Comparative transcriptome reveals distinct starch-sugar interconversion patterns in potato genotypes contrasting for cold-induced sweetening capacity

Integrated transcriptome and metabolome analysis revealed hub genes and metabolites associated with subzero temperature tolerance following cold acclimation in rapeseed (Brassica rapa L.)

Rapeseed naturally endures low temperature in late autumn and early winter to develop cold adaptation, named as cold acclimation (CA). The underlying mechanism by which CA induces plant resistance to subzero temperature tolerance is unclear. This study examined the transcriptome and metabolome of strong (Longyou 7) and weak (Longyou 99) cold-tolerant rapeseed varieties treated with treatments CA and sub-zero temperatures at fourth leaf stage. Cold shock (CS) treatment was developed by incubating seedlings directly at 0, -3, and -7 °C for 4 day at each temperature. For CA, seedlings were acclimatized at 4 °C for one week and then to 0, -3, and -7 °C for four days in each temperature. By transcriptome analysis 5364 and 6534 DEGs were detected in both varieties following CA. Functional enrichment analysis of DEGs showed that carbohydrate metabolism and biosynthesis of secondary metabolic pathways were enriched following CA. A weighted gene co-expression network analysis revealed hub genes AMY2, DREB, MYB, PBL, and GFT1 from three biological modules that can be employed as candidate genes to investigate the network regulation pathway of rapeseed in response to CA treatment. Metabolome profiling revealed phenylalanine, purine, amino sugar and nucleotide sugar, and flavonoid biosynthesis were the most enriched pathways in rapeseed seedlings following CA. Contemporaneous analysis of transcriptomics and metabolomic changes following CA revealed the dynamics of specific gene-metabolite relationships in rapeseed. DEGs and DAMs correlation analysis showed that genes DREB, RAP, TCP2, ZAT12, ASP1, ASP3, ASP4, and the metabolites N-acetyl-D-glucosamine, 2-glycitein, and 3-hydroxybenzyl alcohol glucoside, played an important role in rapeseed following CA. This study's findings elucidate the molecular and regulatory mechanisms enabling rapeseed to withstand subzero temperatures following CA.

Carbohydrate and hormone regulatory networks driving dormancy release of Cardiocrinum giganteum (Wall.) Makino bulbs induced by low temperature

Bulb physiological dormancy significantly limits the development and utilization of Cardiocrinum giganteum (Wall.) Makino, a valuable medicinal, edible and ornamental plant. In the current study, to break the dormancy and reveal its mechanism, metabolome and transcriptome analyses using bulbs stored at 4°C for 0, 30, and 60 days (d) were conducted. Results revealed that bulb dormancy release and development were linked to hormones such as ABA, IAA, GA and ZR, as well as sucrose and starch. Total soluble sugars initially increased and then decreased within 60 days of low temperature treatment, contrary to the behaviour of starch content. Dormancy release predominantly relied on GA accumulation and ABA degradation. Additionally, genes involved in carbohydrate metabolism, including HK, SPS, BGLU, and SuSy, were up-regulated in the later stage. The energy production during carbohydrate metabolism mainly depended on the tricarboxylic acid cycle and glycolysis pathway. Hormone-mediated regulation and hormone signal transduction metabolism pathways were also obviously changed. Co-expression analysis indicated that key genes, such as NCED, PP2C and DELLA, related to the ABA signal transduction pathway, and GA2ox, ARF and SAUR, related to the IAA and GA signal transduction pathway, played a crucial role in dormancy release. Moreover, ZR signal transduction genes such as CRE, ARR-B, ARR-A and TRIT1 involved in cell division were up-regulated in bulbs treated at 4°C for 30 or 60 d. This study provides evidence for understanding the molecular mechanism underlying bulb dormancy release and is a guide for industry development and utilization of Cardiocrinum giganteum (Wall.) Makino.

