Starch Metabolism Research Articles

Using transcriptome sequencing (RNA-Seq) to screen genes involved in β-glucan biosynthesis and accumulation during oat seed development.

Oat (Avena sativa L.) is an annual grass that has a high nutritional value and therapeutic benefits. β-glucan is one of the most important nutrients in oats. In this study, we investigated two oat varieties with significant differences in β-glucan content (high β-glucan oat varieties BY and low β-glucan content oat variety DY) during different filling stages. We also studied the transcriptome sequencing of seeds at different filling stages. β-glucan accumulation was highest at days 6-16 in the filling stage. Differentially expressed genes (DEGs) were selected from the dataset of transcriptome sequencing. Among them, three metabolic pathways were closely related to the biosynthesis of β-glucan by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, including xyloglucan:xyloglucosyl transferase activity, starch and sucrose metabolism, and photosynthesis. By analyzing the expression patterns of DEGs, we identified one CslF2 gene and 32 transcription factors. Five modules were thought to be positively correlated with β-glucan accumulation by weighted gene co-expression network analysis (WGCNA). Moreover, the expression levels of candidate genes obtained from the transcriptome sequencing were further validated by quantitative real-time PCR (RT-qPCR) analysis. Our study provides a novel way to identify the regulatory mechanism of β-glucan synthesis and accumulation in oat seeds and offers a possible pathway for the genetic engineering of oat breeding for higher-quality seeds.

Dissection of genetic architecture for desirable traits in sugarcane by integrated transcriptomics and metabolomics

Sugarcane is an important sugar and energy crop. Breeding varieties with high yield and sugar, strong stress tolerance, as well as beneficial for mechanized harvesting are the goal of sugarcane breeder. In the present study, transcriptomics and metabolomics were conducted to explore the molecular basis for outstanding performance of five elite varieties GT42, GT44, LC05-136, YZ08-1609, and YZ05-51, along with the cross-parent CP72-1210 compared to ROC22. Transcriptomics revealed a total of 18,353 differentially expressed genes (DEGs) and several regulatory pathways, including carbon fixation, starch and sucrose metabolism, phenylpropanoids biosynthesis, flavonoid biosynthesis, cysteine and methionine metabolism, as well as zeatin biosynthesis. Expression patterns of genes involved in these pathways confirmed their role in determining the agronomic traits. Besides, metabolomics disclosed 175 differentially accumulated metabolites (DAMs), including specific metabolites of amino acids and secondary metabolites. Furthermore, conjoint analysis of transcriptomics and metabolomics highlighted the manipulation of 113 genes led to changed levels of 20 metabolites associated with carbon fixation, sucrose accumulation, phytohormone response and secondary metabolism. Finally, we depicted here a blueprint outlining the genetic basis underlying the desirable traits in sugarcane. This study will accelerate the dissection of the molecular basis for sugarcane traits and provide targets for molecular breeding.

The genomes of Australian wild limes

Australian wild limes occur in highly diverse range of environments and are a unique genetic resource within the genus Citrus. Here we compare the haplotype-resolved genome assemblies of six Australian native limes, including four new assemblies generated using PacBio HiFi and Hi-C sequencing data. The size of the genomes was between 315 and 391 Mb with contig N50s from 29.5 to 35 Mb. Gene completeness of the assemblies was estimated to be from 98.4 to 99.3% and the annotations from 97.7 to 98.9% based upon BUSCO, confirming the high contiguity and completeness of the assembled genomes. High collinearity was observed among the genomes and the two haplotype assemblies for each species. Gene duplication and evolutionary analysis demonstrated that the Australian citrus have undergone only one ancient whole-genome triplication event during evolution. The highest number of species-specific and expanded gene families were found in C. glauca and they were primarily enriched in purine, thiamine metabolism, amino acids and aromatic amino acids metabolism which might help C. glauca to mitigate drought, salinity, and pathogen attacks in the drier environments in which this species is found. Unique genes related to terpene biosynthesis, glutathione metabolism, and toll-like receptors in C. australasica, and starch and sucrose metabolism genes in both C. australis and C. australasica might be important candidate genes for HLB tolerance in these species. Expanded gene families were not lineage specific, however, a greater number of genes related to plant-pathogen interactions, predominantly disease resistant protein, was found in C. australasica and C. australis.

