Temporal profiling of physiological, histological, and transcriptomic dissection during auxin-induced adventitious root formation in tetraploid Robinia pseudoacacia micro-cuttings.

MAIN CONCLUSION: Optimal levels of indole-3-butyric acid (IBA) applied at the stem base promote adventitious root (AR) initiation and primordia formation, thus promoting the rooting of leafy micro-cuttings of tetraploid Robinia pseudoacacia. Tetraploid Robinia pseudoacacia L. is a widely cultivated tree in most regions of China that has a hard-rooting capability, propagated by stem cuttings. This study utilizes histological, physiological, and transcriptomic approaches to explore how root primordia are induced after indole butyric acid (IBA) treatment of micro-cuttings. IBA application promoted cell divisions in some cells within the vasculature, showing subcellular features associated with adventitious root (AR) founder cells. The anatomical structure explicitly showed that AR initiated from the cambium layer and instigate the inducible development of AR primordia. Meanwhile, the hormone data showed that similar to that of indole-3-acetic acid, the contents of trans-zeatin and abscisic acid peaked at early stages of AR formation and increased gradually in primordia formation across the subsequent stages, suggesting their indispensable roles in AR induction. On the contrary, 24-epibrassinolide roughly maintained at extremely high levels during primordium initiation thoroughly, indicating its presence was involved in cell-specific reorganization during AR development. Furthermore, antioxidant activities transiently increased in the basal region of micro-cuttings and may serve as biochemical indicators for distinct rooting phases, potentially aiding in AR formation. Transcriptomic analysis during the early stages of root formation shows significant downregulation of the abscisic acid and jasmonate signaling pathways, while ethylene and cytokinin signaling seems upregulated. Network analysis of genes involved in carbon metabolism and photosynthesis indicates that the basal region of the micro-cuttings undergoes rapid reprogramming, which results in the breakdown of sugars into pyruvate. This pyruvate is then utilized to fuel the tricarboxylic acid cycle, thereby sustaining growth through aerobic respiration. Collectively, our findings provide a time-course morphophysiological dissection and also suggest the regulatory role of a conserved auxin module in AR development in these species.

MADS-box transcription factors MADS11 and DAL1 interact to mediate the vegetative-to-reproductive transition in pine.

The reproductive transition is an important event that is crucial for plant survival and reproduction. Relative to the thorough understanding of the vegetative phase transition in angiosperms, a little is known about this process in perennial conifers. To gain insight into the molecular basis of the regulatory mechanism in conifers, we used temporal dynamic transcriptome analysis with samples from seven different ages of Pinus tabuliformis to identify a gene module substantially associated with aging. The results first demonstrated that the phase change in P. tabuliformis occurred as an unexpectedly rapid transition rather than a slow, gradual progression. The age-related gene module contains 33 transcription factors and was enriched in genes that belong to the MADS (MCMl, AGAMOUS, DEFICIENS, SRF)-box family, including six SOC1-like genes and DAL1 and DAL10. Expression analysis in P. tabuliformis and a late-cone-setting P. bungeana mutant showed a tight association between PtMADS11 and reproductive competence. We then confirmed that MADS11 and DAL1 coordinate the aging pathway through physical interaction. Overexpression of PtMADS11 and PtDAL1 partially rescued the flowering of 35S::miR156A and spl1,2,3,4,5,6 mutants in Arabidopsis (Arabidopsis thaliana), but only PtMADS11 could rescue the flowering of the ft-10 mutant, suggesting PtMADS11 and PtDAL1 play different roles in flowering regulatory networks in Arabidopsis. The PtMADS11 could not alter the flowering phenotype of soc1-1-2, indicating it may function differently from AtSOC1 in Arabidopsis. In this study, we identified the MADS11 gene in pine as a regulatory mediator of the juvenile-to-adult transition with functions differentiated from the angiosperm SOC1.

The Transcriptional Landscape and Hub Genes Associated with Physiological Responses to Drought Stress in Pinus tabuliformis.

