Gene expression profiles predictive of cold-induced sweetening in potato

Integration of transcriptomic and metabolomic analysis unveils the response mechanism of sugar metabolism in Cyclocarya paliurus seedlings subjected to PEG-induced drought stress

Cyclocarya paliurus (Batal.) Iljinskaja is a multiple function tree species used for functional food and valued timber production. Carbohydrates, especially water-soluble carbohydrates, play an important role in osmotic protection, signal transduction and carbon storage. Under the circumstance of global climate change the abiotic stress would restrict the development of C. paliurus plantation, whereas there is few knowledge on the regulatory mechanisms of sugar metabolism under drought stress in C. paliurus. To investigate the drought response of C. paliurus at molecular level, we conducted an integrated analysis of transcriptomic and metabolomic of C. paliurus at three PEG-induced drought stress levels (0%: control; 15%: moderate drought; 25%: severe drought) in short term. Both moderate and severe drought treatments activated the chemical defense with lowering relative water content, and enhancing the contents of soluble protein, proline and malondialdehyde in the leaves. Meanwhile, alterations in the expression of differentially expressed genes and carbohydrate metabolism profiles were observed among the treatments. Weighted gene co-expression network analysis (WGCNA) showed 3 key modules, 8 structural genes (such as genes encoding beta-fructofuranosidase (INV), sucrose synthase (SUS), raffinose synthase (RS)) and 14 regulatory transcription factors were closely linked to sugar metabolism. Our results provided the foundation to understand the response mechanism of sugar metabolism in C. paliurus under drought stress, and would drive progress in breeding of drought-tolerant varieties and plantation development of the species.

Evolutionary and Integrative Analysis of Gibberellin-Dioxygenase Gene Family and Their Expression Profile in Three Rosaceae Genomes (F. vesca, P. mume, and P. avium) Under Phytohormone Stress

The gibberellin-dioxygenase (GAox) gene family plays a crucial role in regulating plant growth and development. GAoxs, which are encoded by many gene subfamilies, are extremely critical in regulating bioactive GA levels by catalyzing the subsequent stages in the biosynthesis process. Moreover, GAoxs are important enzymes in the GA synthesis pathway, and the GAox gene family has not yet been identified in Rosaceae species (Prunus avium L., F. vesca, and P. mume), especially in response to gibberellin and PCa (prohexadione calcium; reduce biologically active GAs). In the current investigation, 399 GAox members were identified in sweet cherry, Japanese apricot, and strawberry. Moreover, they were further classified into six (A-F) subgroups based on phylogeny. According to motif analysis and gene structure, the majority of the PavGAox genes have a remarkably well-maintained exon-intron and motif arrangement within the same subgroup, which may lead to functional divergence. In the systematic investigation, PavGAox genes have several duplication events, but segmental duplication occurs frequently. A calculative analysis of orthologous gene pairs in Prunus avium L., F. vesca, and P. mume revealed that GAox genes are subjected to purifying selection during the evolutionary process, resulting in functional divergence. The analysis of cis-regulatory elements in the upstream region of the 140 PavGAox members suggests a possible relationship between genes and specific functions of hormone response-related elements. Moreover, the PavGAox genes display a variety of tissue expression patterns in diverse tissues, with most of the PavGAox genes displaying tissue-specific expression patterns. Furthermore, most of the PavGAox genes express significant expression in buds under phytohormonal stresses. Phytohormones stress analysis demonstrated that some of PavGAox genes are responsible for maintaining the GA level in plant-like Pav co4017001.1 g010.1.br, Pav sc0000024.1 g340.1.br, and Pav sc0000024.1 g270.1.mk. The subcellular localization of PavGAox protein utilizing a tobacco transient transformation system into the tobacco epidermal cells predicted that GFP signals were mostly found in the cytoplasm. These findings will contribute to a better understanding of the GAox gene family's interaction with prohexadione calcium and GA, as well as provide a strong framework for future functional characterization of GAox genes in sweet cherry.

