Cellulose Synthase-Like D1 is integral to normal cell division, expansion, and leaf development in maize

Genome-wide analysis of the Amorphophallus konjac AkCSLA gene family and its functional characterization in drought tolerance of transgenic arabidopsis

BACKGROUND

Amorphophallus konjac (A. konjac), a perennial tuberous plant, is widely cultivated for its high konjac glucomannan (KGM) content, a heteropolysaccharide with diverse applications. The cellulose synthase-like (CSL) gene family is known to be a group of processive glycan synthases involved in the synthesis of cell-wall polysaccharides and plays an important role in the biological process of KGM. However, in A. konjac the classification, structure, and function of the AkCSLA superfamily have been studied very little.

RESULTS

Bioinformatics methods were used to identify the 11 AkCSLA genes from the whole genome of Amorphophallus konjac and to systematically analyze their characteristics, phylogenetic evolution, promoter cis-elements, expression patterns, and subcellular locations. Phylogenetic analysis revealed that the AkCSLA gene family can be divided into three subfamilies (Groups I- III), which have close relationships with Arabidopsis. The promoters of most AkCSLA family members contain MBS elements and ABA response elements. Analysis of expression patterns in different tissues showed that most AkCSLAs are highly expressed in the corms. Notably, PEG6000 induced down-regulation of the expression of most AkCSLAs, including AkCSLA11. Subcellular localization results showed that AkCSLA11 was localized to the plasma membrane, Golgi apparatus and endoplasmic reticulum. Transgenic Arabidopsis experiments demonstrated that overexpression of AkCSLA11 reduced the plant's drought tolerance. This overexpression also inhibited the expression of drought response genes and altered the sugar components of the cell wall. These findings provide new insights into the response mechanisms of A. konjac to drought stress and may offer potential genetic resources for improving crop drought resistance.

CONCLUSION

In conclusion, the study reveals that the AkCSLA11 gene from A. konjac negatively impacts drought tolerance when overexpressed in Arabidopsis. This discovery provides valuable insights into the mechanisms of plant response to drought stress and may guide future research on crop improvement for enhanced resilience.

Expanding the BonnMu sequence-indexed repository of transposon induced maize (Zea mays L.) mutations in dent and flint germplasm

The BonnMu resource is a transposon tagged mutant collection designed for functional genomics studies in maize. To expand this resource, we crossed an active Mutator (Mu) stock with dent (B73, Co125) and flint (DK105, EP1, and F7) germplasm, resulting in the generation of 8064 mutagenized BonnMu F2-families. Sequencing of these Mu-tagged families revealed 425 924 presumptive heritable Mu insertions affecting 36 612 (83%) of the 44 303 high-confidence gene models of maize (B73v5). On average, we observed 12 Mu insertions per gene (425 924 total insertions/36 612 affected genes) and 53 insertions per BonnMu F2-family (425 924 total insertions/8064 families). Mu insertions and photos of seedling phenotypes from segregating BonnMu F2-families can be accessed through the Maize Genetics and Genomics Database (MaizeGDB). Downstream examination via the automated Mutant-seq Workflow Utility (MuWU) identified 94% of the presumptive germinal insertion sites in genic regions and only a small fraction of 6% inserting in non-coding intergenic sequences of the genome. Consistently, Mu insertions aligned with gene-dense chromosomal arms. In total, 42% of all BonnMu insertions were located in the 5' untranslated region of genes, corresponding to accessible chromatin. Furthermore, for 38% of the insertions (163 843 of 425 924 total insertions) Mu1, Mu8 and MuDR were confirmed to be the causal Mu elements. Our publicly accessible European BonnMu resource has archived insertions covering two major germplasm groups, thus facilitating both forward and reverse genetics studies.

Decrypting Molecular Mechanisms Involved in Counteracting Copper and Nickel Toxicity in Jack Pine (Pinus banksiana) Based on Transcriptomic Analysis

The remediation of copper and nickel-afflicted sites is challenged by the different physiological effects imposed by each metal on a given plant system. Pinus banksiana is resilient against copper and nickel, providing an opportunity to build a valuable resource to investigate the responding gene expression toward each metal. The objectives of this study were to (1) extend the analysis of the Pinus banksiana transcriptome exposed to nickel and copper, (2) assess the differential gene expression in nickel-resistant compared to copper-resistant genotypes, and (3) identify mechanisms specific to each metal. The Illumina platform was used to sequence RNA that was extracted from seedlings treated with each of the metals. There were 449 differentially expressed genes (DEGs) between copper-resistant genotypes (RGs) and nickel-resistant genotypes (RGs) at a high stringency cut-off, indicating a distinct pattern of gene expression toward each metal. For biological processes, 19.8% of DEGs were associated with the DNA metabolic process, followed by the response to stress (13.15%) and the response to chemicals (8.59%). For metabolic function, 27.9% of DEGs were associated with nuclease activity, followed by nucleotide binding (27.64%) and kinase activity (10.16%). Overall, 21.49% of DEGs were localized to the plasma membrane, followed by the cytosol (16.26%) and chloroplast (12.43%). Annotation of the top upregulated genes in copper RG compared to nickel RG identified genes and mechanisms that were specific to copper and not to nickel. NtPDR, AtHIPP10, and YSL1 were identified as genes associated with copper resistance. Various genes related to cell wall metabolism were identified, and they included genes encoding for HCT, CslE6, MPG, and polygalacturonase. Annotation of the top downregulated genes in copper RG compared to nickel RG revealed genes and mechanisms that were specific to nickel and not copper. Various regulatory and signaling-related genes associated with the stress response were identified. They included UGT, TIFY, ACC, dirigent protein, peroxidase, and glyoxyalase I. Additional research is needed to determine the specific functions of signaling and stress response mechanisms in nickel-resistant plants.

SMALL PLANT AND ORGAN 1 (SPO1) Encoding a Cellulose Synthase-like Protein D4 (OsCSLD4) Is an Important Regulator for Plant Architecture and Organ Size in Rice

Plant architecture and organ size are considered as important traits in crop breeding and germplasm improvement. Although several factors affecting plant architecture and organ size have been identified in rice, the genetic and regulatory mechanisms remain to be elucidated. Here, we identified and characterized the small plant and organ 1 (spo1) mutant in rice (Oryza sativa), which exhibits narrow and rolled leaf, reductions in plant height, root length, and grain width, and other morphological defects. Map-based cloning revealed that SPO1 is allelic with OsCSLD4, a gene encoding the cellulose synthase-like protein D4, and is highly expressed in the roots at the seedling and tillering stages. Microscopic observation revealed the spo1 mutant had reduced number and width in leaf veins, smaller size of leaf bulliform cells, reduced cell length and cell area in the culm, and decreased width of epidermal cells in the outer glume of the grain. These results indicate the role of SPO1 in modulating cell division and cell expansion, which modulates plant architecture and organ size. It is showed that the contents of endogenous hormones including auxin, abscisic acid, gibberellin, and zeatin tested in the spo1 mutant were significantly altered, compared to the wild type. Furthermore, the transcriptome analysis revealed that the differentially expressed genes (DEGs) are significantly enriched in the pathways associated with plant hormone signal transduction, cell cycle progression, and cell wall formation. These results indicated that the loss of SPO1/OsCSLD4 function disrupted cell wall cellulose synthase and hormones homeostasis and signaling, thus leading to smaller plant and organ size in spo1. Taken together, we suggest the functional role of SPO1/OsCSLD4 in the control of rice plant and organ size by modulating cell division and expansion, likely through the effects of multiple hormonal pathways on cell wall formation.

Cellulose synthase-like D movement in the plasma membrane requires enzymatic activity

Cellulose Synthase-Like D (CSLD) proteins, important for tip growth and cell division, are known to generate β-1,4-glucan. However, whether they are propelled in the membrane as the glucan chains they produce assemble into microfibrils is unknown. To address this, we endogenously tagged all eight CSLDs in Physcomitrium patens and discovered that they all localize to the apex of tip-growing cells and to the cell plate during cytokinesis. Actin is required to target CSLD to cell tips concomitant with cell expansion, but not to cell plates, which depend on actin and CSLD for structural support. Like Cellulose Synthase (CESA), CSLD requires catalytic activity to move in the plasma membrane. We discovered that CSLD moves significantly faster, with shorter duration and less linear trajectories than CESA. In contrast to CESA, CSLD movement was insensitive to the cellulose synthesis inhibitor isoxaben, suggesting that CSLD and CESA function within different complexes possibly producing structurally distinct cellulose microfibrils.

