Starch Metabolism Research Articles

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.

Bioturbation effect of high - Yield pyrazine strain on the microbial community and flavour metabolites of fortified Daqu

In order to comprehensively explore the regulatory effect of bioturbation on the assembly and overall metabolic characteristics of Daqu microbial community. This study used metatranscriptomics and metabolomics to investigate the composition of the microbial community, physicochemical properties, and overall metabolic profile of Daqu before and after bioturbation by Bacillus velezensis. The results demonstrated that the acidity, moisture, amino acid nitrogen, and starch content of Daqu exhibited a significant increase following bioturbation. The symbol microorganisms of Daqu have also changed significantly, from the original Aspergillus chevalieri, Rasamsonia emersonii, Aspergillus ruber, Aspergillus glaucus, Aspergillus wentii and Aspergillus cristatus to Paecilomyces varioti, Trichomonascus ciferrii and Staphylococcus gallinarum. Correlation analyses and integration pathways indicated that altered microbial community abundance also promoted the metabolism of starch, ethanol, fatty acids, and pyrazine, resulting in a significant enhancement of Daqu's saccharification and liquefaction power, as well as the content of some volatile and non-volatile metabolites, with pyrazines increased by 24.50%. The application of fortified Daqu to Baijiu fermentation can significantly enhance the content of various pyrazines in Baijiu. These results are helpful to elucidate the mechanism of biochemical changes, microbial assembly and flavor production of Daqu after biodisturbance.

Interactions at the Oviposition Scar: Molecular and Metabolic Insights into Elaeagnus angustifolia's Resistance Response to Anoplophora glabripennis.

The Russian olive (Elaeagnus angustifolia), which functions as a "dead-end trap tree" for the Asian long-horned beetle (Anoplophora glabripennis) in mixed plantations, can successfully attract Asian long-horned beetles for oviposition and subsequently kill the eggs by gum. This study aimed to investigate gum secretion differences by comparing molecular and metabolic features across three conditions-an oviposition scar, a mechanical scar, and a healthy branch-using high-performance liquid chromatography and high-throughput RNA sequencing methods. Our findings indicated that the gum mass secreted by an oviposition scar was 1.65 times greater than that secreted by a mechanical scar. Significant differences in gene expression and metabolism were observed among the three comparison groups. A Kyoto Encyclopedia of Genes and Genomes annotation and enrichment analysis showed that an oviposition scar significantly affected starch and sucrose metabolism, leading to the discovery of 52 differentially expressed genes and 7 differentially accumulated metabolites. A network interaction analysis of differentially expressed metabolites and genes showed that EaSUS1, EaYfcE1, and EaPGM1 regulate sucrose, uridine diphosphate glucose, α-D-glucose-1P, and D-glucose-6P. Although the polysaccharide content in the OSs was 2.22 times higher than that in the MSs, the sucrose content was lower. The results indicated that the Asian long-horned beetle causes Russian olive sucrose degradation and D-glucose-6P formation. Therefore, we hypothesized that damage caused by the Asian long-horned beetle could enhance tree gum secretions through hydrolyzed sucrose and stimulate the Russian olive's specific immune response. Our study focused on the first pair of a dead-end trap tree and an invasive borer pest in forestry, potentially offering valuable insights into the ecological self-regulation of Asian long-horned beetle outbreaks.

Role of auxin and gibberellin under low light in enhancing saffron corm starch degradation during sprouting

