Starch Metabolism Genes Research Articles

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.

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.

Integrated transcriptomic and proteomic analyses reveal the molecular mechanism underlying the thermotolerant response of Spodoptera frugiperda

Spodoptera frugiperda (Lepidoptera: Noctuidae) is a highly destructive invasive pest with remarkable adaptability to extreme climatic conditions, posing a substantial global threat. Although the effects of temperature stress on the biological and ecological properties of S. frugiperda have been elucidated, the molecular mechanisms underlying its responses remain unclear. Herein, we combined transcriptomic and proteomic analyses to explore the key genes and proteins involved in thermotolerance regulation in S. frugiperda larvae at 42 °C. Overall, 1528 differentially expressed genes (DEGs) and 154 differentially expressed proteins (DEPs) were identified in S. frugiperda larvae under heat stress, including antioxidant enzymes, heat shock proteins (Hsps), cytochrome P450s, starch and sucrose metabolism genes, and insulin signaling pathway genes, indicating their involvement in heat tolerance regulation. Correlation analysis of DEGs and DEPs revealed that seven and eight had the same and opposite expression profiles, respectively. After nanocarrier-mediated RNA interference knockdown of SfHsp29, SfHsp20.4, SfCAT, and SfGST, the body weight and mortality of S. frugiperda larvae significantly decreased and increased under heat stress, respectively. This indicates that SfHsp29, SfHsp20.4, SfCAT, and SfGST play a crucial role in the thermotolerance of S. frugiperda larvae. These results provide insight into the mechanism of heat tolerance in S. frugiperda.

Integrated Bioinformatics and Multi-Omics Analyses Reveal Possible Molecular Mechanisms for Seed Starch Content Differences between Glycine max and Cicer arietinum

Although soybean and chickpea belong to the legume family, their seed starch content is very different. Currently, many studies focus on the molecular mechanisms of starch synthesis within a single species. However, the key genes and regulatory relationships responsible for the difference in seed starch content between the two species remain unknown. To elucidate the molecular mechanisms responsible for the above difference, multi-omics and bioinformatics analyses were used here to analyze gene expression patterns, protein–protein interaction networks, gene-transcription factor co-expression networks, and miRNA–gene regulatory relationships based on reported sucrose and starch metabolic genes in Arabidopsis. The results were as follows. First, seven differential expression genes of the two species in starch synthesis metabolism, including GBSS1, APL3, APS1, SS2, PTST, SBE2, and ISA, and the starch degradation gene BMY in soybean and chickpea, may contribute to their seed starch content differences. Then, the protein–protein interaction between DPEs and PHS may facilitate seed starch synthesis in chickpea. Finally, the positive regulation of two starch degradation genes (GmBMY and GmPHS) and four sucrose metabolism genes (GmHXK, GmPFK, GmTPS, and GmFRK) by transcription factors may lead to lower seed starch content in soybean. This study elucidates the possible molecular mechanisms underlying the difference in seed starch content between the two species and addresses the scientific problem of why soybean seeds have lower starch content than chickpea seeds.

The transcription factors ZmNAC128 and ZmNAC130 coordinate with Opaque2 to promote endosperm filling in maize.

Endosperm filling in maize (Zea mays), which involves nutrient uptake and biosynthesis of storage reserves, largely determines grain yield and quality. However, much remains unclear about the synchronization of these processes. Here, we comprehensively investigated the functions of duplicate NAM, ATAF1/2, and CUC2 (NAC)-type transcription factors, namely, ZmNAC128 and ZmNAC130, in endosperm filling. The gene-edited double mutant zmnac128 zmnac130 exhibits a poorly filled kernel phenotype such that the kernels have an inner cavity. RNA sequencing and protein abundance analysis revealed that the expression of many genes involved in the biosynthesis of zein and starch is reduced in the filling endosperm of zmnac128 zmnac130. Further, DNA affinity purification and sequencing combined with chromatin-immunoprecipitation quantitative PCR and promoter transactivation assays demonstrated that ZmNAC128 and ZmNAC130 are direct regulators of 3 (16-, 27-, and 50-kD) γ-zein genes and 6 important starch metabolism genes (Brittle2 [Bt2], pullulanase-type starch debranching enzyme [Zpu1], granule-bound starch synthase 1 [GBSS1], starch synthase 1 [SS1], starch synthase IIa [SSIIa], and sucrose synthase 1 [Sus1]). ZmNAC128 and ZmNAC130 recognize an additional cis-element in the Opaque2 (O2) promoter to regulate its expression. The triple mutant zmnac128 zmnac130 o2 exhibits extremely poor endosperm filling, which results in more than 70% of kernel weight loss. ZmNAC128 and ZmNAC130 regulate the expression of the transporter genes sugars that will eventually be exported transporter 4c (ZmSWEET4c), sucrose and glucose carrier 1 (ZmSUGCAR1), and yellow stripe-like2 (ZmYSL2) and in turn facilitate nutrient uptake, while O2 plays a supporting role. In conclusion, ZmNAC128 and ZmNAC130 cooperate with O2 to facilitate endosperm filling, which involves nutrient uptake in the basal endosperm transfer layer (BETL) and the synthesis of zeins and starch in the starchy endosperm (SE).

