Transcriptome analysis of harvested bell peppers (Capsicum annuum L.) in response to cold stress

Molecular Regulatory Mechanism of Exogenous Hydrogen Sulfide in Alleviating Low-Temperature Stress in Pepper Seedlings

Pepper (Capsicum annuum L.) is sensitive to low temperatures, with low-temperature stress affecting its plant growth, yield, and quality. In this study, we analyzed the effects of exogenous hydrogen sulfide (H2S) on pepper seedlings subjected to low-temperature stress. Exogenous H2S increased the content of endogenous H2S and its synthetase activity, enhanced the antioxidant capacity of membrane lipids, and protected the integrity of the membrane system. Exogenous H2S also promoted the Calvin cycle to protect the integrity of photosynthetic organs; enhanced the photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), and photosynthesis; and reduced the intercellular CO2 concentration (Ci). Moreover, the activities of superoxide dismutase, peroxidase, catalase, and anti-cyclic glutathione (ASA-GSH) oxidase were improved to decompose excess reactive oxygen species (ROS), enhance the oxidative stress and detoxification ability of pepper seedlings, and improve the resistance to low-temperature chilling injury in 'Long Yun2' pepper seedlings. In addition, the H2S scavenger hypotaurine (HT) aggravated the ROS imbalance by reducing the endogenous H2S content, partially eliminating the beneficial effects of H2S on the oxidative stress and antioxidant defense system, indicating that H2S can effectively alleviate the damage of low temperature on pepper seedlings. The results of transcriptome analysis showed that H2S could induce the MAPK-signaling pathway and plant hormone signal transduction; upregulate the expression of transcription factors WRKY22 and PTI6; induce defense genes; and activate the ethylene and gibberellin synthesis receptors ERF1, GDI2, and DELLA, enhancing the resistance to low-temperature chilling injury of pepper seedlings. The plant-pathogen interaction was also significantly enriched, suggesting that exogenous H2S also promotes the expression of genes related to plant-pathogen interaction. The results of this study provide novel insights into the molecular mechanisms and genetic modifications of H2S that mitigate the hypothermic response.

CaHMA1 promotes Cd accumulation in pepper fruit

The main planting areas for pepper (Capsicum sp.) are high in cadmium (Cd), which is the most prevalent heavy metal pollutant worldwide. Breeding pepper cultivars with low Cd levels can promote sustainable agricultural production and ensure the safety of pepper products. To identify breeding targets for reducing Cd accumulation in pepper fruits, we performed a genome-wide association study on 186 accessions. Polymorphisms were associated with fruit Cd content in a genomic region containing a homolog of Arabidopsis (Arabidopsis thaliana) Heavy metal-transporting ATPase 1 (HMA1) encoding a P-type ATPase. In two cultivars with contrasting Cd accumulation, transcriptome analysis revealed differentially expressed genes enriched for carbohydrate metabolism and photosynthesis in fruits with high Cd accumulation, and a Cd2+/Zn2+-exporting ATPase gene (HMA). Heterologous expression of CaHMA1 in yeast increases Cd sensitivity. Overexpression of CaHMA1 conferred a severe increase in Cd content in Arabidopsis plants, whereas reduced CaHMA1 expression in pepper fruits decreased Cd content. We propose that CaHMA1 expression may be an important component of the high Cd accumulation in pepper plants.

Transcriptomic analysis of bell pepper (Capsicum annuum L.) revealing key mechanisms in response to low temperature stress

BACKGROUND

Bell pepper (Capsicum annuum L.) is one of the most economically and nutritionally important vegetables worldwide. However, its production can be affected by various abiotic stresses, such as low temperature. This causes various biochemical, morphological and molecular changes affecting membrane lipid composition, photosynthetic pigments, accumulation of free sugars and proline, secondary metabolism, as well as a change in gene expression. However, the mechanism of molecular response to this type of stress has not yet been elucidated.

