Building Feedback-Regulation System Through Atomic Design for Highly Active SO_(2)Sensing

Reasonably constructing an atomic interface is pronouncedly essential for surface-related gas-sensing reaction.Herein,we present an ingen-ious feedback-regulation system by changing the interactional mode between single Pt atoms and adjacent S species for high-efficiency SO_(2)sensing.We found that the single Pt sites on the MoS_(2)surface can induce easier volatiliza-tion of adjacent S species to activate the whole inert S plane.Reversely,the activated S species can provide a feedback role in tailoring the antibonding-orbital electronic occupancy state of Pt atoms,thus creating a combined system involving S vacancy-assisted single Pt sites(Pt-Vs)to synergistically improve the adsorption ability of SO_(2)gas molecules.Further-more,in situ Raman,ex situ X-ray photoelectron spectroscopy testing and density functional theory analysis demonstrate the intact feedback-regulation system can expand the electron transfer path from single Pt sites to whole Pt-MoS_(2)supports in SO_(2)gas atmosphere.Equipped with wireless-sensing modules,the final Pt1-MoS_(2)-def sensors array can further realize real-time monitoring of SO_(2)levels and cloud-data storage for plant growth.Such a fundamental understanding of the intrinsic link between atomic interface and sensing mechanism is thus expected to broaden the rational design of highly effective gas sensors.

Physiological and transcriptome analyses of Chinese cabbage in response to drought stress

Chinese cabbage is an important leafy vegetable crop with high water demand and susceptibility to drought stress.To explore the molecular mechanisms underlying the response to drought,we performed a transcriptome analysis of drought-tolerant and-sensitive Chinese cabbage genotypes under drought stress,and uncovered core drought-responsive genes and key signaling pathways.A co-expression network was constructed by a weighted gene coexpression network analysis(WGCNA)and candidate hub genes involved in drought tolerance were identified.Furthermore,abscisic acid(ABA)biosynthesis and signaling pathways and their drought responses in Chinese cabbage leaves were systemically explored.We also found that drought treatment increased the antioxidant enzyme activities and glucosinolate contents significantly.These results substantially enhance our understanding of the molecular mechanisms underlying drought responses in Chinese cabbage.

Gene expression,transcription factor binding and histone modification predict leaf adaxial-abaxial polarity related genes

Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process remains unclear.To uncover critical genes involved in leaf ad-abaxial patterning,we applied a combination of in silico prediction using machine learning(ML)and experimental analysis.A Random Forest model was trained using genes known to influence ad-abaxial polarity as ground truth.Gene expression data from various tissues and conditions as well as promoter regulation data derived from transcription factor chromatin immunoprecipitation sequencing(ChIP-seq)was used as input,enabling the prediction of novel ad-abaxial polarity-related genes and additional transcription factors.Parallel to this,available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial sides.Based on these analyses,we obtained a set of 111 novel genes which are involved in leaf ad-abaxial specialization.To explore implications for vegetable crop breeding,we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell transcriptomics.The results demonstrated the utility of our computational approach for predicting candidate genes in crop species.Our findings expand the understanding of the genetic networks governing leaf ad-abaxial differentiation in agriculturally important vegetables,enhancing comprehension of natural variation impacting leaf morphology and development,with demonstrable breeding applications.

Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies

Brassica rapa comprises several important cultivated vegetables and oil crops.Current reference genome assemblies of Brassica rapa are quite fragmented and not highly contiguous,thereby limiting extensive genetic and genomic analyses.Here,we report an improved assembly of the B.rapa genome(v3.0)using single-molecule sequencing,optical mapping,and chromosome conformation capture technologies(Hi-C).Relative to the previous reference genomes,our assembly features a contig N50 size of 1.45 Mb,representing a~30-fold improvement.We also identified a new event that occurred in the B.rapa genome~1.2 million years ago,when a long terminal repeat retrotransposon(LTR-RT)expanded.Further analysis refined the relationship of genome blocks and accurately located the centromeres in the B.rapa genome.The B.rapa genome v3.0 will serve as an important community resource for future genetic and genomic studies in B.rapa.This resource will facilitate breeding efforts in B.rapa,as well as comparative genomic analysis with other Brassica species.

