Epigenetic control on transcription of vernalization genes and whole-genome gene expression profile induced by vernalization in common wheat

Vernalization is necessary for winter wheat to flower.However,it is unclear whether vernalization is also required for spring wheat,which is frequently sown in fall,and what molecular mechanisms underlie the vernalization response in wheat varieties.In this study,we examined the molecular mechanisms that regulate vernalization response in winter and spring wheat varieties.For this purpose,we determined how major vernalization genes(VRN1,VRN2,and VRN3)respond to vernalization in these varieties and whether modifications to histones play a role in changes in gene expression.We also identified genes that are differentially regulated in response to vernalization in winter and spring wheat varieties.We found that in winter wheat,but not in spring wheat,VRN1 expression decreases when returned to warm temperature following vernalization.This finding may be associated with differences between spring and winter wheat in the levels of tri-methylation of lysine 27 on histone H3(H3K27me3)and tri-methylation of lysine 4 on histone H3(H3K4me3)at the VRN1 gene.Analysis of winter wheat transcriptomes before and after vernalization revealed that vernalization influences the expression of several genes,including those involved in leucine catabolism,cysteine biosynthesis,and flavonoid biosynthesis.These findings provide new candidates for further study on the mechanism of vernalization regulation in wheat.

Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification

Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors(TFs)in intricate regulatory networks in a cell-type specific manner.Here we introduced a comprehensive single-cell transcriptomic atlas of Arabidopsis seedlings.This atlas is the result of meticulous integration of 63 previously published scRNA-seq datasets,addressing batch effects and conserving biological variance.This integration spans a broad spectrum of tissues,including both below-and above-ground parts.Utilizing a rigorous approach for cell type annotation,we identified 47 distinct cell types or states,largely expanding our current view of plant cell compositions.We systematically constructed cell-type specific gene regulatory networks and uncovered key regulators that act in a coordinated manner to control cell-type specific gene expression.Taken together,our study not only offers extensive plant cell atlas exploration that serves as a valuable resource,but also provides molecular insights into gene-regulatory programs that varies from different cell types.

Hexagonal boron nitride based slippery liquid infused porous surface with anti-corrosion, anti-contaminant and anti-icing properties for protecting magnesium alloy

In an era where the concept of green development is deeply rooted, magnesium(Mg) alloy as a light metal has a long-term development prospect in the process of energy saving, emission reduction and environmental improvement. However, anti-corrosion performance of Mg alloy is poor due to the high chemical activity and low equilibrium potential, which limits the development of Mg alloy products.Herein, three-dimensional mesopore hollow polypyrrole spheres(MHPS) were prepared, and the MHPS was inserted into the middle of the stacked hexagon boron nitride(h-BN) lamellae, which allowed the hBN to be separated forming a further composite with abundant pore structure. Subsequently, the MHPS/hBN-OH composite was uniformly sprayed on the Mg alloy surface via simple spraying method to form the superhydrophobic surface(SHS). Finally, the slippery liquid infused porous surface(SLIPS) was successfully fabricated by applying drops of silicone lubricant on the superhydrophobic coating surface. After a series of characterization and testing, the results showed that the stacking of h-BN lamellae was significantly reduced after h-BN was successfully embedded by MHPS. In addition, the fabricated SLIPS have excellent self-cleaning, mechanical stability, anti-icing and anti-corrosion properties. Therefore, the method of embedding polymer microspheres not only offers a new strategy for h-BN exfoliation, but also the successful prepared SLIPS largely retards the corrosion of Mg alloy while providing new ideas for the development of SLIPS.

Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat

Spike architecture influences both grain weight and grain number per spike,which are the two major components of grain yield in bread wheat(Triticum aestivum L.).However,the complex wheat genome and the influence of various environmental factors pose challenges in mapping the causal genes that affect spike traits.Here,we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in wheat.We identified 170 loci that are responsible for variations in spike length,spikelet number per spike,and grain number per spike through genome-wide association study and meta-QTL analyses.We constructed gene regulatory networks for young inflorescences at the double ridge stage and thefloret primordium stage,in which the spikelet meristem and thefloret meristem are predominant,respec-tively,by integrating transcriptome,histone modification,chromatin accessibility,eQTL,and protein–pro-tein interactome data.From these networks,we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike traits.The functions of TaZF-B1,VRT-B2,and TaSPL15-A/D in establishment of wheat spike architecture were verified.This study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.

Overcoming genotypic dependency and bypassing immature embryos in wheat transformation by using morphogenic regulators

Dear Editor,Agrobacterium-mediated transformation technology is of vital importance for functional genomics studies and precision breeding in crops due to low cost and clear genetic manifestation.A morphogenic gene pair,BABY BOOM and WUSCHEL(BBM-WUS).

scPlant:A versatile framework for single-cell transcriptomic data analysis in plants

Single-cell transcriptomics has been fully embraced in plant biological research and is revolutionizing our understanding of plant growth,development,and responses to external stimuli.However,single-cell tran-scriptomic data analysis in plants is not trivial,given that there is currently no end-to-end solution and that integration of various bioinformatics tools involves a large number of required dependencies.Here,we pre-sent scPlant,a versatile framework for exploring plant single-cell atlases with minimuminput data provided by users.The scPlant pipeline is implemented with numerous functions for diverse analytical tasks,ranging from basic data processing to advanced demands such as cell-type annotation and deconvolution,trajec-tory inference,cross-species data integration,and cell-type-specific gene regulatory network construc-tion.In addition,a variety of visualization tools are bundled in a built-in Shiny application,enabling explo-ration of single-cell transcriptomic data on the fly.

Meeting partners at the right time promises varied flowering

Photoperiodic flowering is critical for adaptability and high yield in rice.In this issue of Molecular Plant,Hu et al.(2022)report the autophagy-mediated degradation of Hd1 protein in the dark as a major regulatory mechanisrp of photoperiodic flowering,which promotes rice flowering under both short-day(SD)and long-day(LD)conditions.The established regualtory mechanism links the cellular autophagy to plant climate adaptation and also explains the multiple functions of Hd1 in rice photoperiodic flowering.

Exploitation of genetic resources based on regulome and gene editing in crops

Future breeding programs have to meet diverse demands of different consumers, which require massive genetic resources and variations. However, the number of natural existing haplotypes is always limited due to domestication and breeding process (Tanksley and Mc Couch, 1997). Compared with traditional genetic cloning approaches, elucidating how one gene is transcribed and how it regulates downstream workhorses will generate more information on the casual mutation(s) of the gene and its downstream targets.