DNA methylation patterns of banana leaves in response to Fusarium oxysporum f. sp. cubense tropical race 4

Fusarium wilt of banana, which is caused by Fusarium oxysporum f. sp. cubense tropical race 4 （Foc TR4）, is a serious soil-borne fungal disease. Now, the epigenetic molecular pathogenic basis is elusive. In this study, with methylation-sensitive amplification polymorphism （MSAP） technique, DNA methylation was compared between the leaves inoculated with Foc TR4 and the mock-inoculated leaves at different pathogenic stages. With 25 pairs of primers, 1 144 and 1 255 fragments were amplified from the infected and mock-inoculated leaves, respectively. DNA methylation was both changed and the average methylated CCGG sequences were 34.81 and 29.26% for the infected and the mock-inoculated leaves. And DNA hypermethylation and hypomethylation were induced by pathogen infection during all pathogenic stages. Further, 69 polymorphic fragments were sequenced and 29 of them showed sequence similarity to genes with known functions. And RT-PCR results of four genes indicated that their expression patterns were consistent with their methylation patterns. Our results suggest that DNA methylation plays important roles in pathogenic response to Foc TR4 for banana.

Identification of QTLs for grain size and characterization of the beneficial alleles of grain size genes in large grain rice variety BL129

Grain size is one of the most important agronomic components of grain yield. Grain length, width and thickness are controlled by multiple quantitative trait loci （QTLs）. To understand genetic basis of large grain shape and explore the beneficial alleles for grain size improvement, we perform QTL analysis using an F2 population derived from a cross between the japonica variety Beilu 129 （BL129, wide and thick grain） and the elite indica variety Huazhan （HZ, narrow and long grain）. A total number of eight major QTLs are detected on three different chromosomes. QTLs for grain width （qGW）, grain thickness （qGT）, brown grain width （qBGW）, and brown grain thickness （qBGT） explained 77.67, 36.24, 89.63, and 39.41% of total phenotypic variation, respectively. The large grain rice variety BL129 possesses the beneficial alleles of GW2 and qSW5/ GW5, which have been known to control grain width and weight, indicating that the accumulation of the beneficial alleles causes large grain shape in BL129. Further results reveal that the rare gw2 allele from BL129 increases grain width, thickness and weight of the elite indica variety Huazhan, which is used as a parental line in hybrid rice breeding. Thus, our findings will help breeders to carry out molecular design breeding on rice grain size and shape.

Identification and characterization of MeERF genes and their targets in pathogen response by cassava(Manihot esculenta)

Cassava,Manihot esculenta Crantz (Me),is a major dietary source of calories for over 700 million people in tropical regions.The production of cassava is constantly threatened by cassava bacterial blight (CBB),caused by Xanthomonas axonopodis pv.manihotis (Xam).The gene resources for CBB-resistant breeding of cassava are limited.In model plant species,ethylene response factors play important roles in response to pathogen infection.In this study,cassava ethylene response factors (MeERFs) were identified and characterized as the first step in studying their potential for CBB-resistant breeding of cassava.In the cassava genome 155 MeERFs were identified,of which 23 were induced by Xam infection.The promoter regions of204 genes harbored GCC-box that had the potential to interact with MeERFs.Using 37 transcriptomes derived from Xam infection treatment,four gene co-expression modules for the MeERFs and GCC-box containing genes were constructed.Six MeERFs were associated with two GCC-box containing genes:transcription initiation factor TFIIE subunit beta (MeTFIIE),and histone-lysine N-methyltransferase ASHR1 (MeASHR1).Dual-luciferase reporter assays showed that MeERF10 and MeERF58 positively regulated Me TFIIE;MeERF137 negatively regulated Me TFIIE;MeERF10 and MeERF137 positively regulated Me ASHR1;and MeERF35 negatively regulated Me ASHR1.The four MeERFs may mediate pathogen response by regulating the expression of the two GCC-box containing genes.

The receptor-like cytoplasmic kinase OsRLCK118 regulates plant development and basal immunity in rice(Oryza sativa L.)