Drought stress has an extensive impact on regulating various physiological, metabolic, and molecular responses. In the present study, the Pinus tabuliformis transcriptome was studied to evaluate the drought-responsive genes using RNA- Sequencing approache. The results depicted that photosynthetic rate and H2O conductance started to decline under drought but recovered 24 h after re-watering; however, the intercellular CO2 concentration (Ci) increased with the onset of drought. We identified 84 drought-responsive transcription factors, 62 protein kinases, 17 transcriptional regulators, and 10 network hub genes. Additionally, we observed the expression patterns of several important gene families, including 2192 genes positively expressed in all 48 samples, and 40 genes were commonly co-expressed in all drought and recovery stages compared with the control samples. The drought-responsive transcriptome was conserved mainly between P. tabuliformis and A. thaliana, as 70% (6163) genes had a homologous in arabidopsis, out of which 52% homologous (3178 genes corresponding to 2086 genes in Arabidopsis) were also drought response genes in arabidopsis. The collaborative network exhibited 10 core hub genes integrating with ABA-dependent and independent pathways closely conserved with the ABA signaling pathway in the transcription factors module. PtNCED3 from the ABA family genes had shown significantly different expression patterns under control, mild, prolonged drought, and recovery stages. We found the expression pattern was considerably increased with the prolonged drought condition. PtNCED3 highly expressed in all drought-tested samples; more interestingly, expression pattern was higher under mild and prolonged drought. PtNCED3 is reported as one of the important regulating enzymes in ABA synthesis. The continuous accumulation of ABA in leaves increased resistance against drought was due to accumulation of PtNCED3 under drought stress in the pine needles.

Identification of GH17 gene family in Vitis vinifera and expression analysis of GH17 under various adversities.

Glycoside hydrolase (GH, EC 3.2.1) is a group of enzymes that hydrolyzes glycosidic bonds and play a role in the hydrolysis and synthesis of sugars in living organisms. Vitis vinifera is an important fruit crop and it harbors GH17 gene family however, their function in grapes has not been systematically investigated. In this study, a total of 870 GH17 genes were identified from 14 plant species and their structural domain, sequence alignment, phylogenetic tree, collinear analysis, with the expression profiles of VviGH17 gene family was performed. The promoter analysis of VviGH17 gene showed the presence of cis-acting elements, which are responsive to plant growth and development. In addition, elements for plant hormones were found that are triggered in response to abiotic/biological stress. Transcriptomic data led to the identification of several VviGH17 genes, which are associated with bud dormancy and in response to abiotic stress. Transcript analysis was carried out for some of the selected VviGH17 genes RT-qPCR. VviGH17-16 and VviGH17-30 genes were differentially expressed during bud dormancy, fruit development and different abiotic stresses. Moreover, VviGH17-37 and VviGH17-44 were differentially expressed at fruit development, in response to abiotic stress. In addition, subcellular localization predicts that the VviGH17-16, VviGH17-30, and VviGH17-37 genes were located in the cell membrane, while VviGH17-44 gene was located in the vacuole. In conclusion, our study led to the identification of several GH17s and their probable role in development and stress. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01014-1.

Demethylation alters transcriptome profiling of buds and leaves in 'Kyoho' grape.

BACKGROUND: Grape buds and leaves are directly associated with the physiology and metabolic activities of the plant, which is monitored by epigenetic modifications induced by environment and endogenous factors. Methylation is one of the epigenetic regulators that could be involved in DNA levels and affect gene expression in response to stimuli. Therefore, changes of gene expression profile in leaves and bud through inhibitors of DNA methylation provide a deep understanding of epigenetic effects in regulatory networks. RESULTS: In this study, we carried out a transcriptome analysis of 'Kyoho' buds and leaves under 5-azacytidine (5-azaC) exposure and screened a large number of differentially expressed genes (DEGs). GO and KEGG annotations showed that they are mainly involved in photosynthesis, flavonoid synthesis, glutathione metabolism, and other metabolic processes. Functional enrichment analysis also provided a holistic perspective on the transcriptome profile when 5-azaC bound to methyltransferase and induced demethylation. Enrichment analysis of transcription factors (TFs) also showed that the MYB, C2H2, and bHLH families are involved in the regulation of responsive genes under epigenetic changes. Furthermore, hormone-related genes have also undergone significant changes, especially gibberellin (GA) and abscisic acid (ABA)-related genes that responded to bud germination. We also used protein-protein interaction network to determine hub proteins in response to demethylation. CONCLUSIONS: These findings provide new insights into the establishment of molecular regulatory networks according to how methylation as an epigenetic modification alters transcriptome patterns in bud and leaves of grape.

