Holomics - a user-friendly R shiny application for multi-omics data integration and analysis.

An organism's observable traits, or phenotype, result from intricate interactions among genes, proteins, metabolites and the environment. External factors, such as associated microorganisms, along with biotic and abiotic stressors, can significantly impact this complex biological system, influencing processes like growth, development and productivity. A comprehensive analysis of the entire biological system and its interactions is thus crucial to identify key components that support adaptation to stressors and to discover biomarkers applicable in breeding programs or disease diagnostics. Since the genomics era, several other 'omics' disciplines have emerged, and recent advances in high-throughput technologies have facilitated the generation of additional omics datasets. While traditionally analyzed individually, the last decade has seen an increase in multi-omics data integration and analysis strategies aimed at achieving a holistic understanding of interactions across different biological layers. Despite these advances, the analysis of multi-omics data is still challenging due to their scale, complexity, high dimensionality and multimodality. To address these challenges, a number of analytical tools and strategies have been developed, including clustering and differential equations, which require advanced knowledge in bioinformatics and statistics. Therefore, this study recognizes the need for user-friendly tools by introducing Holomics, an accessible and easy-to-use R shiny application with multi-omics functions tailored for scientists with limited bioinformatics knowledge. Holomics provides a well-defined workflow, starting with the upload and pre-filtering of single-omics data, which are then further refined by single-omics analysis focusing on key features. Subsequently, these reduced datasets are subjected to multi-omics analyses to unveil correlations between 2-n datasets. This paper concludes with a real-world case study where microbiomics, transcriptomics and metabolomics data from previous studies that elucidate factors associated with improved sugar beet storability are integrated using Holomics. The results are discussed in the context of the biological background, underscoring the importance of multi-omics insights. This example not only highlights the versatility of Holomics in handling different types of omics data, but also validates its consistency by reproducing findings from preceding single-omics studies.

[Study of 2,6-di(propan-2-yl)phenol stability in biomaterial]. / Izuchenie ustoichivosti 2,6-di(propan-2-il)fenola v biologicheskom materiale.

The aim of this study is to research the stability of 2.6-di(propan-2-yl)phenol in biomaterial. GC-MS (column DB-5MS EVIDEX (25 m×0.2 mm); stationary liquid phase of 5%-phenyl-95% dimethylpolysiloxane), TLC (Sorbfil plates, mobile phase of hexane-diethyl ether (9:1) and spectrophotometry (solvent medium - 95% ethanol) were used as methods of analysis. 2.6-di(propan-2-yl)phenol was isolated from the biomatrix (liver tissue) by infusion with a mixture of ethyl acetate-acetone (7:3). The analyte was purified by combining extraction (water-ethyl acetate system) and semi-preparative chromatography on a column of silica gel L 40/100 µm, eluent - hexane-acetone (7:3). It was found that at -22 °C, 0 °C, 12 °C, 20 °C and 30 °C 2.6-di(propan-2-yl)phenol can be present in the liver tissue for 119, 98, 70, 56 and 42 days, respectively. The possibility of mathematical description of analyte decomposition dynamics in biomaterial (liver tissue) at the considered temperatures on the basis of hyperbola equation has been studied. The experimentally calculated coefficients in the hyperbola equation (km) for temperatures -22 °C, 0 °C, 12 °C, 20 °C and 30 °C are equal to 1823, 1130, 697, 510, and 255, respectively. The dependence km on the conserving temperature (tо) was educed. The equation for the description of dependence is offered: km=30.61∙(50-to)-402.39. It is shown that this equation can be the basis for prediction of 2.6-di(propan-2-yl)phenol stability in biomaterial (liver tissue) in the temperature range from -22 °C to 30 °C.

Unraveling metabolic patterns and molecular mechanisms underlying storability in sugar beet.

BACKGROUND: Sugar beet is an important crop for sugar production. Sugar beet roots are stored up to several weeks post-harvest waiting for processing in the sugar factories. During this time, sucrose loss and invert sugar accumulation decreases the final yield and processing quality. To improve storability, more information about post-harvest metabolism is required. We investigated primary and secondary metabolites of six sugar beet varieties during storage. Based on their variety-specific sucrose loss, three storage classes representing well, moderate, and bad storability were compared. Furthermore, metabolic data were visualized together with transcriptome data to identify potential mechanisms involved in the storage process. RESULTS: We found that sugar beet varieties that performed well during storage have higher pools of 15 free amino acids which were already observable at harvest. This storage class-specific feature is visible at harvest as well as after 13 weeks of storage. The profile of most of the detected organic acids and semi-polar metabolites changed during storage. Only pyroglutamic acid and two semi-polar metabolites, including ferulic acid, show higher levels in well storable varieties before and/or after 13 weeks of storage. The combinatorial OMICs approach revealed that well storable varieties had increased downregulation of genes involved in amino acid degradation before and after 13 weeks of storage. Furthermore, we found that most of the differentially genes involved in protein degradation were downregulated in well storable varieties at both timepoints, before and after 13 weeks of storage. CONCLUSIONS: Our results indicate that increased levels of 15 free amino acids, pyroglutamic acid and two semi-polar compounds, including ferulic acid, were associated with a better storability of sugar beet taproots. Predictive metabolic patterns were already apparent at harvest. With respect to elongated storage, we highlighted the role of free amino acids in the taproot. Using complementary transcriptomic data, we could identify potential underlying mechanisms of sugar beet storability. These include the downregulation of genes for amino acid degradation and metabolism as well as a suppressed proteolysis in the well storable varieties.