Understanding starch biosynthesis in potatoes for metabolic engineering to improve starch quality: A detailed review

Potato tubers accumulate substantial quantities of starch, which serves as their primary energy reserve. As the predominant component of potato tubers, starch strongly influences tuber yield, processing quality, and nutritional attributes. Potato starch is distinguished from other food starches by its unique granule morphology and compositional attributes. It possesses large, oval granules with amylose content ranging from 20 to 33 % and high phosphorus levels, which collectively determine the unique physicochemical characteristics. These physicochemical properties direct the utility of potato starch across diverse food and industrial applications. This review synthesizes current knowledge on the molecular factors controlling potato starch biosynthesis and structure-function relationships. Key topics covered are starch granule morphology, the roles and regulation of major biosynthetic enzymes, transcriptional and hormonal control, genetic engineering strategies, and opportunities to tailor starch functionality. Elucidating the contributions of different enzymes in starch biosynthesis has enabled targeted modification of potato starch composition and properties. However, realizing the full potential of this knowledge faces challenges in optimizing starch quality without compromising plant vigor and yield. Overall, integrating multi-omics datasets with advanced genetic and metabolic engineering tools can facilitate the development of elite cultivars with enhanced starch yield and tailored functionalities.

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.

Exogenous 5-Aminolevulinic acid improved low-temperature tolerance tomato seedling by regulating starch content and phenylalanine metabolism

Tomato is an important horticultural cash crop, and low-temperature stress has seriously affected the yield and quality of tomato. 5-Aminolevulinic acid (ALA) is widely used in agriculture as an efficient and harmless growth regulator. It is currently unclear whether exogenous ALA can cope with low-temperature stress by regulating tomato starch content and phenylalanine metabolism. In this study, exogenous ALA remarkably improved the low-temperature tolerance of tomato seedlings. RNA-sequencing results showed that exogenous ALA affected starch metabolism and phenylalanine metabolism in tomato seedling leaves under low-temperature stress. Subsequently, we used histochemical staining, observation of chloroplast microstructure, substance content determination, and qRT-PCR analysis to demonstrate that exogenous ALA could improve the low-temperature tolerance of tomato seedlings by regulating starch content and phenylalanine metabolism (SlPAL, SlPOD1, and SlPOD2). Simultaneously, we found that exogenous ALA induced the expression of SlMYBs and SlWRKYs under low-temperature stress. In addition, dual luciferase, yeast one hybrid, and electrophoretic mobility shift assays indicate that SlMYB4 and SlMYB88 could regulate the expression of SlPOD2 in phenylalanine metabolism. We demonstrated that exogenous ALA could improve the low-temperature tolerance of tomato seedlings by regulating starch content and phenylalanine metabolism.

Starch and sucrose metabolism plays an important role in the stem development in Medicago sativa

The forage quality of alfalfa (Medicago sativa ) stems is greater than the leaves. Sucrose hydrolysis provides energy for stem development, with starch being enzymatically converted into sucrose to maintain energy homeostasis. To understand the physiological and molecular networks controlling stem development, morphological characteristics and transcriptome profiles in the stems of two alfalfa cultivars (Zhungeer and WL168) were investigated. Based on transcriptome data, we analysed starch and sugar contents, and enzyme activity related to starch-sugar interconversion. Zhungeer stems were shorter and sturdier than WL168, resulting in significantly higher mechanical strength. Transcriptome analysis showed that starch and sucrose metabolism were significant enriched in the differentially expressed genes of stems development in both cultivars. Genes encoding INV , bglX , HK , TPS and glgC downregulated with the development of stems, while the gene encoding was AMY upregulated. Weighted gene co-expression network analysis revealed that the gene encoding glgC was pivotal in determining the variations in starch and sucrose contents between the two cultivars. Soluble carbohydrate, sucrose, and starch content of WL168 were higher than Zhungeer. Enzyme activities related to sucrose synthesis and hydrolysis (INV, bglX, HK, TPS) showed a downward trend. The change trend of enzyme activity was consistent with gene expression. WL168 stems had higher carbohydrate content than Zhungeer, which accounted for more rapid growth and taller plants. WL168 formed hollow stems were formed during rapid growth, which may be related to the redistribution of carbohydrates in the pith tissue. These results indicated that starch and sucrose metabolism play important roles in the stem development in alfalfa.

