Cell Wall Modification Genes Research Articles

Impacts of Fruit Frosting Coverage on Postharvest Softening of Prunes under Vibration Stress

The surface of prune fruit has a thick layer of frosting, which is easily damaged and lost during prunes harvest or postharvest handling, and there is no clear information on the effect of prune surface frost on postharvest storage quality. To investigate the effect of fruit frosting on the softening of prune fruits during storage under vibration stress, prunes were divided into three grades according to fruit frosting in this study and were vibrated for 8 h at a frequency of 5 Hz at 4 °C; then, samples were selected once every 8 d. The results showed that the heavy fruit frosting (HFF) group maintained higher hardness (21.47%), L* (20.85%), and total soluble solids (12.79%) levels at the end of storage and inhibited cell wall-modifying enzyme activities (polygalacturonase, pectin methylesterase, glycosidase, β-glucosidase, and cellulase) compared to frosting-less fruit (FF) group. This group also showed improved expression of key cell wall-modification genes (ADPG2, PME31, CESA1, BGAL3, XTH33, BGLU41) as well as chelate-soluble pectin (72.11%), Na2CO3-soluble pectin (42.83%), and cellulose (36.89%) solubilization and maintained lower water-soluble pectin (34.23%). Microscopic observations showed that the fruit frosting could delay the dissolution of pectin components and protect the cell wall structure. In summary, fruit frosting can effectively inhibit fruit softening and maintain fruit quality.

Ficus carica ERF12 improves fruit firmness at ripening

Fig fruit firmness decreases rapidly during ripening and after harvest, resulting in poor storability and transportation loss, which severely restricts development of the fresh fig industry. APETALA2/ethylene-responsive factor (AP2/ERF) transcription factors are downstream components of the ethylene-signaling pathway that play crucial roles in quality formation during fruit ripening. In this study, Ficus carica (Fc) ERF12 was clustered in repressor subfamily VIII of ERFs through phylogenetic analysis, and further recruited by its two EAR motifs and expression pattern during fig ripening. DNA affinity purification sequencing analysis indicated that FcERF12 binds to the promoter or gene body regions of multiple ripening-related genes, including cell wall-modification genes FcPG, FcXTH and FcPME, and ethylene-biosynthesis genes FcACS and FcACO. Yeast two-hybrid assay demonstrated that FcERF12 interacts with TOPLESS (TPL) co-repressors FcTPL1, FcTPL4 and FcTPL5, and histone deacetylases FcHDA6 and FcHDA19; interaction with FcTPL4 and FcTPL5 relied on the C-terminal EAR motif. Overexpressing FcERF12 in tomato did not change fruit size or yield, but resulted in an 18.37% increment in fruit firmness and a 49.62% reduction in ethylene-release rate at fruit ripening, accompanied by a significant decrease in seed number per fruit. Transcriptomic analysis revealed downregulation of tomato cell wall-modification genes SlPL, SlEXP and SlPG, and ethylene-synthesis genes SlACO and SlACS. Metabolomic profiling identified 82 differentially accumulated flavonoid metabolites, 61 of them showing significantly decreased contents. Taken together, our results exhibit the negative regulatory role of FcERF12 in fig ethylene-signal transduction, providing new information on precise control of fruit firmness and other quality traits at ripening.

Genomic and Transcriptomic Analyses Illuminates Unique Traits of Elusive Night Flowering Jasmine Parijat (Nyctanthes arbor‐tristis)

AbstractThe night‐flowering Jasmine, Nyctanthes arbor‐tristis also known as Parijat, is a perennial woody shrub belonging to the family of Oleaceae. It is popular for its fragrant flowers that bloom in the night and is a potent source of secondary metabolites. However, knowledge about its genome and the expression of genes regulating flowering or secondary metabolite accumulation is lacking. In this study, we generated whole genome sequencing data to assemble the first de novo assembly of Parijat and use it for comparative genomics and demographic history reconstruction. The temporal dynamics of effective population size (Ne) experienced a positive influence of colder climates suggesting the switch to night flowering may have provided an evolutionary advantage. We employed multi‐tissue transcriptome sequencing of floral stages/parts to obtain insights into the transcriptional regulation of nocturnal flower development and the production of volatiles/metabolites. Tissue‐specific transcripts for mature flowers revealed key players in circadian regulation and flower development, including the auxin pathway and cell wall modifying genes. Furthermore, we identified tissue‐specific transcripts responsible for producing numerous secondary metabolites, mainly terpenoids and carotenoids. The diversity and specificity of Terpene Synthase (TPS) and CCDs (Carotenoid Cleavage Deoxygenases) mediate the bio‐synthesis of specialised metabolites in Parijat. Our study establishes Parijat as a novel non‐model species to understand the molecular mechanisms of nocturnal blooming and secondary metabolite production.