Phenotypic Analysis and Gene Cloning of Rice Floury Endosperm Mutant wcr (White-Core Rice).

The composition and distribution of storage substances in rice endosperm directly affect grain quality. A floury endosperm mutant, wcr (white-core rice), was identified, exhibiting a loose arrangement of starch granules with a floury opaque appearance in the inner layer of mature grains, resulting in reduced grain weight. The total starch and amylose content remained unchanged, but the levels of the four component proteins in the mutant brown rice significantly decreased. Additionally, the milled rice (inner endosperm) showed a significant decrease in total starch and amylose content, accompanied by a nearly threefold increase in albumin content. The swelling capacity of mutant starch was reduced, and its chain length distribution was altered. The target gene was mapped on chromosome 5 within a 65 kb region. A frameshift mutation occurred due to an insertion of an extra C base in the second exon of the cyOsPPDKB gene, which encodes pyruvate phosphate dikinase. Expression analysis revealed that wcr not only affected genes involved in starch metabolism but also downregulated expression levels of genes associated with storage protein synthesis. Overall, wcr plays a crucial role as a regulator factor influencing protein synthesis and starch metabolism in rice grains.

GC–MS metabolomics of French lettuce (Lactuca Sativa L. var capitata) leaves exposed to bisphenol A via the hydroponic media

IntroductionBisphenol A (BPA), an organic compound used to produce polycarbonate plastics and epoxy resins, has become a ubiquitous contaminant due to its high-volume production and constant release to the environment. Plant metabolomics can trace the stress effects induced by environmental contaminants to the variation of specific metabolites, making it an alternative way to study pollutants toxicity to plants. Nevertheless, there is an important knowledge gap in metabolomics applications in this area.ObjectiveEvaluate the influence of BPA in French lettuce (Lactuca Sativa L. var capitata) leaves metabolic profile by gas chromatography coupled to mass spectrometry (GC–MS) using a hydroponic system.MethodsLettuces were cultivated in the laboratory to minimize biological variation and were analyzed 55 days after sowing (considered the plant’s adult stage). Hexanoic and methanolic extracts with and without derivatization were prepared for each sample and analyzed by GC–MS.ResultsThe highest number of metabolites was obtained from the hexanoic extract, followed by the derivatized methanolic extract. Although no physical differences were observed between control and contaminated lettuce leaves, the multivariate analysis determined a statistically significant difference between their metabolic profiles. Pathway analysis of the most affected metabolites showed that galactose metabolism, starch and fructose metabolism and steroid biosynthesis were significantly affected by BPA exposure.ConclusionsThe preparation of different extracts from the same sample permitted the determination of metabolites with different physicochemical properties. BPA alters the leaves energy and membrane metabolism, plant growth could be affected at higher concentrations and exposition times.

Integrated miRNA and mRNA Transcriptome Analysis Reveals Regulatory Mechanisms in the Response of Winter Brassica rapa to Drought Stress.

Drought is a major abiotic stress factor that reduces agricultural productivity. Understanding the molecular regulatory network of drought response in winter rape is of great significance for molecular Brassica rapa. In order to comprehensively analyze the network expression of DEGs and DEMIs in winter rape under drought stress, in this study we used Longyou 7 as the experimental material to identify DEGs and DEMIs related to drought stress by transcriptome and miRNA sequencing. A total of 14-15 key differential mRNA genes related to drought stress and biological stress were screened out under different treatments in the three groups. and 32 differential miRNAs were identified through targeted regulatory relationships, and the mRNA expression of 20 target genes was negatively regulated by the targeting regulatory relationship. It is mainly enriched in starch and sucrose metabolism, carbon metabolism and other pathways. Among them, gra-MIR8731-p3_2ss13GA18GA regulated the expression of multiple mRNAs in the three treatments. miRNA is mainly involved in the drought resistance of Chinese cabbage winter rape by regulating the expression of target genes, such as starch and sucrose metabolism, amino acid biosynthesis, and carbon metabolism. These miRNAs and their target genes play an indispensable role in winter rapeseed drought stress tolerance regulation.