Evaluation of altered starch mutants and identification of candidate genes responsible for starch variation in wheat

BackgroundInduction of mutation through chemical mutagenesis is a novel approach for preparing diverse germplasm. Introduction of functional alleles in the starch biosynthetic genes help in the improvement of the quality and yield of cereals.ResultsIn the present study, a set of 350 stable mutant lines were used to evaluate dynamic variation of the total starch contents. A megazyme kits were used for measuring the total starch content, resistant starch, amylose, and amylopectin content. Analysis of variance showed significant variation (p < 0.05) in starch content within the population. Furthermore, two high starch mutants (JE0173 and JE0218) and two low starch mutants (JE0089 and JE0418) were selected for studying different traits. A multiple comparison test showed that significant variation in all physiological and morphological traits, with respect to the parent variety (J411) in 2019–2020 and 2020–2021. The quantitative expression of starch metabolic genes revealed that eleven genes of JE0173 and twelve genes of JE0218 had consistent expression in high starch mutant lines. Similarly, in low starch mutant lines, eleven genes of JE0089 and thirteen genes of JE0418 had consistent expression in all stages of seed development. An additional two candidate genes showed over-expression (PHO1, PUL) in the high starch mutant lines, indicating that other starch metabolic genes may also contribute to the starch biosynthesis. The overexpression of SSII, SSIII and SBEI in JE0173 may be due to presence of missense mutations in these genes and SSI also showed overexpression which may be due to 3-primer_UTR variant. These mutations can affect the other starch related genes and help to increase the starch content in this mutant line (JE0173).ConclusionsThis study screened a large scale of mutant population and identified mutants, could provide useful genetic resources for the study of starch biosynthesis and genetic improvement of wheat in the future. Further study will help to understand new genes which are responsible for the fluctuation of total starch.

Transcriptomic analysis of mesocarp tissue during fruit development of the oil palm revealed specific isozymes related to starch metabolism that control oil yield.

The oil palm (Elaeis guineensis Jacq.) produces a large amount of oil from the fruit. However, increasing the oil production in this fruit is still challenging. A recent study has shown that starch metabolism is essential for oil synthesis in fruit-producing species. Therefore, the transcriptomic analysis by RNA-seq was performed to observe gene expression alteration related to starch metabolism genes throughout the maturity stages of oil palm fruit with different oil yields. Gene expression profiles were examined with three different oil yields group (low, medium, and high) at six fruit development phases (4, 8, 12, 16, 20, and 22 weeks after pollination). We successfully identified and analyzed differentially expressed genes in oil palm mesocarps during development. The results showed that the transcriptome profile for each developmental phase was unique. Sucrose flux to the mesocarp tissue, rapid starch turnover, and high glycolytic activity have been identified as critical factors for oil production in oil palms. For starch metabolism and the glycolytic pathway, we identified specific gene expressions of enzyme isoforms (isozymes) that correlated with oil production, which may determine the oil content. This study provides valuable information for creating new high-oil-yielding palm varieties via breeding programs or genome editing approaches.

Effects of Source Strength and Sink Size on Starch Metabolism, Starch Properties and Grain Quality of Rice (Oryza sativa L.)

