer RNA(tRNA)genes and 3 ribosomal RNA(rRNA)genes.Our study also examined repetitive sequences,RNA editing sites,and intracellular sequence transfers within the mtDNA.Furthermore,we conducted a phylogenetic analy-sis between E.urophylla×E.grandis and 30 closely related species based on genetic affinities.The outcomes furnish a high-quality organelle genome for E.urophylla×E.grandis,thereby explaining basic insights into organelle genome evo-lution and phylogenetic relationships.
基金supported by grants from the National Natural Science Foundation of China(32272120)the Guangdong Basic and Applied Basic Research Foundation(2024A1515012120)+3 种基金the Guangzhou Basic and Applied Basic Research Foundation(2023A04J00359)Special Foundation for Introduction of Scientific Talents of GDAAS(R2022YJ-YB1003,R2021YJ-XD001)the Seed Industry Revitalization Project of Special Fund for Rural Revitalization Strategy in Guangdong Province(2024-NPY-00-001)Guangdong Key Laboratory of Rice Science and Technology(2023B1212060042)。
文摘The canonical CRISPR/Cas editors are constrained by the requirement for specific PAMs,which substantially limits their editable target range.Rice(particularly indica rice)is sensitive to low temperature,which impacts the yield and restricts the geographic distribution of rice.In this study,we developed PAM-flexible multiplex genome editing tools based on Sp G(recognising NGN-PAMs)and Sp RY(recognising NNN-PAMs)variants.We then tested the feasibility of using a sweet potato leaf curl virus(SPLCV)replicon-based expression vector and single-stranded DNA-binding domain(DBD)to improve the editing efficiency of these PAM-flexible editors.Furthermore,we used Sp G-mediated multiplex genome editing to achieve comprehensive improvement in cold tolerance in indica rice by editing WRKY transcription factors Os WRKY53 and Os WRKY63,to generate high cold-resistant indica rice lines.We concluded that these PAM-flexible multiplex genome editors are powerful tools for multi-gene editing for crop genetic improvement.
基金supported by the National Natural Science Foundation of China(no.32570426)the Key Basic Research Program of Yunnan Province,China(202101BC070003)+1 种基金the Fundamental Research Funds for the Central Universities(QNTD202502)the STI 2030—Major Program(2022ZD0401605-2).
文摘Tetracentron sinense is a‘living fossil’tree in East Asia.Understanding how this‘living fossil’responds to climate change and adapts to local environments is critical for its conservation.Here,we used resequenced genomes to clarify the evolutionary history and adaptive potential of T.sinense.We identifiedsix divergent lineages in T.sinense:three lineages from southwestern China(Yunnan Province)and three lineages from the central subtropical region of China.Additionally,we detected hybridization events between some adjacent lineages.Demographic analysis revealed that over the past 10,000 years the effective population size(Ne)of three T.sinense lineages(i.e.,NORTH,SWEST,and YNWEST)increased after their last bottleneck and then remained stable,whereas that of the remaining three lineages(i.e.,YSEAST,YC,and EAST)declined steadily.The decline in effective population size in the Yunnan lineages aligned well with the decrease in genome-wide diversity and a significantincrease in the frequency of runs of homozygosity.Deleterious variants and positively selected sites were involved in the evolution of different lineages.Further,genotype–environment association(GEA)analyses indicated adaptation to temperature-and precipitation-related factors.Genomic offset analyses found the most vulnerable populations,while SC and SC-yad were predicted to better handle extreme changes.Our findingsprovide insights into the evolutionary history and conservation of T.sinense and enhance our understanding of the evolution of living fossil species.
基金supported by the National Natural Science Foundation of China(32270217,31970205,31770211)Metasequoia funding of Nanjing Forestry University to YY。
文摘Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,1999;One Thousand Plant Transcriptomes Initiative,2019).Due to its unique phylogenetic status,it holds tremendous interest for botanists.The nuclear and mitochondrial genomes of Amborella were first published in 2013,providing valuable resources for studies on genome and gene family evolution,phylogenomics,and flower development,despite the fact that the assembly is heavily fragmented(Amborella Genome Project,2013;Rice et al.,2013).In 2024,a haplotype-resolved Amborella genome assembly was published,showing significant improvement in quality and completeness(Carey et al.,2024).