Metabolomics, phytohormone and transcriptomics strategies to reveal the mechanism of barley heading date regulation to responds different photoperiod

BackgroundThe correlation between heading date and flowering time significantly regulates grain filling and seed formation in barley and other crops, ultimately determining crop productivity. In this study, the transcriptome, hormone content detection, and metabolome analysis were performed systematically to analyze the regulatory mechanism of heading time in highland barley under different light conditions. The heading date of D18 (winter highland barley variety, Dongqing18) was later than that of K13 (vernal highland barley variety) under normal growth conditions or long-day (LD) treatment, while this situation will reverse with short-day (SD) treatment.ResultsThe circadian rhythm plant, plant hormone signaling transduction, starch and sucrose metabolism, and photosynthesis-related pathways are significantly enriched in barley under SD and LD to influence heading time. In the plant circadian rhythm pathway, the key genes GI (Gigantea), PRR (Pesudoresponseregulator), FKF1 (Flavin-binding kelch pepeat F-Box 1), and FT (Flowering locus T) are identified as highly expressed in D18SD3 and K13SD2, while they are significantly down-regulated in K13SD3. These genes play an important role in regulating the heading date of D18 earlier than that of K13 under SD conditions. In photosynthesis-related pathways, a-b binding protein and RBS were highly expressed in K13LD3, while NADP-dependent malic enzyme, phosphoenolpyruvate carboxylase, fructose-bisphosphate aldolase, and triosephosphate isomerase were significantly expressed in D18SD3. In the starch and sucrose metabolism pathway, 41 DEGs (differentially expressed genes) and related metabolites were identified as highly expressed and accumulated in D18SD3. The DEGs SAUR (Small auxin-up RNA), ARF (Auxin response factor), TIR1 (Transport inhibitor response 1), EIN3 (Ethylene-insensitive 3), ERS1 (Ethylene receptor gene), and JAZ1 (Jasmonate ZIM-domain) in the plant hormone pathway were significantly up-regulated in D18SD3. Compared with D18LD3, the content of N6-isopentenyladenine, indole-3-carboxylic acid, 1-aminocyclopropanecarboxylic acid, trans-zeatin, indole-3-carboxaldehyde, 1-O-indol-3-ylacetylglucose, and salicylic acid in D18SD3 also increased. The expression levels of vernalization genes (HvVRN1, HvVRN2, and HvVRN3), photoperiod genes (PPD), and PPDK (Pyruvate phosphate dikinase) that affect photosynthetic efficiency in barley are also analyzed, which play important regulatory roles in barley heading date. The WGCNA analysis of the metabolome data and circadian regulatory genes identified the key metabolites and candidate genes to regulate the heading time of barley in response to the photoperiod.ConclusionThese studies will provide a reference for the regulation mechanism of flowering and the heading date of highland barley.

Profiling the lncRNA–miRNA–mRNA interaction network in the cold-resistant exercise period of grape (Vitis amurensis Rupr.)

BackgroundGrape is a plant that is sensitive to low temperature and vulnerable to low-temperature damage. However, little is known about the roles of lncRNAs, miRNAs and mRNAs in regulating the hypothermia response mechanism in Vitis amurensis Rupr.MethodsIn this study, the expression and regulatory network of low-temperature response genes were studied in the phloem of grape under different low-temperature stress.ResultsHere, we performed analyses related to RNA-seq and miRNA-seq on grape phloem tissues from five periods of cold resistance campaigns. Three RNAs (lncRNAs, miRNAs and mRNAs) obtained by KEGG and GO analyses were used to identify starch and sucrose metabolism associated with cold resistance, and specific changes in BP, CC, and MF were identified in four comparisons. Venn diagrams, thermograms and pathway maps were used to analyze the differentially expressed genes (DEGs), and their specific gene expression during the cold exercise were obtained. The six DEGs finally selected were used for qRT-PCR to verify the RNA-seq data. In addition, we found that the regulatory networks of miRNAs and lncRNAs correspond to the six DEGs. This study will contribute to further experimental studies to elucidate the cold resistance mechanism of Vitis amurensis Rupr.ConclusionsThe low-temperature response genes of grape are mainly enriched in the starch and sucrose metabolism, and they are regulated by miRNAs and lncRNAs. The conclusions will provide basic information for further understanding of the cold resistance mechanism of grape in the future.Graphical

Morphological and Transcriptomic Analyses Reveal the Involvement of Key Metabolic Pathways in Male Sterility in Chimonanthus praecox (L.) Genotypes.