ERF54 regulates cold tolerance in Rosa multiflora through DREB/COR signalling pathways

Ethylene-responsive factors (ERFs) participate in a wide range of physiological and biological processes. However, many of the functions of ERFs in cold stress responses remain unclear. We, therefore, characterised the cold responses of RmERF54 in Rosa multiflora, a rose-related cold-tolerant species. Overexpression of RmERF54, which is a nuclear transcription factor, increases the cold resistance of transgenic tobacco and rose somatic embryos. In contrast, virus-induced gene silencing (VIGS) of RmERF54 increased cold susceptibility of R. multiflora. The overexpression of RmERF54 resulted in extensive transcriptional reprogramming of stress response and antioxidant enzyme systems. Of these, the levels of transcripts encoding the PODP7 peroxidase and the cold-related COR47 protein showed the largest increases in the somatic embryos with ectopic expression of RmERF54. RmERF54 binds to the promoters of the RmPODP7 and RmCOR47 genes and activates expression. RmERF54-overexpressing lines had higher antioxidant enzyme activities and considerably lower levels of reactive oxygen species. Opposite effects on these parameters were observed in the VIGS plants. RmERF54 was identified as a target of Dehydration-Responsive-Element-Binding factor (RmDREB1E). Taken together, provide new information concerning the molecular mechanisms by which RmERF54 regulates cold tolerance.

The DREB transcription factor, a biomacromolecule, responds to abiotic stress by regulating the expression of stress-related genes

Abiotic stress is a crucial factor that affects plant survival and growth and even leads to plant death in severe cases. Transcription factors can enhance the ability of plants to fight against various stresses by controlling the expression of downstream genes. The dehydration response element binding protein (DREB) is the most extensive subfamily of AP2/ERF transcription factors involved in abiotic stress. However, insufficient research on the signal network of DREB transcription factors has limited plant growth and reproduction. Furthermore, field planting of DREB transcription factors and their roles under multiple stress also require extensive research. Previous reports on DREB transcription factors have focused on the regulation of DREB expression and its roles in plant abiotic stress. In recent years, there has been new progress in DREB transcription factors. Here, the structure and classification, evolution and regulation, role in abiotic stress, and application in crops of DREB transcription factors were reviewed. And this paper highlighted the evolution of DREB1/CBF, as well as the regulation of DREB transcription factors under the participation of plant hormone signals and the roles of subgroups in abiotic stress. In the future, it will lay a solid foundation for further study of DREB transcription factors and pave the way for the cultivation of resistant plants.

Kiwifruit bZIP transcription factor AcePosF21 elicits ascorbic acid biosynthesis during cold stress

Cold stress seriously affects plant development, resulting in heavy agricultural losses. L-ascorbic acid (AsA, vitamin C) is an antioxidant implicated in abiotic stress tolerance and metabolism of reactive oxygen species (ROS). Understanding whether and how cold stress elicits AsA biosynthesis to reduce oxidative damage is important for developing cold-resistant plants. Here, we show that the accumulation of AsA in response to cold stress is a common mechanism conserved across the plant kingdom, from single-cell algae to angiosperms. We identified a basic leucine zipper domain (bZIP) transcription factor (TF) of kiwifruit (Actinidia eriantha Benth.), AcePosF21, which was triggered by cold and is involved in the regulation of kiwifruit AsA biosynthesis and defense responses against cold stress. AcePosF21 interacted with the R2R3-MYB TF AceMYB102 and directly bound to the promoter of the gene encoding GDP-L-galactose phosphorylase 3 (AceGGP3), a key conduit for regulating AsA biosynthesis, to up-regulate AceGGP3 expression and produce more AsA, which neutralized the excess ROS induced by cold stress. On the contrary, VIGS or CRISPR-Cas9-mediated editing of AcePosF21 decreased AsA content and increased the generation of ROS in kiwifruit under cold stress. Taken together, we illustrated a model for the regulatory mechanism of AcePosF21-mediated regulation of AceGGP3 expression and AsA biosynthesis to reduce oxidative damage by cold stress, which provides valuable clues for manipulating the cold resistance of kiwifruit.