Identification of miRNAs Mediating Seed Storability of Maize during Germination Stage by High-Throughput Sequencing, Transcriptome and Degradome Sequencing.

Seed storability is an important trait for improving grain quality and germplasm conservation, but little is known about the regulatory mechanisms and gene networks involved. MicroRNAs (miRNAs) are small non-coding RNAs regulating the translation and accumulation of their target mRNAs by means of sequence complementarity and have recently emerged as critical regulators of seed germination. Here, we used the germinating embryos of two maize inbred lines with significant differences in seed storability to identify the miRNAs and target genes involved. We identified a total of 218 previously known and 448 novel miRNAs by miRNA sequencing and degradome analysis, of which 27 known and 11 newly predicted miRNAs are differentially expressed in two maize inbred lines, as measured by Gene Ontology (GO) enrichment analysis. We then combined transcriptome sequencing and real-time quantitative polymerase chain reaction (RT-PCR) to screen and confirm six pairs of differentially expressed miRNAs associated with seed storability, along with their negative regulatory target genes. The enrichment analysis suggested that the miRNAs/target gene mediation of seed storability occurs via the ethylene activation signaling pathway, hormone synthesis and signal transduction, as well as plant organ morphogenesis. Our results should help elucidate the mechanisms through which miRNAs are involved in seed storability in maize.

Understanding the Palatability, Flavor, Starch Functional Properties and Storability of Indica-Japonica Hybrid Rice.

The rice quality and starch functional properties, as well as the storability of three YY-IJHR cultivars, which included YY12 (biased japonica type YY-IJHR), YY1540 (intermedius type YY-IJHR) and YY15 (biased indica type YY-IJHR), were studied and compared to N84 (conventional japonica rice). The study results suggested that the three YY-IJHR varieties all had greater cooking and eating quality than N84, as they had lower amylose and protein content. The starch of YY-IJHR has a higher pasting viscosity and digestibility, and there was a significant difference among the three YY-IJHR cultivars. Rice aroma components were revealed by GC-IMS, which indicated that the content of alcohols vola-tile components of YY-IJHR were generally lower, whereas the content of some aldehydes and esters were higher than N84. In addition, YY-IJHR cultivars' FFA and MDA contents were lower, which demonstrated that YY-IJHR had a higher palatability and storability than those of N84 in fresh rice and rice stored for 12 months. In conclusion, this study suggested that YY-IJHR had better rice quality and storability than N84. PCA indicated that the grain quality and storability of YY12 and YY15 were similar and performed better than YY1540, while the aroma components and starch functional properties of YY-IJHR cultivars all had significant differences.

Integrative transcriptomics reveals genotypic impact on sugar beet storability.

KEY MESSAGE: An integrative comparative transcriptomic approach on six sugar beet varieties showing different amount of sucrose loss during storage revealed genotype-specific main driver genes and pathways characterizing storability. Sugar beet is next to sugar cane one of the most important sugar crops accounting for about 15% of the sucrose produced worldwide. Since its processing is increasingly centralized, storage of beet roots over an extended time has become necessary. Sucrose loss during storage is a major concern for the sugar industry because the accumulation of invert sugar and byproducts severely affect sucrose manufacturing. This loss is mainly due to ongoing respiration, but changes in cell wall composition and pathogen infestation also contribute. While some varieties can cope better during storage, the underlying molecular mechanisms are currently undiscovered. We applied integrative transcriptomics on six varieties exhibiting different levels of sucrose loss during storage. Already prior to storage, well storable varieties were characterized by a higher number of parenchyma cells, a smaller cell area, and a thinner periderm. Supporting these findings, transcriptomics identified changes in genes involved in cell wall modifications. After 13 weeks of storage, over 900 differentially expressed genes were detected between well and badly storable varieties, mainly in the category of defense response but also in carbohydrate metabolism and the phenylpropanoid pathway. These findings were confirmed by gene co-expression network analysis where hub genes were identified as main drivers of invert sugar accumulation and sucrose loss. Our data provide insight into transcriptional changes in sugar beet roots during storage resulting in the characterization of key pathways and hub genes that might be further used as markers to improve pathogen resistance and storage properties.

Development and characterization of marker-free and transgene insertion site-defined transgenic wheat with improved grain storability and fatty acid content.

