Rice Brittle Culm19 Encoding Cellulose Synthase Subunit CESA4 Causes Dominant Brittle Phenotype But has No Distinct Influence on Growth and Grain Yield

Genome-Wide Identification and Hormone Response Analysis of the COBL Gene Family in Barley

Barley (Hordeum vulgare L.), a diverse cereal crop, exhibits remarkable versatility in its applications, ranging from food and fodder to industrial uses. The content of cellulose in barley is significantly influenced by the COBRA genes, which encode the plant glycosylphosphatidylinositol (GPI)-anchored protein (GAP) that plays a pivotal role in the deposition of cellulose within the cell wall. The COBL (COBRA-Like) gene family has been discovered across numerous species, yet the specific members of this family in barley remain undetermined. In this study, we discovered 13 COBL genes within the barley genome using bioinformatics methods, subcellular localization, and protein structure analysis, finding that most of the barley COBL proteins have a signal peptide structure and are localized on the plasma membrane. Simultaneously, we constructed a phylogenetic tree and undertook a comprehensive analysis of the evolutionary relationships. Other characteristics of HvCOBL family members, including intraspecific collinearity, gene structure, conserved motifs, and cis-acting elements, were thoroughly characterized in detail. The assessment of HvCOBL gene expression in barley under various hormone treatments was conducted through qRT-PCR analysis, revealing jasmonic acid (JA) as the predominant hormonal regulator of HvCOBL gene expression. In summary, this study comprehensively identified and analyzed the barley COBL gene family, aiming to provide basic information for exploring the members of the HvCOBL gene family and to propose directions for further research.

A Comprehensive Molecular, Biochemical, Histochemical, and Spectroscopic Characterization of Early and Medium Duration Rice Genotypes Investigating Dry Matter Accumulation Efficiencies

Investigation on accumulation of cell wall components over critical growth stages will surely provide a new insight into dry matter accumulation studies in rice. An elevated biomass production provides an alternative strategy of yield improvement, which in turn maneuvers the species concerned as potential dual-purpose crop. On that note, present study was carried on 33 early and 39 medium duration rice genotypes. The average cellulose accumulation was 6.51% and 8.17% in early and medium duration genotypes, respectively, at flowering stage, which later on dipped to 1.43% and 3.46%, respectively, at physiological maturity. The gene specific marker MDgsp-5.a exhibited highest estimate of polymorphic information content (PIC), i.e., 0.685, closely followed by MDgsp-6.a with polymorphic information content (PIC) of 0.683. The control genotypes, i.e., Pratap and Mandakini, are grouped under the same cluster, i.e., Cluster-I.A, indicating their inherent genetic divergence from that of potential accumulators pertaining to cellulose accumulation. Pratap and Mandakini failed to produce peaks of conspicuous form at 3342 cm-1 and 1635 cm-1, bearing out by their low performance pertaining to cellulose and lignin accumulation at the later stages of development, respectively. From histochemistry studies, it was observed that the cell walls of sclerenchyma, peripheral vascular bundles, and parenchyma of the culm transections in control genotypes stained lightly than that of prolific accumulator cell walls, thus corroborating the findings of compositional analysis. The variation in cell wall thickening is primarily accounted due to altered carbohydrate accumulation across the growth stages as explored under scanning electron micrograph.

Effects of Supplemental Lighting on Flavonoid and Anthocyanin Biosynthesis in Strawberry Flesh Revealed via Metabolome and Transcriptome Co-Analysis

The spectral composition of light influences the biosynthesis of flavonoids in many plants. However, the detailed composition of flavonoids and anthocyanins and the molecular basis for their biosynthesis in strawberry fruits under two light-quality treatments, red light supplemented with blue light (RB) and ultraviolet B (UVB) irradiation, remain unclear. In this study, the content of flavonoids and anthocyanins was significantly increased in strawberry fruits under RB light and UVB, respectively. The content of flavonoids and anthocyanins in strawberry fruits under UVB light was dramatically higher than that in strawberry fruits irradiated with RB light, and a total of 518 metabolites were detected by means of LC-MS/MS analysis. Among them, 18 phenolic acids, 23 flavonoids, and 8 anthocyanins were differentially accumulated in the strawberry fruits irradiated with red/blue (RB) light compared to 30 phenolic acids, 46 flavonoids, and 9 anthocyanins in fruits irradiated with UVB. The major genes associated with the biosynthesis of flavonoids and anthocyanins, including structural genes and transcription factors (TFs), were differentially expressed in the strawberry fruits under RB and UVB irradiation, as determined through RNA-seq data analysis. A correlation test of transcriptome and metabolite profiling showed that the expression patterns of most genes in the biosynthesis pathway of flavonoids and anthocyanins were closely correlated with the differential accumulation of flavonoids and anthocyanins. Two TFs, bZIP (FvH4_2g36400) and AP2 (FvH4_1g21210), induced by RB and UVB irradiation, respectively, exhibited similar expression patterns to most structural genes, which were closely correlated with six and eight flavonoids, respectively. These results indicated that these two TFs regulated the biosynthesis of flavonoids and anthocyanins in strawberry fruit under RB light and UVB, respectively. These results provide a systematic and comprehensive understanding of the accumulation of flavonoids and anthocyanins and the molecular basis for their biosynthesis in strawberry fruits under RB light and UVB.