Targeted expression of bgl23-D, a dominant-negative allele of ATCSLD5, affects cytokinesis of guard mother cells and exine formation of pollen in Arabidopsis thaliana

Targeted expression of bgl23-D, a dominant-negative allele of ATCSLD5, is a useful genetic approach for functional analysis of ATCSLDs in specific cells and tissues in plants. Stomata are key cellular structures for gas and water exchange in plants and their development is influenced by several genes. We found the A. thaliana bagel23-D (bgl23-D) mutant showing abnormal bagel-shaped single guard cells. The bgl23-D was a novel dominant mutation in the A. thaliana cellulose synthase-like D5 (ATCSLD5) gene that was reported to function in the division of guard mother cells. The dominant character of bgl23-D was used to inhibit ATCSLD5 function in specific cells and tissues. Transgenic A. thaliana expressing bgl23-D cDNA with the promoter of stomata lineage genes, SDD1, MUTE, and FAMA, showed bagel-shaped stomata as observed in the bgl23-D mutant. Especially, the FAMA promoter exhibited a higher frequency of bagel-shaped stomata with severe cytokinesis defects. Expression of bgl23-D cDNA in the tapetum with SP11 promoter or in the anther with ATSP146 promoter induced defects in exine pattern and pollen shape, novel phenotypes that were not shown in the bgl23-D mutant. These results indicated that bgl23-D inhibited unknown ATCSLD(s) that exert the function of exine formation in the tapetum. Furthermore, transgenic A. thaliana expressing bgl23-D cDNA with SDD1, MUTE, and FAMA promoters showed enhanced rosette diameter and increased leaf growth. Taken together, these findings suggest that the bgl23-D mutation could be a helpful genetic tool for functional analysis of ATCSLDs and manipulating plant growth.

Combined linkage mapping and association analysis uncovers candidate genes for 25 leaf-related traits across three environments in maize

Combined linkage and association analysis revealed five co-localized genetic loci across multiple environments. The key gene Zm00001d026491 was further verified to influence leaf length by candidate gene association analysis. Leaf morphology and number determine the canopy structure and thus affect crop yield. Herein, the genetic basis and key genes for 25 leaf-related traits, including leaf lengths (LL), leaf widths (LW), and leaf areas (LA) of eight continuous leaves under the tassel, and the number of leaves above the primary ear (LAE), were dissected by using an association panel and a biparental population. Using an intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, 290 quantitative trait loci (QTL) controlling these traits were detected across different locations, among which 115 QTL were individually repeatedly identified in at least two environments. Using the association panel, 165 unique significant single-nucleotide polymorphisms (SNPs) were associated with target traits (P < 2.15E-06), of which 35 were separately detected across multiple environments. In total, 42 pleiotropic QTL/SNPs (pQTL/SNPs) were responsible for at least two of the LL, LW, LA, and LAE traits across multiple environments. Combining the QTL mapping and association study, five unique SNPs were located within the confidence intervals of seven QTL, and 77 genes were identified based on the linkage disequilibrium regions of co-localized SNP loci. Gene-based association studies verified that the intragenic variants in the candidate gene Zm00001d026491 influenced LL of the third leaf counted from the top node. These findings will provide vital information to understanding the genetic basis of leaf-related traits and help to cultivate maize varieties with ideal plant architecture.

Molecular mapping of quantitative trait loci for 3 husk traits using genotyping by sequencing in maize (Zea mays L.)

The maize (Zea mays L.) husk consists of multiple leaf layers and plays an important role in grain growth and development. Despite significant achievements in physiological and morphological research, few studies have focused on the detection of genetic loci underlying husk-related traits due to the lack of efficient tools. In this study, we constructed an ultra-high-density linkage map using genotyping by sequencing based on a recombinant inbred line population to estimate the genetic variance and heritability of 3 husk traits, i.e. husk length, husk width, and husk layer number in 3 field environments and the combined environment. The 3 husk traits showed broad phenotypic variation and high heritability; the broad-sense heritability (H²) was 0.92, 0.84, and 0.86. Twenty quantitative trait loci were consistently detected more than 1 environment, including 9 for husk length, 6 for husk width, and 5 for husk layer number. These loci were considered as stable quantitative trait loci. Based on the quantitative trait loci mapping in the recombinant inbred line population, qHL6 and qHN4 were detected across all environments and inferred to be reliable and major-effect quantitative trait loci for husk length and husk layer number, respectively. In addition, several predicted candidate genes were identified in the region of qHL6 and qHN4, of which 17 candidate genes potentially play a role in biological processes related to development process and energy metabolism. These results will be as a useful resource for performing functional studies aimed at understanding the molecular pathways involved in husk growth and development.

Identification and bioinformatic analysis of the CaCesA/Csls family members and the expression of the CaCslD1 in the flower buds of CMS/Rf system in pepper

The cellulose synthase gene superfamily contains cellulose synthase (CesA) and cellulose synthase-like (Csl) gene families, which synthesize cellulose and hemicellulose in plant cell walls and play a crucial role in plant growth and development. However, the CesA/Csl gene family has not been reported in pepper. Therefore, the genome-wide research of the CaCesA/CaCsl gene family was conducted in pepper. In this study, a total of 39 CaCesA/CaCsls genes (10 CesAs genes and 29 Csls genes) were identified in pepper and unevenly distributed on 11 chromosomes. These CaCesA/Csls were divided into seven subfamilies (CesAs, CslAs, CslBs, CslCs, CslDs, CslEs, CslGs), and most of CaCesA/Csls genes are closely related to AtCesA/Csls genes. The cis-acting elements in the promoters of CaCesA/Csls genes are mainly related to hormone response and stress response. There are ten collinear gene pairs between the CesA/Csls gene family of pepper and Arabidopsis, and four fragment duplication gene pairs of the CaCesA/Csls genes were discovered. RNA-seq analysis shows that the majority of CaCesA/Csls are expressed in a variety of plant tissues, indicating that most CaCesA/Csls gene expression patterns are not organ-specific, and CaCslD1/D4 have the highest expression in anthers, followed by petal, ovary, and F9. RNA-seq analysis shows that most CaCesA/Csls are responsive to five hormones (IAA, GA₃, ABA, SA, and MeJA). The tissue-specific expression analysis of the CaCslD1 gene shows that the CaCslD1 gene is expressed specifically in flowers. In the flower buds IV of cytoplasmic male sterility (CMS) and its restoration of fertility (Rf) system, CaCslD1 reach the highest expression respectively. However, the relative expression level of CaCslD1 in the fertile accessions is extremely significantly higher than in the sterile accessions. This study shows an overall understanding of the CaCesA/Csls gene family and provides a new insight for understanding the function of CaCslD1 in pollen development and exploring the fertility restoration of CMS in pepper.

Expression of Exogenous GFP-CesA6 in Tobacco Enhances Cell Wall Biosynthesis and Biomass Production

Simple Summary

Cellulose is synthesized at the plasma membrane by an enzymatic complex constituted by different cellulose synthase (CesA) proteins. The overexpression of CesA genes has been assessed for increasing cellulose biosynthesis and plant biomass. In this study, we analyzed transgenic tobacco plants (F₃1 line), stably expressing the Arabidopsis CesA6 fused to GFP, for possible variations in the cellulose biosynthesis. We found that F₃1 plants were bigger than the wild-type (wt), showing significant increases of stem height, root length, and leaf area. They bloomed about 3 weeks earlier and yielded more flowers and seeds than wt. In the F₃1 leaves, the expression of the exogenous GFP-CesA6 prompted the overexpression of all CesAs involved in the synthesis of primary cell wall cellulose and of other proteins responsible for plant cell wall building and remodeling. Instead, secondary cell wall CesAs were not affected. In the F₃1 stem, showing a 3.3-fold increase of the secondary xylem thickness, both primary and secondary CesAs expression was differentially modulated. Significantly, the amounts of cellulose and matrix polysaccharides increased in the transformed seedlings. The results evidence the potentiality to overexpress primary CesAs in tobacco for biomass production increase.

Abstract

Improved cellulose biosynthesis and plant biomass represent important economic targets for several biotechnological applications including bioenergy and biofuel production. The attempts to increase the biosynthesis of cellulose by overexpressing CesAs proteins, components of the cellulose synthase complex, has not always produced consistent results. Analyses of morphological and molecular data and of the chemical composition of cell walls showed that tobacco plants (F₃1 line), stably expressing the Arabidopsis CesA6 fused to GFP, exhibits a “giant” phenotype with no apparent other morphological aberrations. In the F₃1 line, all evaluated growth parameters, such as stem and root length, leaf size, and lignified secondary xylem, were significantly higher than in wt. Furthermore, F₃1 line exhibited increased flower and seed number, and an advance of about 20 days in the anthesis. In the leaves of F₃1 seedlings, the expression of primary CesAs (NtCesA1, NtCesA3, and NtCesA6) was enhanced, as well as of proteins involved in the biosynthesis of non-cellulosic polysaccharides (xyloglucans and galacturonans, NtXyl4, NtGal10), cell wall remodeling (NtExp11 and XTHs), and cell expansion (NtPIP1.1 and NtPIP2.7). While in leaves the expression level of all secondary cell wall CesAs (NtCesA4, NtCesA7, and NtCesA8) did not change significantly, both primary and secondary CesAs were differentially expressed in the stem. The amount of cellulose and matrix polysaccharides significantly increased in the F₃1 seedlings with no differences in pectin and hemicellulose glycosyl composition. Our results highlight the potentiality to overexpress primary CesAs in tobacco plants to enhance cellulose synthesis and biomass production.