Functional Characterization of VvSK Gene Family in Grapevine (Vitis vinifera L.) Revealing their Role in Berry Ripening.

The glycogen synthase kinase 3/shaggy kinase (GSK3) is a serine/threonine kinase that plays important roles in brassinosteroid signaling, abiotic stress responses, cell division, and elongation, etc. In this study, we characterized seven grape GSK3 genes, showing high similarities with homologs from other species including Arabidopsis, white pear, apple, orange, and peach. Gene chip microarray data derived from an online database revealed very diverse developmental and tissue-specific expression patterns of VvSKs. VvSK3 and VvSK7 showed much higher expression levels in almost every tissue compared with other members. VvSK7 was highly enriched in young tissues like berries before the veraison stage, young leaves and green stems, etc., but immediately downregulated after these tissues entered maturation or senescence phases. Prediction of cis-elements in VvSK promoters indicated that VvSKs might be sensitive to light stimulation, which is further confirmed by the qPCR data. Constitutive overexpression of VvSK7 in Arabidopsis leads to dwarf plants that resembles BR-deficient mutants. The photosynthetic rate was significantly reduced in these plants, even though they accumulated more chlorophyll in leaves. Transient overexpression of VvSKs in tomatoes delayed the fruit ripening process, consistent with the observation in grapevine which blocks VvSKs by EBR- or BIKININ-promoted berry expansion and soluble solids accumulation. Data presented in the current study may serve as a theoretical basis for the future application of BRs or related compounds in quality grape production.

Characterization of Vv-miR156: Vv-SPL pairs involved in the modulation of grape berry development and ripening.

SPL is a plant-specific transcription factor family. Many researchers reported that SPL members targeted by miR156s could play crucial roles in the modulation of plant growth and development. Although there are similar reports on grapes, till now little is known about grape berry development and ripening. To gain more insight into how grape miR156s (Vv-miR156s) modulated the above given processes of grape berries by mediating their target gene Vv-SPLs, here we identified the precise sequences of Vv-miR156s in 'Giant Rose' grape berries, predicted their potential targets, and revealed that the matching degree of various Vv-miR156: Vv-SPL pairs exhibited some discrepancy, implying the divergence of their interaction. Subsequently, we also discovered similar motifs such as ABRE, CGTCA and ERE, which are more specific to berry development and ripening, within the promoters of both Vv-MIR156s and Vv-SPLs. With berry development and ripening, meanwhile, Vv-miR156a, b/c/d, e and f/g/i exhibited an overall increasing expression trend, while their targets showed opposite trends at the corresponding stages. Additionally, exogenous ABA and NAA application promoted or curbed the expression of Vv-miR156s to some extent, before grape berry ripening stage. The cleavage products, sites and frequencies of Vv-miR156a, b/c/d, e, f/g/i and their respective targets (Vv-SPL2, 9, 10, 16) during grape berry development and ripening process were validated by our developed PPM-RACE and modified RLM-RACE together with qRT-PCR, which demonstrated that Vv-miR156s can be involved in the modulation of grape berry development and ripening process by mediating the expression of Vv-SPL2, 9, 10, 16. Our findings lay an important foundation for further recognizing their functions in grape berries, and enrich the knowledge of the regulatory mechanism of miRNA-mediated grape berry development and ripening.

Characterization of VvPAL-like promoter from grapevine using transgenic tobacco plants.