Genome triplication drove the diversification of Brassica plants

The genus Brassica belongs to the plant family Brassicaceae,which includes many important crop species that are used as oilseed,condiments,or vegetables throughout the world.Brassica plants comprise many diverse species,and each species contains rich morphotypes showing extreme traits.Brassica species experienced an extra whole genome triplication(WGT)event compared with the model plant Arabidopsis thaliana.Whole genome sequencing of the Brassica species Brassica rapa,Brassica oleracea and others demonstrated that WGT plays an important role in the speciation and morphotype diversification of Brassica plants.Comparative genomic analysis based on the genome sequences of B.rapa and A.thaliana clearly identified the WGT event and further demonstrated that the translocated Proto-Calepine Karyotype(tPCK,n57)was the diploid ancestor of the three subgenomes in B.rapa.Following WGT,subsequent extensive genome fractionation,block reshuffling and chromosome reduction accompanied by paleocentromere descent from the three tPCK subgenomes during the rediploidization process produced stable diploid species.Genomic rearrangement of the diploid species and their hybridization then contributed to Brassica speciation.The subgenome dominance effect and biased gene retention,such as the over-retention of auxin-related genes after WGT,promoted functional gene evolution and thus propelled the expansion of rich morphotypes in the Brassica species.In conclusion,the WGT event initiated subsequent genomic and gene-level evolution,which further drove Brassica speciation and created rich morphotypes in each species.

A naturally occurring variation in the BrMAM-3 gene is associated with aliphatic glucosinolate accumulation in Brassica rapa leaves

Glucosinolate profiles significantly vary among Brassica rapa genotypes.However,the molecular basis of these variations is largely unknown.In this study,we investigated a major quantitative trait locus(QTL)controlling aliphatic glucosinolate accumulation in B.rapa leaves.The QTL,which encompasses three tandem MAM genes and two MYB genes,was detected in two BC2DH populations.Among the five-candidate genes,only the expression level of BrMAM-3(Bra013007)was significantly correlated with the accumulation of aliphatic glucosinolates in B.rapa leaves.We identified a naturally occurring insertion within exon 1 of BrMAM-3,which is predicted to be a loss-of-function mutation,as confirmed by qRT-PCR.We determined that the loss of function was associated with the low glucosinolate content in B.rapa accessions.Furthermore,overexpressing the BrMAM-3 gene resulted in an increase in total aliphatic glucosinolates in Arabidopsis transgenic lines.Our study provides insights into the molecular mechanism underlying the accumulation of aliphatic glucosinolates in B.rapa leaves,thereby facilitating in the manipulation of total aliphatic glucosinolate content in Brassica crops.

Development of InDel Markers for Brassica rapa Based on a High-resolution Melting Curve

Brassica rapa is one of the most important leafy vegetable crops with large cultivated area in China.To increase the availability of DNA markers in B.rapa,we developed insertion-deletion(InDel)markers utilizing high-resolution melting(HRM)curve analysis.We designed primers for 252 InDels(≥3 bp)evenly distributed in the genome and tested gene polymorphisms with eight accessions.In total,208 markers were specifically amplified,and 148 InDels with polymorphism were genotyped successfully using HRM.We further analyzed the correlation with InDel size,GC number,and predicted the difference in Tm values(Tm)using 208 markers with specific amplification.We found that the success rate of InDel markers was correlated with the GC number of InDel and the predicted-Tm,but not clearly correlated with the length of InDel.When the GC number within InDel was≥8,the successful rate exceeded 90.0%.When the predicted-Tm reached 0.5°C,the success rate was greater than 90.0%,and when it was≥0.6°C,the rate climbed to 100.0%,indicating their role as the optimal parameter for successful development of an applicable InDel marker.The polymorphic InDel markers can be easily genotyped using HRM.They are of great value in genetic analysis,construction of linkage map,and molecular marker-assisted selection in B.rapa.