Strong culm: a crucial trait for developing next-generation climate-resilient rice lines

Lodging, a phenomenon characterized by the bending or breaking of rice plants, poses substantial constraints on productivity, particularly during the harvesting phase in regions susceptible to strong winds. The rice strong culm trait is influenced by the intricate interplay of genetic, physiological, epigenetic, and environmental factors. Stem architecture, encompassing morphological and anatomical attributes, alongside the composition of both structural and non-structural carbohydrates, emerges as a critical determinant of lodging resistance. The adaptive response of the rice culm to various biotic and abiotic environmental factors further modulates the propensity for lodging. Advancements in next-generation sequencing technologies have expedited the genetic dissection of lodging resistance, enabling the identification of pertinent genes, quantitative trait loci, and novel alleles. Concurrently, contemporary breeding strategies, ranging from biparental approaches to more sophisticated methods such as multi-parent-based breeding, gene pyramiding, genomic selection, genome-wide association studies, and haplotype-based breeding, offer perspectives on the genetic underpinnings of culm strength. This review comprehensively delves into physiological attributes, culm histology, epigenetic determinants, and gene expression profiles associated with lodging resistance, with a specialized focus on leveraging next-generation sequencing for candidate gene discovery.

Integrative transcriptome and metabolome analysis reveals the discrepancy in the accumulation of active ingredients between Lycium barbarum cultivars

MAIN CONCLUSION

The combined analysis of transcriptome and metabolome provided molecular insight into the dynamics of multiple active ingredients biosynthesis and accumulation across different cultivars of Lycium barbarum. Lycium barbarum L. has a high concentration of active ingredients and is well known in traditional Chinese herbal medicine for its therapeutic properties. However, there are many Lycium barbarum cultivars, and the content of active components varies, resulting in inconsistent quality between Lycium barbarum cultivars. At present, few research has been conducted to reveal the difference in active ingredient content among different cultivars of Lycium barbarum at the molecular level. Therefore, the transcriptome of 'Ningqi No.1' and 'Qixin No.1' during the three development stages (G, T, and M) was constructed in this study. A total of 797,570,278 clean reads were obtained. Between the two types of wolfberries, a total of 469, 2394, and 1531 differentially expressed genes (DEGs) were obtained in the 'G1 vs. G10,' 'T1 vs. T10,' and 'M1 vs. M10,' respectively, and were annotated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology identifiers. Using these transcriptome data, most DEGs related to the metabolism of the active ingredients in 'Ningqi No.1' and 'Qixin No.1' were identified. Moreover, a widely targeted metabolome analysis of the metabolites of 'Ningqi 1' and 'Qixin 1' fruits at the maturity stage revealed 1,135 differentially expressed metabolites (DEMs) in 'M1 vs. M10,' and many DEMs were associated with active ingredients such as flavonoids, alkaloids, terpenoids, and so on. We further quantified the flavonoid, lignin, and carotenoid contents of the two Lycium barbarum cultivars during the three developmental stages. The present outcome provided molecular insight into the dynamics of multiple active ingredients biosynthesis and accumulation across different cultivars of Lycium barbarum, which would provide the basic data for the formation of Lycium barbarum fruit quality and the breeding of outstanding strains.