Genomic Architecture and Evolution of the Cellulose synthase Gene Superfamily as Revealed by Phylogenomic Analysis

The Cellulose synthase superfamily synthesizes cellulose and different hemicellulosic polysaccharides in plant cell walls. While much has been discovered about the evolution and function of these genes, their genomic architecture and relationship with gene (sub-)functionalization and evolution remains unclear. By using 242 genomes covering plant evolution from green algae to eudicots, we performed a large-scale analysis of synteny, phylogenetic, and functional data of the CesA superfamily. Results revealed considerable gene copy number variation across species and gene families, and also two patterns - singletons vs. tandem arrays - in chromosomic gene arrangement. Synteny analysis revealed exceptional conservation of gene architecture across species, but also lineage-specific patterns across gene (sub-)families. Synteny patterns correlated with gene sub-functionalization into primary and secondary CesAs and distinct CslD functional isoforms. Furthermore, a genomic context shift of a group of cotton secondary CesAs was associated with peculiar properties of cotton fiber synthesis. Finally, phylogenetics suggested that primary CesA sequences appeared before the secondary CesAs, while phylogenomic analyses unveiled the genomic trace of the CslD duplication that initiated the CslF family. Our results describe in detail the genomic architecture of the CesA superfamily in plants, highlighting its crucial relevance for gene diversification and sub-functionalization, and for understanding their evolution.

Cell biology of primary cell wall synthesis in plants

Building a complex structure such as the cell wall, with many individual parts that need to be assembled correctly from distinct sources within the cell, is a well-orchestrated process. Additional complexity is required to mediate dynamic responses to environmental and developmental cues. Enzymes, sugars, and other cell wall components are constantly and actively transported to and from the plasma membrane during diffuse growth. Cell wall components are transported in vesicles on cytoskeletal tracks composed of microtubules and actin filaments. Many of these components, and additional proteins, vesicles, and lipids are trafficked to and from the cell plate during cytokinesis. In this review, we first discuss how the cytoskeleton is initially organized to add new cell wall material or to build a new cell wall, focusing on similarities during these processes. Next, we discuss how polysaccharides and enzymes that build the cell wall are trafficked to the correct location by motor proteins and through other interactions with the cytoskeleton. Finally, we discuss some of the special features of newly formed cell walls generated during cytokinesis.

Morphological Characterization and Transcriptome Analysis of New Dwarf and Narrow-Leaf (dnl2) Mutant in Maize

Lodging is the primary factor limiting high yield under a high plant density. However, an optimal plant height and leaf shape can effectively decrease the lodging risk. Here we studied an ethyl methanesulfonate (EMS)-induced dwarf and a narrow-leaf mutant, dnl2. Gene mapping indicated that the mutant was controlled by a gene located on chromosome nine. Phenotypic and cytological observations revealed that dnl2 showed inhibited cell growth, altered vascular bundle patterning, and disrupted secondary cell wall structure when compared with the wild-type, which could be the direct cause of the dwarf and narrow-leaf phenotype. The phytohormone levels, especially auxin and gibberellin, were significantly decreased in dnl2 compared to the wild-type plants. Transcriptome profiling of the internodes of the dnl2 mutant and wild-type revealed a large number of differentially expressed genes enriched in the cell wall biosynthesis, remodeling, and hormone biosynthesis and signaling pathways. Therefore, we suggest that crosstalk between hormones (the altered vascular bundle and secondary cell wall structure) may contribute to the dwarf and narrow-leaf phenotype by influencing cell growth. These results provide a foundation for DNL2 gene cloning and further elucidation of the molecular mechanism of the regulation of plant height and leaf shape in maize.

Identification and Fine Mapping of the Recessive Gene BK-5, Which Affects Cell Wall Biosynthesis and Plant Brittleness in Maize

The cellulose of the plant cell wall indirectly affects the cell shape and straw stiffness of the plant. Here, the novel brittleness mutant brittle stalk-5 (bk-5) of the maize inbred line RP125 was characterized. We found that the mutant displayed brittleness of the stalk and even the whole plant, and that the brittleness phenotype existed during the whole growth period from germination to senescence. The compressive strength was reduced, the cell wall was thinner, and the cellulose content was decreased compared to that of the wild type. Genetic analysis and map-based cloning indicated that bk-5 was controlled by a single recessive nuclear gene and that it was located in a 90.2-Kb region on chromosome 3 that covers three open reading frames (ORFs). Sequence analysis revealed a single non-synonymous missense mutation, T-to-A, in the last exon of Zm00001d043477 (B73: version 4, named BK-5) that caused the 951th amino acid to go from leucine to histidine. BK-5 encodes a cellulose synthase catalytic subunit (CesA), which is involved with cellulose synthesis. We found that BK-5 was constitutively expressed in all tissues of the germinating stage and silking stage, and highly expressed in the leaf, auricula, and root of the silking stage and the 2-cm root and bud of the germinating stage. We found that BK-5 mainly localized to the Golgi apparatus, suggesting that the protein might move to the plasma membrane with the aid of Golgi in maize. According to RNA-seq data, bk-5 had more downregulated genes than upregulated genes, and many of the downregulated genes were enzymes and transcription factors related to cellulose, hemicellulose, and lignin biosynthesis of the secondary cell wall. The other differentially expressed genes were related to metabolic and cellular processes, and were significantly enriched in hormone signal transduction, starch and sucrose metabolism, and the plant-pathogen interaction pathway. Taken together, we propose that the mutation of gene BK-5 causes the brittle stalk phenotype and provides important insights into the regulatory mechanism of cellulose biosynthesis and cell wall development in maize.

A kelch-repeat superfamily gene, ZmNL4, controls leaf width in maize (Zea mays L.)

Leaf width (LW) is an important component of plant architecture that extensively affects both light capture during photosynthesis and grain yield, particularly under dense planting conditions. However, the genetic and molecular mechanisms regulating LW remain largely elusive in maize (Zea mays L.). In this study, qLW4a, a major quantitative trait locus controlling LW, was identified in a population constructed with maize inbred lines PH6WC, with wide leaves, and Lin387, with narrow leaves. Map-based cloning revealed that ZmNL4, a kelch-repeat superfamily gene, emerged to be the candidate for qLW4a, and a single-base deletion in the conserved SMC_prok_B domain of ZmNL4 in Lin387 caused a frame shift, leading to premature termination. Consistently, the knockout of ZmNL4 by CRISPR/Cas9 editing significantly reduced the LW, which was attributed to a reduction in the cell number instead of cell size, indicating a role of ZmNL4 in regulating cell division. Transcriptomic comparison of ZmNL4 knockout lines with the wild type B73-329 revealed that ZmNL4 might participate in cell wall biogenesis, asymmetric cell division, metabolic processes, transmembrane transport and response to external stimulus, etc. These results provide insights into the genetic and molecular mechanisms of ZmNL4 in controlling LW and could potentially contribute to optimizing plant architecture for maize breeding.

Developmental genetics of maize vegetative shoot architecture

More than 1.1 billion tonnes of maize grain were harvested across 197 million hectares in 2019 (FAOSTAT 2020). The vast global productivity of maize is largely driven by denser planting practices, higher yield potential per area of land, and increased yield potential per plant. Shoot architecture, the three-dimensional structural arrangement of the above-ground plant body, is critical to maize grain yield and biomass. Structure of the shoot is integral to all aspects of modern agronomic practices. Here, the developmental genetics of the maize vegetative shoot is reviewed. Plant architecture is ultimately determined by meristem activity, developmental patterning, and growth. The following topics are discussed: shoot apical meristem, leaf architecture, axillary meristem and shoot branching, and intercalary meristem and stem activity. Where possible, classical and current studies in maize developmental genetics, as well as recent advances leveraged by "-omics" analyses, are highlighted within these sections.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01208-1.