Chimonanthus praecox (Calycanthaceae family) is a unique ornamental and economic flowering tree in China, and after thousands of years of cultivation, it has produced several varieties and varietal types. Notably, male sterility is common in flowering plants and is an important tool for the genetic improvement in plants and optimization using hybrid plant technology; however, there have been no reports on male-sterile material or related studies on C. praecox. To our knowledge, this is the first time that C. praecox male sterility is dissected unveiling the involvement of key metabolic pathways. Notably, male sterility in C. praecox was observed during the budding period and likely occurred during the premature stage of pollen cell maturation. Additionally, differentially expressed genes in the starch and sucrose metabolism pathway and the plant hormone signal transduction pathway showed regular expression trends. This study reports on significant genetic differences that contribute to male sterility in C. praecox and provides a basis for further research and breeding strategies.

Multi-omics analyses reveal the mechanisms underlying the responses of Casuarina equisetifolia ssp. incana to seawater atomization and encroachment stress

Casuarina equisetifolia trees are used as windbreaks in subtropical and tropical coastal zones, while C. equisetifolia windbreak forests can be degraded by seawater atomization (SA) and seawater encroachment (SE). To investigate the mechanisms underlying the response of C. equisetifolia to SA and SE stress, the transcriptome and metabolome of C. equisetifolia seedlings treated with control, SA, and SE treatments were analyzed. We identified 737, 3232, 3138, and 3899 differentially expressed genes (SA and SE for 2 and 24 h), and 46, 66, 62, and 65 differentially accumulated metabolites (SA and SE for 12 and 24 h). The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that SA and SE stress significantly altered the expression of genes related to plant hormone signal transduction, plant–pathogen interaction, and starch and sucrose metabolism pathways. The accumulation of metabolites associated with the biosynthetic pathways of phenylpropanoid and amino acids, as well as starch and sucrose metabolism, and glycolysis/gluconeogenesis were significantly altered in C. equisetifolia subjected to SA and SE stress. In conclusion, C. equisetifolia responds to SA and SE stress by regulating plant hormone signal transduction, plant–pathogen interaction, biosynthesis of phenylpropanoid and amino acids, starch and sucrose metabolism, and glycolysis/gluconeogenesis pathways. Compared with SA stress, C. equisetifolia had a stronger perception and response to SE stress, which required more genes and metabolites to be regulated. This study enhances our understandings of how C. equisetifolia responds to two types of seawater stresses at transcriptional and metabolic levels. It also offers a theoretical framework for effective coastal vegetation management in tropical and subtropical regions.

Integrated cytological, physiological, and comparative transcriptome profiling reveals the regulatory network for male sterility in Welsh onion (Allium fistulosum L.)

Welsh onion (Allium fistulosum L.) is a specialty crop with value as a vegetable, condiment, and medicine. However, the molecular mechanisms related to pollen abortion and cytoplasmic male sterility are poorly understood, limiting the heterosis utilization and hybrid production of A. fistulosum. This study investigated the dynamic differences between male-sterile (MS) plants and male-fertile (MF) plants at different anther developmental stages based on integrated cytological, physiological, and transcriptomic analyses. Cytological observations revealed that pollen abortion in the MS plants began during the tetrad stage and was caused by vacuolated microspores, abnormal degradation of the tapetum, and inadequate nutrient supply. The physiological results showed that MS plants exhibited low total soluble sugar and starch contents and decreased antioxidant enzyme activities (peroxidase and catalase). Comparative transcriptome analysis identified 7005 differentially expressed genes (DEGs) and functional enrichment analysis indicated that significant transcriptomic differences were related to oxidative phosphorylation, starch and sucrose metabolism, and cutin, suberine, and wax biosynthesis. The relative expression levels of key DEGs in these three important metabolic pathways were determined using quantitative real-time polymerase chain reaction. On this basis, a core transcriptome-mediated MS network was proposed for MS plants with four functional components: inhibited sucrose synthesis and transport; blocked cutin, suberine, and wax synthesis; accelerated reactive oxygen species generation; and abnormal tapetal programmed cell death. These results provide theoretical guidance for further exploring the molecular mechanisms of male sterility in A. fistulosum.