The source strength and sink demand as well as their interaction have been demonstrated to co-regulate the synthesis of starch and determine the grain quality, but the knowledge of the underlying physiological mechanisms is limiting. An indica variety, Yangdao 6, and a japonica variety, Jinxiangyu 1, were planted with three treatments, including normal growth plant (CK), leaf-cutting (LC) and spikelet-thinning (ST). The transcript levels of starch metabolic genes, physicochemical characteristics of starch and appearance, milling, cooking and tasting qualities of rice under different treatments were determined. The ST treatment increased the relative expression of genes related to the synthesis of short branch-chains of amylopectin (SSI, BEI, BEIIb) and amylose (GBSSI) and reduced the relative expression of medium-long to long branch-chains of amylopectin synthesis genes (SSIIa, SSIIIa, SSIIIb, ISA1). When comparing ST with the CK treatment, starch granules became smoother with higher contents of short branch-chains and lower ratios of medium-long and long branch-chains of amylopectin; the crystallinity and the value of 1045/1022 cm−1 was decreased; for pasting properties, the setback and pasting temperature were decreased; the peak viscosity, hot viscosity, breakdown and final viscosity were significantly increased. Meanwhile, the ST treatment improved the appearance, milling and cooking and tasting qualities. The opposite results were observed under the LC treatment. These results indicated that source strength and sink size would regulate expression levels of starch metabolic genes, which is pivotal for the contents of amylose and short/long branch chains ratio of amylopectin, thus changing the structure and physicochemical properties of starch and grain quality. Here, we speculated that the improved source strength in terms of higher leaf/canopy photosynthesis and small sink size, such as small panicle size, would be preferred traits in high grain quality rice breeding.

Identification and Characterization of Long Non-Coding RNAs: Implicating Insights into Their Regulatory Role in Kiwifruit Ripening and Softening during Low-Temperature Storage.

Long non-coding RNAs (lncRNAs) are crucial players regulating many biological processes in plants. However, limited knowledge is available regarding their roles in kiwifruit ripening and softening. In this study, using lncRNA-seq technology, 591 differentially expressed (DE) lncRNAs (DELs) and 3107 DE genes (DEGs) were identified from kiwifruit stored at 4 °C for 1, 2, and 3 weeks in comparison with non-treated control fruits. Of note, 645 DEGs were predicted to be targets of DELs (DEGTLs), including some DE protein-coding genes (such as β-amylase and pectinesterase). DEGTL-based GO enrichment analysis revealed that these genes were significantly enriched in cell wall modification and pectinesterase activity in 1 W vs. CK and 3 W vs. CK, which might be closely related to the fruit softening during low-temperature storage. Moreover, KEGG enrichment analysis revealed that DEGTLs were significantly associated with starch and sucrose metabolism. Our study revealed that lncRNAs play critical regulatory roles in kiwifruit ripening and softening under low-temperature storage, mainly by mediating the expression of starch and sucrose metabolism and cell wall modification related genes.

Response of sugar metabolism in the cotyledons and roots of Ricinus communis subjected to salt stress.

Ricinus communis is an important oilseed crop worldwide and is also considered one of the best potential plants for salt-affected soil improvement in northeast China. However, little is known about photosynthesis and carbohydrate metabolism in this plant, nor the distribution of carbohydrates in cotyledons and roots under salinity stress. In the present study, seedling growth, gas exchange parameters (PN , E, gs and Ci ), carbohydrate (fructose, sucrose, glucose, soluble sugar and starch) metabolism and related enzymes and genes were measured in Ricinus plants. Under salt stress, PN of cotyledons decreased significantly (P< 0.05), resulting in weak photosynthetic capacity. Furthermore, salt stress increased sucrose and glucose content in cotyledons, but decreased soluble sugar and starch content. However, sucrose increased and starch decreased in roots. This may be correlated with the increasing sugar metabolism under salinity, including notable changes in sugar-related enzyme activities (SPS, SuSy, α-amylase and β-amylase) and gene expression of RcINV, RcSUS, RcAmY, RcBAM and RcGBE1. The results suggest that salinity reduces photosynthesis of cotyledons, alters carbohydrate allocation between cotyledons and roots and also promotes starch utilization in cotyledons and starch biosynthesis in roots, leading to a functional imbalance between cotyledons and roots. Together, these findings provide insights into the crucial role of sugar metabolism in improving salt-tolerance of Ricinus during the early seedling growth stage.