SHI family transcription factors regulate an interspecific barrier.

Pre-zygotic interspecies incompatibility in angiosperms is an important mechanism to prevent unfavourable hybrids between species. Here we report our identification of STIGMATIC PRIVACY 2 (SPRI2), a transcription factor that has a zinc-finger domain and regulates interspecies barriers in Arabidopsis thaliana, via genome-wide association study. Knockout analysis of SPRI2/SRS7 and its paralogue SPRI2-like/SRS5 demonstrated their necessity in rejecting male pollen from other species within female pistils. Additionally, they govern mRNA transcription of xylan O-acetyltransferases (TBL45 and TBL40) related to cell wall modification, alongside SPRI1, a pivotal transmembrane protein for interspecific pollen rejection. SPRI2/SRS7 is localized as condensed structures in the nucleus formed via liquid-liquid phase separation (LLPS), and a prion-like sequence in its amino-terminal region was found to be responsible for the formation of the condensates. The LLPS-regulated SPRI2/SRS7 discovered in this study may contribute to the establishment of interspecific reproductive barriers through the transcriptional regulation of cell wall modification genes and SPRI1.

Tissues and mechanisms associated with Verticillium wilt resistance in tomato using bi-grafted near-isogenic lines.

Host resistance is the primary means to control Verticillium dahliae, a soil-borne pathogen causing major losses on a broad range of plants, including tomato. The tissues and mechanisms responsible for resistance remain obscure. In the field, resistant tomato used as rootstocks does not confer resistance. Here, we created bi-grafted plants with near-isogenic lines (NILs) exhibiting (Ve1) or lacking (ve1) resistance to V. dahliae race 1. Ten days after inoculation, scion and rootstock tissues were subjected to differential gene expression and co-expression network analyses. Symptoms only developed in susceptible scions regardless of the rootstock. Infection caused more dramatic alteration of tomato gene expression in susceptible compared to resistant tissues, including pathogen receptor, signaling pathway, PR protein, and cell wall modification genes. Differences were observed between scions and rootstocks, primarily related to physiological processes in these tissues. Gene expression in scions was influenced by the rootstock genotype. A few genes were associated with the Ve1 genotype, which was independent of infection or tissue type. Several were physically clustered, some near the Ve1 locus on chromosome 9. Transcripts mapped to V. dahliae were dominated by secreted candidate effector proteins. These findings advance knowledge of molecular mechanisms underlying the tomato-V. dahliae interaction.

Genome and Transcriptome Identification of a Rice Germplasm with High Cadmium Uptake and Translocation.

The safe production of food on Cd-polluted land is an urgent problem to be solved in South China. Phytoremediation or cultivation of rice varieties with low Cd are the main strategies to solve this problem. Therefore, it is very important to clarify the regulatory mechanism of Cd accumulation in rice. Here, we identified a rice variety with an unknown genetic background, YSD, with high Cd accumulation in its roots and shoots. The Cd content in the grains and stalks were 4.1 and 2.8 times that of a commonly used japonica rice variety, ZH11, respectively. The Cd accumulation in the shoots and roots of YSD at the seedling stage was higher than that of ZH11, depending on sampling time, and the long-distance transport of Cd in the xylem sap was high. Subcellular component analysis showed that the shoots, the cell wall, organelles, and soluble fractions of YSD, showed higher Cd accumulation than ZH11, while in the roots, only the cell wall pectin showed higher Cd accumulation. Genome-wide resequencing revealed mutations in 22 genes involved in cell wall modification, synthesis, and metabolic pathways. Transcriptome analysis in Cd-treated plants showed that the expression of pectin methylesterase genes was up-regulated and the expression of pectin methylesterase inhibitor genes was down-regulated in YSD roots, but there were no significant changes in the genes related to Cd uptake, translocation, or vacuole sequestration. The yield and tiller number per plant did not differ significantly between YSD and ZH11, but the dry weight and plant height of YSD were significantly higher than that of ZH11. YSD provides an excellent germplasm for the exploration of Cd accumulation genes, and the cell wall modification genes with sequence- and expression-level variations provide potential targets for phytoremediation.