Genome-wide investigation and comparative analysis of MATE gene family in Rosaceae species and their regulatory role in abiotic stress responses in Chinese pear (Pyrus bretschneideri)

The Multidrug and Toxic Compound Extrusion (MATE) protein belongs to a secondary transporter gene family, which plays a primary role in transporting many kinds of substrates such as organic compounds, secondary metabolites, and phytohormones. MATE protein members exist in both prokaryotes and eukaryotes. However, evolution and comprehensive analysis of the MATE genes has not been performed in Rosaceae species. In the present study, a total of 404 MATEs genes were identified from six Rosaceae genomes (Prunus avium, Pyrus bretschneideri, Prunus persica, Fragaria vesca, Prunus mume, and Malus domestica) and classified into eight main subfamilies (I-VII) based on structural and phylogenetic analysis. Microcollinearity analysis showed that whole-genome duplication events might play a vital role in the expansion of the MATE genes family. The Ka/Ks analysis, chromosomal localization, subcellular localization, and molecular characteristics (length, weight, and pI) were performed using various bioinformatics tools. Furthermore, different subfamilies have different introns-exons structures, cis-acting elements, and conserved motifs analysis, indicating functional divergence in the MATE family. Subsequently, RNA-seq analysis and real-time qRT-PCR were conducted during Chinese pear fruit development. Moreover, PbMATE genes were significantly expressed under hormonal treatments of MeJA (methyl jasmonate), SA (salicylic acid), and ABA (abscisic acid). Overall, our results provide helpful insights into the functions, expansion complexity, and evolutions of the MATE genes in Chinese pear and five Rosaceae species.

New insights into the effects of ethylene on ABA catabolism, sweetening and dormancy in stored potato tubers

Continuous ethylene supplementation suppresses postharvest sprouting, but it can increase reducing sugars, limiting its use as an alternative to chlorpropham for processing potatoes. To elucidate the mechanisms involved, tubers were treated after curing with or without the ethylene binding inhibitor 1-methylcyclopropene (1-MCP at 1 μL L^-1 for 24 h), and then stored in air or air supplemented with continuous ethylene (10 μL L^-1). Across three consecutive seasons, changes in tuber physiology were assessed alongside transcriptomic and metabolomic analysis. Exogenous ethylene alone consistently induced a respiratory rise and the accumulation of undesirable reducing sugars. The transient respiratory peak was preceded by the strong upregulation of two genes encoding 1-aminocyclopropane-1-carboxylate oxidase (ACO), typical of wound and stress induced ethylene production. Profiles of parenchymatic tissue highlighted that ethylene triggered abscisic acid (ABA) catabolism, evidenced by a steep fall in ABA levels and a transient rise in the catabolite phaseic acid, accompanied by upregulation of transcripts encoding an ABA 8'-hydroxylase. Moreover, analysis of non-structural carbohydrate-related genes revealed that ethylene strongly downregulated the expression of the Kunitz-type invertase inhibitor, already known to be involved in cold-induced sweetening. All these ethylene-induced effects were negated by 1-MCP with one notable exception: 1-MCP enhanced the sprout suppressing effect of ethylene whilst preventing ethylene-induced sweetening. This study supports the conclusions that: i) tubers adapt to ethylene by regulating conserved pathways (e.g. ABA catabolism); ii) ethylene-induced sweetening acts independently from sprout suppression, and is similar to cold-induced sugar accumulation.

Transcriptomic and metabolomic analyses of non-structural carbohydrates in red maple leaves

Plant sugars serve to balance nutrition, regulate development, and respond to biotic and abiotic stresses, whereas non-structural carbohydrates (NSCs) are essential energy sources that facilitate plant growth, metabolism, and environmental adaptation. To better elucidate the mechanisms of NSCs in red maple, ultrahigh-performance liquid chromatograph Q extractive mass spectrometry (UHPLC-QE-MS) and high-throughput RNA-sequencing were performed on green, red, and yellow leaves from a selected red maple mutant. In green leaves, the fructose phosphorylation process exhibited greater flux. In yellow leaves, sucrose and starch had a stronger capacity for synthesis and degradation, whereas in red leaves, there was a greater accumulation of trehalose and manninotriose. ArTPS5 positively regulated amylose, which was negatively regulated by ArFBP2, whereas ArFRK2 and ArFBP13 played a positive role in the biosynthesis of Sucrose-6P. Sucrose-6P also regulated anthocyanins and abscisic acid in red maple by affecting transcription factors. The results of this paper can assist with the control and optimization of the biosynthesis of NSCs in red maple, which may ultimately provide the foundation for influencing sugar production in Acer.

Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice

BACKGROUND

Low temperature is a limiting factor of rice productivity and geographical distribution. Wild rice (Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance to many abiotic stresses, including cold stress, but little is known about the mechanism underlying its resistance to cold.

RESULTS

This study elucidated the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12-4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44-68.71 million readings were obtained, resulting in the alignment of 29,128 and 30,131 genes in genotypes 253 and Y12-4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in the cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in the cold-tolerant genotype than in the cold-sensitive genotype at four stages under cold stress. Gene ontology enrichment analyses based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity indicated more upregulated genes than downregulated ones in the cold-tolerant genotype than in the cold-sensitive genotype. Quantitative real-time polymerase chain reaction was performed on seven randomly selected DEGs to confirm the RNA Sequencing (RNA-seq) data. These genes showed similar expression patterns corresponding with the RNA-Seq method. Weighted gene co-expression network analysis (WGCNA) revealed Y12-4 showed more positive genes than 253 under cold stress. We also explored the cold tolerance gene LTG5 (Low Temperature Growth 5) encoding a UDP-glucosyltransferase. The overexpression of the LTG5 gene conferred cold tolerance to indica rice.

CONCLUSION

Gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crops.

Changes in gene expression in potato meristems treated with the sprout suppressor 1,4-dimethylnaphthalene are dependent on tuber age and dormancy status

Commercial storage of potatoes often relies on the use of sprout inhibitors to prolong storage and reduce spoilage. The compound 1,4-dimethylnaphthalene (DMN) has seen increase application as a sprout inhibitor in the potato industry as older chemistries are being phased out. The mode of action of DMN is poorly understood as is the sensitivity of potato tissues to this new class of inhibitor. During storage potato tubers transition from a state of endo-dormant to eco-dormant and it is not known if the DMN response is consistent across this developmental transition. RNA-seq gene expression profiling was used to establish if stored potato tubers (Solanum tuberosum cv La Chipper) have differential sensitivity to DMN as tubers age. DMN was applied at three different times during storage; just after harvest when tubers are in endo-dormancy, midwinter at early eco-dormancy, and in spring during late eco-dormancy when sprouting was prevented via exposure to cold storage temperatures. Changes in gene expression were lowest during endo-dormancy while midwinter and spring treatments exhibited a greater and more diverse expression response. Functional analysis of differential gene expression demonstrated gene sets associated with DNA replication, cell division, and DNA methylation are suppressed after DMN treatment. However, gene sets associated with salicylic acid, jasmonic acid, abiotic and biotic stress responses are elevated by DMN only after endodormancy terminates. Gene clusters associated with pathogenesis related proteins PR-4 and PR-5 are also upregulated in response to DMN. These results indicate that DMN sensitivity changes as potato tubers age and transition from endo-dormant to eco-dormant in storage and the overall response is a shift in gene classes that regulate growth and response to stress.

Cold storage reveals distinct metabolic perturbations in processing and non-processing cultivars of potato (Solanum tuberosum L.)

Cold-induced sweetening (CIS) causes considerable losses to the potato processing industry wherein the selection of potato genotypes using biochemical information has found to be advantageous. Here, ¹H NMR spectroscopy was performed to identify metabolic perturbations from tubers of five potato cultivars (Atlantic, Frito Lay-1533, Kufri Jyoti, Kufri Pukhraj, and PU1) differing in their CIS ability and processing characteristics at harvest and after cold storage (4 °C). Thirty-nine water-soluble metabolites were detected wherein significantly affected metabolites after cold storage were categorized into sugars, sugar alcohols, amino acids, and organic acids. Multivariate statistical analysis indicated significant differences in the metabolic profiles among the potato cultivars. Pathway enrichment analysis revealed that carbohydrates, amino acids, and organic acids are the key players in CIS. Interestingly, one of the processing cultivars, FL-1533, exhibited a unique combination of metabolites represented by low levels of glucose, fructose, and asparagine accompanied by high citrate levels. Conversely, non-processing cultivars (Kufri Pukhraj and Kufri Jyoti) showed elevated glucose, fructose, and malate levels. Our results indicate that metabolites such as glucose, fructose, sucrose, asparagine, glutamine, citrate, malate, proline, 4-aminobutyrate can be potentially utilized for the prediction, selection, and development of potato cultivars for long-term storage, nutritional, as well as processing attributes.