Receptor-like cytoplasmic kinases(RLCKs),which belong to a large subgroup of receptor-like kinases in plants,play crucial roles in plant development and immunity.However,their functions and regulatory mechanisms in plants remain unclear.Here,we report functional characterization of OsRLCK118 from the OsRLCK34 subgroup in rice(Oryza sativa L.).Expression of OsRLCK118 could be induced by infections with Xanthomonas oryzae pv.oryzae(Xoo)strains PXO68 and PXO99.Silencing of OsRLCK118 altered plant height,flag-leaf angle and second-topleaf angle.Silencing of OsRLCK118 also resulted in increasing susceptibility to Xoo and Magnaporthe oryzae(M.oryzae)in rice plants.OsRLCK118 knock-out plants were more sensitive to bacterial blight whereas OsRLCK118 overexpressor plants exhibited increased disease resistance.Expression levels of pathogenesis-related genes of OsPAL1,OsNH1,OsICS1,OsPR1a,OsPR5 and OsPR10 were reduced in the rlck118 mutant compared to wild-type rice(Dongjin)and knock-out of OsRLCK118 compromised the production of reactive oxygen species.These results suggest that OsRLCK118 may modulate basal resistance to Xoo and M.oryzae,possibly through regulation of ROS burst and hormone mediated defense signaling pathway.

Single-cell RNA landscape of the special fiber initiation process in Bombax ceiba

As a new source of natural fibers,the Bombax ceiba tree can provide thin,light,extremely soft and warm fiber material for the textile industry.Natural fibers are an ideal model system for studying cell growth and differentiation,but the molecular mechanisms that regulate fiber initiation are not fully understood.In B.ceiba,we found that fiber cells differentiate from the epidermis of the inner ovary wall.Each initiated cell then divides into a cluster of fiber cells that eventually develop into mature fibers,a process very different from the classical fiber initiation process of cotton.We used high-throughput single-cell RNA sequencing(scRNA-seq)to examine the special characteristics of fiber initiation in B.ceiba.A total of 15567 high-quality cells were identified from the inner wall of the B.ceiba ovary,and 347 potential marker genes for fiber initiation cell types were identified.Two major cell types,initiated fiber cells and epidermal cells,were identified and verified by RNA in situ hybridization.A developmental trajectory analysis was used to reconstruct the process of fiber cell differentiation in B.ceiba.Comparative analysis of scRNAseq data from B.ceiba and cotton(Gossypium hirsutum)confirmed that the additional cell division process in B.ceiba is a novel species-specific mechanismfor fiber cell development.Candidate genes and key regulators that may contribute to fiber cell differentiation and division in B.ceiba were identified.This work reveals gene expression signatures during B.ceiba fiber initiation at a single-cell resolution,providing a new strategy and viewpoint for investigation of natural fiber cell differentiation and development.

The Structure and Function of Major Plant Metabolite Modifications

Plants produce a myriad of structurally and functionally diverse metabolites that play many different roles in plant growth and development and in plant response to continually changing environmental conditions as well as abiotic and biotic stresses. This metabolic diversity is, to a large extent, due to chemical modification of the basic skeletons of metabolites. Here, we review the major known plant metabolite modifications and summarize the progress that has been achieved and the challenges we are facing in the field. We focus on discussing both technical and functional aspects in studying the influences that various modifications have on biosynthesis, degradation, transport, and storage of metabolites, as well as their bioactivity and toxicity. Finally, we discuss some emerging insights into the evolution of metabolic pathways and metabolite functionality.

Tomato SlRUP is a negative regulator of UV-B photomorphogenesis

Introduction Sunlight is an environmental factor regulating plant growth and development.Plants have evolved a battery of photoreceptors to sense and respond to different wavelengths of light(Jenkins,2017;Liu et al.,2020a).UV-B(280–315 nm)comprises the shortest wavelength of sunlight on the earth surface.In general,low fluence rate UV-B does not generate damage effects on plants,rather it induces plant photomorphogenic responses(Yin and Ulm,2017).High fluence rate UV-B may damage macromolecules,including nucleic acids,protein and membranes(Hideg et al.,2013).The UV-B photoreceptor UVR8 protein((UV RESISTANCE LOCUS 8)perceives the low dose UV-B and triggers UV-B specific signal transduction.