Author Correction:Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies

Since the publication of this article,the authors have noticed that the total gene models(45,985),tandem arrays(2077),tandem genes(4963),redundancy removed(43,099),syntenic genes(39,858),nonsyntenic genes(3241),genes on chromosomes(45,411),genes on scaffolds(574)of B.rapa reference genome v3.0 were mistaken in the article.

Wild Brassica and Its Close Relatives in Turkey,the Genetic Treasures

Brassica taxa occur naturally and are also cultivated in Turkey.Due to their economic importance,several cultivars have been extensively cultivated in certain regions of the country.Alongside extensive cultivation for vegetable production of the other species of the genus,Brassica juncea has very limited cultivation.Five native species of Brassica are known from restricted locations in Turkey with only a few collections.Among them,Brassica elongata is distributed all over the Central and Eastern parts of the country and it prefers unfertile soils on hillsides.Highlighting the current data about the Brassica taxa would lead to new initiatives for Brassica research dealing with both the genetic structure and the origin of the taxa.Diagnostic characters of the genera closely related to Brassica have been discussed under the relevant genera.Additionally,an overview for the Turkish Brassiceae tribe,both native and cultivated,has been presented and the relevant identification keys have been supplied for updating.

Segmental Translocation Contributed to the Origin of the Brassica S-locus

Self-incompatibility(SI),which has recurred during the evolution of plants,is one of the most important cross-pollination mating systems.Three S-loci have been reported in Brassicaceae,namely,Arabidopsis lyrata(Al),Brassica(Br),and Leavenworthia alabamica(La)S-loci.Here,through multi-genomic comparative analysis of 20 species,we revealed that the most ancient S-locus was formed prior to the divergence of Brassicaceae lineage I and II.Itwas retained and inherited by Arabidopsis,as the Al S-locus in Brassicaceae lineage I.Furthermore,we found that the Br S-locus,which has been widely used in the breeding of Brassica crops to generate hybrid seeds,was formed through segmental translocation(ST)in the hexaploid ancestor of Brassica in Brassicaceae lineage II.The Br S-locus was evolved through a ST from one of the triplicated ancestral S-locus paralogs in the Brassica hexaploidy ancestor,while the other two S-locus paralogs were lost.Together with the previous discovery that the La S-locus was formed through a secondary origin in Brassicaceae lineage I,we conclude the monophyletic origin of Al and Br S-loci and clarify the evolutionary route of S-loci in the Brassicaceae family.Our findings will contribute to evolutionary studies and breeding applications of the S-locus in Brassicaceae.

Divergence of three BRX homoeologs in Brassica rapa and its effect on leaf morphology

The leafy head characteristic is a special phenotype of Chinese cabbage resulting from artificial selection during domestication and breeding.BREVIS RADIX(BRX)has been suggested to control root elongation,shoot growth,and tiller angle in Arabidopsis and rice.In Brassica rapa,three BrBRX homoeologs have been identified,but only BrBRX.1 and BrBRX.2 were found to be under selection in leaf-heading accessions,indicating their functional diversification in leafy head formation.Here,we show that these three BrBRX genes belong to a plant-specific BRX gene family but that they have significantly diverged from other BRX-like members on the basis of different phylogenetic classifications,motif compositions and expression patterns.Moreover,although the expression of these three BrBRX genes differed,compared with BrBRX.3,BrBRX.1,and BrBRX.2 displayed similar expression patterns.Arabidopsis mutant complementation studies showed that only BrBRX.1 could rescue the brx root phenotype,whereas BrBRX.2 and BrBRX.3 could not.However,overexpression of each of the three BrBRX genes in Arabidopsis resulted in similar pleiotropic leaf phenotypes,including epinastic leaf morphology,with an increase in leaf number and leaf petiole length and a reduction in leaf angle.These leaf traits are associated with leafy head formation.Further testing of a SNP(T/C)in BrBRX.2 confirmed that this allele in the heading accessions was strongly associated with the leaf-heading trait of B.rapa.Our results revealed that all three BrBRX genes may be involved in the leaf-heading trait,but they may have functionally diverged on the basis of their differential expression.