Genome Sequence and Analysis ofNicotiana benthamiana, the Model Plant for Interactions between Organisms

Nicotiana benthamiana is widely used as a model plant for dicotyledonous angiosperms. In fact, the strains used in research are highly susceptible to a wide range of viruses. Accordingly, these strains are subject to plant pathology and plant-microbe interactions. In terms of plant-plant interactions, N. benthamiana is one of the plants that exhibit grafting affinity with plants from different families. Thus, N. benthamiana is a good model for plant biology and has been the subject of genome sequencing analyses for many years. However, N. benthamiana has a complex allopolyploid genome, and its previous reference genome is fragmented into 141,000 scaffolds. As a result, molecular genetic analysis is difficult to perform. To improve this effort, de novo whole-genome assembly was performed in N. benthamiana with Hifi reads, and 1,668 contigs were generated with a total length of 3.1 Gb. The 21 longest scaffolds, regarded as pseudomolecules, contained a 2.8-Gb sequence, occupying 95.6% of the assembled genome. A total of 57,583 high-confidence gene sequences were predicted. Based on a comparison of the genome structures between N. benthamiana and N. tabacum, N. benthamiana was found to have more complex chromosomal rearrangements, reflecting the age of interspecific hybridization. To verify the accuracy of the annotations, the cell wall modification genes involved in grafting were analyzed, which revealed not only the previously indeterminate untranslated region, intron and open reading frame sequences but also the genomic locations of their family genes. Owing to improved genome assembly and annotation, N. benthamiana would increasingly be more widely accessible.

MaHDA6-MaNAC154 module regulates the transcription of cell wall modification genes during banana fruit ripening

Fruit ripening and softening is a complex physiological process that is governed by the expression of a wide range of genes, and histone modification is a critical mechanism for precise gene expression. Although previous studies have indicated that NAC transcription factor (TF) and histone deacetylase individually play important roles in fruit ripening, the molecular connection between these two proteins within the regulatory system underlying banana fruit ripening is poorly understood. Here, we characterized a banana NAC MaNAC154 that was a negative regulator of banana fruit ripening. MaNAC154 was shown to localize in the nucleus, and it could target the promoters of MaEXP1/2, MaPL2, MaPG1/X3 and MaXTH5/23/28 to repress their transcription. Importantly, MaNAC154 was found to interact with a histone deacetylase MaHDA6, and their interaction significantly enhanced MaNAC154-mediated transcriptional repression capacity. Moreover, the acetylation levels of histones H3 and H4 of MaEXP1/2, MaPL2, MaPG1/X3 and MaXTH5/23/28 were elevated in the ripening stage. Overall, our data establish a coordinated mechanism underpinning histone deacetylation and TF-mediated gene repression for banana fruit ripening, providing a novel molecular basis for controlling mechanism of fruit ripening and softening.

The mechanism of gibberellins treatment suppressing kiwifruit postharvest ripening processes by transcriptome analysis

Gibberellins (GAs) control numerous processes in plants, including fruit ripening. However, the role of GAs in kiwifruit ripening is not well characterized. Here, we noticed that GA3 treatment in postharvest kiwifruit delayed the ripening process and many physiological traits were detected such as firmness, starch/total soluble solid content, cell-wall components (pectin, cellulose and hemicellulose), ethylene and ester production, and ascorbic acid (vitamin C) concentration. Transcriptome analysis supplied a molecular basis for investigating the inhibiting mechanism of GA3 and metabolic variations during kiwifruit ripening. A total of 3116 differently expressed genes (DEGs) were identified, including 51 genes involved in plant hormone signal transduction pathways and 36 structural genes related to these physiological traits. 16 major DEGs were analyzed by real-time PCR during the whole storage period. The expression of most of them was significantly suppressed by GA3 treatment, such as two ethylene biosynthesis genes (ACOs ), two β-amylase (BAMs), five cell-wall modification genes, one GA2ox, and one GA receptor GID1, whereas the expression of Actinidia29942 (JAZ) was enhanced by GA3 treatment. Correlation analysis between multiple physiological indicators and candidate genes showed that GA3 could regulate kiwifruit postharvest ripening effectively and comprehensively. Together, these GA-responsive genes may play important roles in controlling kiwifruit ripening, and GA treatment could be a promising approach for the preservation of postharvest kiwifruit.