A Tos17 transposon insertion in OsCesA9 causes brittle culm in rice

The mechanical strength of rice stalks plays an important role in rice growth and development. In this study, the brittle culm mutant bc26 was identified from a tissue culture-derived line of the japonica rice cultivar 'ZH15'. bc26 plants showed fragile leaves and stalks and reduced plant height and spike number compared with wild-type 'ZH15'. Analysis of cell wall components revealed that the cellulose content of stems, leaves, roots and spikes of bc26 plants was significantly lower than that of the wild type, while the hemicellulose content in these tissues of bc26 plants was significantly higher than that of the wild type. Further sequencing using a mixed pool bulked segregant analysis sequencing (BSA-Seq) of brittle plants from the F2 populations localized the bc26 gene to chromosome 9, and a Tos17 transposon insertion in the bc6 gene near the highest SNP-index point was associated with a loss of gene function. Therefore, the bc26 gene was tentatively identified as a new allele of the Bc6 gene, resulting in the brittle culm trait caused by the insertion of the Tos17 transposon.

Reciprocal regulation of cellulose and lignin biosynthesis by the transcription factor OsTCP19

This article comments on:

Lv S, Lin Z, Shen J, Luo L, Xu Q, Li L, Gui J. 2024. OsTCP19 coordinates inhibition of lignin biosynthesis and promotion of cellulose biosynthesis to modify lodging resistance in rice. Journal of Experimental Botany 75, 123–136.

Genetic linkage analysis of stable QTLs in Gossypium hirsutum RIL population revealed function of GhCesA4 in fiber development

INTRODUCTION

Upland cotton is an important allotetrapolyploid crop providing natural fibers for textile industry. Under the present high-level breeding and production conditions, further simultaneous improvement of fiber quality and yield is facing unprecedented challenges due to their complex negative correlations.

OBJECTIVES

The study was to adequately identify quantitative trait loci (QTLs) and dissect how they orchestrate the formation of fiber quality and yield.

METHODS

A high-density genetic map (HDGM) based on an intraspecific recombinant inbred line (RIL) population consisting of 231 individuals was used to identify QTLs and QTL clusters of fiber quality and yield traits. The weighted gene correlation network analysis (WGCNA) package in R software was utilized to identify WGCNA network and hub genes related to fiber development. Gene functions were verified via virus-induced gene silencing (VIGS) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 strategies.

RESULTS

An HDGM consisting of 8045 markers was constructed spanning 4943.01 cM of cotton genome. A total of 295 QTLs were identified based on multi-environmental phenotypes. Among 139 stable QTLs, including 35 newly identified ones, seventy five were of fiber quality and 64 yield traits. A total of 33 QTL clusters harboring 74 QTLs were identified. Eleven candidate hub genes were identified via WGCNA using genes in all stable QTLs and QTL clusters. The relative expression profiles of these hub genes revealed their correlations with fiber development. VIGS and CRISPR/Cas9 edition revealed that the hub gene cellulose synthase 4 (GhCesA4, GH_D07G2262) positively regulate fiber length and fiber strength formation and negatively lint percentage.

CONCLUSION

Multiple analyses demonstrate that the hub genes harbored in the QTLs orchestrate the fiber development. The hub gene GhCesA4 has opposite pleiotropic effects in regulating trait formation of fiber quality and yield. The results facilitate understanding the genetic basis of negative correlation between cotton fiber quality and yield.

A comprehensive review on genetic modification of plant cell wall for improved saccharification efficiency

The focus is now on harnessing energy from green sources through sustainable technology to minimize environmental pollution. Several crop residues including rice and wheat straw are having enormous potential to be used as lignocellulosic source material for bioenergy production. The lignocellulosic feedstock is primarily composed of cellulose, hemicellulose, and lignin cell wall polymers. The hemicellulose and lignin polymers induce crosslinks in the cell wall, by firmly associating with cellulose microfibrils, and thereby, denying considerable access of cellulose to cellulase enzymes. This issue has been addressed by various researchers through downregulating several genes associated in monolignol biosynthesis in Arabidopsis, Poplar, Rice and Switchgrass to increase ethanol recovery. Similarly, xylan biosynthetic genes are also targeted to genetically culminate its accumulation in the secondary cell walls. Regulation of cellulose synthases (CesA) proves to be an effective tool in addressing the negative impact of these two factors. Modification in the expression of cellulose synthase aids in reducing cellulose crystallinity as well as polymerisation degree which in turn increases ethanol recovery. The engineered bioenergy crops and various fungal strains with state of art biomass processing techniques presents the most recent integrative biotechnology model for cost effective green fuels generation along with production of key value-added products with minuscule disturbances in the environment. Plant breeding strategies utilizing the existing variability for biomass traits will be key in developing dual purpose varieties. For this purpose, reorientation of conventional breeding techniques for incorporating useful biomass traits will be effective.