METHODS AND RESULTS

To further investigate the response mechanism to this abiotic stress, we performed an RNA-Seq transcriptomic analysis to obtain the transcriptomic profile of Capsicum annuum exposed to low temperature stress, where libraries were constructed from reads of control and low temperature stress samples, varying on average per treatment from 22,952,190.5-27,305,327 paired reads ranging in size from 30 to 150 bp. The number of differentially expressed genes (DEGs) for each treatment was 388, 417 and 664 at T-17 h, T-22 h and T-41 h, respectively, identifying 58 up-regulated genes and 169 down-regulated genes shared among the three exposure times. Likewise, 23 DEGs encoding TFs were identified at T-17 h, 30 DEGs at T-22 h and 47 DEGs at T-42 h, respectively. GO analysis revealed that DEGs were involved in catalytic activity, response to temperature stimulus, oxidoreductase activity, stress response, phosphate ion transport and response to abscisic acid. KEGG pathway analysis identified that DEGs were related to flavonoid biosynthesis, alkaloid biosynthesis and plant circadian rhythm pathways in the case of up-regulated genes, while in the case of down-regulated genes, they pertained to MAPK signaling and plant hormone signal transduction pathways, present at all the three time points of low temperature exposure. Validation of the transcriptomic method was performed by evaluation of five DEGs by quantitative polymerase chain reaction (q-PCR).

CONCLUSIONS

The data obtained in the present study provide new insights into the transcriptome profiles of Capsicum annuum stem in response to low temperature stress. The data generated may be useful for the identification of key candidate genes and molecular mechanisms involved in response to this type of stress.

Effects of Fogging System and Nitric Oxide on Growth and Yield of 'Naomi' Mango Trees Exposed to Frost Stress

In years with unfavorable weather, winter frost during the blossoming season can play a significant role in reducing fruit yield and impacting the profitability of cultivation. The mango Naomi cultivar Mangifera indica L. has a low canopy that is severely affected by the effects of frost stress. As a result of the canopy being exposed to physiological problems, vegetative development is significantly inhibited. The current investigation aimed to study the influence of spraying nitric oxide and fogging spray systems on Naomi mango trees grafted on 'Succary' rootstock under frost stress conditions. The treatments were as follows: nitric oxide (NO) 50 and 100 μM, fogging spray system, and control. In comparison to the control, the use of nitric oxide and a fogging system significantly improved the leaf area, photosynthesis pigments of the leaf, the membrane stability index, yield, and physical and chemical characteristics of the Naomi mango cultivar. For instance, the application of 50 μM NO, 100 μM NO, and the fogging spray system resulted in an increase in yield by 41.32, 106.12, and 121.43% during the 2020 season, and by 39.37, 101.30, and 124.68% during the 2021 season compared to the control, respectively. The fogging spray system and highest level of NO decreased electrolyte leakage, proline content, total phenolic content, catalase (CAT), peroxidases (POX), and polyphenol oxidase (PPO) enzyme activities in leaves. Furthermore, the number of damaged leaves per shoot was significantly reduced after the application of fogging spray systems and nitric oxide in comparison to the control. Regarding vegetative growth, our results indicated that the fogging spray system and spraying nitric oxide at 100 μM enhanced the leaf surface area compared to the control and other treatments. A similar trend was noticed regarding yield and fruit quality, whereas the best values were obtained when the fogging spray system using nitric oxide was sprayed at a concentration of 100 μM. The application of fogging spray systems and nitric oxide can improve the production and fruit quality of Naomi mango trees by reducing the effects of adverse frost stress conditions.

Integrated transcriptomics and metabolomics analysis reveals key regulatory network that response to cold stress in common Bean (Phaseolus vulgaris L.)