基金supported by the National Natural Science Foundation of China(NSFC)grants(32030020,32288101,32470649,323B2013,32300499,32270665)the National Key Research and Development Program of China(2023YFC2605400)+1 种基金the Shanghai Science and Technology Commission Program(25JS2810100,23JS1410100,QNKJ2024023)the Office of Global Partnerships(Key Projects Development Fund).
文摘Recent advancements in genome sequencing have enabled the estimation of genetic load through deleterious mutation profiling.However,Chinese populations remain underexplored in this context.We analyze whole-exome sequencing data from 5002 individuals,encompassing major Han subgroups―North Han(NHan),South Han(S-Han),and Guangxi Han(G-Han)―as well as 13 ethnic minorities.Notably,G-Han exhibits significant genetic affinity with the Zhuang population.Systematic curation of 2110 ClinVar pathogenic or likely pathogenic variants reveals 93.4%are ultra-rare.Exceptions include GJB2 rs72474224-A(hearing loss),which shows higher frequencies in Zhuang and G-Han,and β-thalassemia-associated HBB variants(rs33986703-A and rs33950507-T),which are elevated in G-Han compared to other Han subgroups.Among 96 autosomal dominant mutation carriers,LDLR variants are predominant(~25%),with comparable frequencies across Han subgroups.Adaptive signatures highlight gene-environment interactions:MTHFR rs1801133-A(UV adaptation)declines southward,while ALDH2 rs671-A(alcohol metabolism)displays the opposite trend.ABCC11 rs17822931-A,associated with cold adaptation,is particularly low frequency in G-Han.Gene-based rare-variant collapsing analyses identify an elevated risk of retinitis pigmentosa in S-Han(PRPF4,TUB).Our findings demonstrate that genetic load in Chinese populations is influenced by demographic history,population structure,and regional adaptation,emphasizing the importance of population-specific frameworks in precision medicine.
基金funded by the National Natural Science Foundation of China(31372019)Key Laboratory of Urban Agriculture(North China)Ministry of Agriculture,P.R.China(kf2017015)the Beijing Municipal Education Commission(CEFF-PXM2017_014207_000043)
文摘CBF/DREB proteins play a critical role in abiotic stress-mediated gene expression and represent attractive regulons for plant breeding programs.However,no study has been conducted for CBF/DREB protein-related genes in jujube(Ziziphus jujuba Mill.).In this study,twenty-five ZjDREB genes were identified and annotated from the jujube(Z.jujuba‘Dongzao’)genome.Detailed analysis,including gene classification,annotation,phylogenetic evaluation,conserved motif determination and expression profiling were performed on all genes.Phylogenetic analysis showed that ZjDREB proteins were divided into five subgroups(A1–A5),but lacking a subgroup A6 corresponding to AtDREBs.The ZjDREB genes were distributed in nine of twelve chromosomes in the genome.Additionally,the expression patterns of the DREB genes under different abiotic stresses were investigated using q RT-PCR.Nineteen ZjDREB genes were down-regulated under low temperature,in contrast six ZjDREB genes(01,03,05,11,23 and 24)were up-regulated.Under drought,salinity and high temperature conditions,expression of ZjDREB03,09,10,14,15,17 and 20 genes were induced and showed similar expression patterns,suggesting that various stress conditions share common elements in the signaling pathway.The results suggest that the family of DREB genes play an important role in abiotic stresses in jujube,and provide a foundation for further functional studies of this important class of transcriptional regulators.
基金the National Basic Research Program of China (No 2007CB116307)Forestry Scientific and Technical Supporting Programs (No 2006BAD01A15-3)
文摘Polygalacturonase-inhibiting proteins （PGIPs） are extracellular proteins that belong to the leucine-rich repeat （LRR） protein superfamily. PGIPs inhibit fungal polygalacturonases （PGs） and promote accumulation of oligogalacturonides, which activate plant defense responses. PGIPs play important roles in resistance to infection of pathogens. In this study, reverse transcriptase-polymerase chain reaction （RT-PCR） and RNA ligase-mediated rapid amplification of cDNA ends （RLM-RACE） were used to isolate the full-length PGIP cDNA from Populus deltoides （GenBank accession no. of PdPGIP2 and PdPGIP4：EF684913 and EF684912）. Domain analysis revealed that the deduced amino acid sequences of PdPGIP2 and PdPGIP4 had a typical PGIP topology. Phylogenetic analysis of known PGIPs indicated that the two PdPGIPs were clustered to the defense-related PGIP clade. Using real-time RT-PCR, the expression patterns of the two PdPGIPs following treatment with a fungal pathogen and defense-related signaling molecules were studied. The expression levels of PdPGIP2 and PdPGIP4 were both up-regulated when inoculated with the phytopathogenic fungus Marssonina brunnea. Therefore, it was proposed that the two PGIPs might be involved in the resistance to Marssonina brunnea in P. deltoides.