The mechanisms by which low light accelerates starch macromolecules degradation by auxin and gibberellin (GA) in geophytes during sprouting remain largely unknown. This study investigated these mechanisms in saffron, grown under low light (50 μmol m−2 s−1) and optimal light (200 μmol m−2 s−1) during the sprouting phase. Low light reduced starch concentration in corms by 34.0 % and increased significantly sucrose levels in corms, leaves, and leaf sheaths by 19.2 %, 9.8 %, and 134.5 %, respectively. This was associated with a 33.3 % increase in GA3 level and enhanced auxin signaling. Leaves synthesized IAA under low light, which was transported to the corms to promote GA synthesis, facilitating starch degradation through a 228.7 % increase in amylase activity. Exogenous applications of GA and IAA, as well as the use of their synthesis or transport inhibitors, confirmed the synergistic role of these phytohormones in starch metabolism. The unigenes associated with GA biosynthesis and auxin signaling were upregulated under low light, highlighting the IAA-GA module role in starch degradation. Moreover, increased respiration rate and invertase activity, crucial for ATP biosynthesis and the tricarboxylic acid cycle, were consistent with the upregulation of related unigenes, suggesting that auxin signaling accelerates starch degradation by promoting energy metabolism. Upregulated of auxin signaling (CsSAUR32) and starch metabolism (CsSnRK1) genes under low light suggests that auxin directly regulate starch degradation in saffron corms. This study elucidates that low light modulates auxin and GA interactions to accelerate starch degradation in saffron corms during sprouting, offering insights for optimizing agricultural practices under suboptimal light conditions.

Source leaves are regulated by sink strengths through non-coding RNAs and alternative polyadenylation in cucumber (Cucumis sativus L.)

BackgroundThe yield of major crops is generally limited by sink capacity and source strength. Cucumber is a typical raffinose family oligosaccharides (RFOs)–transporting crop. Non-coding RNAs and alternative polyadenylation (APA) play important roles in the regulation of growth process in plants. However, their roles on the sink‒source regulation have not been demonstrated in RFOs–translocating species.ResultsHere, whole–transcriptome sequencing was applied to compare the leaves of cucumber under different sink strength, that is, no fruit-carrying leaves (NFNLs) and fruit-carrying leaves (FNLs) at 12th node from the bottom. The results show that 1101 differentially expressed (DE) mRNAs, 79 DE long non–coding RNAs (lncRNAs) and 23 DE miRNAs were identified, which were enriched in photosynthesis, energy production and conversion, plant hormone signal transduction, starch and carbohydrate metabolism and protein synthesis pathways. Potential co–expression networks like, DE lncRNAs–DE mRNAs/ DE miRNAs–DE mRNAs, and competing endogenous RNA (ceRNA) regulation models (DE lncRNAs–DE miRNAs–DE mRNAs) associated with sink‒source allocation, were constructed. Furthermore, 37 and 48 DE genes, which enriched in MAPK signaling and plant hormone signal transduction pathway, exist differentially APA, and SPS (CsaV3_2G033300), GBSS1 (CsaV3_5G001560), ERS1 (CsaV3_7G029600), PNO1 (CsaV3_3G003950) and Myb (CsaV3_3G022290) may be regulated by both ncRNAs and APA between FNLs and NFNLs, speculating that ncRNAs and APA are involved in the regulation of gene expression of cucumber sink‒source carbon partitioning.ConclusionsThese results reveal a comprehensive network among mRNAs, ncRNAs, and APA in cucumber sink–source relationships. Our findings also provide valuable information for further research on the molecular mechanism of ncRNA and APA to enhance cucumber yield.

SlNAP1 promotes tomato fruit ripening by regulating carbohydrate metabolism

Many studies showed NAC transcription factors play an important role in fruit ripening. Moreover, sucrose and starch metabolism is also closely related to fruit ripening. However, there are a few studies focus on whether NAC regulates sucrose and starch metabolism to influence fruit ripening. In this study, virus-induced gene silencing (VIGS) of SlNAP1 suppressed fruit ripening and delayed color transformation. The chlorophyll (including Chla, Chlb, and Chla + b) degradation and carotenoid synthesis in SlNAP1-silenced fruits were dramatically suppressed. Silencing SlNAP1 decreased soluble sugar and reducing sugar accumulation in fruits, and increased starch content. The activity of starch degrading enzymes, including α amylase (AMY) and β amylase (BAM) was significantly lower in SlNAP1-silenced fruits than in the control fruits, whereas denosine diphosphoglucose pyrophosphorylase (AGP) activity was significantly higher. In addition, the expression of starch degradation-related genes (SlAMY1, SlAMY2, SlBAM1, SlBAM7, SlGWD, SlPWD) in SlNAP1-silenced fruits was significantly suppressed, while starch synthesis-related genes (SlAGPase1, SlAGPase2) was significantly increased. Compared with the control fruits, SlNAP1-silenced fruits showed significantly lower sucrose and glucose content. The expression level of sucrose and glucose metabolism-related genes such as Slsus1, Slsus3, SlSPS, SlHxk1, SlHxk2, SlPK1, and SlPK2 was significantly lower in SlNAP1-silenced fruits than in the control fruits. Overall, this study revealed that SlNAP1 gene might positively regulate fruit ripening by influencing carbohydrate metabolism.

