The anthocyanin formation of purple leaf is associated with the activation of LfiHY5 and LfiMYB75 in crape myrtle

Purple-leafed plants not only have a higher resistance to biotic and abiotic stresses,but also have higher ornamental value.Anthocyanins are vital for leaf color formation,growth and development of purple leaves.However,the molecular mechanism underlying purple leaf formation in Lagerstroemia indica remains unclear.Metabolomic and transcriptomic analysis of purple-leafed cultivar‘Ebony Embers’and greenleafed cultivar‘Arapahoe’showed that the high expression of anthocyanin structure genes induced hyperaccumulation of cyanidin and pelargonidin derivatives,making the leaves purple.LfiHY5,LfiMYB75 and LfibHLH1 were identified using correlation analysis and weighted gene co-expression network analysis.In‘Arapahoe’‘Ebony Embers’population,LfiHY5 and LfiMYB75 showed significant positive correlation with leaf anthocyanin content.Transient expression of LfiMYB75 and LfiHY5 in tobacco and purple-leafed crape myrtle indicated that the two genes activated anthocyanin synthesis.Yeast two-hybrid analysis showed that LfiMYB75 and LfibHLH1 could form a complex that enhanced anthocyanin synthesis.Yeast monohybrid and dual-luciferase assays confirmed that LfiHY5 activated the expression of LfiMYB75,to activate the transcription of anthocyanin structural genes LfiCHS and LfiANS.Moreover,there were three alleles of LfiHY5 in crape myrtle,and the different sequences had different activation effects on LfiMYB75.In conclusion,the results showed that LfiHY5 led to upregulate the transcription of LfiMYB75,and LfiMYB75 formed a complex with LfibHLH1,which increased the transcription level of LfiCHS and LfiANS to affect anthocyanin synthesis in crape myrtle.

Photoperiod-and temperature-mediated control of the ethylene response and winter dormancy induction in Prunus mume

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.

Establishment and Verification of An Efficient Virus-induced Gene Silencing System in Forsythia

To understand the functional identification of large-scale genomic sequences in Forsythia,tobacco rattle virus(TRV)-mediated virus-induced gene silencing(VIGS),suitable for the plant,was explored in this study.The results showed that the TRV-mediated VIGS system could be successfully used in Forsythia for silencing the reporter gene FsPDS(Forsythia phytoene desaturase)using stem infiltration and leaf infiltrationmethods.All the treated plants were pruned below the injection site after 7–15 d infection;the FsPDS was silenced and typical photobleaching symptoms were observed in newly sprouted leaves at the whole-plant level.Meanwhile,this system has been successfully tested and verified through virus detection and qRT-PCR analysis.After the optimization,Forsythia magnesium chelatase subunit H(FsChlH)was silenced successfully in Forsythia using this system,resulting in yellow leaveswith decreased chlorophyll content.The system was stable,highly efficient and had greater rapidity and convenience,which made it suitable to study the function of genes related to physiological pathways such as growth and development,and metabolic regulation in Forsythia.

Transcriptome profiles reveal that gibberellin-related genes regulate weeping traits in crape myrtle

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.

Expansion of PmBEAT genes in the Prunus mume genome induces characteristic floral scent production

Prunus mume is the only plant in the genus Prunus of the Rosaceae family with a characteristic floral scent,and the main component of this scent is benzyl acetate.By contrast,benzyl acetate is not synthesized in Prunus persica flowers.Here,we searched for benzyl alcohol acetyltransferase(BEAT)genes based on genomic data from P.mume and P.persica and found 44 unique PmBEATs in P.mume.These genes,which were mainly detected in clusters on chromosomes,originated from gene duplication events during the species evolution of P.mume,and retroduplication and tandem duplication were the two dominant duplication patterns.The genes PmBEAT34,PmBEAT36 and PmBEAT37,which were generated by tandem duplication,were highly expressed in flowers,and their highest levels were detected during the blooming stage.In vitro,PmBEAT34,PmBEAT3,and PmBEAT37 all had benzyl alcohol acetyltransferase activity that was localized in the cytoplasm.Overexpression of the PmBEAT36 or PmBEAT37 genes increased benzyl acetate production in the petal protoplasts of P.mume,and interference in the expression of these genes slightly decreased the benzyl acetate content.In addition,light and temperature regulated the expression of the PmBEAT34,PmBEAT36 and PmBEAT37 genes.According to these results,we hypothesize that the expansion of the PmBEAT genes in the genome induce the characteristic floral scent of P.mume.

Genome-wide investigation of the bZIP transcription factor gene family in Prunus mume:Classification, evolution, expression profile and low-temperature stress responses

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.