Genome-Wide Identification of Banana Csl Gene Family and Their Different Responses to Low Temperature between Chilling-Sensitive and Tolerant Cultivars

The cell wall plays an important role in responses to various stresses. The cellulose synthase-like gene (Csl) family has been reported to be involved in the biosynthesis of the hemicellulose backbone. However, little information is available on their involvement in plant tolerance to low-temperature (LT) stress. In this study, a total of 42 Csls were identified in Musa acuminata and clustered into six subfamilies (CslA, CslC, CslD, CslE, CslG, and CslH) according to phylogenetic relationships. The genomic features of MaCsl genes were characterized to identify gene structures, conserved motifs and the distribution among chromosomes. A phylogenetic tree was constructed to show the diversity in these genes. Different changes in hemicellulose content between chilling-tolerant and chilling-sensitive banana cultivars under LT were observed, suggesting that certain types of hemicellulose are involved in LT stress tolerance in banana. Thus, the expression patterns of MaCsl genes in both cultivars after LT treatment were investigated by RNA sequencing (RNA-Seq) technique followed by quantitative real-time PCR (qPCR) validation. The results indicated that MaCslA4/12, MaCslD4 and MaCslE2 are promising candidates determining the chilling tolerance of banana. Our results provide the first genome-wide characterization of the MaCsls in banana, and open the door for further functional studies.

High-density QTL mapping of leaf-related traits and chlorophyll content in three soybean RIL populations

BACKGROUND

Leaf size and shape, which affect light capture, and chlorophyll content are important factors affecting photosynthetic efficiency. Genetic variation of these components significantly affects yield potential and seed quality. Identification of the genetic basis for these traits and the relationship between them is of great practical significance for achieving ideal plant architecture and high photosynthetic efficiency for improved yield.

RESULTS

Here, we undertook a large-scale linkage mapping study using three mapping populations to determine the genetic interplay between soybean leaf-related traits and chlorophyll content across two environments. Correlation analysis revealed a significant negative correlation between leaf size and shape, while both traits were positively correlated with chlorophyll content. This phenotypic relationship was verified across the three mapping populations as determined by principal component analysis, suggesting that these traits are under the control of complex and interrelated genetic components. The QTLs for leaf-related traits and chlorophyll are partly shared, which further supports the close genetic relationship between the two traits. The largest-effect major loci, q20, was stably identified across all population and environments and harbored the narrow leaflet gene Gm-JAG1 (Ln/ln), which is a key regulator of leaflet shape in soybean.

CONCLUSION

Our results uncover several major QTLs (q4-1, q4-2, q11, q13, q18 and q20) and its candidate genes specific or common to leaf-related traits and chlorophyll, and also show a complex epistatic interaction between the two traits. The SNP markers closely linked to these valuable QTLs could be used for molecular design breeding with improved plant architecture, photosynthetic capacity and even yield.

Cotton CSLD3 restores cell elongation and cell wall integrity mainly by enhancing primary cellulose production in the Arabidopsis cesa6 mutant

Overexpression of cotton cellulose synthase like D3 (GhCSLD3) gene partially rescued growth defect of atcesa6 mutant with restored cell elongation and cell wall integrity mainly by enhancing primary cellulose production. Among cellulose synthase like (CSL) family proteins, CSLDs share the highest sequence similarity to cellulose synthase (CESA) proteins. Although CSLD proteins have been implicated to participate in the synthesis of carbohydrate-based polymers (cellulose, pectins and hemicelluloses), and therefore plant cell wall formation, the exact biochemical function of CSLD proteins remains controversial and the function of the remaining CSLD genes in other species have not been determined. In this study, we attempted to illustrate the function of CSLD proteins by overexpressing Arabidopsis AtCSLD2, -3, -5 and cotton GhCSLD3 genes in the atcesa6 mutant, which has a background that is defective for primary cell wall cellulose synthesis in Arabidopsis. We found that GhCSLD3 overexpression partially rescued the growth defect of the atcesa6 mutant during early vegetative growth. Despite the atceas6 mutant having significantly reduced cellulose contents, the defected cell walls and lower dry mass, GhCSLD3 overexpression largely restored cell wall integrity (CWI) and improved the biomass yield. Our result suggests that overexpression of the GhCSLD protein enhances primary cell wall synthesis and compensates for the loss of CESAs, which is required for cellulose production, therefore rescuing defects in cell elongation and CWI.

Tomato locule number and fruit size controlled by natural alleles of lc and fas

Improving yield by increasing the size of produce is an important selection criterion during the domestication of fruit and vegetable crops. Genes controlling meristem organization and organ formation work in concert to regulate the size of reproductive organs. In tomato, lc and fas control locule number, which often leads to enlarged fruits compared to the wild progenitors. LC is encoded by the tomato ortholog of WUSCHEL (WUS), whereas FAS is encoded by the tomato ortholog of CLAVATA3 (CLV3). The critical role of the WUS-CLV3 feedback loop in meristem organization has been demonstrated in several plant species. We show that mutant alleles for both loci in tomato led to an expansion of the SlWUS expression domain in young floral buds 2-3 days after initiation. Single and double mutant alleles of lc and fas maintain higher SlWUS expression during the development of the carpel primordia in the floral bud. This augmentation and altered spatial expression of SlWUS provided a mechanistic basis for the formation of multilocular and large fruits. Our results indicated that lc and fas are gain-of-function and partially loss-of-function alleles, respectively, while both mutations positively affect the size of tomato floral meristems. In addition, expression profiling showed that lc and fas affected the expression of several genes in biological processes including those involved in meristem/flower development, patterning, microtubule binding activity, and sterol biosynthesis. Several differentially expressed genes co-expressed with SlWUS have been identified, and they are enriched for functions in meristem regulation. Our results provide new insights into the transcriptional regulation of genes that modulate meristem maintenance and floral organ determinacy in tomato.

Effects of Naphthazarin (DHNQ) Combined with Lawsone (NQ-2-OH) or 1,4-Naphthoquinone (NQ) on the Auxin-Induced Growth of Zea mays L. Coleoptile Segments

Naphthoquinones, plants secondary metabolites are known for their antibacterial, antifungal, anti-inflammatory, anti-cancer and anti-parasitic properties. The biological activity of naphthoquinones is connected with their ability to generate reactive oxygen species and to modify biological molecules at their nucleophilic sites. In our research, the effect of naphthazarin (DHNQ) combined with 2-hydroxy-1,4-naphthoquinone (NQ-2-OH) or 1,4-naphthoquinone (1,4-NQ) on the elongation growth, pH changes of the incubation medium, oxidative stress and redox activity of maize coleoptile cells were investigated. This paper describes experiments performed with maize (Zea mays L.) coleoptile segments, which is a classical model system to study plant cell elongation growth. The data presented clearly demonstrate that lawsone and 1,4-naphthoquinone combined with naphthazarin, at low concentrations (1 and 10 nM), reduced the endogenous and IAA-induced (Indole-3-Acetic Acid) elongation growth of maize coleoptile segments. Those changes in growth correlated with the proton concentration in the incubation medium, which suggests that the changes in the growth of maize coleoptile segments observed in the presence of naphthoquinones are mediated through the activity of PM H⁺-ATPase. The presence of naphthoquinones induced oxidative stress in the maize coleoptile tissue by producing hydrogen peroxide and causing changes in the redox activity. Moreover, the incubation of maize segments with both naphthoquinones combined with naphthazarin resulted in lipid peroxidation and membrane damage. The regulation of PM H⁺-ATPase activity, especially its inhibition, may result from two major types of reaction: first, a direct interaction between an enzyme and naphthoquinone, which leads to the covalent modification of the protein thiols and the generation of thioethers, which have been found to alter the activity of the PM H⁺-ATPases; second, naphthoquinones induce reactive oxygen species (ROS) production, which inhibits PM H⁺-ATPases by increasing cytosolic Ca2+. This harmful effect was stronger when naphthazarin and 1,4-naphthoquinone were added together. Taking these results into account, it can be suggested that by combining naphthoquinones in small quantities, an alternative to synthetic pesticides could be developed.

Characterization of Cellulose synthase-like D (CSLD) family revealed the involvement of PtrCslD5 in root hair formation in Populus trichocarpa

Cellulose synthase-like D (CSLD) family was characterized for their expression and functions in Populus trichocarpa. Ten members, PtrCslD1-10, were identified in the P. trichocarpa genome, and they belong to 4 clades by phylogenetic tree analysis. qRT-PCR and promoter:GUS assays in Arabidopsis and P. trichocarpa displayed divergent expression patterns of these 10 PtrCSLD genes in root hairs, root tips, leaves, vascular tissues, xylem and flowers. Among PtrCslD2, PtrCslD4, PtrCslD5, PtrCslD6, and PtrCslD8 that all exhibited expression in root hairs, only PtrCslD5 could restore the root hairless phenotype of the atcsld3 mutant, demonstrating that PtrCslD5 is the functional ortholog of AtCslD3 for root hair formation. Our results suggest more possible functions for other PtrCslD genes in poplar.