Allele-defined genome reveals biallelic differentiation during cassava evolution

Dear Editor,Generation of heterozygous genomes by hybridization between or within species can help maintain plant diversity and serve as a potential source of new species(Baek et al.,2018).Moreover,genomic heterozygosity is associated with genomic coadaptation,developmental stability,and heterosis.Accurate definition of alleles in haplotypes is necessary to precisely characterize allelic variation controlling agriculturally important traits(Shi et al.,2019).Currently,most released genomes have mosaic assembly of haplotypes due to random selection or collapse of alleles during genome assembly(Shi et al.,2019),which masked allelic variation and functional differentiation of divergent alleles in heterozygous species.

Arabidopsis PED_2 positively modulates plant drought stress resistance

Abscisic acid (ABA) is an important phytohormone that functions in seed germination, plant development, and multiple stress responses. Arabidopsis Peroxisome defective 2 (AtPED2) (also known as AtPEXOXIN14, AtPEX14), is involved in the intracellular transport of thiolase from the cytosol to glyoxysomes, and perosisomal matrix protein import in plants. In this study, we assigned a new role for AtPED2 in drought stress resistance. The transcript level of AtPED2 was downregulated by ABA and abiotic stress treatments. AtPED2 knockout mutants were insensitive to ABA-mediated seed germination, primary root elongation, and stomatal response, while AtPED2 over-expressing plants were sensitive to ABA in comparison to wide type (WT). AtPED2 also positively regulated drought stress resistance, as evidenced by the changes of water loss rate, electrolyte leakage, and survival rate. Notably, AtPED2 positively modulated expression of several stress-responsive genes (RAB18, RD22, RD29A, and RD29B), positively affected underlying antioxidant enzyme activities and negatively regulated reactive oxygen species (ROS) level under drought stress conditions. Moreover, multiple carbon metabolites including amino acids, organic acids, sugars, sugar alcohols, and aromatic amines were also positively regulated by AtPED2. Taken together, these results indicated a positive role for AtPED2 in drought resistance, through modulation of stress-responsive genes expression, ROS metabolism, and metabolic homeostasis, at least partially.

The lncRNA39896–miR166b–HDZs module affects tomato resistance to Phytophthora infestans

The yield and quality of tomatoes(Solanum lycopersicum)is seriously affected by Phytophthora infestans.The long non-coding RNA(lnc RNA)Sl-lnc RNA39896 is induced after P.infestans infection and was previously predicted to act as an endogenous target mimic(eTM)for the micro RNA Sl-miR166b,which function in stress responses.Here,we further examined the role of Sl-lncRNA39896 and Sl-mi R166b in tomato resistance to P.infestans.Sl-miR166b levels were higher in Sl-lnc RNA39896-knockout mutants than in wild-type plants,and the mutants displayed enhanced resistance to P.infestans.A six-point mutation in the region of Sl-lncRNA39896 that binds to Sl-miR166b disabled the interaction,suggesting that Sl-lnc RNA39896 acts as an e TM for Sl-mi R166b.Overexpressing Sl-miR166b yielded a similar phenotype to that produced by Sl-lncRNA39896-knockout,whereas silencing of Sl-mi R166b impaired resistance.We verified that Sl-miR166b cleaved transcripts of its target classⅢhomeodomain-leucine zipper genes Sl HDZ34and Sl HDZ45.Silencing of Sl HDZ34/45 decreased pathogen accumulation in plants infected with P.infestans.Additionally,jasmonic acid and ethylene contents were elevated following infection in the plants with enhanced resistance.Sl-lnc RNA39896is the first known lnc RNA to negatively regulate resistance to P.infestans in tomato.We propose a novel mechanism in which the lnc RNA39896–mi R166b–HDZ module modulates resistance to P.infestans.

Arabidopsis Roots and Light:Complex Interactions

Unlike actively moving animals,plants actively change their body architecture via growth of their diverse organs in response to environmental clues and stresses.For example,changes in Arabidopsis thaliana root apex zonation under phosphate(Pi)deficiency is considered to be such an active response,including inhibition of primary root elongation and increasing densities of lateral roots and root hairs(Abel,2017).However,a recent study by Zheng et al.(2019)modifies this hypothesis,which is based on the transparent Petri dish-based culture method of young Arabidopsis seedlings causing illumination of roots.In this issue,Zheng et al.(2019)report that Pi deficiency not only increases malate secretion from Arabidopsis root apices via the ALMT1 transporter but also that blue light(BL)triggers a malate-mediated photo-Fenton reaction in the rhizosphere,increasing the OH radical levels.