基金supported by National Key R&D Program of China(2017YFD0600404-1)Medium and Long Scientific Research Project for Young Teachers in Beijing Forestry University(2015ZCQ-SW-02)+2 种基金the Project of National Natural Science Foundation of China(31370658)Program for Changjiang Scholars and Innovative Research Team in University(IRT13047)the Project of Beijing Gardening and Greening Bureau(CEG-2016-01)
文摘Larix principis-rupprechtii Mayr is a dominant species in coniferous forests of North China.However,early selection of L.principis-rupprechtii for growth traits is poorly characterised.To explore the optimal selection age for this species,heights(HT)and diameters at breast(DBH)of 40 half-sib families were measured at ages 3,12,22,and 28 years in a progeny test population established in the town of Kangjiahui,Shanxi Province.Age trends in heritability,age–age genetic correlations,and early selection efficiency for height and DBH were analysed.The individual heritability of these growth traits varied over time,and maximized at different ages(0.55 at age 12 for HT and 0.48 at age 28 for DBH).The age–age genetic correlations were always positive,and the majority were high(0.790–0.953)between the juvenile and mature ages for HT and DBH.For the same pairs of measurements,HT demonstrated higher age–age genetic correlations than DBH,and both age–age genetic correlation data sets were described well by the linear relationship with the logarithm of the age ratio(r^(2)>0.90).The regression slope for DBH was lower than that for HT.Based on the early selection efficiency estimates,the optimal selection age could be as early as age 6 for DBH and 8–9 years for HT.The results of this study provide information that can be used to assist early selection practices in L.principis-rupprechtii improvement programs in Shanxi Province.
基金supported by the National Natural Science Foundation of China (31360543 and 31760655)the earmarked fund for the China Agriculture Research System (CARS-39)+1 种基金the Open Project of Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, China (2016D03017)the Postdoctoral Science Foundation, China (2017M623287)
文摘As a member of the Frizzled family, Frizzled3 (FZD3) is a receptor of the canonical Wnt signaling pathway and plays a vital role in mammalian hair follicle developmental processes. However, its effects on wool traits are not clear. The objectives of this study were to identify the single nucleotide polymorphisms (SNPs) and the expression patterns of FZD3 gene, and then to determine whether it affected wool traits of Chinese Merino sheep (Xinjiang Type) or not. PCR-single stranded conformational polymorphism (PCR-SSCP) and sequencing were used to identify mutation loci, and general linear model (GLM) with SAS 9.1 was used for the association analysis between wool traits and SNPs. Quantitative real-time PCR (qRT-PCR) was used to investigate FZD3 gene expression levels. The results showed that six exons of FZD3 gene were amplified and two mutation loci were identified in exon 1 (NC_019459.2: g.101771685 T>C (SNP1)) and exon 3 (NC_019459.2: g.101810848, A>C (SNP2)), respectively. Association analysis showed that SNP1 was significantly associated with mean fiber diameter (MFD)(P=0.04) and live weight (LW)(P=0.0004), SNP2 was significantly associated with greasy fleece weight (GFW)(P=0.04). The expression level of FZD3 gene in skin tissues of the superfine wool (SF) group was significantly lower (P<0.05) than that of the fine wool (F) group. Moreover, it had a higher expression level (P<0.01) in skin tissues than in other tissues of Chinese Merino ewes. While, its expression level had a fluctuant expression in skin tissues at different developmental stages of embryos and born lambs, with the highest expression levels (P<0.01) at the 65th day of embryos. Our study revealed the genetic relationship between FZD3 variants and wool traits and two identified SNPs might serve as potential and valuable genetic markers for sheep breeding and lay a molecular genetic foundation for sheep marker-assisted selection (MAS).