Genome-wide characterization of the cellulose synthase gene superfamily in Solanum lycopersicum

The cellulose synthase gene superfamily, which includes the cellulose synthase (CesA) and cellulose synthase-like (Csl) gene families, plays a vital role in the biosynthesis of cellulose and hemicellulose in plants. However, these genes have not been extensively studied in tomato (Solanum lycopersicum), a model for Solanaceae plants and for fleshy fruit development. Here, we identified and systematically analyzed 38 CesA/Csl family members that contained cellulose synthase domain regions, and categorized their encoded proteins into 6 subfamilies (CesA, CslA, CslB, CslD, CslE, and CslG) based on phylogenetic analysis. Most CesA/Csl genes from tomato are closely related to those from Arabidopsis, but the families have distinct features regarding gene structure, chromosome distribution and localization, phylogeny, and deduced protein sequence, indicating that they arose via different evolutionary process. Furthermore, expression analysis of CesA/Csl genes in different tissues at various developmental stages showed that most CesAs were constitutively expressed with differential expression levels in various organs; three CslD genes were expressed specifically in flowers, and four CesA and five Csl putative genes were preferentially expressed in fruits. Our results provide insight into the general characteristics of the CesA/Csl genes in tomato, and lay the foundation for further functional studies of CesA/Csl genes in tomato and other Solanaceae species.

Cellulose synthase-like D1 controls organ size in maize

BACKGROUND

Plant architecture is a critical factor that affects planting density and, consequently, grain yield in maize. The genes or loci that determine organ size are the key regulators of plant architecture. Thus, understanding the genetic and molecular mechanisms of organ size will inform the use of a molecular manipulation approach to improve maize plant architecture and grain yield.

RESULTS

A total of 18 unique quantitative trait loci (QTLs) were identified for 11 agronomic traits in the F₂ and F_2:3 segregating populations derived from a cross between a double haploid line with a small plant architecture (MT03-1) and an inbred line with a large plant architecture (LEE-12). Subsequently, we showed that one QTL, qLW10, for multiple agronomic traits that relate to plant organ size reflects allelic variation in ZmCSLD1, which encodes a cellulose synthase-like D protein. ZmCSLD1 was localized to the trans-Golgi and was highly expressed in the rapidly growing regions. The loss of ZmCSLD1 function decreased cell division, which resulted in smaller organs with fewer cell numbers and, in turn, pleiotropic effects on multiple agronomic traits. In addition, intragenic complementation was investigated for two Zmcsld1 alleles with nonsynonymous SNPs in different functional domains, and the mechanism of this complementation was determined to be through homodimeric interactions.

CONCLUSIONS

Through positional cloning by using two populations and allelism tests, qLW10 for organ size was resolved to be a cellulose synthase-like D family gene, ZmCSLD1. ZmCSLD1 has pleiotropic effects on multiple agronomic traits that alter plant organ size by changing the process of cell division. These findings provide new insight into the regulatory mechanism that underlies plant organ development.

Outside-in control - does plant cell wall integrity regulate cell cycle progression?

During recent years it has become accepted that plant cell walls are not inert objects surrounding all plant cells but are instead highly dynamic, plastic structures. They are involved in a large number of cell biological processes and contribute actively to plant growth, development and interaction with environment. Therefore, it is not surprising that cellular processes can control plant cell wall integrity (CWI) while, simultaneously, CWI can influence cellular processes. In yeast and animal cells such a bidirectional relationship also exists between the yeast/animal extracellular matrices and the cell cycle. In yeast, the CWI maintenance mechanism and a dedicated plasma membrane integrity checkpoint are mediating this relationship. Recent research has yielded insights into the mechanism controlling plant cell wall metabolism during cytokinesis. However, the knowledge regarding putative regulatory pathways controlling adaptive modifications in plant cell cycle activity in response to changes in the state of the plant cell wall are not yet identified. In this review, we summarize similarities and differences in regulatory mechanisms coordinating extracellular matrices and cell cycle activity in animal and yeast cells, discuss the available evidence supporting the existence of such a mechanism in plants and suggest that the plant CWI maintenance mechanism might also control cell cycle activity in plant cells.

Three AtCesA6-like members enhance biomass production by distinctively promoting cell growth in Arabidopsis

Cellulose is an abundant biopolymer and a prominent constituent of plant cell walls. Cellulose is also a central component to plant morphogenesis and contributes the bulk of a plant's biomass. While cellulose synthase (CesA) genes were identified over two decades ago, genetic manipulation of this family to enhance cellulose production has remained difficult. In this study, we show that increasing the expression levels of the three primary cell wall AtCesA6-like genes (AtCesA2, AtCesA5, AtCesA6), but not AtCesA3, AtCesA9 or secondary cell wall AtCesA7, can promote the expression of major primary wall CesA genes to accelerate primary wall CesA complex (cellulose synthase complexes, CSCs) particle movement for acquiring long microfibrils and consequently increasing cellulose production in Arabidopsis transgenic lines, as compared with wild-type. The overexpression transgenic lines displayed changes in expression of genes related to cell growth and proliferation, perhaps explaining the enhanced growth of the transgenic seedlings. Notably, overexpression of the three AtCesA6-like genes also enhanced secondary cell wall deposition that led to improved mechanical strength and higher biomass production in transgenic mature plants. Hence, we propose that overexpression of certain AtCesA genes can provide a biotechnological approach to increase cellulose synthesis and biomass accumulation in transgenic plants.

AtCSLD3 and GhCSLD3 mediate root growth and cell elongation downstream of the ethylene response pathway in Arabidopsis

CSLD3, a gene of the cellulose synthase-like D family, affects root hair elongation, but its interactions with ethylene signaling and phosphate-starvation are poorly understood. Here, we aim to understand the role of CSLD3 in the context of the ethylene signaling and phosphate starvation pathways in Arabidopsis plant growth. Therefore, we performed a comparative analysis of the csld3-1 mutant, CSLD3-overexpressing lines, and ethylene-response mutants, such as the constitutive ethylene-response mutant i-ctr1. We found that CSLD3 overexpression enhanced root and hypocotyl growth by increasing cell elongation, and that the root growth was highly sensitive to ethylene treatment (1 µM ACC), in particular under phosphate starvation. However, the CSLD3-mediated hypocotyl elongation occurred independently of the ethylene signaling pathway. Notably, the typical induction of root hair and root elongation by ethylene and phosphate-starvation was completely abolished in the csld3-1 mutant. Furthermore, i-ctr1 csld3-1 double-mutants were hairless like the csld3-1 parent, confirming that CSLD3 acts downstream of the ethylene signaling pathway during root growth. Moreover, the CSLD3 levels positively correlated with cellulose levels, indicating a role of CSLD3 in cellulose synthesis, which may explain the observed growth effects. Our results establish how CSLD3 works in the context of the ethylene signaling and phosphate-starvation pathways during root hair growth, cell elongation, and cell wall biosynthesis.

Identification and Fine-Mapping of a Major Maize Leaf Width QTL in a Re-sequenced Large Recombinant Inbred Lines Population

Leaf width (LW) influences canopy architecture of population-cultured maize and can thus contribute to density breeding. In previous studies, almost all maize LW-related mutants have extreme effect on leaf development or accompanied unfavorable phenotypes. In addition, the identification of quantitative trait loci (QTLs) has been resolution-limited, with cloning and fine-mapping rarely performed. Here, we constructed a bin map for 670 recombinant inbred lines (RILs) using ∼1.2 billion 100-bp re-sequencing reads. QTL analysis of the LW trait directly narrowed the major effect QTL, qLW4, to a ∼270-kb interval. A fine-mapping population and near-isogenic lines (NILs) were quickly constructed using a key RIL harboring heterozygous genotypes across the qLW4 region. A recombinant-derived progeny testing strategy was subsequently used to further fine-map qLW4 to a 55-kb interval. Examination of NILs revealed that qLW4 has a completely dominant effect on LW, with no additional effect on leaf length. Candidate gene analysis suggested that this locus may be a novel LW controlling allele in maize. Our findings demonstrate the advantage of large-population high-density bin mapping, and suggest a strategy for efficiently fine-mapping or even cloning of QTLs. These results should also be helpful for further dissection of the genetic mechanism of LW variation, and benefit maize density breeding.

Genome-wide analysis of the cellulose synthase-like (Csl) gene family in bread wheat (Triticum aestivum L.)

BACKGROUND

Hemicelluloses are a diverse group of complex, non-cellulosic polysaccharides, which constitute approximately one-third of the plant cell wall and find use as dietary fibres, food additives and raw materials for biofuels. Genes involved in hemicellulose synthesis have not been extensively studied in small grain cereals.