Cold temperatures can be detrimental to crop survival and productivity. Breeding progress can be improved by understanding the molecular basis of low temperature tolerance. We investigated the key routes and critical metabolites related to low temperature resistance in cold-tolerant and -sensitive common bean cultivars 120 and 093, respectively. Many potential genes and metabolites implicated in major metabolic pathways during the chilling stress response were identified through transcriptomics and metabolomics research. Under chilling stress, the expression of many genes involved in lipid, amino acid, and flavonoid metabolism, as well as metabolite accumulation increased in the two bean types. Malondialdehyde (MDA) content was lower in 120 than in 093. Regarding amino acid metabolism, 120 had a higher concentration of acidic amino acids than 093, whereas 093 had a higher concentration of basic amino acids. Methionine accumulation was clearly higher in 120 than in 093. In addition, 120 had a higher concentration of many types of flavonoids than 093. Flavonoids, methionine and malondialdehyde could be used as biomarkers of plant chilling injury. Transcriptome analysis of hormone metabolism revealed considerably greater, expression of abscisic acid (ABA), gibberellin (GA), and jasmonic acid (JA) in 093 than in 120 during chilling stress, indicating that hormone regulation modes in 093 and 120 were different. Thus, chilling stress tolerance is different between 093 and 120 possibly due to transcriptional and metabolic regulation.

Genetic and biotechnological tools to identify breeding targets for improving postharvest quality and extending shelf life of peppers

Improved postharvest storage is a major target for pepper-crop production. The three main components of postharvest improvement of pepper fruit are reducing water-loss rate, reducing chilling susceptibility, and increasing resistance to pathogens. To date, a small number of Quantitative Trait Locus (QTL) studies have been reported for reduced water loss and enhanced tolerance to chilling and anthracnose. More effort is needed to screen germplasm collections for accessions with improved postharvest traits. Molecular studies have enabled the identification of candidate genes conferring reduced susceptibility to chilling injury and pathogen infection in pepper fruit, and in related crops such as tomato - which may be implemented in pepper. Manipulation of the activity of these genes by genome editing can improve postharvest pepper quality.

Exogenous Application of Melatonin to Green Horn Pepper Fruit Reduces Chilling Injury during Postharvest Cold Storage by Regulating Enzymatic Activities in the Antioxidant System

Chilling injury (CI) caused by exposure to low temperatures is a serious problem in the postharvest cold storage of pepper fruit. Melatonin (MT) has been reported to minimize CI in several plants. To evaluate the effectiveness of MT to minimize CI in green horn pepper and the possible mechanism involved, freshly picked green horn peppers were treated with MT solution at 100 μmol L−1 or water and then stored at 4 °C for 25 d. Results showed that MT treatment reduced CI in green horn pepper fruit, as evidenced by lower CI rate and CI index. MT treatment maintained lower postharvest metabolism rate and higher fruit quality of green horn peppers, as shown by reduced weight loss and respiratory rate, maintened fruit firmness and higher contents of chlorophyll, total phenols, flavonoids, total soluble solids and ATP. Additionally, the contents of hydrogen peroxide, superoxide radical, and malondialdehyde were kept low in the MT-treated fruit, and the activities of the enzymes peroxidase, superoxide dismutase, and catalase were significantly elevated. Similarly, the ascorbate–glutathione cycle was enhanced by elevating the activities of ascorbate peroxidase, glutathione reductase, dehydroascorbate reductase, and monodehydroascorbate reductase, to increase the regeneration of ascorbic acid and glutathione. Our results show that MT treatment protected green horn pepper fruit from CI and maintained high fruit quality during cold storage by triggering the antioxidant system

The CaMYB340 transcription factor induces chilling injury in post-harvest bell pepper by inhibiting fatty acid desaturation

Bell pepper (Capsicum annuum L.) is a tradable and desirable crop; however, its perishable nature requires low-temperature handling. Paradoxically, cold causes chilling injury (CI) and post-harvest waste. Current knowledge about CI in pepper is limited. The mechanism of CI is multi-faceted; therefore, we focused on fatty acid (FA) desaturation. We identified an upstream nuclear transcription factor (TF), CaMYB340, belonging to the R2R3 MYB subfamily, that negatively regulates FA desaturation and CaCBF3 expression and whose gene and protein expression is induced by low temperature (4°C). Specifically, McrBC treatment and bisulfite sequencing PCR indicate that exposure to cold triggers DNA methylation on one of the CHH sites in the CaMYB340 promoter. This epigenetic event at least partly contributes to the upregulation of CaMYB340 transcript levels. Increased expression of CaMYB340 results in the formation of protein complexes with CabHLH93 and CaMYB1R1, which in turn downregulate the expression of downstream genes. For peppers held at low temperature, transient overexpression of CaMYB340 reduced unsaturated FA content and membrane fluidity, resulting in cold-induced poor peel texture. Transient CaMYB340 silencing increased FA desaturation and lowered electrolyte leakage, enhancing cold tolerance in CaMYB340 knockdown fruits. Overall, these results underscore the intricacy of transcriptional networks in plants and highlight the role of CaMYB340 in CI occurrence in pepper fruits.