Surface-localized glycoproteins act through class C ARFs to fine-tune gametophore initiation in Physcomitrium patens.

Arabinogalactan proteins are functionally diverse cell wall structural glycoproteins that have been implicated in cell wall remodeling, although the mechanistic actions remain elusive. Here, we identify and characterize two AGP glycoproteins, SLEEPING BEAUTY (SB) and SB-like (SBL), that negatively regulate the gametophore bud initiation in Physcomitrium patens by dampening cell wall loosening/softening. Disruption of SB and SBL led to accelerated gametophore formation and altered cell wall compositions. The function of SB is glycosylation dependent and genetically connected with the class C auxin response factor (ARF) transcription factors PpARFC1B and PpARFC2. Transcriptomics profiling showed that SB upregulates PpARFC2, which in turn suppresses a range of cell wall-modifying genes that are required for cell wall loosening/softening. We further show that PpARFC2 binds directly to multiple AuxRE motifs on the cis-regulatory sequences of PECTIN METHYLESTERASE to suppress its expression. Hence, our results demonstrate a mechanism by which the SB modulates the strength of intracellular auxin signaling output, which is necessary to fine-tune the timing of gametophore initials formation.

Modified Atmosphere Packaging and 1-Methylcyclopropene Treatments Maintain the Fruit Quality of 'Wonmi' Persimmons during Export Simulation.

Persimmons are one of the most important export fruits in South Korea, where several tons are exported across the globe each year. In this study, the quality attributes of 'Wonmi' persimmon fruits were evaluated during an export simulation at 0 °C, 10 °C, and 24 °C with a combination of 1-Methylcyclopropene (1-MCP) and modified atmosphere packaging (MAP) treatments. The relative humidity during the export simulation was greater at room temperature (75-92%) and 0 °C (85% to 93%) than at 10 °C (42% to 60%). The results show that the application of 1-MCP and MAP treatments during the export simulation were effective in delaying the ripening of 'Wonmi' persimmons by reducing respiration and ethylene production. The suppressed expression of ethylene synthesis genes and cell wall modification genes reduced the ethylene production and maintain the fruit firmness, respectively. In addition, 1-MCP and MAP treatments were effective in maintaining SSC and color of 'Wonmi' persimmon fruits during the export simulation. Thus, by adopting these treatments, the overall quality of persimmon exports from South Korea can significantly improve.

Combined effects of temperature and humidity on the interaction between tomato and Botrytis cinerea revealed by integration of histological characteristics and transcriptome sequencing.

The environment significantly impacts the interaction between plants and pathogens, thus remarkably affecting crop disease occurrence. However, the detailed combined mechanisms of temperature and humidity influencing this interaction remain unclear. In this study, the interaction between tomato and Botrytis cinerea in various temperature and humidity conditions was analyzed by histological observation and a dual RNA-seq approach. Results showed that low humidity was not favorable for mycelial growth, resulting in infection failure. Both high and low temperatures at high humidity successfully inhibited pathogenic infection and disease incidence in the tomato plants, thus enhancing their resistance to B. cinerea. The high temperature and high humidity (HH) treatment induced the upregulation of light reaction genes, increased the net photosynthetic rate, and expanded the chloroplast morphology of infected tomatoes. The HH treatment also inhibited the expression of cell cycle-related genes of B. cinerea, interfered with conidial germination and mycelial growth, and damaged mycelial cell structure. Low temperature and high humidity (LH) treatment induced the expression of cell wall modification genes and remodeled the cell wall morphology of tomatoes in response to B. cinerea. In addition, the downregulated fungal catabolic genes and the abnormal increase in electron density of mycelial cells under LH treatment subsequently reduced the infection ability of B. cinerea. These results further explain the coupled effects of temperature and humidity on plant defenses and pathogen virulence, and provide a potential means to control gray mold.