RESULTS

In efforts to isolate the sequences for the cellulose synthase-like (Csl) gene family from wheat, we identified 108 genes (hereafter referred to as TaCsl). Each gene was represented by two to three homeoalleles, which are named as TaCslXY_ZA, TaCslXY_ZB, or TaCslXY_ZD, where X denotes the Csl subfamily, Y the gene number and Z the wheat chromosome where it is located. A quarter of these genes were predicted to have 2 to 3 splice variants, resulting in a total of 137 putative translated products. Approximately 45% of TaCsl genes were located on chromosomes 2 and 3. Sequences from the subfamilies C and D were interspersed between the dicots and grasses but those from subfamily A clustered within each group of plants. Proximity of the dicot-specific subfamilies B and G, to the grass-specific subfamilies H and J, respectively, points to their common origin. In silico expression analysis in different tissues revealed that most of the genes were expressed ubiquitously and some were tissue-specific. More than half of the genes had introns in phase 0, one-third in phase 2, and a few in phase 1.

CONCLUSION

Detailed characterization of the wheat Csl genes has enhanced the understanding of their structural, functional, and evolutionary features. This information will be helpful in designing experiments for genetic manipulation of hemicellulose synthesis with the goal of developing improved cultivars for biofuel production and increased tolerance against various stresses.

Leaf primordium size specifies leaf width and vein number among row-type classes in barley

Exploring genes with impact on yield-related phenotypes is the preceding step to accomplishing crop improvements while facing a growing world population. A genome-wide association scan on leaf blade area (LA) in a worldwide spring barley collection (Hordeum vulgare L.), including 125 two- and 93 six-rowed accessions, identified a gene encoding the homeobox transcription factor, Six-rowed spike 1 (VRS1). VRS1 was previously described as a key domestication gene affecting spike development. Its mutation converts two-rowed (wild-type VRS1, only central fertile spikelets) into six-rowed spikes (mutant vrs1, fully developed fertile central and lateral spikelets). Phenotypic analyses of mutant and wild-type leaves revealed that mutants had an increased leaf width with more longitudinal veins. The observed significant increase of LA and leaf nitrogen (%) during pre-anthesis development in vrs1 mutants also implies a link between wider leaf and grain number, which was validated from the association of vrs1 locus with wider leaf and grain number. Histological and gene expression analyses indicated that VRS1 might influence the size of leaf primordia by affecting cell proliferation of leaf primordial cells. This finding was supported by the transcriptome analysis of mutant and wild-type leaf primordia where in the mutant transcriptional activation of genes related to cell proliferation was detectable. Here we show that VRS1 has an independent role on barley leaf development which might influence the grain number.

Evolution, gene expression profiling and 3D modeling of CSLD proteins in cotton

BACKGROUND

Among CESA-like gene superfamily, the cellulose synthase-like D (CSLD) genes are most similar to cellulose synthase genes and have been reported to be involved in tip-growing cell and stem development. However, there has been no genome-wide characterization of this gene subfamily in cotton. We thus sought to analyze the evolution and functional characterization of CSLD proteins in cotton based on fully sequenced cotton genomes.

RESULTS

A total of 23 full-length CSLD proteins were identified in Gossypium raimondii, Gossypium arboreum and Gossypium hirsutum. The phylogenetic tree divided the CSLD proteins into five clades with strong support: CSLD1, CSLD2/3, CSLD4, CSLD5 and CSLD6. The total expression of GhCSLD genes was the highest in androecium & gynoecium (mostly contributed by CSLD1 and CSLD4) compared with other CSL genes. CSLD1 and CSLD4 were only highly expressed in androecium & gynoecium (A&G), and showed tissue-specific expression. The total expression of CSLD2/3, 5 and 6 was highest in the specific tissues. These results suggest that CSLD genes showed the different pattern of expression. Cotton CSLD proteins were subjected to different evolutionary pressures, and the CSLD1 and CSLD4 proteins exhibited episodic and long-term shift positive selection. The predicted three-dimensional structure of GrCSLD1 suggested that GrCSLD1 belongs to glycosyltransferase family 2. The amino acid residues under positive selection in the CSLD1 lineage are positioned in a region adjacent to the class-specific region (CSR), β1-strand and transmembrane helices (TMHs) in the GrCSLD1structure.

CONCLUSION

Our results characterized the CSLD proteins by an integrated approach containing phylogeny, transcriptional profiling and 3D modeling. The study added to the understanding about the importance of the CSLD family and provide a useful reference for selecting candidate genes and their associations with the biosynthesis of the cell wall in cotton.

The Maize MID-COMPLEMENTING ACTIVITY Homolog CELL NUMBER REGULATOR13/NARROW ODD DWARF Coordinates Organ Growth and Tissue Patterning

Organogenesis occurs through cell division, expansion, and differentiation. How these cellular processes are coordinated remains elusive. The maize (Zea mays) leaf provides a robust system to study cellular differentiation due to its distinct tissues and cell types. The narrow odd dwarf (nod) mutant displays defects at both the cellular and tissue level that increase in severity throughout growth. nod mutant leaves have reduced size due to fewer and smaller cells compared with the wild type. The juvenile-to-adult transition is delayed, and proximal distal-patterning is abnormal in this mutant. Differentiation of specialized cells such as those forming stomata and trichomes is incomplete. Analysis of nod-1 sectors suggests that NOD plays a cell-autonomous function in the leaf. We cloned nod positionally and found that it encodes CELL NUMBER REGULATOR13 (CNR13), the maize MID-COMPLEMENTING ACTIVITY homolog. CNR13/NOD is localized to the membrane and is enriched in dividing tissues. Transcriptome analysis of nod mutants revealed overrepresentation of cell wall, hormone metabolism, and defense gene categories. We propose that NOD coordinates cell activity in response to intrinsic and extrinsic cues.

The Core Subunit of A Chromatin-Remodeling Complex, ZmCHB101, Plays Essential Roles in Maize Growth and Development

ATP-dependent chromatin remodeling complexes play essential roles in the regulation of diverse biological processes by formulating a DNA template that is accessible to the general transcription apparatus. Although the function of chromatin remodelers in plant development has been studied in A. thaliana, how it affects growth and development of major crops (e.g., maize) remains uninvestigated. Combining genetic, genomic and bioinformatic analyses, we show here that the maize core subunit of chromatin remodeling complex, ZmCHB101, plays essential roles in growth and development of maize at both vegetative and reproductive stages. Independent ZmCHB101 RNA interference plant lines displayed abaxially curling leaf phenotype due to increase of bulliform cell numbers, and showed impaired development of tassel and cob. RNA-seq-based transcriptome profiling revealed that ZmCHB101 dictated transcriptional reprogramming of a significant set of genes involved in plant development, photosynthesis, metabolic regulation, stress response and gene expressional regulation. Intriguingly, we found that ZmCHB101 was required for maintaining normal nucleosome density and 45 S rDNA compaction. Our findings suggest that the SWI3 protein, ZmCHB101, plays pivotal roles in maize normal growth and development via regulation of chromatin structure.

Genome-wide association study (GWAS) reveals the genetic architecture of four husk traits in maize

Background

Maize (Zea mays) husk referring to the leafy outer enclosing the ear, plays an important role in grain production by directly contributing photosynthate and protecting ear from pathogen infection. Although the physiological functions related to husk have been extensively studied, little is known about its morphological variation and genetic basis in natural population.

Results

Here we utilized a maize association panel including 508 inbred lines with tropical, subtropical and temperate backgrounds to decipher the genetic architecture attributed to four husk traits, i.e. number of layers, length, width and thickness. Evaluating the phenotypic diversity at two different environments showed that four traits exhibit broadly natural variations and moderate levels of heritability with 0.64, 0.74, 0.49 and 0.75 for number, length, width and thickness, respectively. Diversity analysis indicated that different traits have dissimilar responses to subpopulation effects. A series of significantly positive or negative correlations between husk phenotypes and other agronomic traits were identified, indicating that husk growth is coordinated with other developmental processes. Combining husk traits with about half of a million of single nucleotide polymorphisms (SNPs) via genome-wide association study revealed a total of 9 variants significantly associated with traits at P < 1.04 × 10^-5, which are implicated in multiple functional categories, such as cellular trafficking, transcriptional regulation and metabolism.

Conclusions

These results provide instrumental information for understanding the genetic basis of husk development, and further studies on identified candidate genes facilitate to illuminate molecular pathways regulating maize husk growth.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3229-6) contains supplementary material, which is available to authorized users.

Characterization of maize roothairless6 which encodes a D-type cellulose synthase and controls the switch from bulge formation to tip growth

Root hairs are tubular extensions of the epidermis. Root hairs of the monogenic recessive maize mutant roothairless 6 (rth6) are arrested after bulge formation during the transition to tip growth and display a rough cell surface. BSR-Seq in combination with Seq-walking and subsequent analyses of four independently generated mutant alleles established that rth6 encodes CSLD5 a plasma membrane localized 129 kD D-type cellulose synthase with eight transmembrane domains. Cellulose synthases are required for the biosynthesis of cellulose, the most abundant biopolymer of plant cell walls. Phylogenetic analyses revealed that RTH6 is part of a monocot specific clade of D-type cellulose synthases. D-type cellulose synthases are highly conserved in the plant kingdom with five gene family members in maize and homologs even among early land plants such as the moss Physcomitrella patens or the clubmoss Selaginella moellendorffii. Expression profiling demonstrated that rth6 transcripts are highly enriched in root hairs as compared to all other root tissues. Moreover, in addition to the strong knock down of rth6 expression in young primary roots of the mutant rth6, the gene is also significantly down-regulated in rth3 and rth5 mutants, while it is up-regulated in rth2 mutants, suggesting that these genes interact in cell wall biosynthesis.