An optimized protocol for detecting guard cell specific gene expression by in situ RT-PCR in Brassica rapa

It is important to detect specific genes expressed in the guard cells,which control gas exchange and play key roles in response to drought and salt stresses.Due to the genetic transformation of Chinese cabbage(Brassica rapa)has not been well developed,in situ RT-PCR is a valuable option for detecting guard cell specific genes.We reported an optimized protocol of in situ RT-PCR by using an FAMA homologous gene Bra001929 in Brassica rapa.FAMA in Arabidopsis has been verified to be specially expressed in guard cells.We designed specific RT-PCR primers and optimized the protocol in terms of the(a)reverse transcription time,(b)blocking time,(c)antigen-antibody incubation time,and(d)washing temperature.Our approach provides a sensitive and effective in situ RT-PCR method for locating expression in the guard cells in Brassica rapa.Moreover,we proved the guard cell specific expression of Bra001929 in the epidermis indicating its’applicability as a marker gene for guard cells of Brassica rapa.

Identification of a male-specific region(MSR)in Spinacia oleracea

Dioecy,the presence of male and female individual,has evolved independently from hermaphroditism in multiple flowering plant lineages.Spinach,an important leafy vegetable crop worldwide,is a dioecious species with an XY sex-determination system.Although some markers that are fully linked to male-determination locus were identified,the male-specific region(MSR)remained unclear.In this research,five male individuals and five female lines were resequenced to identify the male-specific region.We identified a region(∼21 kb)on chromosome 4(putative sex chromosome)where the five females had a low reads coverage,while the five males had high coverage.A KASP marker,SponR,developed from a single nucleotide polymorphism(SNP)closely linked to the MSR was co-segregating with the sex determination gene in the population of 958 individuals,suggesting that the MSR might be specifically present in male spinach plants.

The APETALA2 homolog CaFFN regulates flowering time in pepper

Flowering time is an important agronomic trait that contributes to fitness in plants.However,the genetic basis of flowering time has not been extensively studied in pepper.To understand the genetics underlying flowering time,we constructed an F 2 population by crossing a spontaneous early flowering mutant and a late-flowering pepper line.Using bulked segregant RNA-seq,a major locus controlling flowering time in this population was mapped to the end of chromosome 2.An APETALA2(AP2)homolog(CaFFN)cosegregated with flowering time in 297 individuals of the F 2 population.A comparison between the parents revealed a naturally occurring rare SNP(SNP2T>C)that resulted in the loss of a start codon in CaFFN in the early flowering mutant.Transgenic Nicotiana benthamiana plants with high CaFFN expression exhibited a delay in flowering time and floral patterning defects.On the other hand,pepper plants with CaFFN silencing flowered early.Therefore,the CaFFN gene acts as a flowering repressor in pepper.CaFFN may function as a transcriptional activator to activate the expression of CaAGL15 and miR156e and as a transcriptional repressor to repress the expression of CaAG,CaAP1,CaSEP3,CaSOC1,and miR172b based on a qRT-PCR assay.Direct activation of CaAGL15 by CaFFN was detected using yeast one-hybrid and dual-luciferase reporter assays,consistent with the hypothesis that CaFFN regulates flowering time.Moreover,the CaFFN gene association analysis revealed a significant association with flowering time in a natural pepper population,indicating that the CaFFN gene has a broad effect on flowering time in pepper.Finally,the phylogeny,evolutionary expansion and expression patterns of CaFFN/AP2 homologs were analyzed to provide valuable insight into CaFFN.This study increases our understanding of the involvement of CaFFN in controlling flowering time in pepper,thus making CaFFN a target gene for breeding early maturing pepper.