Potato tonoplast sugar transporter 1 controls tuber sugar accumulation during postharvest cold storage

Cold-induced sweetening (CIS), the undesirable sugar accumulation in cold-stored potato (Solanum tuberosum L.) tubers, is a severe postharvest issue in the potato processing industry. Although the process of sucrose hydrolysis by vacuolar invertase during potato CIS is well understood, there is limited knowledge about the transportation of sucrose from the cytosol to the vacuole during postharvest cold storage. Here, we report that among the three potato tonoplast sugar transporters (TSTs), StTST1 exhibits the highest expression in tubers during postharvest cold storage. Subcellular localization analysis demonstrates that StTST1 is a tonoplast-localized protein. StTST1 knockdown decreases reducing sugar accumulation in tubers during low-temperature storage. Compared to wild-type, potato chips produced from StTST1-silenced tubers displayed significantly lower acrylamide levels and lighter color after cold storage. Transcriptome analysis manifests that suppression of StTST1 promotes starch synthesis and inhibits starch degradation in cold-stored tubers. We further establish that the increased sucrose content in the StTST1-silenced tubers might cause a decrease in the ABA content, thereby inhibiting the ABA-signaling pathway. We demonstrate that the down-regulation of β-amylase StBAM1 in StTST1-silenced tubers might be directly controlled by ABA-responsive element-binding proteins (AREBs). Altogether, we have shown that StTST1 plays a critical role in sugar accumulation and starch metabolism regulation during postharvest cold storage. Thus, our findings provide a new strategy to improve the frying quality of cold-stored tubers and reduce the acrylamide content in potato chips.

Low temperature reduces potato wound formation by inhibiting phenylpropanoid metabolism and fatty acid biosynthesis

INTRODUCTION

Potato tubers have the healing capacity to prevent surface water transpiration and pathogen invasion after mechanical damage. Previous research has shown the inability to form healing periderm in potatoes under low temperatures, but the potential mechanism is still unclear.

METHODS

To explore the effects and mechanisms of low-temperature potato healing, wounded potatoes were stored at low temperature (4°C) and room temperature (22°C), respectively.

RESULTS

In this study, compared with 22°C healing, low temperature reduced the content of hydrogen peroxide, and the down-regulation of StAMY23 inhibited the conversion of starch to sugar, alleviated the degradation of starch, and reduced the content of soluble sugars and sucrose. Meanwhile, inhibition of phenylalanine metabolism by suppression of StPAL1 and St4CL expression reduced lignin accumulation. Low temperature also down-regulated the expression of StKCS6, StFAOH, StGPAT5, and StPrx, causing the lower deposition amount of suberin in wounds of potato tubers.

DISCUSSION

The above results suggested that low temperature led to less wound tissue deposition at the wound surfaces via suppressing phenylpropanoid metabolism and fatty acid biosynthesis in potato tubers.