The barley (Hordeum vulgare) cellulose synthase-like D2 gene (HvCslD2) mediates penetration resistance to host-adapted and nonhost isolates of the powdery mildew fungus

Cell walls and cellular turgor pressure shape and suspend the bodies of all vascular plants. In response to attack by fungal and oomycete pathogens, which usually breach their host's cell walls by mechanical force or by secreting lytic enzymes, plants often form local cell wall appositions (papillae) as an important first line of defence. The involvement of cell wall biosynthetic enzymes in the formation of these papillae is still poorly understood, especially in cereal crops. To investigate the role in plant defence of a candidate gene from barley (Hordeum vulgare) encoding cellulose synthase-like D2 (HvCslD2), we generated transgenic barley plants in which HvCslD2 was silenced through RNA interference (RNAi). The transgenic plants showed no growth defects but their papillae were more successfully penetrated by host-adapted, virulent as well as avirulent nonhost isolates of the powdery mildew fungus Blumeria graminis. Papilla penetration was associated with lower contents of cellulose in epidermal cell walls and increased digestion by fungal cell wall degrading enzymes. The results suggest that HvCslD2-mediated cell wall changes in the epidermal layer represent an important defence reaction both for nonhost and for quantitative host resistance against nonadapted wheat and host-adapted barley powdery mildew pathogens, respectively.

Genetic dissection of maize plant architecture with an ultra-high density bin map based on recombinant inbred lines

Background

Plant architecture attributes, such as plant height, ear height, and internode number, have played an important role in the historical increases in grain yield, lodging resistance, and biomass in maize (Zea mays L.). Analyzing the genetic basis of variation in plant architecture using high density QTL mapping will be of benefit for the breeding of maize for many traits. However, the low density of molecular markers in existing genetic maps has limited the efficiency and accuracy of QTL mapping. Genotyping by sequencing (GBS) is an improved strategy for addressing a complex genome via next-generation sequencing technology. GBS has been a powerful tool for SNP discovery and high-density genetic map construction. The creation of ultra-high density genetic maps using large populations of advanced recombinant inbred lines (RILs) is an efficient way to identify QTL for complex agronomic traits.

Results

A set of 314 RILs derived from inbreds Ye478 and Qi319 were generated and subjected to GBS. A total of 137,699,000 reads with an average of 357,376 reads per individual RIL were generated, which is equivalent to approximately 0.07-fold coverage of the maize B73 RefGen_V3 genome for each individual RIL. A high-density genetic map was constructed using 4183 bin markers (100-Kb intervals with no recombination events). The total genetic distance covered by the linkage map was 1545.65 cM and the average distance between adjacent markers was 0.37 cM with a physical distance of about 0.51 Mb. Our results demonstrated a relatively high degree of collinearity between the genetic map and the B73 reference genome. The quality and accuracy of the bin map for QTL detection was verified by the mapping of a known gene, pericarp color 1 (P1), which controls the color of the cob, with a high LOD value of 80.78 on chromosome 1. Using this high-density bin map, 35 QTL affecting plant architecture, including 14 for plant height, 14 for ear height, and seven for internode number were detected across three environments. Interestingly, pQTL10, which influences all three of these traits, was stably detected in three environments on chromosome 10 within an interval of 14.6 Mb. Two MYB transcription factor genes, GRMZM2G325907 and GRMZM2G108892, which might regulate plant cell wall metabolism are the candidate genes for qPH10.

Conclusions

Here, an ultra-high density accurate linkage map for a set of maize RILs was constructed using a GBS strategy. This map will facilitate identification of genes and exploration of QTL for plant architecture in maize. It will also be helpful for further research into the mechanisms that control plant architecture while also providing a basis for marker-assisted selection.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2555-z) contains supplementary material, which is available to authorized users.

DNL1, encodes cellulose synthase-like D4, is a major QTL for plant height and leaf width in rice (Oryza sativa L.)

To better understand the genetic of rice agronomic traits, we selected two different rice germplasms in phenotypes, Xian80 and Suyunuo, to construct genetic population for QTL analysis. A total of 25 QTLs for six traits were found in a 175 F2 population. Major QTLs, qPH12,qLW12.2, qLL12 and qGW12.1, explaining 50.00%, 57.08%, 15.41% and 22.51% phenotypic variation for plant height, leaf width, leaf length and grain width, respectively, were located on the same interval of chromosome 12 flanking SSR markers RM519 and RM1103. In consideration of the great effects on plant height and leaf width, the locus was named DNL1 (Dwarf and Narrowed Leaf 1). Using a segregating population derived from F2 heterozygous individuals, a total of 1363 dwarfism and narrowed-leaf individuals was selected for screening recombinants. By high-resolution linkage analysis in 141 recombination events, DNL1 was narrowed to a 62.39kb region of InDel markers ID12M28 and HF43. The results of ORF analysis in target region and nucleotide sequence alignment indicated that DNL1 encodes cellulose synthase-like D4 protein, and a single nucleotide substitution (C2488T) in dnl1 result in decrease in plant height and leaf width. Bioinformatical analysis demonstrated that a conserved role for OsCSLD4 in the regulation of plant growth and development. Expression analysis for OsCSLDs showed OsCSLD4 highly expressed in roots, while other CSLD members had comparatively lower expression levels. However, no clear evidence about CSLD4/DNL1 expression was associated with its function.

Divergent roles for maize PAN1 and PAN2 receptor-like proteins in cytokinesis and cell morphogenesis

Pangloss1 (PAN1) and PAN2 are leucine-rich repeat receptor-like proteins that function cooperatively to polarize the divisions of subsidiary mother cells (SMCs) during stomatal development in maize (Zea mays). PANs colocalize in SMCs, and both PAN1 and PAN2 promote polarization of the actin cytoskeleton and nuclei in these cells. Here, we show that PAN1 and PAN2 have additional functions that are unequal or divergent. PAN1, but not PAN2, is localized to cell plates in all classes of dividing cells examined. pan1 mutants exhibited no defects in cell plate formation or in the recruitment or removal of a variety of cell plate components; thus, they did not demonstrate a function for PAN1 in cytokinesis. PAN2, in turn, plays a greater role than PAN1 in directing patterns of postmitotic cell expansion that determine the shapes of mature stomatal subsidiary cells and interstomatal cells. Localization studies indicate that PAN2 impacts subsidiary cell shape indirectly by stimulating localized cortical actin accumulation and polarized growth in interstomatal cells. Localization of PAN1, Rho of Plants2, and PIN1a suggests that PAN2-dependent cell shape changes do not involve any of these proteins, indicating that PAN2 function is linked to actin polymerization by a different mechanism in interstomatal cells compared with SMCs. Together, these results demonstrate that PAN1 and PAN2 are not dedicated to SMC polarization but instead play broader roles in plant development. We speculate that PANs may function in all contexts to regulate polarized membrane trafficking either directly or indirectly via their influence on actin polymerization.

Phenotype to genotype using forward-genetic Mu-seq for identification and functional classification of maize mutants

In pursuing our long-term goals of identifying causal genes for mutant phenotypes in maize, we have developed a new, phenotype-to-genotype approach for transposon-based resources, and used this to identify candidate genes that co-segregate with visible kernel mutants. The strategy incorporates a redesigned Mu-seq protocol (sequence-based, transposon mapping) for high-throughput identification of individual plants carrying Mu insertions. Forward-genetic Mu-seq also involves a genetic pipeline for generating families that segregate for mutants of interest, and grid designs for concurrent analysis of genotypes in multiple families. Critically, this approach not only eliminates gene-specific PCR genotyping, but also profiles all Mu-insertions in hundreds of individuals simultaneously. Here, we employ this scalable approach to study 12 families that showed Mendelian segregation of visible seed mutants. These families were analyzed in parallel, and 7 showed clear co-segregation between the selected phenotype and a Mu insertion in a specific gene. Results were confirmed by PCR. Mutant genes that associated with kernel phenotypes include those encoding: a new allele of Whirly1 (a transcription factor with high affinity for organellar and single-stranded DNA), a predicted splicing factor with a KH domain, a small protein with unknown function, a putative mitochondrial transcription-termination factor, and three proteins with pentatricopeptide repeat domains (predicted mitochondrial). Identification of such associations allows mutants to be prioritized for subsequent research based on their functional annotations. Forward-genetic Mu-seq also allows a systematic dissection of mutant classes with similar phenotypes. In the present work, a high proportion of kernel phenotypes were associated with mutations affecting organellar gene transcription and processing, highlighting the importance and non-redundance of genes controlling these aspects of seed development.