Screening of Induced Mutants Led to the Identification of Starch Biosynthetic Genes Associated with Improved Resistant Starch in Wheat.

Several health benefits are obtained from resistant starch, also known as healthy starch. Enhancing resistant starch with genetic modification has huge commercial importance. The variation of resistant starch content is narrow in wheat, in relation to which limited improvement has been attained. Hence, there is a need to produce a wheat population that has a wide range of variations in resistant starch content. In the present study, stable mutants were screened that showed significant variation in the resistant starch content. A megazyme kit was used for measuring the resistant starch content, digestible starch, and total starch. The analysis of variance showed a significant difference in the mutant population for resistant starch. Furthermore, four diverse mutant lines for resistant starch content were used to study the quantitative expression patterns of 21 starch metabolic pathway genes; and to evaluate the candidate genes for resistant starch biosynthesis. The expression pattern of 21 starch metabolic pathway genes in two diverse mutant lines showed a higher expression of key genes regulating resistant starch biosynthesis (GBSSI and their isoforms) in the high resistant starch mutant lines, in comparison to the parent variety (J411). The expression of SBEs genes was higher in the low resistant starch mutants. The other three candidate genes showed overexpression (BMY, Pho1, Pho2) and four had reduced (SSIII, SBEI, SBEIII, ISA3) expression in high resistant starch mutants. The overexpression of AMY and ISA1 in the high resistant starch mutant line JE0146 may be due to missense mutations in these genes. Similarly, there was a stop_gained mutation for PHO2; it also showed overexpression. In addition, the gene expression analysis of 21 starch metabolizing genes in four different mutants (low and high resistant starch mutants) shows that in addition to the important genes, several other genes (phosphorylase, isoamylases) may be involved and contribute to the biosynthesis of resistant starch. There is a need to do further study about these new genes, which are responsible for the fluctuation of resistant starch in the mutants.

Transcriptome Analysis Reveals Critical Genes and Pathways in Carbon Metabolism and Ribosome Biogenesis in Poplar Fertilized with Glutamine.

Exogenous Gln as a single N source has been shown to exert similar roles to the inorganic N in poplar ‘Nanlin895′ in terms of growth performance, yet the underlying molecular mechanism remains unclear. Herein, transcriptome analyses of both shoots (L) and roots (R) of poplar ‘Nanlin895’ fertilized with Gln (G) or the inorganic N (control, C) were performed. Compared with the control, 3109 differentially expressed genes (DEGs) and 5071 DEGs were detected in the GL and GR libraries, respectively. In the shoots, Gln treatment resulted in downregulation of a large number of ribosomal genes but significant induction of many starch and sucrose metabolism genes, demonstrating that poplars tend to distribute more energy to sugar metabolism rather than ribosome biosynthesis when fertilized with Gln-N. By contrast, in the roots, most of the DEGs were annotated to carbon metabolism, glycolysis/gluconeogenesis and phenylpropanoid biosynthesis, suggesting that apart from N metabolism, exogenous Gln has an important role in regulating the redistribution of carbon resources and secondary metabolites. Therefore, it can be proposed that the promotion impact of Gln on poplar growth and photosynthesis may result from the improvement of both carbon and N allocation, accompanied by an efficient energy switch for growth and stress responses.

Transcription factor OsSGL is a regulator of starch synthesis and grain quality in rice.

Starch biosynthesis during rice endosperm development is important for grain quality, as it influences grain size and physico-chemical properties, which together determine rice eating quality. Cereal starch biosynthetic pathways have been comprehensively investigated; however, their regulation, especially by transcriptional repressors remains largely unknown. Here, we identified a DUF1645 domain-containing protein, STRESS_tolerance and GRAIN_LENGTH (OsSGL), that participates in regulating rice starch biosynthesis. Overexpression of OsSGL reduced total starch and amylose content in the endosperm compared with the wild type. Chromatin immunoprecipitation sequencing and RNA-seq analyses indicated that OsSGL targets the transcriptional activity of several starch and sucrose metabolism genes. In addition, ChIP-qPCR, yeast one-hybrid, EMSA and dual-luciferase assays demonstrated that OsSGL directly inhibits the expression of SUCROSE SYNTHASE 1 (OsSUS1) in the endosperm. Furthermore, OsSUS1 interacts with OsSGL to release its transcriptional repression ability. Unexpectedly, our results also show that knock down and mutation of OsSGL disrupts the starch biosynthetic pathway, causing lower starch and amylose content. Therefore, our findings demonstrate that accurate control of OsSGL homeostasis is essential for starch synthesis and grain quality. In addition, we revealed the molecular mechanism of OsSGL in regulating starch biosynthesis-related genes, which are required for grain quality.