Chromosome-level genome assembly of Dongxiang wild rice (Oryza rufipogon) provides insights into resistance to disease and freezing

Dongxiang wild rice (DXWR, Oryza rufipogon Griff.) belongs to common wild rice O. rufipogon, which is the well-known ancestral progenitor of cultivated rice, possessing important gene resources for rice breeding. However, the distribution of DXWR is decreasing rapidly, and no reference genome has been published to date. In this study, we constructed a chromosome-level reference genome of DXWR by Oxford Nanopore Technology (ONT) and High-through chromosome conformation capture (Hi-C). A total of 58.41 Gb clean data from ONT were de novo assembled into 231 contigs with the total length of 413.46 Mb and N50 length of 5.18 Mb. These contigs were clustered and ordered into 12 pseudo-chromosomes covering about 97.39% assembly with Hi-C data, with a scaffold N50 length of 33.47 Mb. Moreover, 54.10% of the genome sequences were identified as repeat sequences. 33,862 (94.21%) genes were functionally annotated from a total of predicted 35,942 protein-coding sequences. Compared with other species of Oryza genus, the genes related to disease and cold resistance in DXWR had undergone a large-scale expansion, which may be one of the reasons for the stronger disease resistance and cold resistance of DXWR. Comparative transcriptome analysis also determined a list of differentially expressed genes under normal and cold treatment, which supported DXWR as a cold-tolerant variety. The collinearity between DXWR and cultivated rice was high, but there were still some significant structural variations, including a specific inversion on chromosome 11, which may be related to the differentiation of DXWR. The high-quality chromosome-level reference genome of DXWR assembled in this study will become a valuable resource for rice molecular breeding and genetic research in the future.

Functional characterization of a cell wall invertase inhibitor StInvInh1 revealed its involvement in potato microtuber size in vitro

Cell wall invertase (CWI) is as an essential coordinator in carbohydrate partitioning and sink strength determination, thereby playing key roles in plant development. Emerging evidence revealed that the subtle regulation of CWI activity considerably depends on the post-translational mechanism by their inhibitors (INHs). In our previous research, two putative INHs (StInvInh1 and StInvInh3) were expected as targets of CWI in potato (Solanum tubersum), a model species of tuberous plants. Here, transcript analysis revealed that StInvInh1 showed an overall higher expression than StInhInh3 in all tested organs. Then, StInvInh1 was further selected to study. In accordance with this, the activity of StInvInh1 promoter increased with the development of leaves in plantlets but decreased with the development of microtubers in vitro and mainly appeared in vascular bundle. The recombinant protein StInvInh1 displayed inhibitory activities on the extracted CWI in vitro and StInvInh1 interacted with a CWI StcwINV2 in vivo by bimolecular fluorescence complementation. Furthermore, silencing StInvInh1 in potato dramatically increased the CWI activity without changing activities of vacuolar and cytoplasmic invertase, indicating that StInvInh1 functions as a typical INH of CWI. Releasing CWI activity in StInvInh1 RNA interference transgenic potato led to improvements in potato microtuber size in coordination with higher accumulations of dry matter in vitro. Taken together, these findings demonstrate that StInvInh1 encodes an INH of CWI and regulates the microtuber development process through fine-tuning apoplastic sucrose metabolism, which may provide new insights into tuber development.

The transcription factor StTINY3 enhances cold-induced sweetening resistance by coordinating starch resynthesis and sucrose hydrolysis in potato

The accumulation of reducing sugars in cold-stored tubers, known as cold-induced sweetening (CIS), negatively affects potato processing quality. The starch to sugar interconversion pathways that are altered in cold-stored CIS tubers have been elucidated, but the mechanism that regulates them remains largely unknown. This study identified a CBF/DREB transcription factor (StTINY3) that enhances CIS resistance by both activating starch biosynthesis and repressing the hydrolysis of sucrose to reducing sugars in detached cold-stored tubers. Silencing StTINY3 in a CIS-resistant genotype decreased CIS resistance, while overexpressing StTINY3 in a CIS-sensitive genotype increased CIS resistance, and altering StTINY3 expression was associated with expression changes in starch resynthesis-related genes. We showed first that overexpressing StTINY3 inhibited sucrose hydrolysis by enhancing expression of the invertase inhibitor gene StInvInh2, and second that StTINY3 promoted starch resynthesis by up-regulating a large subunit of the ADP-glucose pyrophosphorylase gene StAGPaseL3, and the glucose-6-phosphate transporter gene StG6PT2. Using electrophoretic mobility shift assays, we revealed that StTINY3 is a nuclear-localized transcriptional activator that directly binds to the dehydration-responsive element/CRT cis-element in the promoters of StInvInh2 and StAGPaseL3. Taken together, these findings established that StTINY3 influences CIS resistance in cold-stored tubers by coordinately modulating the starch to sugar interconversion pathways and is a good target for improving potato processing quality.