A 2000-bp 5'-flanking region of VvPAL-like was isolated from 'Summer Black' grapevine by PCR amplification, named pVvPAL-like. To gain a better understanding of the expression and regulatory mechanism of VvPAL-like, a chimeric expression unit consisting of the ß-glucuronidase (GUS) reporter gene under the control of a 2000-bp fragment of the VvPAL-like promoter was transformed into tobacco via Agrobacterium tumefaciens. Histochemical staining showed that the full-length promoter directs efficient expression of the reporter gene in cotyledons and hypocotyls, stigma, style, anthers, pollen, ovary, trichomes, and vascular bundles of transgenic plants. A series of 5' progressive deletions of the promoter revealed the presence of a negative regulatory region (-424 to -292) in the VvPAL-like promoter. Exposure of the transgenic tobacco plants to various abiotic stresses demonstrated that the full-length construct could be induced by light, copper (Cu), abscisic acid (ABA), indole-3-acetic (IAA), methyl jasmonate (MeJA) (N-1-naphthylphthalamic acid), ethylene, and drought. Furthermore, the ethylene-responsive region was found to be located in the -1461/-930 fragment, while the element(s) for the MeJA-responsive expression may be present in the -424/-292 region in the VvPAL-like promoter. These findings will help us to better understand the molecular mechanisms by which VvPAL-like participates in biosynthesis of flavonoids and stress responses.

Jasmonic acid involves in grape fruit ripening and resistant against Botrytis cinerea.

Fruit ripening is a complex process that is regulated by a signal network. Whereas the regulatory mechanism of abscisic acid has been studied extensively in non-climacteric fruit, little is know about other signaling pathways involved in this process. In this study, we performed that plant hormone jasmonic acid plays an important role in grape fruit coloring and softening by increasing the transcription levels of several ripening-related genes, such as the color-related genes PAL1, DFR, CHI, F3H, GST, CHS, and UFGT; softening-related genes PG, PL, PE, Cell, EG1, and XTH1; and aroma-related genes Ecar, QR, and EGS. Lastly, the fruit anthocyanin, phenol, aroma, and cell wall materials were changed. Jasmonic acid positively regulated its biosynthesis pathway genes LOS, AOS, and 12-oxophytodienoate reductase (OPR) and signal pathway genes COI1 and JMT. RNA interference of grape jasmonic acid pathway gene VvAOS in strawberry fruit appeared fruit un-coloring phenotypes; exogenous jasmonic acid rescued this phenotypes. On the contrary, overexpression of grape jasmonic acid receptor VvCOI1 in the strawberry fruit accelerated the fruit-ripening process and induced some plant defense-related gene expression level. Furthermore, jasmonic acid treatment or strong jasmonic acid signal pathway in strawberry fruit make the fruit resistance against Botrytis cinerea.

Association between Chloroplast and Mitochondrial DNA sequences in Chinese Prunus genotypes (Prunus persica, Prunus domestica, and Prunus avium).

BACKGROUND: The nuclear DNA is conventionally used to assess the diversity and relatedness among different species, but variations at the DNA genome level has also been used to study the relationship among different organisms. In most species, mitochondrial and chloroplast genomes are inherited maternally; therefore it is anticipated that organelle DNA remains completely associated. Many research studies were conducted simultaneously on organelle genome. The objectives of this study was to analyze the genetic relationship between chloroplast and mitochondrial DNA in three Chinese Prunus genotypes viz., Prunus persica, Prunus domestica, and Prunus avium. RESULTS: We investigated the genetic diversity of Prunus genotypes using simple sequence repeat (SSR) markers relevant to the chloroplast and mitochondria. Most of the genotypes were genetically similar as revealed by phylogenetic analysis. The Y2 Wu Xing (Cherry) and L2 Hong Xin Li (Plum) genotypes have a high similarity index (0.89), followed by Zi Ye Li (0.85), whereas; L1 Tai Yang Li (plum) has the lowest genetic similarity (0.35). In case of cpSSR, Hong Tao (Peach) and L1 Tai Yang Li (Plum) genotypes demonstrated similarity index of 0.85 and Huang Tao has the lowest similarity index of 0.50. The mtSSR nucleotide sequence analysis revealed that each genotype has similar amplicon length (509 bp) except M5Y1 i.e., 505 bp with CCB256 primer; while in case of NAD6 primer, all genotypes showed different sizes. The MEHO (Peach), MEY1 (Cherry), MEL2 (Plum) and MEL1 (Plum) have 586 bps; while MEY2 (Cherry), MEZI (Plum) and MEHU (Peach) have 585, 584 and 566 bp, respectively. The CCB256 primer showed highly conserved sequences and minute single polymorphic nucleotides with no deletion or mutation. The cpSSR (ARCP511) microsatellites showed the harmonious amplicon length. The CZI (Plum), CHO (Peach) and CL1 (Plum) showed 182 bp; whileCHU (Peach), CY2 (Cherry), CL2 (Plum) and CY1 (Cherry) showed 181 bp amplicon lengths. CONCLUSIONS: These results demonstrated high conservation in chloroplast and mitochondrial genome among Prunus species during the evolutionary process. These findings are valuable to study the organelle DNA diversity in different species and genotypes of Prunus to provide in depth insight in to the mitochondrial and chloroplast genomes.