Integration of mRNA and miRNA profiling reveals the heterosis of three hybrid combinations of Capsicum annuum varieties

Capsicum annuum is also known as chili which is one of the most important vegetable crops grown in the world. Breeding new varieties with heterosis could improve the quality of pepper, increase yield, growth potential, disease resistance, adaptability, and seed viability. To investigate the heterosis among three cross combinations of different parents, the mRNA-miRNA integrated analysis was performed. A total number of 22,659,009 to 36,423,818 clean data were generated from mRNA-seq with 81 libraries, and the unique mapped reads were from 35,495,567 (86.81%) to 46,466,622 (88.95%). The plant-hormone signal transduction pathway (40 genes) was detected with a higher DEG number. The SAUR32L, GID1, PYR1, EIN2. ERF1, PR1, JAR1-like, IAA from this pathway play a key role in plant development. From the miRNA-seq, the number of clean reads was ranging from 12,132,221 to 25,632,680. A total of 220 miRNAs were predicted in this study, and all of them were identified as novel miRNA. The top three candidate KEGG pathways of miRNA were ribosome signaling pathway (13 miRNAs), spliceosome pathway (13 miRNAs), and plant hormone signal transduction pathways (10 miRNAs). With the mRNA and miRNA integrated analysis, we found some key genes were regulated by some miRNAs. Among them, the scarecrow-like 6 protein can be up or down regulated by mir8, mir120, mir184, mir_214, mir125, and mir130. The function of Della protein was regulated by mir24, mir74, mir94, mir139, and mir190. This study contributes to understanding how heterosis regulates the traits, such as crop production, fruit weight, and fruit length.

Arbuscular mycorrhiza in combating abiotic stresses in vegetables: An eco-friendly approach

Vegetable production is hampered by several abiotic stresses which are very common in this era of climate change. There is a huge pressure on the plants to survive and yield better results even in the prevalence of various environmental stresses such as cold stress, drought, heat stress, salinity etc. This necessitates the need of robust plant growth which is possible with mycorrhizal association. Mycorrhiza improves plants tolerance to several abiotic stresses by various physiological, functional and biochemical changes in plants. The application of arbuscular mycorrhiza (AM) as vegetable biofertilizers doesn’t only influence the plant health, but moreover discursively it lowers the demand for harmful chemical fertilizers. Overall, it may be concluded that inoculation of vegetables with arbuscular mycorrhizal fungi can be used, as it easily guards plants against undesirable abiotic stresses. In this work, information is provided based on several examples from the literature based on the application of AM to combat harmful abiotic stresses in vegetable crops. This paper reviews the impacts of AM fungi on the plant parameters, its functional activities and molecular mechanisms which makes it more adaptable and underline the future prospects of using AM fungi as a biofertilizer in the stress condition.

Advance in yellowing mechanism and the regulation technology of post-harvested broccoli

Yellowing is one of the main problems of quality deterioration in the storage, transportation, and sales of post-harvested broccoli, which seriously affects the commodity value of broccoli. Therefore, it is of significance to understand the mechanism of the process and develop effective regulation technology. In this review, we expounded the changes in the appearance of the flower ball, bud morphology, and calyx cell structure, as well as endogenous pigment metabolism, accompanying the yellowing process of broccoli. In addition, recent research on the molecular mechanism of yellowing was summarized from the aspects of transcriptome analysis and transcription regulation. Finally, the progress on the control technology of broccoli yellowing was reviewed.