Transcriptome profiling reveals insight into the cold response of perennial ryegrass genotypes with contrasting freezing tolerance

Low freezing tolerance threatens the survival and productivity of perennial ryegrass under northern climate. In this study, we aimed to identify transcriptional changes in plants subjected to low and freezing temperatures as well as to elucidate differences between tolerant and sensitive genotypes. Response to freezing stress was evaluated in a panel of 160 perennial ryegrass genotypes by measuring electrolyte leakage after exposure to -12 °C and -14 °C for 24 h. Two tolerant and two sensitive genotypes were selected for the transcriptome analysis. Crown tissue samples were collected at six treatments: before the start of cold acclimation (control point), at the start of acclimation, after one week of acclimation, after three weeks of acclimation, after freezing at -5 °C and freezing at -10 °C. A total of 11,125 differentially expressed genes (DEGs) were identified in the sensitive and 12,937 DEGs in the tolerant genotypes, when comparing the control vs. each of the acclimation and freezing treatments, as well as the end of acclimation vs. freezing treatments. Among the identified DEGs 3323 were unique to the sensitive genotypes, 5135 were unique to the tolerant genotypes and 7802 were shared. Genes upregulated during cold acclimation and freezing stress were linked to the MAPK signalling pathway, circadian rhythm, starch and sucrose metabolism, plant-pathogen interaction, carbon fixation, alpha-linoleic acid metabolism, carotenoid metabolism, glyoxylate and dicarboxylate metabolism pathways. Downregulated genes were linked to ATP-dependent chromatin remodelling, fatty acid elongation and DNA replication. The downregulation of fatty acid elongation and glutathione metabolism DEGs could indicate that the studied genotypes respond to cold stress in a novel or not yet well-characterized manner.

Multi-omics study on the mixed culture of Trichoderma reesei and Aspergillus niger with improved lignocellulase production

The mixed culture of Trichoderma reesei and Aspergillus niger were found to improve lignocellulase production and ameliorate the composition (Fang et al., 2010; Fang et al., 2013; Zhao et al., 2018) [1-3]. However, the mechanism behind remained unclear. Here we conducted multi-omics study of the mixed culture to elucidate the mechanism comprehensively, including proteomics of the secretomes, metabolomics of the fermentation broths and transcriptomics. The mechanisms at transcriptional, proteomic and metabolomic levels were clarified. Proteomics show many proteins in the secretomes were up-regulated by the mix culture of T. reesei and A. niger, and lignocellulase production and the composition were improved, but the protein numbers and abundances of the lignocellulases were reduced. Transcriptomics demonstrate that lignocellulase gene expressions, stress responses and anti-stress were co-regulated in T. reesei, and that most lignocellulase genes in T. reesei were up-regulated and most A. niger lignocellulase genes were down-regulated. Metabolomics reveal the chemicals and the mechanism of the communication between T. reesei and A. niger in the mixed culture for improved lignocellulase production. The secondary metabolites such as p-cresol, nodularin and tolazoline could play important roles. Integrative analyses indicate that the secondary metabolites, stress-response, anti-stress, starch and sucrose metabolism and lignocellulase gene expressions were orchestrated. As a result, the roles of T. reesei and A. niger in the mixed culture were defined. The mechanism of the mixed culture for improved lignocellulase production was obtained, in short T. reesei was the major role and A. niger the minor. This work provides theory and targets as basis to obtain complete understanding of the mechanism and guide engineering of the microbial consortium of T. reesei and A. niger for further improvements.