Starch content changes and metabolism-related gene regulation of Chinese cabbage synergistically induced by Plasmodiophora brassicae infection.

Clubroot is one of the major diseases adversely affecting Chinese cabbage (Brassica rapa) yield and quality. To precisely characterize the Plasmodiophora brassicae infection of Chinese cabbage, we developed a dual fluorescent staining method for simultaneously examining the pathogen, cell structures, and starch grains. The number of starch (amylopectin) grains increased in B. rapa roots infected by P. brassicae, especially from 14 to 21 days after inoculation. Therefore, the expression levels of 38 core starch metabolism genes were investigated by quantitative real-time PCR. Most genes related to starch synthesis were up-regulated at 7 days after P. brassicae inoculation, whereas the expression levels of starch degradation-related genes were increased at 14 days after inoculation. Then, genes encoding the core enzymes involved in starch metabolism were investigated by assessing their chromosomal distributions, structures, duplication events, and synteny among Brassica species. Genome comparisons indicated that 38 non-redundant genes belonging to six core gene families related to starch metabolism are highly conserved among Arabidopsis thaliana, B. rapa, Brassica nigra, and Brassica oleracea. Previous genome sequencing projects have revealed that P. brassicae obtained host nutrients by manipulating plant metabolism. Starch may serve as a carbon source for P. brassicae colonization, as indicated by histological observations and transcriptomic analysis. Results of this study may elucidate the evolution and expression of core starch metabolism genes and provide researchers with novel insights into the pathogenesis of clubroot in B. rapa.

Transcriptomic and physiological analysis reveals interplay between salicylic acid and drought stress in citrus tree floral initiation.

Salicylic acid (SA) and drought stress promote more flowering in sweet orange. The physiological response and molecular mechanism underlying stress-induced floral initiation were discovered by transcriptome profiling. Numerous flowering-regulated genes were identified, and ectopically expressed CsLIP2A promotes early flowering in Arabidopsis. Floral initiation is a critical developmental mechanism associated with external factors, and citrus flowering is mainly regulated by drought stress. However, little is known about the intricate regulatory network involved in stress-induced flowering in citrus. To understand the molecular mechanism of floral initiation in citrus, flower induction was performed on potted Citrus sinensis trees under the combined treatment of salicylic acid (SA) and drought (DR). Physiological analysis revealed that SA treatment significantly normalized the drastic effect of drought stress by increasing antioxidant enzyme activities (SOD, POD, and CAT), relative leaf water content, total chlorophyll, and proline contents and promoting more flowering than drought treatment. Analysis of transcriptome changes in leaves from different treatments showed that 1135, 2728 and 957 differentially expressed genes (DEGs) were revealed in response to DR, SD (SA + DR), and SA (SA + well water) treatments in comparison with the well watered plants, respectively. A total of 2415, 2318 and 1933 DEGs were expressed in DR, SD, and SA in comparison with water recovery, respectively. Some key flowering genes were more highly expressed in SA-treated drought plants than in DR-treated plants. GO enrichment revealed that SA treatment enhances the regulation and growth of meristem activity under drought conditions, but no such a pathway was found to be highly enriched in the control. Furthermore, we focused on various hormones, sugars, starch metabolism, and biosynthesis-related genes. The KEGG analysis demonstrated that DEGs enriched in starch sucrose metabolism and hormonal signal transduction pathways probably account for stress-induced floral initiation in citrus. In addition, a citrus LIPOYLTRANSFERSAE 2A homologous (LIP2A) gene was upregulated by SD treatment. Ectopic expression of CsLIP2A exhibited early flowering in transgenic Arabidopsis. Taken together, this study provides new insight that contributes to citrus tree floral initiation under the SA-drought scenario as well as an excellent reference for stress-induced floral initiation in woody trees.