Genome assembly and resequencing analyses provide new insights into the evolution, domestication and ornamental traits of crape myrtle

Crape myrtle(Lagerstroemia indica)is a globally used ornamental woody plant and is the representative species of Lagerstroemia.However,studies on the evolution and genomic breeding of L.indica have been hindered by the lack of a reference genome.Here we assembled the first high-quality genome of L.indica using PacBio combined with Hi-C scaffolding to anchor the 329.14-Mb genome assembly into 24 pseudochromosomes.We detected a previously undescribed independent whole-genome triplication event occurring 35.5 million years ago in L.indica following its divergence from Punica granatum.After resequencing 73 accessions of Lagerstroemia,the main parents of modern crape myrtle cultivars were found to be L.indica and L.fauriei.During the process of domestication,genetic diversity tended to decrease in many plants,but this was not observed in L.indica.We constructed a high-density genetic linkage map with an average map distance of 0.33 cM.Furthermore,we integrated the results of quantitative trait locus(QTL)using genetic mapping and bulk segregant analysis(BSA),revealing that the major-effect interval controlling internode length(IL)is located on chr1,which contains CDL15,CRG98,and GID1b1 associated with the phytohormone pathways.Analysis of gene expression of the red,purple,and white flower-colour flavonoid pathways revealed that differential expression of multiple genes determined the flower colour of L.indica,with white flowers having the lowest gene expression.In addition,BSA of purple-and green-leaved individuals of populations of L.indica was performed,and the leaf colour loci were mapped to chr12 and chr17.Within these intervals,we identified MYB35,NCED,and KAS1.Our genome assembly provided a foundation for investigating the evolution,population structure,and differentiation of Myrtaceae species and accelerating the molecular breeding of L.indica.

Identification of the PmWEEP locus controlling weeping traits in Prunus mume through an integrated genome-wide association study and quantitative trait locus mapping

Weeping Prunus mume(mei)has long been cultivated in East Asia for its specific ornamental value.However,little is known about the regulatory mechanism of the weeping trait in mei,which limits molecular breeding for the improvement of weeping-type cultivars.Here,we quantified the weeping trait in mei using nested phenotyping of 214 accessions and 342 F 1 hybrids.Two major associated loci were identified from the genome-wide association study(GWAS),which was conducted using 3,014,409 single nucleotide polymorphisms(SNPs)derived from resequencing,and 8 QTLs and 55 epistatic loci were identified from QTL mapping using 7,545 specific lengths amplified fragment(SLAF)markers.Notably,an overlapping PmWEEP major QTL was fine mapped within a 0.29 Mb region on chromosome 7(Pa7),and a core SNP locus closely associated with the weeping trait was screened and validated.Furthermore,a total of 22 genes in the PmWEEP QTL region were expressed in weeping or upright mei based on RNA-seq analysis.Among them,only a novel gene(Pm024213)containing a thioredoxin(Trx)domain was found to be close to the core SNP and specifically expressed in buds and branches of weeping mei.Co-expression analysis of Pm024213 showed that most of the related genes were involved in auxin and lignin biosynthesis.These findings provide insights into the regulatory mechanism of the weeping trait and effective molecular markers for molecular-assisted breeding in Prunus mume.

The genomics of ornamental plants: current status and opportunities

With the rapid development of sequencing technologies,followed by the reduction of sequencing cost,numerous ornamental plants have been sequenced,resulting in their genomic studies shifting from gene cloning and marker development to whole genome profiling.A profound understanding of genome structure and function at the whole genome level can not only help to modify ornamental traits,such as fragrance,color and flower shape,through genetic engineering,but also infer the genetic relationship and evolutionary history of ornamental plants via comparative genomics analysis.In this paper,we review the current situation of sequencing strategies and the application of genomics to study the origin and evolution of ornamental plants.We highlight challenges of ornamental plant genomic research.The use of cutting-edge technologies,such as genomics,gene editing and molecular design polymerization breeding,can facilitate our understanding of genetic regulation mechanisms and the germplasm innovation of important traits in ornamental plants.The results can be expected to significantly increase the breeding efficiency of ornamental plants.

Mapping the genetic architecture of developmental modularity in ornamental plants

Developmental modularity,i.e.,coherent organization and function of developmentally related traits,is an emergent property of organismic development and evolution.However,knowledge about how modular variation and evolution are driven genetically is still limited.Here,using ornamental plants as an example,we propose a computational framework to map,visualize and annotate the genetic architecture of trait modularity by integrating modularity theory into system mapping,a statistical model for multifaceted genetic mapping of complex traits.A developmental module can be viewed as an ecosystem,in which the constituting components compete for space and resources or cooperate symbiotically to organize its function and behavior.This interactive process is quantified by mathematical models and evolutionarily interpreted by game theory.The proposed framework can test whether and how genes regulate the coordination of different but interconnected traits through their competition or cooperation to downstream developmental modularity.

BULKED SEGREGANT RNA SEQUENCING(BSR-SEQ)IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN PRUNUS MUME

Weeping species are used both as ornamental plants and for breeding dwarf plant types.However,exploration of casual genes controlling weeping traits is rather limited.Here,we identified individuals with contrasting phenotypes from an Fx bi-parental mapping population of Prunus mume which was developed from a cross between the upright cultivar/Liuban,and the weeping cultivar'Fentai Chuizhi'.Bulked segregant RNA sequencing was used and five QTLs on chromosome 7 were identified.The Pm024074(PmilGT72B3)allele,belonging to the UDP-glycosyltransferase superfamily containing the coniferyl-alcohol glucosyltransferase domain,was identified in a genomic region overlapping with a previously identified QTL;and had a synonymous transition of T66(upright)to C(weeping)in the coding sequence and a 470-bp deletion in the promoter region.Pm024074 had exceptionally high expression in buds and stems of weeping P.mume.Weighted correlation network analysis indicates that genes neighboring Pm024074 were significantly associated with plant architecture.In addition,a reliable single nucleotide polymorphism marker was developed based on the variation in the Pm024074 gene,providing precise marker-assisted breeding for weeping traits.This study provides insights into the genetic mechanism governing the weeping trait in P.mume,and indicates potential applications for the manipulation of tree architecture.