Conserved noncoding sequences correlate with distant gene contacts in Arabidopsis and Brassica

Physical contact between genes distant on chromosomes is a potentially important way for genes to coordinate their expressions.To investigate the potential importance of distant contacts,we performed high-throughput chromatin conformation capture(Hi-C)experiments on leaf nuclei isolated from Brassica rapa and Brassica oleracea.We then combined our results with published Hi-C data from Arabidopsis thaliana.We found that distant genes come into physical contact and do so preferentially between the proximal promoter of one gene and the downstream region of another gene.Genes with higher numbers of conserved noncoding sequences(CNSs)nearby were more likely to have contact with distant genes.With more CNSs came higher numbers of transcription factor binding sites and more histone modifications associated with the activity.In addition,for the genes we studied,distant contacting genes with CNSs were more likely to be transcriptionally coordinated.These observations suggest that CNSs may enrich active histone modifications and recruit transcription factors,correlating with distant contacts to ensure coordinated expression.This study advances our knowledge of gene contacts and provides insights into the relationship between CNSs and distant gene contacts in plants.

The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceaepolyploidizationandits distinct traits

Orychophragmus violaceus,referred to as‘‘eryuelan’’(February orchid)in China,is an early-flowering ornamental plant.The high oil content and abundance of unsaturated fatty acids in O.violaceus seeds make it a potential high-quality oilseed crop.Here,we generated a whole-genome assembly for O.violaceus using Nanopore and Hi-C sequencing technologies.The assembled genome of O.violaceus was~1.3 Gb in size,with 12 pairs of chromosomes.Through investigation of ancestral genome evolution,we determined that the genome of O.violaceus experienced a tetraploidization event from a diploid progenitor with the translocated proto-Calepineae karyotype.Comparisons between the reconstructed subgenomes of O.violaceus identified indicators of subgenome dominance,indicating that subgenomes likely originated via allotetraploidy.O.violaceus was phylogenetically close to the Brassica genus,and tetraploidy in O.violaceus occurred approximately 8.57 million years ago,close in time to the whole-genome triplication of Brassica that likely arose via an intermediate tetraploid lineage.However,the tetraploidization in Orychophragmus was independent of the hexaploidization in Brassica,as evidenced by the results from detailed phylogenetic analyses and comparisons of the break and fusion points of ancestral genomic blocks.Moreover,identification of multi-copy genes regulating the production of high-quality oil highlighted the contributions of both tetraploidization and tandem duplication to functional innovation in O.violaceus.These findings provide novel insights into the polyploidization evolution of plant species and will promote both functional genomic studies and domestication/breeding efforts in O.violaceus.