Preharvest Mandarin Rind Disorder: Insights into Varietal Differences and Preharvest Treatments Effects on Postharvest Quality.

The citrus industry loses a significant amount of mandarin fruits either before or shortly after harvesting due to rind disorder. Different citrus cultivars are impacted by a physiological rind disorder that lowers fruit quality and marketability. Although the primary etiology of this condition is unknown, changes in relative humidity (RH) and rind water status can make it worse. The damage is initiated in the fall, especially following rain. It begins with irregular water-soaked areas that develop into dark-brown, necrotic lesions covering large portions of the fruit's surface. The damage is evident in some citrus types such as Satsuma Owari mandarins and other cultivars. In this study, we attempted to understand and control the occurrence of this kind of rind disorder in Satsuma Owari mandarins growing under California conditions. Our data showed that fruit located in the outer part of the canopy suffer more than fruit in the interior canopy. We were able to reduce this damage in Satsuma Owari mandarins by applying 2,4-dichlorophenoxyacetic acid (2,4-D) at 16 milligrams/Liter (mg/L), gibberellic acid (GA3) at 20 mg/L, or Vapor Gard® at 0.5 percent (v/v) at the color break stage. However, GA3 caused a delay in color development by approximately four weeks. GA3-treated fruit changed their color completely four weeks after the control, and the rind damage was at a very low percentage. Delaying rind senescence could be a good strategy to reduce the damage in mandarin orchards. Data showed that in addition to the benefits of the different treatments on preventing rind disorder at harvest, they have some beneficial effects during storage for four weeks either at 0.5 or 7.5 °C.

Geographical location influence 'Cabernet Franc' fruit quality in Shandong province.

Grape quality is a key factor in determining wine quality, and it depends not only on management skills, but also on the geographic location of the producing area. In China, Shandong is the province with the largest wine production, and 'Cabernet Franc' is widely planted. This study evaluated the 'Cabernet Franc' fruit quality in relation to geographical conditions in five 'Cabernet Franc' producing districts of Shandong province, China, including Dezhou Aodeman Winery (DZ), Tai'an Zhongqingsongshi Winery (TA), Penglai Longhu Winery (PL), Rushan Taiyihu Winery (RS), and Rizhao Taiyangcheng Winery (RZ). At the time of veraison and maturity, fruit was harvested from five areas, and compared for cosmetic and internal fruit quality. The soluble sugar content in the Rizhao area was rich, and the weight and volume of single fruit were relatively large. The titratable acid of the berries in Tai'an area was high. RNA-seq analysis showed that the number of genes in the véraison stage was 19,571-20,750, and the number of genes in the mature stage was 19,176-20,735. The analysis found that areas with multiple high-quality characteristics tended to have more DEGs (differential expressed genes). And the DEGs in different areas were mainly distributed on chromosome 7, and at least on chromosome 15. DEGs in 5 areas were enriched on 855 GO terms and 116 KEGG pathways during berries development. Among them, it was found that the up/down-regulation of DEGs was related to the formation of berry quality, which helps to explain the impact of environment on grape quality components. In summary, this study is helpful to understand the influence of cultivation location on the quality of 'Cabernet Franc' in different production areas in Shandong province, and further provide a reference for the production of high-quality wine grapes and winemaking.

Metabolomic analyses provide insights into the preharvest rind disorder in Satsuma Owari Mandarin.