基金supported by the National Natural Science Foundation of China (Grant No. 32071816)the Opening Preject of State Key Laboratory of Tree Genetics and Breeding (Grant No. K2021101)Special Fund for Beijing Common Construction Project。
文摘Prunus mume is an important woody plant that has high ornamental and economic value, widely distributed and used in landscape architecture in East Asia. In plants, basic(region) leucine zipper(bZIP) transcription factors play important regulatory roles in growth, development,dormancy and abiotic stress. To date, bZIP transcription factors have not been systematically studied in P. mume. In this study, 49 bZIP genes were first identified in P. mume, and the PmbZIP family was divided into 12 groups according to the grouping principles for the Arabidopsis thaliana bZIP family. For the first time, we constructed a detailed model of the PmbZIP domains(R-x_(3)–N-(x)_7-R/K-x_(2)-K-x_(6)-L-x_(6)-L-_(6)-L). Phylogenetic and synteny analyses showed that PmbZIPs duplication events might have occurred during the large-scale genome duplication events. A relatively short time of speciation and the finding that 91.84% of the bZIP genes formed orthologous pairs between P. mume and Prunus armeniaca provided evidence of a close relationship. Gene expression patterns were analysed in different tissues and periods, indicating that PmbZIP genes with the same motifs exhibited similar expression patterns. The gene expression results showed that PmbZIP31/36/41 genes played a more prominent role in the response to freezing stress than cold stress. The expression level of almost all subset Ⅲ genes was upregulated under freezing treatment, especially after cold exposure. We analysed the gene expression patterns of PmbZIP12/31/36/41/48 and their responses to low-temperature stress, which provided useful resources for future studies on the cold/freezing-tolerant molecular breeding of P. mume.
基金supported by the Beijing High-Precision Discipline Project,Discipline of Ecological Environment of Urban and Rural Human Settlements and the National Key R&D Program of China(2019YFD1000400)。
文摘Rose is a highly significant ornamental plant with substantial edible and medicinal value,cultivated worldwide primarily for perfume production.Recently,Rosa yangii,a new species found in northwestern Yunnan,China,has drawn attention due to its strong sweet scented flowers.In this study,the floral components of R.yangii were extracted at different flowering stages using solid phase micro extraction(SPME)and analyzed through gas chromatography-mass spectrometry(GC-MS).A total of 131 volatile organic compounds(VOCs)were detected from R.yangii,including 69 odor compounds.The production and release of floral VOCs were the highest during the initial-open stage,making it the most suitable time for harvesting as a significant number of floral components were synthesized and preserved.The analysis of the odor activity values(OAV)highlighted several key aromatic ingredients of R.yangii,such as eugenol,methyleugenol,benzeneacetaldehyde and phenylethylalcohol,heptanal,decanal,(E)-2-hexen-1-yl acetate,caryophyllene,and others.Metabolome and time-order gene co-expression networks(TO-GCN)revealed that VOCs and benzenoids/phenylpropanoids,along with associated genes,played a pivotal role in the overall floral regulatory network of R.yangii.MYB and bHLH were identified as the essential regulatory factors governing the regulation of eugenol synthase(EGS)and isoeugenol synthase(IGS),consequently influencing the sweet scent of R.yangii.The findings of this study provide a scientific foundation for enhancing fragrance through molecular breeding of ornamental plants.Furthermore,the study facilitated the development and utilization of this new plant’s essential oil material in various industries,including food storage,aromatherapy,cosmetic,and perfumery.
基金the National Natural Science Foundation of China(No.31800595 and 31471906)the National Key Research and Development Program of China(2018YFD1000401)the Special Fund for Beijing Common Construction Project.
文摘The term‘ornamental plant’refers to all plants with ornamental value,which generally have beautiful flowers or special plant architectures.China is rich in ornamental plant resources and known as the“mother of gardens”.Genomics is the science of studying genomes and is useful for carrying out research on genome evolution,genomic variations,gene regulation,and important biological mechanisms based on detailed genome sequence information.Due to the diversity of ornamental plants and high sequencing costs,the progress of genome research on ornamental plants has been slow for a long time.With the emergence of new sequencing technologies and a reduction in costs since the whole-genome sequencing of the first ornamental plant(Prunus mume)was completed in 2012,whole-genome sequencing of more than 69 ornamental plants has been completed in<10 years.In this review,whole-genome sequencing and resequencing of ornamental plants will be discussed.We provide analysis with regard to basic data from whole-genome studies of important ornamental plants,the regulation of important ornamental traits,and application prospects.
