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.

Expression changes of mi RNA-regulated genes associated with the formation of the leafy head in cabbage

The vegetative development of cabbage(Brassica oleracea var.capitata)passes through seedling,rosette,folding and heading stages.Leaves that form the rosette are large and mostly flat.In the following developmental stages,the plants produce leaves that curve inward to produce the leafy head.Many microRNAs and their target genes have been described participating in leaf development and leaf curvature.The aim of this study is to investigate the role of miRNA-regulated genes in the transition from the rosette to the heading stage.We compared the mi RNA and gene abundances between emerging rosette and heading leaves.To remove transcripts(miRNAs and genes)whose regulation was most likely associated with plant age rather than the change from rosette to heading stage,we utilized a non-heading collard green(B.oleracea var.acephala)morphotype as control.This resulted in 33 DEMs and 1998 DEGs with likely roles in the transition from rosette to heading stage in cabbage.Among these 1998 DEGs,we found enriched GO terms related to DNA-binding transcription factor activity,transcription regulator activity,iron ion binding,and photosynthesis.We predicted the target genes of these 33 DEMs and focused on the subset that was differentially expressed(1998DEGs)between rosette and heading stage leaves to construct mi RNA-target gene interaction networks.Our main finding is a role for miR396b-5p targeting two Arabidopsis thaliana orthologues of GROWTH REGULATING FACTORs 3(GRF3)and 4(GRF4)in pointed cabbage head formation.

番茄植株与白粉病菌互作过程中叶片胞间蛋白变化的初步分析

利用SDS -PAGE方法分析番茄抗白粉病过程中番茄叶片胞间蛋白 (IntercellularProtein)的变化趋势 ,比较了含有Ol 1的抗病品种和感病品种间的差异 ,从分泌蛋白的角度研究了番茄抗白粉病的机理。

Genome-wide transcriptome analysis reveals molecular pathways involved in leafy head formation of Chinese cabbage(Brassica rapa)

Chinese cabbage plants go through seedling and rosette stages before forming their leafy head.Chinese cabbage plants resemble pak-choi plants at their seedling stage,but in their rosette stage the leaves of Chinese cabbage differentiate,as they increase in size with shorter petioles.In order to understand the molecular pathways that play a role in leafy head formation,transcript abundance of young emerging leaves was profiled during development of two Chinese cabbage genotypes and a single pak-choi genotype.The two Chinese cabbages differed in many aspects,among others earliness,leaf size and shape,leaf numbers,and leafy head shape.Genome-wide transcriptome analysis clearly separated the seedling stages of all three genotypes together with the later stages from pak-choi,from the later developmental stages of both Chinese cabbages(rosette,folding,and heading).Weighted correlation network analysis and hierarchical clustering using Euclidean distances resulted in gene clusters with transcript abundance patterns distinguishing the two Chinese cabbages from pak-choi.Three clusters included genes with transcript abundance affected by both genotype and developmental stage,whereas two clusters showed only genotype effects.This included a genotype by developmental stage cluster highly enriched with the MapMan category photosynthesis,with high expression during rosette and folding in Chinese cabbages and low expression in the heading inner leaves that are not exposed to light.The other clusters contained many genes in the MapMan categories Cell,showing again differences between pak-choi and both Chinese cabbages.We discuss how this relates to the differences in leaf blade growth between Chinese cabbage and pak-choi,especially at the rosette stage.Overall,comparison of the transcriptome between leaves of two very different Chinese cabbages with pak-choi during plant development allowed the identification of specific gene categories associated with leafy head formation.

What makes turnips:anatomy,physiology and transcriptome during early stages of its hypocotyl-tuber development

Brassica species are characterized by their tremendous intraspecific diversity,exemplified by leafy vegetables,oilseeds,and crops with enlarged inflorescences or above ground storage organs.In contrast to potato tubers that are edible storage organs storing energy as starch and are the vegetative propagation modules,the storage organs of turnips,grown from true seed,are swollen hypocotyls with varying degrees of root and stem that mainly store glucose and fructose.To highlight their anatomical origin,we use the term“hypocotyl-tuber”for these turnip vegetative storage organs.We combined cytological,physiological,genetic and transcriptomic approaches,aiming to identify the initial stages,molecular pathways and regulatory genes for hypocotyl-tuber induction in turnips(B.rapa subsp.rapa).We first studied the development of the hypocotyl zone of turnip and Pak choi and found that 16 days after sowing(DAS)morphological changes occurred in the xylem which indicated the early tuberization stage.Tissue culture experiments showed a clear effect of auxin on hypocotyl-tuber growth.Differentially expressed genes between 1 and 6 weeks after sowing in turnip hypocotyls,located in genomic regions involved in tuber initiation and/or tuber growth defined by QTL and selective sweeps for tuber formation,were identified as candidate genes that were studied in more detail for their role in hypocotyl-tuber formation.This included a Bra-FLOR1 paralogue with increased expression 16 DAS,when the hypocotyl starts swelling,suggesting dual roles for duplicated flowering time genes in flowering and hypocotyltuber induction.Bra-CYP735A2 was identified for its possible role in tuber growth via trans-zeatin.Weigthed Coexpression Network Analysis(WGCNA)identified 59 modules of co-expressed genes.Bra-FLOR1 and Bra-CYP735A2 were grouped in a module that included several genes involved in carbohydrate transport and metabolism,cell-wall growth,auxin regulation and secondary metabolism that serve as starting points to illuminate the transcriptional regulation of hypocotyl-tuber formation and development.

Genetic analysis of the “head top shape” quality trait of Chinese cabbage and its association with rosette leaf variation

The agricultural and consumer quality of Chinese cabbage is determined by its shape.The shape is defined by the folding of the heading leaves,which defines the head top shape(HTS).The overlapping HTS,in which the heading leaves curve inward and overlap at the top,is the shape preferred by consumers.To understand the genetic regulation of HTS,we generated a large segregating F 2 population from a cross between pak choi and Chinese cabbage,with phenotypes ranging from nonheading to heading with either outward curving or inward curving overlapping heading leaves.HTS was correlated with plant height,outer/rosette leaf length,and petiole length.A high-density genetic map was constructed.Quantitative trait locus(QTL)analysis resulted in the identification of 22 QTLs for leafy head-related traits,which included five HTS QTLs.Bulked segregant analysis(BSA)was used to confirm HTS QTLs and identify candidate genes based on informative single-nucleotide polymorphisms.Interestingly,the HTS QTLs colocalized with QTLs for plant height,outer/rosette leaf,and petiole length,consistent with the observed phenotypic correlations.Combined QTL analysis and BSA laid a foundation for molecular marker-assisted breeding of Chinese cabbage HTS and directions for further research on the genetic regulation of this trait.