Citrus fruit's appearance is the primary criterion used to assess its quality for the fresh market, hence the rind's condition is a crucial quality trait. Pre-harvest rind disorder is one of the major physiological problems in mandarins. The disorder occurs right before harvest following rain events in some Mandarin varieties. Despite the economic damage caused by this kind of disorder, very limited information is available about the molecular mechanisms underlying the occurrence of this disorder. In the present study, we evaluated the primary metabolites, antioxidants, and hormones associated with the pre-harvest rind disorder in Mandarins. The study was carried out using ten-year-old 'Owari' Satsuma mandarin trees grafted on 'Carrizo' rootstock and grown in a commercial orchard in San Joaquin Valley, California, USA. Samples were collected from healthy tissue of healthy fruit (HF_HT), healthy tissue of damaged fruit (DF_HT), and damaged tissue of damaged fruit (DF_DT). Damaged fruit (DF_HT and DF_DT) showed lower cellulose concentrations than healthy fruit tissues (HF_HT), however, had similar contents of pectin and hemicellulose. The antioxidant activities showed no significant difference in all paired comparisons between samples as expressed in the malondialdehyde (MDA) content. However, DF_DT had a higher H2O2 content compared to HF_HT, but DF_HT had a similar content to that of HF_HT. Furthermore, peroxidase (POD) and polyphenol oxidase (PPO) activities were increased in DF_DT compared to HF_HT (P = 0.0294) and DF_HT (P = 0.0044), respectively. Targeted metabolomics analysis revealed that a total of 76 metabolites were identified in Satsuma rind tissues, and the relative concentrations of 43 metabolites were significantly different across studied samples. The hormonal analysis showed the involvement of jasmonate O-methyltransferase, jasmonic acid-amido synthetase JAR1-like, and JA-isoleucine may key role in causing the rind disorder in mandarins. In addition, the damaged fruit tissues have a higher level of jasmonic acid (JA), 12-oxo-phytodienoic acid, and JA-isoleucine than undamaged tissue.

Whole-genome re-sequencing, diversity analysis, and stress-resistance analysis of 77 grape rootstock genotypes.

Introduction: Grape rootstocks play critical role in the development of the grape industry over the globe for their higher adaptability to various environments, and the evaluation of their genetic diversity among grape genotypes is necessary to the conservation and utility of genotypes. Methods: To analyze the genetic diversity of grape rootstocks for a better understanding multiple resistance traits, whole-genome re-sequencing of 77 common grape rootstock germplasms was conducted in the present study. Results: About 645 billion genome sequencing data were generated from the 77 grape rootstocks at an average depth of ~15.5×, based on which the phylogenic clusters were generated and the domestication of grapevine rootstocks was explored. The results indicated that the 77 rootstocks originated from five ancestral components. Through phylogenetic, principal components, and identity-by-descent (IBD) analyses, these 77 grape rootstocks were assembled into ten groups. It is noticed that the wild resources of V. amurensis and V. davidii, originating from China and being generally considered to have stronger resistance against biotic and abiotic stresses, were sub-divided from the other populations. Further analysis indicated that a high level of linkage disequilibrium was found among the 77 rootstock genotypes, and a total of 2,805,889 single nucleotide polymorphisms (SNPs) were excavated, GWAS analysis among the grape rootstocks located 631, 13, 9, 2, 810, and 44 SNP loci that were responsible to resistances to phylloxera, root-knot nematodes, salt, drought, cold and waterlogging traits. Discussion: This study generated a significant amount of genomic data from grape rootstocks, thus providing a theoretical basis for further research on the resistance mechanism of grape rootstocks and the breeding of resistant varieties. These findings also reveal that China originated V. amurensis and V. davidii could broaden the genetic background of grapevine rootstocks and be important germplasm used in breeding high stress-resistant grapevine rootstocks.

Characterization of Simple Sequence Repeat (SSR) Markers Mined in Whole Grape Genomes.