Genome-Wide Identification of microRNAs Associated with Starch Biosynthesis and Endosperm Development in Foxtail Millet.

Foxtail millet is one of the oldest crops, and its endosperm contains up to 70% of starch. Grain filling is an important starch accumulation process associated with foxtail millet yield and quality. However, the molecular mechanisms of grain filling in foxtail millet are relatively unclear. Here, we investigate the genes and regulated miRNAs associated with starch synthesis and metabolism in foxtail millet using high-throughput small RNA, mRNA and degradome sequencing. The regulation of starch synthesis and quality is carried out mainly at the 15 DAA to 35 DAA stage during grain filling. The DEGs between waxy and non-waxy foxtail millet were significant, especially for GBSS. Additionally, ptc-miR169i_R+2_1ss21GA, fve-miR396e_L-1R+1, mtr-miR162 and PC-5p-221_23413 regulate the expression of genes associated with the starch synthesis pathway in foxtail millet. This study provides new insights into the molecular mechanisms of starch synthesis and quality formation in foxtail millet.

Identification of candidate genes associated with double flowers via integrating BSA-seq and RNA-seq in Brassica napus

As a Brassica crop, Brassica napus typically has single flowers that contain four petals. The double-flower phenotype of rapeseed has been a desirable trait in China because of its potential commercial value in ornamental tourism. However, few double-flowered germplasms have been documented in B. napus, and knowledge of the underlying genes is limited. Here, B. napus D376 was characterized as a double-flowered strain that presented an average of 10.92 ± 1.40 petals and other normal floral organs. F1, F2 and BC1 populations were constructed by crossing D376 with a single-flowered line reciprocally. Genetic analysis revealed that the double-flower trait was a recessive trait controlled by multiple genes. To identify the key genes controlling the double-flower trait, bulk segregant analysis sequencing (BSA-seq) and RNA-seq analyses were conducted on F2 individual bulks with opposite extreme phenotypes. Through BSA-seq, one candidate interval was mapped at the region of chromosome C05: 14.56–16.17 Mb. GO and KEGG enrichment analyses revealed that the DEGs were significantly enriched in carbohydrate metabolic processes, notably starch and sucrose metabolism. Interestingly, five and thirty-six DEGs associated with floral development were significantly up- and down-regulated, respectively, in the double-flowered plants. A combined analysis of BSA-seq and RNA-seq data revealed that five genes were candidates associated with the double flower trait, and BnaC05.ERS2 was the most promising gene. These findings provide novel insights into the breeding of double-flowered varieties and lay a theoretical foundation for unveiling the molecular mechanisms of floral development in B. napus.

Transcriptomic and Hormonal Changes in Wheat Roots Enhance Growth under Moderate Soil Drying.

Understanding the mechanisms that regulate plant root growth under soil drying is an important challenge in root biology. We observed that moderate soil drying promotes wheat root growth. To understand whether metabolic and hormonic changes are involved in this regulation, we performed transcriptome sequencing on wheat roots under well-watered and moderate soil drying conditions. The genes upregulated in wheat roots under soil drying were mainly involved in starch and sucrose metabolism and benzoxazinoid biosynthesis. Various plant hormone-related genes were differentially expressed during soil drying. Quantification of the plant hormones under these conditions showed that the concentrations of abscisic acid (ABA), cis-zeatin (CZ), and indole-3-acetic acid (IAA) significantly increased during soil drying, whereas the concentrations of salicylic (SA), jasmonic (JA), and glycosylated salicylic (SAG) acids significantly decreased. Correlation analysis of total root length and phytohormones indicated that CZ, ABA, and IAA are positively associated with wheat root length. These results suggest that changes in metabolic pathways and plant hormones caused by moderate soil drying help wheat roots grow into deeper soil layers.