Transcriptome analysis of the winter wheat Dn1 in response to cold stress

BACKGROUND

Heilongjiang Province has a long and cold winter season (the minimum temperature can reach -30 ℃), and few winter wheat varieties can safely overwinter. Dongnongdongmai1 (Dn1) is the first winter wheat variety that can safely overwinter in Heilongjiang Province. This variety fills the gap for winter wheat cultivation in the frigid region of China and greatly increases the land utilization rate. To understand the molecular mechanism of the cold response, we conducted RNA-sequencing analysis of Dn1 under cold stress.

RESULTS

Approximately 120,000 genes were detected in Dn1 under cold stress. The numbers of differentially expressed genes (DEGs) in the six comparison groups (0 ℃ vs. 5 ℃, -5 ℃ vs. 5 ℃, -10 ℃ vs. 5 ℃, -15 ℃ vs. 5 ℃, -20 ℃ vs. 5 ℃ and -25 ℃ vs. 5 ℃) were 11,313, 8313, 15,636, 13,671, 14,294 and 13,979, respectively. Gene Ontology functional annotation suggested that the DEGs under cold stress mainly had "binding", "protein kinase" and "catalytic" activities and were involved in "oxidation-reduction", "protein phosphorylation" and "carbohydrate metabolic" processes. Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that the DEGs performed important functions in cold signal transduction and carbohydrate metabolism. In addition, major transcription factors (AP2/ERF, bZIP, NAC, WRKY, bHLH and MYB) participating in the Dn1 cold stress response were activated by low temperature.

CONCLUSION

This is the first study to explore the Dn1 transcriptome under cold stress. Our study comprehensively analysed the key genes involved in cold signal transduction and carbohydrate metabolism in Dn1 under cold stress. The results obtained by transcriptome analysis could help to further explore the cold resistance mechanism of Dn1 and provide basis for breeding of cold-resistant crops.

Comparative transcriptomic analyses of citrus cold-resistant vs. sensitive rootstocks might suggest a relevant role of ABA signaling in triggering cold scion adaption

BACKGROUND

The citrus genus comprises a number of sensitive tropical and subtropical species to cold stress, which limits global citrus distribution to certain latitudes and causes major economic loss. We used RNA-Seq technology to analyze changes in the transcriptome of Valencia delta seedless orange in response to long-term cold stress grafted on two frequently used citrus rootstocks: Carrizo citrange (CAR), considered one of the most cold-tolerant accessions; C. macrophylla (MAC), a very sensitive one. Our objectives were to identify the genetic mechanism that produce the tolerant or sensitive phenotypes in citrus, as well as to gain insights of the rootstock-scion interactions that induce the cold tolerance or sensitivity in the scion.

RESULTS

Plants were kept at 1 ºC for 30 days. Samples were taken at 0, 15 and 30 days. The metabolomic analysis showed a significant increase in the concentration of free sugars and proline, which was higher for the CAR plants. Hormone quantification in roots showed a substantially increased ABA concentration during cold exposure in the CAR roots, which was not observed in MAC. Different approaches were followed to analyze gene expression. During the stress treatment, the 0-15-day comparison yielded the most DEGs. The functional characterization of DEGs showed enrichment in GO terms and KEGG pathways related to abiotic stress responses previously described in plant cold adaption. The DEGs analysis revealed that several key genes promoting cold adaption were up-regulated in the CAR plants, and those repressing it had higher expression levels in the MAC samples.