Characterization and differential expression of sucrose and starch metabolism genes in contrasting chickpea (Cicer arietinum L.) genotypes under low temperature

Low temperature (LT) causes significant yield losses in chickpea (Cicer arietinum L.). The sucrose starch metabolism is associated with abiotic-stress tolerance or sensitivity in plants. The changes in sugars and starch contents under LT in chickpea have already been studied, however, no information is available on LT-induced alterations in transcription of carbohydrate metabolic pathway genes in chickpea. To understand the differences in the regulation of sucrose and starch metabolism under LT, the expression of sucrose and starch metabolism genes was studied in leaves of cold-sensitive (GPF2) and cold-tolerant (ICC 16349) chickpea genotypes. The mRNA sequences of chickpea genes were retrieved from the public databases followed by confirmation of identity and characterization. All the genes were functional in chickpea. Between the two paralogues of cell wall invertase, cell wall invertase 3×2 (CWINx2) was the truncated version of cell wall invertase 3×1 (CWINx1) with the loss of 241 bases in the mRNA and 67 amino acids at N terminal of the protein. Comparison of expression of the genes between control (22°C day / 16°C night) and LT treated (4°C; 72 h) plants revealed that granule bound starch synthase 2 (GBSS2) and β-amylase 3 (BAM3) were upregulated in ICC 16349 whereas sucrose phosphate synthase 2 (SPS2), CWINx1, CWINx2 and β-amylase 1 (BAM1) were downregulated. In contrast to this, SPS2, CWINx1, CWINx2 and BAM1 were upregulated and GBSS2 downregulated in GPF2 under LT. The gene expression data suggested that UGPase, CWINs, GBSS2 and BAM3 are important components of cold-tolerance machinery of chickpea.

Identification of the Carbohydrate and Organic Acid Metabolism Genes Responsible for Brix in Tomato Fruit by Transcriptome and Metabolome Analysis.

BackgroundSugar and organic acids not only contribute to the formation of soluble solids (Brix) but also are an essential factor affecting the overall flavor intensity. However, the possible metabolic targets and molecular synthesis mechanisms remain to be further clarified.MethodsUHPLC-HRMS (ultrahigh-performance liquid chromatography and high-resolution mass spectrometry) combined with comparative transcriptome analysis were performed in fruits at green ripe (S1), turning-color (S2), and red ripe (S3) stages of two tomato genotypes TM-1 (Solanum galapagense L., LA0436) and TM-38 (S. lycopersicum L. cultivar M82, LA3475) that vary in fruit Brix.ResultsThe fruit Brix of TM-1 was nearly twice that of TM-38 at S3. Nevertheless, TM-1 accumulated 1.84- and 2.77-fold the L-malic acid and citric acid in red ripe fruit (S3) compared with TM-38, respectively. D-glucose and D-fructose in TM-1 and TM-38 fruits tended to be similar at S3. Concomitantly, the sugar/organic acid ratio of TM-38 fruits were 23. 08-, 4. 38-, and 2.59-fold higher than that of TM-1 fruits at S1, S2, and S3, respectively. Among starch and sucrose (carbohydrate, CHO) metabolism (ko00500) genes, SUS (Solyc07g042550.3) and BAM (Solyc08g077530.3) were positively (r = 0.885–0.931) correlated with the sugar/organic acid ratio. Besides, INV (Solyc09g010080.3 and Solyc09g010090.5.1), AAM (Solyc04g082090.3), 4-α-GTase (Solyc02g020980.2.1), BGL2 (Solyc06g073750.4, Solyc06g073760.3, and Solyc01g081170.3), TPS (Solyc01g005210.2 and Solyc07g006500.3), and TPP (Solyc08g079060.4) were negatively (r = −0.823 to −0.918) correlated with the sugar/organic acid ratio. The organic acid (TCA cycle) metabolism (ko00020) gene ALMT (Solyc01g096140.3) was also negatively (r = −0.905) correlated with the sugar/organic acid ratio.ConclusionCitric acid may play a more dominant role in the sugar/organic acid ratio of the tomato fruit, and the contribution of both L-malic acid and citric acid to the fruit Brix was much greater than that of D-glucose and D-fructose. Genes involved in CHO and TCA metabolism, which have a significant correlation with the sugar/organic acid ratio were considered to be the contributing factors of fruit Brix.