基金The research was supported by the National Key Research and Development Programof China(Grant No.2019YFD1001500)the National Natural Science Foundation of China(Grant No.31800595)Special Fund for Beijing Common Construction Project.
文摘Plant dormancy is essential for perennial plant survival.Different genotypes of Prunus mume,including Eumume group and Apricot Mei group,undergo leaf senescence and dormancy at different times.In order to verify the cold resistance of P.mume,freeze resistance evaluation was carried out.Our results showed that Apricot Mei group had a stronger freezing tolerance than Eumume group and that leaf senescence and dormancy of Apricot Mei group occurred at an earlier period before winter.Based on phenotypic data in response to seasonal climate change,the significant candidate regions were selected using GWAS.Furthermore,through KEGG pathway and qRT-PCR analyses,we found that the ethylene-related genes,including PmEIL(Pm002057)and PmERF(Pm004265),were significantly upregulated in‘Songchun’Mei(Apricot Mei group)and downregulated in‘Zaohua Lve’Mei(Eumume group).Ethylene-related genes expression models showed that ethylene may be indirectly involved in the induction of dormancy.The PmEIL and PmERF genes were the core genes of the ethylene signal transduction pathway and were regulated by the exogenous ACC or PZA compounds.For non-dormant or weekly dormant perennial plants,application of ACC was able to induce plant dormancy and thus enhance cold/freeze tolerance.Overall,the expression of the major ethylene genes played a significant role in dormancy induction and freezing tolerance in P.mume;accordingly,application of ACC and PZA compounds were an effective approach for enhancing cold/freeze of tolerance of woody plant.
基金supported by the Programme for Science and Technology of Beijing(No.Z181100002418006)the Special Fund for the Beijing Common Construction Project.
文摘Plant architecture includes vital traits that influence and benefit crops,and economically important trees.Different plant architectures provide natural beauty.Weeping ornamental plants are aesthetically appealing to people.The regulatory mechanism controlling the weeping trait is poorly understood in crape myrtle.To investigate the weeping trait mechanism,transcriptional profiling of different organs in weeping and upright crape myrtle was performed based on phenotype.Phenotypic and histological analyses demonstrated that endodermal cells were absent,and that new shoot phenotypes could be rescued by the GA3 treatment of weeping plants.The transcriptional analysis and coexpression network analysis(WGCNA)of differentially expressed genes indicated that GA synthesis and signal transduction pathways play a role in weeping traits.When the expression level of a negative element of GA signaling,LfiGRAS1,was reduced by virus-induced gene silencing(VIGS),new branches grew in infected plants in a negatively geotropic manner.An integrated analysis implied that GA had a strong influence on weeping crape myrtle by interacting with other factors.This study helps to elucidate the mechanism governing the weeping trait and can improve the efficiency of breeding in Lagerstroemia.
基金supported by the National Key R&D Program of China (2019YFE0119000)National Natural Science Foundation of China (31872561)+1 种基金National Science Fund for Distinguished Young Scholars (32225049)Alliance of International Science Organizations (ANSO-CR-PP-2021-03)。
文摘Common carp are among the oldest domesticated fish in the world.As such,there are many food and ornamental carp strains with abundant phenotypic variations due to natural and artificial selection.Hebao red carp(HB,Cyprinus carpio wuyuanensis),an indigenous strain in China,is renowned for its unique body morphology and reddish skin.To reveal the genetic basis underlying the distinct skin color of HB,we constructed an improved highfidelity(HiFi) HB genome with good contiguity,completeness,and correctness.Genome structure comparison was conducted between HB and a representative wild strain,Yellow River carp(YR,C.carpio haematopterus),to identify structural variants and genes under positive selection.Signatures of artificial selection during domestication were identified in HB and YR populations,while phenotype mapping was performed in a segregating population generated by HB×YR crosses.Body color in HB was associated with regions with fixed mutations.The simultaneous mutation and superposition of a pair of homologous genes(mitfa) in chromosomes A06 and B06 conferred the reddish color in domesticated HB.Transcriptome analysis of common carp with different alleles of the mitfa mutation confirmed that gene duplication can buffer the deleterious effects of mutation in allotetraploids.This study provides new insights into genotype-phenotype associations in allotetraploid species and lays a foundation for future breeding of common carp.