CONCLUSIONS

The metabolomic and transcriptomic study herein performed indicates that the mechanisms activated in plants shortly after cold exposure remain active in the long term. Both the hormone quantification and differential expression analysis suggest that ABA signaling might play a relevant role in promoting the cold hardiness or sensitiveness of Valencia sweet orange grafted onto Carrizo citrange or Macrophylla rootstocks, respectively. Our work provides new insights into the mechanisms by which rootstocks modulate resistance to abiotic stress in the production variety grafted onto them.

Transcriptomic and Metabolomic Analyses Reveal Inhibition of Hepatic Adipogenesis and Fat Catabolism in Yak for Adaptation to Forage Shortage During Cold Season

Animals have adapted behavioral and physiological strategies to conserve energy during periods of adverse conditions. Hepatic glucose is one such adaptation used by grazing animals. While large vertebrates have been shown to have feed utilization and deposition of nutrients—fluctuations in metabolic rate—little is known about the regulating mechanism that controls hepatic metabolism in yaks under grazing conditions in the cold season. Hence, the objective of this research was to integrate transcriptomic and metabolomic data to better understand how the hepatic responds to chronic nutrient stress. Our analyses indicated that the blood parameters related to energy metabolism (glucose, total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, lipoprotein lipase, insulin, and insulin-like growth factor 1) were significantly (p < 0.05) lower in the cold season. The RNA-Seq results showed that malnutrition inhibited lipid synthesis (particularly fatty acid, cholesterol, and steroid synthesis), fatty acid oxidation, and lipid catabolism and promoted gluconeogenesis by inhibiting the peroxisome proliferator-activated receptor (PPAR) and PI3K-Akt signaling pathways. For metabolite profiles, 359 metabolites were significantly altered in two groups. Interestingly, the cold season group remarkably decreased glutathione and phosphatidylcholine (18:2 (2E, 4E)/0:0). Moreover, integrative analysis of the transcriptome and metabolome demonstrated that glycolysis or gluconeogenesis, PPAR signaling pathway, fatty acid biosynthesis, steroid biosynthesis, and glutathione metabolism play an important role in the potential relationship between differential expression genes and metabolites. The reduced lipid synthesis, fatty acid oxidation, and fat catabolism facilitated gluconeogenesis by inhibiting the PPAR and PI3K-Akt signaling pathways to maintain the energy homeostasis of the whole body in the yak, thereby coping with the shortage of forages and adapting to the extreme environment of the Qinghai-Tibetan Plateau (QTP).

StRAP2.3, an ERF-VII transcription factor, directly activates StInvInh2 to enhance cold-induced sweetening resistance in potato

Potato invertase inhibitor (StInvInh2) positively regulates cold-induced sweetening (CIS) resistance by inhibiting the activity of vacuolar invertase. The distinct expression patterns of StInvInh2 have been thoroughly characterized in different potato genotypes, but the related CIS ability has not been characterized. The understanding of the regulatory mechanisms that control StInvInh2 transcription is unclear. In this study, we identified an ERF-VII transcription factor, StRAP2.3, that directly regulates StInvInh2 to positively modulate CIS resistance. Acting as a nuclear-localized transcriptional activator, StRAP2.3 directly binds the ACCGAC cis-element in the promoter region of StInvInh2, enabling promoter activity. Overexpression of StRAP2.3 in CIS-sensitive potato tubers induced StInvInh2 mRNA abundance and increased CIS resistance. In contrast, silencing StRAP2.3 in CIS-resistant potato tubers repressed the expression of StInvInh2 and decreased CIS resistance. We conclude that cold-responsive StInvInh2 is due to the binding of StRAP2.3 to the ACCGAC cis-element in the promoter region of StInvInh2. Overall, these findings indicate that StRAP2.3 directly regulates StInvInh2 to positively modulate CIS resistance, which may provide a strategy to improve the processing quality of potatoes.