Tuber transcriptome profiling of eight potato cultivars with different cold-induced sweetening responses to cold storage

Tubers are vegetative reproduction organs formed from underground extensions of the plant stem. Potato tubers are harvested and stored for months. Storage under cold temperatures of 2-4 °C is advantageous for supressing sprouting and diseases. However, development of reducing sugars can occur with cold storage through a process called cold-induced sweetening (CIS). CIS is undesirable as it leads to darkened color with fry processing. The purpose of the current study was to find differences in biological responses in eight cultivars with variation in CIS resistance. Transcriptome sequencing was done on tubers before and after cold storage and three approaches were taken for gene expression analysis: 1. Gene expression correlated with end-point glucose after cold storage, 2. Gene expression correlated with increased glucose after cold storage (after-before), and 3. Differential gene expression before and after cold storage. Cultivars with high CIS resistance (low glucose after cold) were found to increase expression of an invertase inhibitor gene and genes involved in DNA replication and repair after cold storage. The cultivars with low CIS resistance (high glucose after cold) showed increased expression of genes involved in abiotic stress response, gene expression, protein turnover and the mitochondria. There was a small number of genes with similar expression patterns for all cultivars including genes involved in cell wall strengthening and phospholipases. It is proposed that the pattern of gene expression is related to chilling-induced DNA damage repair and cold acclimation and that genetic variation in these processes are related to CIS.

Quantitative trait loci for starch-corrected chip color after harvest, cold storage and after reconditioning mapped in diploid potato

The objective of this study was to map the quantitative trait loci (QTLs) for chip color after harvest (AH), cold storage (CS) and after reconditioning (RC) in diploid potato and compare them with QTLs for starch-corrected chip color. Chip color traits AH, CS, and RC significantly correlated with tuber starch content (TSC). To limit the effect of starch content, the chip color was corrected for TSC. The QTLs for chip color (AH, CS, and RC) and the starch-corrected chip color determined with the starch content after harvest (SCAH), after cold storage (SCCS) and after reconditioning (SCRC) were compared to assess the extent of the effect of starch and the location of genetic factors underlying this effect on chip color. We detected QTLs for the AH, CS, RC and starch-corrected traits on ten potato chromosomes, confirming the polygenic nature of the traits. The QTLs with the strongest effects were detected on chromosomes I (AH, 0 cM, 11.5% of variance explained), IV (CS, 43.9 cM, 12.7%) and I (RC, 49.7 cM, 14.1%). When starch correction was applied, the QTLs with the strongest effects were revealed on chromosomes VIII (SCAH, 39.3 cM, 10.8% of variance explained), XI (SCCS, 79.5 cM, 10.9%) and IV (SCRC, 43.9 cM, 10.8%). Applying the starch correction changed the landscape of QTLs for chip color, as some QTLs became statistically insignificant, shifted or were refined, and new QTLs were detected for SCAH. The QTLs on chromosomes I and IV were significant for all traits with and without starch correction.

Systematic analysis and comparison of the PHD-Finger gene family in Chinese pear (Pyrus bretschneideri) and its role in fruit development

PHD-finger proteins, which belongs to the type of zinc finger family, and that play an important role in the regulation of both transcription and the chromatin state in eukaryotes. Currently, PHD-finger proteins have been well studied in animals, while few studies have been carried out on their function in plants. In the present study, 129 non-redundant PHD-finger genes were identified from 5 Rosaceae species (pear, apple, strawberry, mei, and peach); among them, 31 genes were identified in pear. Subsequently, we carried out a bioinformatics analysis of the PHD-finger genes. Thirty-one PbPHD genes were divided into 7 subfamilies based on the phylogenetic analysis, which are consistent with the intron-exon and conserved motif analyses. In addition, we identified five segmental duplication events, implying that the segmental duplications might be a crucial role in the expansion of the PHD-finger gene family in pear. The microsynteny analysis of five Rosaceae species showed that there were independent duplication events in addition to the genome-wide duplication of the pear genome. Subsequently, ten expressed PHD-finger genes of pear fruit were identified using qRT-PCR, and one of these genes, PbPHD10, was identified as an important candidate gene for the regulation of lignin synthesis. Our research provides useful information for the further analysis of the function of PHD-finger gene family in pear.