Physiological and transcriptomic profiles reveal key regulatory pathways involved in cold resistance in sunflower seedlings

During sunflower growth, cold waves often occur and impede plant growth. Therefore, it is crucial to study the underlying mechanism of cold resistance in sunflowers. In this study, physiological analysis revealed that as cold stress increased, the levels of ROS, malondialdehyde, ascorbic acid, and dehydroascorbic acid and the activities of antioxidant enzymes increased. Transcriptomics further identified 10,903 DEGs between any two treatments. Clustering analysis demonstrated that the expression of MYB44a, MYB44b, MYB12, bZIP2 and bZIP4 continuously upregulated under cold stress. Cold stress can induce ROS accumulation, which interacts with hormone signals to activate cold-responsive transcription factors regulating target genes involved in antioxidant defense, secondary metabolite biosynthesis, starch and sucrose metabolism enhancement for improved cold resistance in sunflowers. Additionally, the response of sunflowers to cold stress may be independent of the CBF pathway. These findings enhance our understanding of cold stress resistance in sunflowers and provide a foundation for genetic breeding.

Comparative Morphological, Physiological, and Transcriptomic Analyses of Diploid and Tetraploid Wucai (Brassica campestris L.).

Polyploid plants often exhibit superior yield, stress resistance, and quality. In this study, homologous tetraploid wucai (Brassica campestris L.) was successfully obtained by spraying seedling growth points with colchicine. The morphological, cytological, and physiological characteristics of diploid and tetraploid wucai were analyzed, and transcriptomic sequencing was performed at three stages of development. Tetraploid seedings grew slowly but exhibited darker leaves, enlarged organs and cells, increased stomatal volume, decreased stomatal density, improved nutritional content, and enhanced photosynthesis. Differentially expressed genes (DEGs) identified in diploid and tetraploid plants at three stages of development were enriched in different pathways. Notably, DEGs identified in the tetraploid plants were specifically enriched in starch and sucrose metabolism, pentose and glucuronate interconversions, and ascorbate and aldarate metabolism. In addition, we found that the light green module was most relevant to ploidy, and DEGs in this module were significantly enriched in the glycolysis/gluconeogenesis and TCA cycle pathways. The differential expression of key glycolysis-associated genes at different developmental stages may be the driver of the observed differences between diploid and tetraploid wucai. This study lays a technical foundation for the development of polyploid wucai germplasm resources as well as the breeding of new varieties with improved quality, yield, and stress resistance. It also provides a good empirical reference for the genetic breeding of closely related Brassica species.

Dynamic changes of starch properties, sweetness, and β-amylases during the development of sweet potato storage roots

Starch and sugar properties and sweetness of storage root (SR) are vital to the economic value of sweet potato. To clarify the factors determining these properties of raw sweet potato, eleven varieties with different SR properties were selected to investigate the changes of starch and sugar-related traits, brix and amylase activities during the growth and development of SRs, and the correlation among these SR properties and the amylase activities were analyzed. Five β-amylase genes expressed in SRs were cloned, and their expression and characteristics were analyzed to reveal the involvement of amylase in these SR properties. The results showed total sugar, soluble sugar, reducing sugar content and brix varied greatly among different varieties and development periods, β-amylase activities were much higher than that of α-amylase in SRs, dynamically changed during the development of SRs, and decreased at the late stage of SR expansion. The expression of three β-amylase encoding genes were positively correlated with the total sugar content, and might play vital roles in starch and sugar metabolism in SRs. The brix of raw SRs was significantly correlated with total starch, amylose, amylopectin, total sugar content and reducing sugar content, but had no significant relationship with soluble sugar content and β-amylase activity. These results indicated that the brix of SR was determined by both starch and sugar components, and multiple β-amylases function together in starch and sugar metabolism in developing SRs. These findings provide important information for the improvement of sweetness and the quality of processed products in sweet potato.