An R2R3-MYB network modulates stem strength by regulating lignin biosynthesis and secondary cell wall thickening in herbaceous peony

Stem strength is an important agronomic trait affecting plant lodging, and plays an essential role in the quality and yield of plants. Thickened secondary cell walls in stems provide mechanical strength that allows plants to stand upright, but the regulatory mechanism of secondary cell wall thickening and stem strength in cut flowers remains unclear. In this study, first, a total of 11 non-redundant Paeonia lactiflora R2R3-MYBs related to stem strength were identified and isolated from cut-flower herbaceous peony, among which PlMYB43, PlMYB83 and PlMYB103 were the most upregulated differentially expressed genes. Then, the expression characteristics revealed that these three R2R3-MYBs were specifically expressed in stems and acted as transcriptional activators. Next, biological function verification showed that these P. lactiflora R2R3-MYBs positively regulated stem strength, secondary cell wall thickness and lignin deposition. Furthermore, yeast-one-hybrid and dual luciferase reporter assays demonstrated that they could bind to the promoter of caffeic acid O-methyltransferase gene (PlCOMT2) and/or laccase gene (PlLAC4), two key genes involved in lignin biosynthesis. In addition, the function of PlLAC4 in increasing lignin deposition was confirmed by virus-induced gene silencing and overexpression. Moreover, PlMYB83 could also act as a transcriptional activator of PlMYB43. The findings of the study propose a regulatory network of R2R3-MYBs modulating lignin biosynthesis and secondary cell wall thickening for improving stem lodging resistance, and provide a resource for molecular genetic engineering breeding of cut flowers.

Mechanical stimulation reprograms the sorghum internode transcriptome and broadly alters hormone homeostasis

Stem structural failure, or lodging, affects many crops including sorghum, and can cause large yield losses. Lodging is typically caused by mechanical forces associated with severe weather like high winds, but exposure to sub-catastrophic forces may strengthen stems and improve lodging resistance. The responses of sorghum internodes at different developmental stages were examined at 2 and 26 h after initiating moderate mechanical stimulation with an automated apparatus. Transcriptome profiling revealed that mechanical stimulation altered the expression of over 900 genes, including transcription factors, cell wall-related and hormone signaling-related genes. IAA, GA₁ and ABA abundances generally declined following mechanical stimulation, while JA increased. Weighted Gene Co-expression Network Analysis (WGCNA) identified three modules significantly enriched in GO terms associated with cell wall biology, hormone signaling and general stress responses, which were highly correlated with mechanical stimulation and with biomechanical and geometrical traits documented in a separate study. Additionally, mechanical stimulation-triggered responses were dependent on the developmental stage of the internode and the duration of stimulation. This study provides insights into the underlying mechanisms of plant hormone-regulated thigmomorphogenesis in sorghum stems. The critical biological processes and hub genes described here may offer opportunities to improve lodging resistance in sorghum and other crops.

A Golgi-localized glycosyltransferase, OsGT14;1, is required for growth of both roots and shoots in rice

Glycosyltransferases (GTs) form a large family in plants and are important enzymes for the synthesis of various polysaccharides, but only a few members have been functionally characterized. Here, through mutant screening with gene mapping, we found that an Oryza sativa (rice) mutant with a short-root phenotype was caused by a frame-shift mutation of a gene (OsGT14;1) belonging to the glycosyltransferase gene family 14. Further analysis indicated that the mutant also had a brittle culm and produced lower grain yield compared with wild-type rice, but the roots showed similar root structure and function in terms of the uptake of mineral nutrients. OsGT14;1 was broadly expressed in all organs throughout the entire growth period, with a relatively high expression in the roots, stems, node I and husk. Furthermore, OsGT14;1 was expressed in all tissues of these organs. Subcellular observation revealed that OsGT14;1 encoded a Golgi-localized protein. Mutation of OsGT14;1 resulted in decreased cellulose content and increased hemicellulose, but did not alter pectin in the cell wall of roots and shoots. The knockout of OsGT14;1 did not affect the tolerance to toxic mineral elements, including Al, As, Cd and salt stress, but did increase the sensitivity to low pH. Taken together, OsGT14;1 located at the Golgi is required for growth of both roots and shoots in rice through affecting cellulose synthesis.