Spermidine promotes lysozyme tolerance and acid stress resistance in Streptococcus pyogenes M3.

Streptococcus pyogenes are Gram-positive opportunistic pathogens residing in the human nasopharynx and skin. Changes in environmental conditions, such as pH, temperature and availability of essential ions, can stimulate the expression of S. pyogenes virulence factors. One such factor could be the availability of an extracellular pool of polyamines. Polyamines are synthesized from amino acids, and are universally present in the environment. Polyamines have been implicated in the ecology of pathogenesis by modulating quorum sensing, host adaptation and virulence. Polyamines mediate pathogenesis and help the pathogen resist environmental stress. In this study, we investigated the ability of the polyamine, spermidine, to promote acid stress survival of S. pyogenes. S. pyogenes does not synthesize spermidine, but the extracellular pool of spermidine constituted by the host and microbiome could be utilized as a signalling molecule. We report that spermidine promotes acid stress resistance in S. pyogenes. Moreover, spermidine affects the morphology of S. pyogenes by decreasing the cell size and increasing the dltA gene expression. Along with dltA, spermidine upregulated the gene expression of cell wall-modifying genes such as mur, pgdA, pepO and srtA, which might help the bacteria to resist acidic stress.

MaMYB4 is a negative regulator and a substrate of RING‐type E3 ligases MaBRG2/3 in controlling banana fruit ripening

Fruit ripening is a complex developmental process, which is modulated by both transcriptional and post-translational events. Control of fruit ripening is important in maintaining moderate quality traits and minimizing postharvest deterioration. In this study, we discovered that the transcription factor MaMYB4 acts as a negative regulator of fruit ripening in banana. The protein levels of MaMYB4 decreased gradually with banana fruit ripening, paralleling ethylene production, and decline in firmness. DNA affinity purification sequencing combined with RNA-sequencing analyses showed that MaMYB4 preferentially binds to the promoters of various ripening-associated genes including ethylene biosynthetic and cell wall modifying genes. Furthermore, ectopic expression of MaMYB4 in tomato delayed tomato fruit ripening, which was accompanied by downregulation of ethylene biosynthetic and cell wall modifying genes. Importantly, two RING finger E3 ligases MaBRG2/3, whose protein accumulation increased progressively with fruit ripening, were found to interact with and ubiquitinate MaMYB4, contributing to decreased accumulation of MaMYB4 during fruit ripening. Transient overexpression of MaMYB4 and MaBRG2/3 in banana fruit ripening delayed or promoted fruit ripening by inhibiting or stimulating ethylene biosynthesis, respectively. Taken together, we demonstrate that MaMYB4 negatively modulates banana fruit ripening, and that MaMYB4 abundance could be regulated by protein ubiquitination, thus providing insights into the role of MaMYB4 in controlling fruit ripening at both transcriptional and post-translational levels.

The NAC transcription factor ANAC017 regulates aluminum tolerance by regulating the cell wall-modifying genes.

Aluminum (Al) toxicity is one of the key factors limiting crop production in acid soils; however, little is known about its transcriptional regulation in plants. In this study, we characterized the role of a NAM, ATAF1/2, and cup-shaped cotyledon 2 (NAC) transcription factors (TFs), ANAC017, in the regulation of Al tolerance in Arabidopsis (Arabidopsis thaliana). ANAC017 was localized in the nucleus and exhibited constitutive expression in the root, stem, leaf, flower, and silique, although its expression and protein accumulation were repressed by Al stress. Loss of function of ANAC017 enhanced Al tolerance when compared with wild-type Col-0 and was accompanied by lower root and root cell wall Al content. Furthermore, both hemicellulose and xyloglucan content decreased in the anac017 mutants, indicating the possible interaction between ANAC017 and xyloglucan endotransglucosylase/hydrolase (XTH). Interestingly, the expression of XTH31, which is responsible for xyloglucan modification, was downregulated in the anac017 mutants regardless of Al supply, supporting the possible interaction between ANAC017 and XTH31. Yeast one-hybrid, dual-luciferase reporter assay, and chromatin immunoprecipitation-quantitative PCR analysis revealed that ANAC017 positively regulated the expression of XTH31 through directly binding to the XTH31 promoter region, and overexpression of XTH31 in the anac017 mutant background rescued its Al-tolerance phenotype. In conclusion, we identified that the tTF ANAC017 acts upstream of XTH31 to regulate Al tolerance in Arabidopsis.