Metagenomic profiling of gut microbiota in Fall Armyworm (Spodoptera frugiperda) larvae fed on different host plants

BackgroundThe fall armyworm (FAW, Spodoptera frugiperda) is a polyphagous pest known for causing significant crop damage. The gut microbiota plays a pivotal role in influencing the biology, physiology and adaptation of the host. However, understanding of the taxonomic composition and functional characteristics of the gut microbiota in FAW larvae fed on different host plants remains limited.MethodsThis study utilized metagenomic sequencing to explore the structure, function and antibiotic resistance genes (ARGs) of the gut microbiota in FAW larvae transferred from an artificial diet to four distinct host plants: maize, sorghum, tomato and pepper.ResultsThe results demonstrated significant variations in gut microbiota structure among FAW larvae fed on different host plants. Firmicutes emerged as the dominant phylum, with Enterococcaceae as the dominant family and Enterococcus as the prominent genus. Notably, Enterococcus casseliflavus was frequently observed in the gut microbiota of FAW larvae across host plants. Metabolism pathways, particularly those related to carbohydrate and amino acid metabolism, played a crucial role in the adaptation of the FAW gut microbiota to different host plants. KEGG orthologs associated with the regulation of the peptide/nickel transport system permease protein in sorghum-fed larvae and the 6-phospho-β-glucosidase gene linked to glycolysis/gluconeogenesis as well as starch and sucrose metabolism in pepper-fed larvae were identified. Moreover, the study identified the top 20 ARGs in the gut microbiota of FAW larvae fed on different host plants, with the maize-fed group exhibiting the highest abundance of vanRC.ConclusionsOur metagenomic sequencing study reveals significant variations in the gut microbiota composition and function of FAW larvae across diverse host plants. These findings underscore the intricate co-evolutionary relationship between hosts and their gut microbiota, suggesting that host transfer profoundly influences the gut microbiota and, consequently, the adaptability and pest management strategies for FAW.

Main metabolic pathways of Solanum nigrum L. hyperaccumulating cadmium except of copper simultaneously through differentially expressed proteins analysis

Determining the hyperaccumulation mechanism of Solanum nigrum L., which exclusively accumulates cadmium (Cd), presents significant challenges due to the difficulty in identifying its unique characteristics. While some metabolic pathways related to Cd accumulation can be explored, there are no methods to ascertain if other heavy metals may share the same pathways. Isobaric tags for relative and absolute quantitation (iTRAQ) were employed to investigate the metabolic pathways associated with Cd hyperaccumulation and Cu accumulation (non-Cu hyperaccumulator) by comparing differentially expressed proteins (DEPs). The results showed that 27 intersecting DEPs reflecting relative metabolic pathways related to Cd accumulation were identified by comparing DEPs in leaves and roots, including carbon metabolism, aminoacyl-tRNA biosynthesis, phagosome, peroxisome, as well as starch and sucrose metabolism. These pathways might be responsible for the values of Cd enrichment factor (EF) and translocation factor (TF) exceeding 1, associated with key proteins participated in phosphoenolpyruvate, carboxylase, chloroplastic catalytic activity, and granule-bound starch synthase I. The combined metabolic pathways identified by 2 intersecting DEPs related to Cu accumulation could result in Cu EF >1 in the 0.2 Cu mg kg−1 treatment, EF <1 in the 5 mg kg−1 treatment, and TF<1 in both treatments, associated with key proteins, which might concern photosynthesis-antenna proteins and hydroxymethylbilane synthase. No metabolic pathways related to simultaneous accumulation of Cd and Cu has been identified. The identified DEPs were validated using Western blotting with five key proteins. Additionally, Western blotting and yeast mutant confirmed the presence of proteins related to carbon fixation in photosynthetic organisms, carbon metabolism, peroxisome, as well as starch and sucrose metabolism. Photosynthetic, O2•−, H2O2 and non-enzymatic antioxidants indices reflecting protein-related differences indirectly supported the above results. These findings are crucial for further exploration of the Cd hyperaccumulation mechanism.