Grain development in Brachypodium and other grasses: possible interactions between cell expansion, starch deposition, and cell-wall synthesis

To explain the low levels of starch, high levels of (1,3;1,4)-β-glucan, and thick cell walls in grains of Brachypodium distachyon L. relative to those in other Pooideae, aspects of grain development were compared between B. distachyon and barley (Hordeum vulgare L.). Cell proliferation, cell expansion, and endoreduplication were reduced in B. distachyon relative to barley and, consistent with these changes, transcriptional downregulation of the cell-cycle genes CDKB1 and cyclin A3 was observed. Similarly, reduced transcription of starch synthase I and starch-branching enzyme I was observed as well as reduced activity of starch synthase and ADP-glucose pyrophosphorylase, which are consistent with the lowered starch content in B. distachyon grains. No change was detected in transcription of the major gene involved in (1,3;1,4)-β-glucan synthesis, cellulose synthase-like F6. These results suggest that, while low starch content results from a reduced capacity for starch synthesis, the unusually thick cell walls in B. distachyon endosperm probably result from continuing (1,3;1,4)-β-glucan deposition in endosperm cells that fail to expand. This raises the possibility that endosperm expansion is linked to starch deposition.

Two poplar cellulose synthase-like D genes, PdCSLD5 and PdCSLD6, are functionally conserved with Arabidopsis CSLD3

Root hairs are tip-growing long tubular outgrowths of specialized epidermal cells, and are important for nutrient and water uptake and interaction with the soil microflora. Here we characterized two poplar cellulose synthase-like D (CSLD) genes, PdCSLD5 and PdCSLD6, the most probable orthologs to the Arabidopsis AtCSLD3/KOJAK gene. Both PdCSLD5 and PdCSLD6 are strongly expressed in roots, including in the root hairs. Subcellular localization experiments showed that these two proteins are located not only in the polarized plasma membrane of root hair tips, but also in Golgi apparatus of the root hair and non-hair-forming cells. Overexpression of these two poplar genes in the atcsld3 mutant was able to rescue most of the defects caused by disruption of AtCSLD3, including root hair morphological changes, altered cell wall monosaccharide composition, increased non-crystalline β-1,4-glucan and decreased crystalline cellulose contents. Taken together, our results provide evidence indicating that PdCSLD5 and PdCSLD6 are functionally conserved with AtCSLD3 and support a role for PdCSLD5 and PdCSL6 specifically in crystalline cellulose production in poplar root hair tips. The results presented here also suggest that at least part of the mechanism of root hair formation is conserved between herbaceous and woody plants.

On the genetic control of planar growth during tissue morphogenesis in plants

Tissue morphogenesis requires extensive intercellular communication. Plant organs are composites of distinct radial cell layers. A typical layer, such as the epidermis, is propagated by stereotypic anticlinal cell divisions. It is presently unclear what mechanisms coordinate cell divisions relative to the plane of a layer, resulting in planar growth and maintenance of the layer structure. Failure in the regulation of coordinated growth across a tissue may result in spatially restricted abnormal growth and the formation of a tumor-like protrusion. Therefore, one way to approach planar growth control is to look for genetic mutants that exhibit localized tumor-like outgrowths. Interestingly, plants appear to have evolved quite robust genetic mechanisms that govern these aspects of tissue morphogenesis. Here we provide a short summary of the current knowledge about the genetics of tumor formation in plants and relate it to the known control of coordinated cell behavior within a tissue layer. We further portray the integuments of Arabidopsis thaliana as an excellent model system to study the regulation of planar growth. The value of examining this process in integuments was established by the recent identification of the Arabidopsis AGC VIII kinase UNICORN as a novel growth suppressor involved in the regulation of planar growth and the inhibition of localized ectopic growth in integuments and other floral organs. An emerging insight is that misregulation of central determinants of adaxial-abaxial tissue polarity can lead to the formation of spatially restricted multicellular outgrowths in several tissues. Thus, there may exist a link between the mechanisms regulating adaxial-abaxial tissue polarity and planar growth in plants.

Rice slender leaf 1 gene encodes cellulose synthase-like D4 and is specifically expressed in M-phase cells to regulate cell proliferation

Cellulose synthase-like (CSL) genes are predicted to catalyse the biosynthesis of non-cellulosic polysaccharides such as the β-D-glycan backbone of hemicelluloses and are classified into nine subfamilies (CSLA-CSLH and CSLJ). The CSLD subfamily is conserved in all land plants, and among the nine CSL subfamilies, it shows the highest sequence similarity to the cellulose synthase genes, suggesting that it plays fundamental roles in plant development. This study presents a detailed analysis of slender leaf 1 (sle1) mutants of rice that showed rolled and narrow leaf blades and a reduction in plant height. The narrow leaf blade of sle1 was caused by reduced cell proliferation beginning at the P3 primordial stage. In addition to the size reduction of organs, sle1 mutants exhibited serious developmental defects in pollen formation, anther dehiscence, stomata formation, and cell arrangement in various tissues. Map-based cloning revealed that SLE1 encodes the OsCSLD4 protein, which was identified previously from a narrow leaf and dwarf 1 mutant. In situ hybridization experiments showed that OsCSLD4 was expressed in a patchy pattern in developing organs. Double-target in situ hybridization and quantitative RT-PCR analyses revealed that SLE1 was expressed specifically during the M-phase of the cell cycle, and suggested that the cell-cycle regulation was altered in sle1 mutants. These results suggest that the OsCSLD4 protein plays a pivotal role in the M phase to regulate cell proliferation. Further study of OsCSLD4 is expected to yield new insight into the role of hemicelluloses in plant development.

Cytoskeletal and membrane dynamics during higher plant cytokinesis

Following mitosis, cytoplasm, organelles and genetic material are partitioned into daughter cells through the process of cytokinesis. In somatic cells of higher plants, two cytoskeletal arrays, the preprophase band and the phragmoplast, facilitate the positioning and de novo assembly of the plant-specific cytokinetic organelle, the cell plate, which develops across the division plane and fuses with the parental plasma membrane to yield distinct new cells. The coordination of cytoskeletal and membrane dynamics required to initiate, assemble and shape the cell plate as it grows toward the mother cell cortex is dependent upon a large array of proteins, including molecular motors, membrane tethering, fusion and restructuring factors and biosynthetic, structural and regulatory elements. This review focuses on the temporal and molecular requirements of cytokinesis in somatic cells of higher plants gleaned from recent studies using cell biology, genetics, pharmacology and biochemistry.

Genetic and molecular analyses of UniformMu transposon insertion lines

The UniformMu transposon population is a large public resource for reverse genetics and functional genomics of maize. Users access the collection of UniformMu genetic stocks that are freely distributed by the Maize Cooperation Stock Center using online tools maintained at MaizeGDB.org. Genetic and molecular analyses of UniformMu stocks (UFMu insertion lines) typically require development of genotyping assays that use a gene-specific polymerase chain reaction (PCR) to follow segregation of transposon insertions in genes of interest. Here we describe methods for accessing the resource and recommended protocols for genotyping of transposon insertion alleles.

Identification of PAN2 by quantitative proteomics as a leucine-rich repeat-receptor-like kinase acting upstream of PAN1 to polarize cell division in maize

Mechanisms governing the polarization of plant cell division are poorly understood. Previously, we identified pangloss1 (PAN1) as a leucine-rich repeat-receptor-like kinase (LRR-RLK) that promotes the polarization of subsidiary mother cell (SMC) divisions toward the adjacent guard mother cell (GMC) during stomatal development in maize (Zea mays). Here, we identify pangloss2 (PAN2) as a second LRR-RLK promoting SMC polarization. Quantitative proteomic analysis identified a PAN2 candidate by its depletion from membranes of pan2 single and pan1;pan2 double mutants. Genetic mapping and sequencing of mutant alleles confirmed the identity of this protein as PAN2. Like PAN1, PAN2 has a catalytically inactive kinase domain and accumulates in SMCs at sites of GMC contact before nuclear polarization. The timing of polarized PAN1 and PAN2 localization is very similar, but PAN2 acts upstream because it is required for polarized accumulation of PAN1 but is independent of PAN1 for its own localization. We find no evidence that PAN2 recruits PAN1 to the GMC contact site via a direct or indirect physical interaction, but PAN2 interacts with itself. Together, these results place PAN2 at the top of a cascade of events promoting the polarization of SMC divisions, potentially functioning to perceive or amplify GMC-derived polarizing cues.