Transcriptome analysis of peach fruit under 1-MCP treatment provides insights into regulation network in melting peach softening

Abstract Peach (Prunus persica L.) displays distinguish texture phenotype during postharvest, which could be classified into three types, including melting flesh (MF), non-melting flesh, and stony-hard. MF peach would soften rapidly with an outbreak of ethylene production, which causes huge wastage during fruit transportation and storage. 1-Methylcyclopropene (1-MCP) was used to alleviate fruit softening. In this study, we performed RNA-sequencing on two MF peach cultivars (‘YuLu’ and ‘Yanhong’) after 1-MCP treatment to identify the candidate genes participating in peach fruit softening. A total of 167 genes were identified by weighted gene coexpression network analysis and correlation analysis that could respond to 1-MCP treatment and might be related to softening. Among them, 5 auxin-related genes including 2 indole-3-acetic acid, 1 auxin response transcription factor and 2 small auxin-up RNAs, and 4 cell wall modifying genes (PpPG1, PpPG2, PpPG24 and PpPMEI) were characterized as key genes participating in MF peach softening. Furthermore, 2 transcription factors, which belong to HD-ZIP and MYB, were predicted as candidates regulating softening process by constructing a transcriptional network of these 4 cell wall modifying genes combined with expression pattern analysis, of which HD-ZIP could trans-activate the promoter of PpPG1.

Acceleration of Aril Cracking by Ethylene in Torreya grandis During Nut Maturation.

Torreya grandis ‘Merrillii’ is a famous nut with great nutritional value and high medicinal value. Aril cracking is an important process for seed dispersal, which is also an indicator of seed maturation. However, the cracking mechanism of T. grandis aril during the maturation stage remains largely unknown. Here, we provided a comprehensive view of the physiological and molecular levels of aril cracking in T. grandis by systematically analyzing its anatomical structure, physiological parameters, and transcriptomic response during the cracking process. These results showed that the length of both epidermal and parenchymatous cell layers significantly increased from 133 to 144 days after seed protrusion (DASP), followed by a clear separation between parenchymatous cell layers and kernel, which was accompanied by a breakage between epidermal and parenchymatous cell layers. Moreover, analyses of cell wall composition showed that a significant degradation of cellular wall polysaccharides occurred during aril cracking. To examine the global gene expression changes in arils during the cracking process, the transcriptomes (96 and 141 DASP) were analyzed. KEGG pathway analysis of DEGs revealed that 4 of the top 10 enriched pathways were involved in cell wall modification and 2 pathways were related to ethylene biosynthesis and ethylene signal transduction. Furthermore, combining the analysis results of co-expression networks between different transcription factors, cell wall modification genes, and exogenous ethylene treatments suggested that the ethylene signal transcription factors (ERF11 and ERF1A) were involved in aril cracking of T. grandis by regulation of EXP and PME. Our findings provided new insights into the aril cracking trait in T. grandis.

Characterization of Two Ethephon-Induced IDA-Like Genes from Mango, and Elucidation of Their Involvement in Regulating Organ Abscission.