The sugar-responsive circadian clock regulator bZIP63 modulates plant growth.

Summary Adjustment to energy starvation is crucial to ensure growth and survival. In Arabidopsis thaliana (Arabidopsis), this process relies in part on the phosphorylation of the circadian clock regulator bZIP63 by SUCROSE non‐fermenting RELATED KINASE1 (SnRK1), a key mediator of responses to low energy.We investigated the effects of mutations in bZIP63 on plant carbon (C) metabolism and growth. Results from phenotypic, transcriptomic and metabolomic analysis of bZIP63 mutants prompted us to investigate the starch accumulation pattern and the expression of genes involved in starch degradation and in the circadian oscillator. bZIP63 mutation impairs growth under light‐dark cycles, but not under constant light. The reduced growth likely results from the accentuated C depletion towards the end of the night, which is caused by the accelerated starch degradation of bZIP63 mutants. The diel expression pattern of bZIP63 is dictated by both the circadian clock and energy levels, which could determine the changes in the circadian expression of clock and starch metabolic genes observed in bZIP63 mutants.We conclude that bZIP63 composes a regulatory interface between the metabolic and circadian control of starch breakdown to optimize C usage and plant growth.

Differential expression of starch and sucrose metabolic genes linked to varying biomass yield in Miscanthus hybrids

BackgroundMiscanthus is a commercial lignocellulosic biomass crop owing to its high biomass productivity and low chemical input requirements. Within an interspecific Miscanthus cross, progeny with high biomass yield were shown to have low concentrations of starch and sucrose but high concentrations of fructose. We performed a transcriptional RNA-seq analysis between selected Miscanthus hybrids with contrasting values for these phenotypes to clarify how these phenotypes are genetically controlled.ResultsWe observed that genes directly involved in the synthesis and degradation of starch and sucrose were down-regulated in high-yielding Miscanthus hybrids. At the same time, glycolysis and export of triose phosphates were up-regulated in high-yielding Miscanthus hybrids. These differentially expressed genes and biological functions were regulated by a well-connected network of less than 25 co-regulated transcription factors.ConclusionsOur results evidence a direct relationship between high expression of essential enzymatic genes in the starch and sucrose pathways and co-expression with their transcriptional regulators, with high starch concentrations and lower biomass production. The strong interconnectivity between gene expression and regulators, chemotype and agronomic traits opens the door to use the expression of well-characterised genes associated with carbohydrate metabolism, particularly in the starch and sucrose pathway, for the early selection of high biomass-yielding genotypes from large Miscanthus populations.

The endosperm-specific transcription factor TaNAC019 regulates glutenin and starch accumulation and its elite allele improves wheat grain quality.

In wheat (Triticum aestivum L.), breeding efforts have focused intensively on improving grain yield and quality. For quality, the content and composition of seed storage proteins (SSPs) determine the elasticity of wheat dough and flour processing quality. Moreover, starch levels in seeds are associated with yield. However, little is known about the mechanisms that coordinate SSP and starch accumulation in wheat. In this study, we explored the role of the endosperm-specific NAC transcription factor TaNAC019 in coordinating SSP and starch accumulation. TaNAC019 binds to the promoters of TaGlu-1 loci, encoding high molecular weight glutenin (HMW-GS), and of starch metabolism genes. Triple knock-out mutants of all three TaNAC019 homoeologs exhibited reduced transcript levels for all SSP types and genes involved in starch metabolism, leading to lower gluten and starch contents, and in flour processing quality parameters. TaNAC019 directly activated the expression of HMW-GS genes by binding to a specific motif in their promoters and interacting with the TaGlu-1 regulator TaGAMyb. TaNAC019 also indirectly regulated the expression of TaSPA, an ortholog of maize Opaque2 that activates SSP accumulation. Therefore, TaNAC019 regulation of starch- and SSP-related genes has key roles in wheat grain quality. Finally, we identified an elite allele (TaNAC019-BI) associated with flour processing quality, providing a candidate gene for breeding wheat with improved quality.