Genome-wide analysis of DNA methylation and transcriptional changes associated with overwintering memory in Brassica rapa L. grown in the field

BackgroundWinter rapeseed, the sole overwintering oilseed crop in northern China, emphasizes winter resilience, yet epigenetic regulatory mechanisms governing overwintering memory remain poorly understood.ResultsIn this study, the root collar tissues from the robust cold-resistant variety Longyou-7 were sampled during the pre-winter period (S1), overwintering periods (S2–S5), and re-greening period (S6), to analyze overall genomic DNA methylation levels using high-performance liquid chromatography (HPLC). The result showed that DNA methylation level exceeded 80% in the S1 stage. Throughout the overwintering periods, methylation levels displayed a decreasing trend in S3, followed by an increase in S5, and a pronounced decrease in S6. Consequently, S1, S3, S5, and S6 periods were chosen for whole-genome bisulfite sequencing analyses to elucidate the overwintering memory mechanisms of Longyou-7. The result revealed that DNA methylation primarily occurs in the CG context in Longyou-7. However, methylation of mC sites is most prevalent in the CHH type, gradually decreasing during overwintering periods. Analysis of methylation patterns in specific genomic regions of Longyou-7 showed that the highest methylation levels in the intergenic region. Moreover, mC sites in repeats and transposon elements are distributed differently across the three contexts. Subsequently, differentially methylated regions and promoters of Longyou-7 were identified during various periods compared to the S1 stage, followed by joint analysis with transcriptome sequencing. Functional enrichment analysis highlighted the involvement of most overlapping genes in the MAPK signaling pathway, plant hormone signal transduction, and starch and sucrose metabolism pathways. Changes in candidate gene expression within these three pathways correlated closely with DNA methylation levels.ConclusionsOur findings underscored the critical role of DNA methylation in regulating the expression of overwintering memory genes in winter rapeseed. These results offer a comprehensive insights into the epigenetic regulatory mechanisms governing winter rapeseed's overwintering memory, while identified overwintering memory genes served as crucial genetic resources for multifaceted breeding of winter-resistant varieties.Graphical

Genome-wide transcriptome and gene family analysis reveal candidate genes associated with potassium uptake of maize colonized by arbuscular mycorrhizal fungi

BackgroundPotassium (K) is an essential nutrient for plant growth and development. Maize (Zea mays) is a widely planted crops in the world and requires a huge amount of K fertilizer. Arbuscular mycorrhizal fungi (AMF) are closely related to the K uptake of maize. Genetic improvement of maize K utilization efficiency will require elucidating the molecular mechanisms of maize K uptake through the mycorrhizal pathway. Here, we employed transcriptome and gene family analysis to elucidate the mechanism influencing the K uptake and utilization efficiency of mycorrhizal maize.Methods and resultsThe transcriptomes of maize were studied with and without AMF inoculation and under different K conditions. AM symbiosis increased the K concentration and dry weight of maize plants. RNA sequencing revealed that genes associated with the activity of the apoplast and nutrient reservoir were significantly enriched in mycorrhizal roots under low-K conditions but not under high-K conditions. Weighted gene correlation network analysis revealed that three modules were strongly correlated with K content. Twenty-one hub genes enriched in pathways associated with glycerophospholipid metabolism, glycerolipid metabolism, starch and sucrose metabolism, and anthocyanin biosynthesis were further identified. In general, these hub genes were upregulated in AMF-colonized roots under low-K conditions. Additionally, the members of 14 gene families associated with K obtain were identified (ARF: 38, ILK: 4, RBOH: 12, RUPO: 20, MAPKK: 89, CBL: 14, CIPK: 44, CPK: 40, PIN: 10, MYB: 174, NPF: 79, KT: 19, HAK/HKT/KUP: 38, and CPA: 8) from maize. The transcript levels of these genes showed that 92 genes (ARF:6, CBL:5, CIPK:13, CPK:2, HAK/HKT/KUP:7, PIN:2, MYB:26, NPF:16, RBOH:1, MAPKK:12 and RUPO:2) were upregulated with AM symbiosis under low-K conditions.ConclusionsThis study indicated that AMF increase the resistance of maize to low-K stress by regulating K uptake at the gene transcription level. Our findings provide a genome-level resource for the functional assignment of genes regulated by K treatment and AM symbiosis in K uptake-related gene families in maize. This may contribute to elucidate the molecular mechanisms of maize response to low K stress with AMF inoculation, and provided a theoretical basis for AMF application in the crop field.

Transcriptome Analysis Reveals the Mechanism of Cold-Induced Sweetening in Chestnut during Cold Storage.