In mango (Mangifera indica L.), fruitlet abscission limits productivity. The INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) peptide acts as a key component controlling abscission events in Arabidopsis. IDA-like peptides may assume similar roles in fruit trees. In this study, we isolated two mango IDA-like encoding-genes, MiIDA1 and MiIDA2. We used mango fruitlet-bearing explants and fruitlet-bearing trees, in which fruitlets abscission was induced using ethephon. We monitored the expression profiles of the two MiIDA-like genes in control and treated fruitlet abscission zones (AZs). In both systems, qRT-PCR showed that, within 24 h, both MiIDA-like genes were induced by ethephon, and that changes in their expression profiles were associated with upregulation of different ethylene signaling-related and cell-wall modifying genes. Furthermore, ectopic expression of both genes in Arabidopsis promoted floral-organ abscission, and was accompanied by an early increase in the cytosolic pH of floral AZ cells—a phenomenon known to be linked with abscission, and by activation of cell separation in vestigial AZs. Finally, overexpression of both genes in an Atida mutant restored its abscission ability. Our results suggest roles for MiIDA1 and MiIDA2 in affecting mango fruitlet abscission. Based on our results, we propose new possible modes of action for IDA-like proteins in regulating organ abscission.

Methylome and transcriptome analysis reveals candidate genes for tuber shape variation in tissue culture-derived potato

We investigated genome-wide DNA methylation and transcriptome (RNA-seq) profiling for tuber shape variation in potato. Mother plant (M1, round) and tissue culture-derived clonal variant plant (M2, elongated) were used. Total number of DNA methylation sites at cytosine contexts (CpG, CHG and CHH) was higher in M2 than M1, where CHH was the highest followed by CHG and CpG. Differential methylation regions (DMRs) analysis in M1 (control) and M2 revealed maximum DMRs number on chromosome 5 in CHG context and hypo-methylation was higher than hyper-methylation. Further, transcriptome analysis revealed that a total of 20,747 genes were differentially expressed between M1 (control) and M2, of which 280 (over-expressed) and 612 (under-expressed) genes were statistically significant (p ≤ 0.05). The gene ontology (GO) annotation showed predominance of molecular function, whereas signal transduction and carbohydrate metabolism were major KEGG (Kyoto encyclopedia of genes and genomes) pathways. RNA-seq gene expression was validated for the ten selected genes by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. Based on the comparative analysis, we observed a few candidate genes associated with tuber developmental processes such as phytohormones-related (e.g. SAUR family protein, abscisic acid environmental stress-inducible protein TAS14), sugar metabolism (e.g. UDP-glucosyltransferase, glycosyltransferase family GT8 protein), transcription factors (e.g. F-box family protein, MYB, WRKY, MADS-box), stress-responsive proteins (e.g. early-responsive to dehydration 3, cytochrome P450, proline-rich protein) and cell wall modifying genes (e.g. endo-1,4-beta-glucanase, glycine-rich cell wall structural protein 1.8, 3-ketoacyl-CoA synthase 10). Our study suggests that these candidate genes probably play key roles in tuber shape variation in potato.

Identification of Candidate Genes Involved in Fruit Ripening and Crispness Retention Through Transcriptome Analyses of a 'Honeycrisp' Population.

Crispness retention is a postharvest trait that fruit of the ’Honeycrisp’ apple and some of its progeny possess. To investigate the molecular mechanisms of crispness retention, progeny individuals derived from a ’Honeycrisp’ × MN1764 population with fruit that either retain crispness (named “Retain”), lose crispness (named “Lose”), or that are not crisp at harvest (named “Non-crisp”) were selected for transcriptomic comparisons. Differentially expressed genes (DEGs) were identified using RNA-Seq, and the expression levels of the DEGs were validated using nCounter®. Functional annotation of the DEGs revealed distinct ripening behaviors between fruit of the “Retain” and “Non-crisp” individuals, characterized by opposing expression patterns of auxin- and ethylene-related genes. However, both types of genes were highly expressed in the fruit of “Lose” individuals and ’Honeycrisp’, which led to the potential involvements of genes encoding auxin-conjugating enzyme (GH3), ubiquitin ligase (ETO), and jasmonate O-methyltransferase (JMT) in regulating fruit ripening. Cell wall-related genes also differentiated the phenotypic groups; greater numbers of cell wall synthesis genes were highly expressed in fruit of the “Retain” individuals and ’Honeycrisp’ when compared with “Non-crisp” individuals and MN1764. On the other hand, the phenotypic differences between fruit of the “Retain” and “Lose” individuals could be attributed to the functioning of fewer cell wall-modifying genes. A cell wall-modifying gene, MdXTH, was consistently identified as differentially expressed in those fruit over two years in this study, so is a major candidate for crispness retention.