The membrane lipid metabolism in horticultural products suffering chilling injury

Horticultural commodities suffer chilling injury following exposure to extremely low temperatures, which results in visible symptoms and considerable quality loss. Therefore, it is of significance to understand the mechanism of this physiological disorder and to develop effective strategies to control it. Chilling stress causes alteration in structure and function of the plasma membrane, which is assumed to be the primary event in response to cold stress. During this process, the membrane lipid metabolism plays a pivotal role in membrane fluidity and stability. In this review, we summarized the possible roles of membrane lipid metabolism in the development of chilling injury, having the potential for developing effective strategies to alleviate chilling injury in horticultural products under refrigerated storage in practice.

Transcriptome analysis of postharvest blueberries (Vaccinium corymbosum 'Duke') in response to cold stress

BACKGROUND

Blueberry (Vaccinium spp.) is a small berry with high economic value. Although cold storage can extend the storage time of blueberry to more than 60 days, it leads to chilling injury (CI) displaying as pedicle pits; and the samples of 0 °C-30 days was the critical point of CI. However, little is known about the mechanism and the molecular basis response to cold stress in blueberry have not been explained definitely. To comprehensively reveal the CI mechanisms in response to cold stress, we performed high-throughput RNA Seq analysis to investigate the gene regulation network in 0d (control) and 30d chilled blueberry. At the same time, the pitting and decay rate, electrolyte leakage (EL), malondialdehyde (MDA) proline content and GSH content were measured.

RESULTS

Two cDNA libraries from 0d (control) and 30d chilled samples were constructed and sequenced, generating a total of 35,060 unigenes with an N50 length of 1348 bp. Of these, 1852 were differentially expressed, with 1167 upregulated and 685 downregulated. Forty-five cold-induced transcription factor (TF) families containing 1023 TFs were identified. The DEGs indicated biological processes such as stress responses; cell wall metabolism; abscisic acid, gibberellin, membrane lipid, energy metabolism, cellular components, and molecular functions were significantly responsed to cold storage. The transcriptional level of 40 DEGs were verified by qRT-PCR.

CONCLUSIONS

The postharvest cold storage leads serious CI in blueberry, which substantially decreases the quality, storability and consumer acceptance. The MDA content, proline content, EL increased and the GSH content decreased in this chilled process. The biological processes such as stress responses, hormone metabolic processes were significantly affected by CI. Overall, the results obtained here are valuable for preventing CI under cold storage and could help to perfect the lack of the genetic information of non-model plant species.

Transcriptome sequencing assisted discovery and computational analysis of novel SNPs associated with flowering in Raphanus sativus in-bred lines for marker-assisted backcross breeding

The sequencing of radish genome aids in the better understanding and tailoring of traits associated with economic importance. In order to accelerate the genomics assisted breeding and genetic selection, transcriptomes of 33 radish inbred lines with diverse traits were sequenced for the development of single nucleotide polymorphic (SNP) markers. The sequence reads ranged from 2,560,543,741 bp to 20,039,688,139 bp with the GC (%) of 47.80-49.34 and phred quality score (Q30) of 96.47-97.54%. A total of 4951 polymorphic SNPs were identified among the accessions after stringent filtering and 298 SNPs with efficient marker assisted backcross breeding (MAB) markers were generated from the polymorphic SNPs. Further, functional annotations of SNPs revealed the effects and importance of the SNPs identified in the flowering process. The SNPs were predominantly associated with the four major flowering related transcription factors such as MYB, MADS box (AG), AP2/EREB, and bHLH. In addition, SNPs in the vital flowering integrator gene (FT) and floral repressors (EMBRYONIC FLOWER 1, 2, and FRIGIDA) were identified among the radish inbred lines. Further, 50 SNPs were randomly selected from 298 SNPs and validated using Kompetitive Allele Specific PCR genotyping system (KASP) in 102 radish inbred lines. The homozygosity of the inbred lines varied from 56 to 96% and the phylogenetic analysis resulted in the clustering of inbred lines into three subgroups. Taken together, the SNP markers identified in the present study can be utilized for the discrimination, seed purity test, and adjusting parental combinations for breeding in radish.