Chestnuts become sweetened with better tastes for fried products after cold storage, but the possible mechanism is not clear. The dynamics of sugar components and related physiological responses, as well as the possible molecular mechanism in chestnuts during cold storage, were investigated. Sucrose accumulation and starch degradation contributed to taste improvement. Sucrose content reached the peak after two months of cold storage, along with the accumulation of reducing sugars of maltose, fructose and glucose to a much lesser extent. Meanwhile, alpha-amylase and beta-amylase maintained high levels, and the activities of acid invertase and sucrose synthase increased. Transcriptome data demonstrated that differentially expressed genes (DEGs) were significantly enriched in the process of starch and sucrose metabolism pathway, revealing the conversion promotion of starch to sucrose. Furthermore, DEGs involved in multiple phytohormone biosynthesis and signal transduction, as well as the transcription regulators, indicated that sucrose accumulation might be interconnected with the dormancy release of chestnuts, with over 90% germinated after two months of cold storage. Altogether, the results indicated that cold storage improved the taste of chestnuts mainly due to sucrose accumulation induced by DEGs of starch and sucrose metabolism pathway in this period, and the sweetening process was interconnected with dormancy release.

Effects of storage period and season on the microecological characteristics of Jiangxiangxing high-temperature Daqu

Metagenomics, non-targeted metabolomics, and metaproteomics were employed to analyze the microecological succession of high-temperature Daqu during storage, elucidate the adaptation mechanism of the microbial community of Daqu to storage environments, and clarify the microecological characteristics of Daqu during different seasons. During storage, the relative abundances of Bacillus, Oceanobacillus, Staphylococcus, and Aspergillus in Daqu had significantly increased, while those of Kroppenstedtia, Saccharopolyspora, Thermoascus, and Thermomyces had significantly decreased. During the first 3 months of storage, compound metabolism of Daqu was primarily dominated by generation of small molecular substances and then shifted to metabolism of amino sugars. During the storage process, homogeneous selection (15.57 %) and homogeneous diffusion (14.86 %) of the microbial communities of Daqu were much larger than during the fermentation process, while the variable selection assembly (29.43 %) was smaller than during the fermentation process. Among the 2509 proteins identified in the four-season Daqu, bacterial protein expression was 1.46-fold greater than that of fungi. Seasonal factors influenced the function of Daqu by alterations to Bacillus subtilis, Oceanobacillus iheyensis, and Aspergillus nidulans and other microbial functions. Carbon and benzoic acid metabolism of Daqu was relatively increased during the spring, while metabolism of alkaloids and tyrosine was upregulated during the summer, amino acid synthesis and starch metabolism were enriched during the autumn, and peptidoglycan synthesis was relatively greater during the winter. Adjusting the moisture content of Daqu during the storage period was shown to reduce microecological differentiation caused by seasonal temperature variations.

Quantitative proteomic analysis reveals hub proteins for high temperature-induced male sterility in bread wheat (Triticum aestivum L.).

High-temperature (HT) stress can induce male sterility in wheat; however, the underlying mechanisms remain poorly understood. This study examined proteomic alterations across three developmental stages between normal and HT-induced male-sterile (HT-ms) anthers in wheat. Utilizing tandem mass tags-based proteomics, we identified 2532 differentially abundant proteins (DAPs): 27 in the tetrad stage, 157 in the binuclear stage, and 2348 in the trinuclear stage. Analyses through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways indicated significant enrichment of these DAPs in seven pathways, namely phenylpropanoid biosynthesis, flavonoid biosynthesis, sphingolipid metabolism, MAPK signaling pathway, starch and sucrose metabolism, response to heat, and response to reactive oxygen species (ROS). Our results indicated the downregulation of DAPs associated with phenylpropanoid biosynthesis and starch and sucrose metabolism, which aligns with anther indehiscence and the lack of starch in HT-ms anthers. By contrast, DAPs in the ROS pathway were upregulated, which aligns with excessive ROS accumulation in HT-ms anthers. Additionally, we conducted protein-protein interaction analysis for the DAPs of these pathways, identifying 15 hub DAPs. The abundance of these hub proteins was confirmed through qRT-PCR, assessing mRNA expression levels of the corresponding transcripts. Collectively, these results offer insights into the molecular mechanisms underlying HT-induced male sterility in wheat at the proteomic level, providing a valuable resource for further research in plant sexual reproduction.