糖尿病视网膜病变患者全视网膜光凝后角膜上皮基底神经丛和朗格汉斯细胞的改变及其相关性

目的:利用结构拼图观察糖尿病(DM)患者全视网膜光凝(PRP)前后角膜上皮基底神经丛(SNP)和朗格汉斯细胞(LC)的变化,并分析二者的相关性。方法:前瞻性临床研究。选取2019年4─11月就诊于山西省眼科医院准备行PRP治疗且双眼糖尿病视网膜病变Ⅳ期的2型DM患者,选择病情较重的眼为治疗眼,对侧眼为对照眼,分别于PRP治疗前、每次光凝后1周和PRP完成后1个月行角膜共焦显微镜检查,观察涡状结构及其周围2~3 mm区域SNP和LC的变化,并测量涡状区神经纤维长度(NFL)值和LC密度。采用重复测量方差分析比较不同观察时间点LC密度和NFL值,并采用SAS软件的MIXED模型分析重复测量的NFL值和LC密度之间的相关性。结果:共纳入患者49例。治疗眼接受PRP后部分患者出现SNP神经纤维变细,伴有不同程度的涡状区神经结构缺失的神经损伤表现;各观察时间点NFL值总体比较差异有统计学意义(F=8.039,P=0.004),且PRP治疗前NFL值[(15.5±3.7)mm/mm^(2)]与第2次光凝后1周[(15.0±3.5)mm/mm^(2)]、第3次光凝后1周[(13.4±4.3)mm/mm^(2)]和第4次光凝后1周[(13.5±4.1)mm/mm^(2)]比较差异均有统计学意义(均P<0.05)。同时,治疗眼LC密度增加,并以涡状区为中心聚集,成熟LC浸润区伴有SNP神经结构的缺失;各观察时间点LC密度总体比较差异有统计学意义(F=12.350,P<0.001),且PRP治疗前LC密度[(40±54)cells/mm^(2)]与第3次光凝后1周[(79±91)cells/mm^(2)]、第4次光凝后1周[(98±126)cells/mm^(2)]以及PRP完成后1个月[(87±102)cells/mm^(2)]比较差异均具有统计学意义(均P<0.05);相关分析显示治疗眼第4次激光后1周LC密度与其基线水平呈正相关(r=0.674,P<0.001);且重复测量的NFL值与LC密度呈负相关(p=-0.041)。结论:PRP多次光凝可以导致LC密度增加;成熟LC可以导致SNP神经结构破坏。

Plant Polyploidy: Origin, Evolution, and Its Influence on Crop Domestication

The prevalence and recurrence of polyploidization in plant species make it one of the most important evolutionary events in plants, and as a result, polyploidization is an extensively investigated research field. Due to the rapid development of sequencing technologies, there is increased evidence to support that polyploidization plays an important role in the diversification of plant species, evolution of genes, and the domestication of crops. Here, we reviewed the influence of polyploidization on various aspects of plant evolution, mainly focused on polyploid origin, characteristics, subsequent genome divergence, and its impact on gene function innovation and crop domestication. The occurrence of many independent polyploidization events in plants was found to be tightly associated with the timing of extreme climate events or natural disasters on earth, leading to mass extinction while possibly facilitating increased polyploidization. Following allo-polyploidization, a distinct phenomenon known as sub-genome dominance occurred during sub-genome evolution, which was found to be associated with the methylation of transposons. Extensive gene fractionations(lost) following polyploidization were reported in almost all paleo-polyploids, and the evolutionary fates of multi-copy genes, such as sub-/neo-functionalization, were further proposed to illustrate their underlying mechanisms. Moreover,polyploidization was found to significantly impact species diversification, with subsequent effects on crop domestication and the development of traits with agronomic importance. Based on the progress of plant polyploidization studies, we discussed several main topics that might further improve our understanding of polyploid evolution and that are likely contribute to the application of polyploidization in crop breeding in the near future.

Variation in Plant Morphology and Sinigrin Content in Ethiopian Mustard(Brassica carinata L.)

Ethiopian mustard(Brassica carinata) is mainly grown as a leafy vegetable and oilseed crop. Sinigrin is predominant glucosinolate in the leaves of Ethiopian mustard. It is hydrolyzed by enzyme myrosinase to produce bioactive product specifically allyl-isothiocyanates. Due to sinigrin content, Ethiopian mustard has a mild flavor and it is a healthy addition to human diet. However, sinigrin concentration depends on genotype.Understanding variations of plant morphology and sinigrin content may be the first step for crop improvement. According to the analyses of various plant characteristics among ninety nine Ethiopian mustard accessions, we found significant differences in plant height, chlorophyll content, and petiole length. In addition, sinigrin content was determined using ultra-performance liquid chromatography tandem quadrupole mass spectrometers/tunable ultraviolet detector(UPLC-TQS/TUV). We found a significant difference in sinigrin content among leaves of 94 Ethiopian mustard accessions. Except for petiole length, the sinigrin content was negatively correlated with leaf area, leaf width, number of primary branches, and plant height. This information will help Ethiopian mustard breeders in screening breeding lines for new accessions.