SSR (simple sequence repeat) DNA markers are widely used for genotype DNA identification, QTL mapping, and analyzing genetic biodiversity. However, SSRs in grapes are still in their early stages, with a few primer pairs accessible. With the whole-genome sequencing (WGS) of several grape varieties, characterization of grape SSR changed to be necessary not only to genomics but to also help SSR development and utility. Based on this, we identified the whole-genome SSR of nine grape cultivars ('PN40024', 'Cabernet Sauvignon', 'Carménère', 'Chardonnay', 'Merlot', 'Riesling', 'Zinfandel', 'Shine Muscat', and 'Muscat Hamburg') with whole-genome sequences released publicly and found that there are great differences in the distribution of SSR loci in different varieties. According to the difference in genome size, the number of SSRs ranged from 267,385 (Cabernet Sauvignon) to 627,429 (Carménère), the density of the SSR locus in the genome of nine cultivars was generally 1 per Kb. SSR motif distribution characteristic analysis of these grape cultivars showed that the distribution patterns among grape cultivars were conservative, mainly enriched in A/T. However, there are some differences in motif types (especially tetranucleotides, pentanucleotides, and hexanucleotides), quantity, total length, and average length in different varieties, which might be related to the size of the assembled genome or the specificity of variety domestication. The distribution characteristics of SSRs were revealed by whole-genome analysis of simple repeats of grape varieties. In this study, 32 pairs of primers with lower polymorphism have been screened, which provided an important research foundation for the development of molecular markers of grape variety identification and the construction of linkage maps of important agronomic traits for crop improvement.

Unraveling the occasional occurrence of berry astringency in table grape cv. Scarlet Royal: a physiological and transcriptomic analysis.

Scarlet Royal, a mid-season ripening table grape, is one of the popular red grape varieties in California. However, its berries develop an undesirable astringent taste under certain conditions. Among the various factors contributing to the degradation of berry attributes, the levels and compositions of polyphenols play a fundamental role in defining berry quality and sensory characteristics. To comprehend the underlying mechanism of astringency development, Scarlet Royal berries with non-astringent attributes at the V7 vineyard were compared to astringent ones at the V9 vineyard. Biochemical analysis revealed that the divergence in berry astringency stemmed from alterations in its polyphenol composition, particularly tannins, during the late ripening stage at the V9 vineyard. Furthermore, transcriptomic profiling of berries positively associated nineteen flavonoid/proanthocyanidins (PAs) structural genes with the accumulation of PAs in V9 berries. The identification of these genes holds significance for table grape genetic improvement programs. At a practical level, the correlation between the taste panel and tannin content revealed a threshold level of tannins causing an astringent taste at approximately 400 mg/L. Additionally, berry astringency at the V9 vineyard was linked to a lower number of clusters and yield during the two study seasons, 2016 and 2017. Furthermore, petiole nutrient analysis at bloom showed differences in nutrient levels between the two vineyards, including higher levels of nitrogen and potassium in V9 vines compared to V7. It's worth noting that V9 berries at harvest displayed a lower level of total soluble solids and higher titratable acidity compared to V7 berries. In conclusion, our results indicate that the accumulation of tannins in berries during the ripening process results in a reduction in their red color intensity but significantly increases the astringency taste, thereby degrading the berry quality attributes. This study also highlights the association of high nitrogen nutrient levels and a lower crop load with berry astringency in table grapes, paving the way for further research in this area.

Strigolactones in Plants and Their Interaction with the Ecological Microbiome in Response to Abiotic Stress.

Phytohormones play an essential role in enhancing plant tolerance by responding to abiotic stresses, such as nutrient deficiency, drought, high temperature, and light stress. Strigolactones (SLs) are carotenoid derivatives that occur naturally in plants and are defined as novel phytohormones that regulate plant metabolism, growth, and development. Strigolactone assists plants in the acquisition of defensive characteristics against drought stress by initiating physiological responses and mediating the interaction with soil microorganisms. Nutrient deficiency is an important abiotic stress factor, hence, plants perform many strategies to survive against nutrient deficiency, such as enhancing the efficiency of nutrient uptake and forming beneficial relationships with microorganisms. Strigolactone attracts various microorganisms and provides the roots with essential elements, including nitrogen and phosphorus. Among these advantageous microorganisms are arbuscular mycorrhiza fungi (AMF), which regulate plant metabolic activities through phosphorus providing in roots. Bacterial nodulations are also nitrogen-fixing microorganisms found in plant roots. This symbiotic relationship is maintained as the plant provides organic molecules, produced in the leaves, that the bacteria could otherwise not independently generate. Related stresses, such as light stress and high-temperature stress, could be affected directly or indirectly by strigolactone. However, the messengers of these processes are unknown. The most prominent connector messengers have been identified upon the discovery of SLs and the understanding of their hormonal effect. In addition to attracting microorganisms, these groups of phytohormones affect photosynthesis, bridge other phytohormones, induce metabolic compounds. In this article, we highlighted the brief information available on SLs as a phytohormone group regarding their common related effects. In addition, we reviewed the status and described the application of SLs and plant response to abiotic stresses. This allowed us to comprehend plants' communication with the ecological microbiome as well as the strategies plants use to survive under various stresses. Furthermore, we identify and classify the SLs that play a role in stress resistance since many ecological microbiomes are unexplained.

DNA and Histone Methylation Regulates Different Types of Fruit Ripening by Transcriptome and Proteome Analyses.

Methylation affects different aspects of genetic material stability, gene expression regulation, and histone modification. The previous reports depicted that DNA and histone methylation regulates plant growth and development. In this study, we evaluated the effects of DNA and histone methylation on 'Hongjia' strawberry and 'Lichun' tomato. We investigated the transient transformation system for arginine methyltransferase (FvPRMT1.5) overexpression and interference and assessed the phenotypic appearance and mRNA and protein expression levels. Results depicted that changes in methylation levels caused inhibition of carotenoids and anthocyanins. Furthermore, the profiling of aroma components was altered in response to 5-azacytidine. DNA hypomethylation induced the expression levels of genes involved in photosynthesis, flavonoid biosynthesis, and hormone signal transduction pathways, while the expression levels of related proteins showed a downward trend. Overall, we proposed a model that reveals the possible regulatory effects of DNA and histone methylation during fruit ripening.

Profiling Analysis of Volatile and Non-volatile Compounds in Vitis Vinifera Berries (cv. Chardonnay) and Spontaneous Bud Mutation.

A novel clonal variety of Vitis vinifera was identified from "Chardonnay" using inter-simple sequence repeat (ISSR) markers and called "bud mutation. " The metabolomic profiles in Chardonnay and bud mutation berries indicated essential differences in the expression of key genes in the pathways of 2-C-methyl-D-erythritol-4-phosphate (MEP) and lipoxygenase-hydroperoxide lyase (LOX-HPL). Bud mutation fruits also matured 10 days earlier than Chardonnay and have higher carotenoid, sugar, and acidic compound contents. Furthermore, the gene expression was examined in the biosynthetic pathways of two ripening-associated hormones, abscisic acid (ABA) and jasmonic acid (JA), which significantly increased in bud mutation compared with the Chardonnay fruit. The synthesis and metabolism of amino acids, terpenes, fatty acids, volatile components, and specialized metabolites significantly increased in bud mutation. Therefore, in comparison with Chardonnay, bud mutation is considered a highly aroma-producing grape variety for an improvement in the beverage industry.

Strawberry Proteome Responses to Controlled Hot and Cold Stress Partly Mimic Post-harvest Storage Temperature Effects on Fruit Quality.

To determine the effect of different temperature on strawberry after harvest, physiological indicator analysis and proteomics analysis were conducted on ripened strawberry ("Sweet Charlie") fruit stored at 4, 23, and 37°C for 10 or 20 days. Results showed that 4°C maintained a better visual quality of strawberry, and the weight loss and firmness remained stable within 3 days. Low temperature negatively affected anthocyanin but positively affected soluble sugars. Though anthocyanin content was higher with increasing temperature, anthocyanin synthesis related proteins were downregulated. Higher indole-acetic acid (IAA) content in seeds and lower abscisic acid (ABA) content were found in berry at 4°C. Antioxidant related proteins were upregulated during storage, showing a significant up-regulation of peroxidase (POD) at 4°C, and ascorbate-glutathione (AsA-GSH) cycle related proteins and heat shock proteins (HSPs) at 37°C. In addition, overexpressed sugar phosphate/phosphate translocator, 1-aminocyclopropane-1-carboxylate oxidase, and aquaporin PIP2-2 had a positive effect in response to low temperature stress for containing higher protopectin content and POD activity.