Development of marker-free and transgene insertion site-defined (MFTID) transgenic plants is essential for safe application of transgenic crops. However, MFTID plants have not been reported for wheat (Triticum aestivum). Here, we prepared a RNAi cassette for suppressing lipoxygenase (LOX) gene expression in wheat grains using a double right border T-DNA vector. The resultant construct was introduced into wheat genome via Agrobacterium-mediated transformation, with four homozygous marker-free transgenic lines (namely GLRW-1, -3, -5 and -8) developed. Aided by the newly published wheat genome sequence, the T-DNA insertion sites in GLRW-3 and GLRW-8 were elucidated at base-pair resolution. While the T-DNA in GLRW-3 inserted in an intergenic region, that of GLRW-8 inactivated an endogenous gene, which was thus excluded from further analysis. Compared to wild -type (WT) control, GLRW-1, -3 and -5 showed decreased LOX gene expression, lower LOX activity and less lipid peroxidation in the grains; they also exhibited significantly higher germination rates and better seedling growth after artificial ageing treatment. Interestingly, the three GLRW lines also had substantially increased contents of several fatty acids (e.g., linoleic acid and linolenic acid) in their grain and flour samples than WT control. Collectively, our data suggest that suppression of grain LOX activity can be employed to improve the storability and fatty acid content of wheat seeds and that the MFTID line GLRW-3 is likely of commercial value. Our approach may also be useful for developing the MFTID transgenic lines of other crops with enhanced grain storability and fatty acid content.

Whole-genome mapping identified novel "QTL hotspots regions" for seed storability in soybean (Glycine max L.).

BACKGROUND: Seed aging in soybean is a serious challenge for agronomic production and germplasm preservation. However, its genetic basis remains largely unclear in soybean. Unraveling the genetic mechanism involved in seed aging, and enhancing seed storability is an imperative goal for soybean breeding. The aim of this study is to identify quantitative trait loci (QTLs) using high-density genetic linkage maps of soybean for seed storability. In this regard, two recombinant inbred line (RIL) populations derived from Zhengyanghuangdou × Meng 8206 (ZM6) and Linhefenqingdou × Meng 8206 (LM6) crosses were evaluated for three seed-germination related traits viz., germination rate (GR), normal seedling length (SL) and normal seedling fresh weight (FW) under natural and artificial aging conditions to map QTLs for seed storability. RESULTS: A total of 34 QTLs, including 13 QTLs for GR, 11 QTLs for SL and 10 QTLs for FW, were identified on 11 chromosomes with the phenotypic variation ranged from 7.30 to 23.16% under both aging conditions. All these QTLs were novel, and 21 of these QTLs were clustered in five QTL-rich regions on four different chromosomes viz., Chr3, Chr5, Chr17 &Chr18, among them the highest concentration of seven and six QTLs were found in "QTL hotspot A" (Chr17) and "QTL hotspot B" (Chr5), respectively. Furthermore, QTLs within all the five QTL clusters are linked to at least two studied traits, which is also supported by highly significant correlation between the three germination-related traits. QTLs for seed-germination related traits in "QTL hotspot B" were found in both RIL populations and aging conditions, and also QTLs underlying "QTL hotspot A" are identified in both RIL populations under artificial aging condition. These are the stable genomic regions governing the inheritance of seed storability in soybean, and will be the main focus for soybean breeders. CONCLUSION: This study uncovers the genetic basis of seed storability in soybean. The newly identified QTLs provides valuable information, and will be main targets for fine mapping, candidate gene identification and marker-assisted breeding. Hence, the present study is the first report for the comprehensive and detailed investigation of genetic architecture of seed storability in soybean.

Preharvest zinc sulfate spray improves the storability of longan (Dimocarpus longan Lour.) fruits by protecting the cell wall components and antioxidants of pericarp.

BACKGROUND: Zinc (Zn) fertilization has been reported to improve the quality and storability of many fruits, but the mechanism had not been systematically studied. In this study, the effect of preharvest 0.2% zinc sulfate (ZnSO4 ) spray on the storability of longan fruits was investigated. RESULTS: The preharvest ZnSO4 spray did not significantly influence the quality but increased the Zn content in longan pericarp by 12.5-fold. More importantly, the treatment significantly reduced the rotting rate, pericarp browning, and aril breakdown of longan fruits stored at room temperature and low temperature. Physiological and biochemical results indicated that the treatment resulted in higher water retention capacity and inhibited the degradation of cellulose, pectin, flavonoid, and phenolics of longan pericarp at the late stages of storage. Consistent with these results, the activity of cellulase, polygalacturonase, polyphenol oxidase, and lipoxygenase was significantly inhibited in the ZnSO4 -treated longan pericarp at the late stages of storage. CONCLUSION: Higher Zn content in the ZnSO4 -treated longan pericarp might help to enhance the resistance against microbial infection, inhibit the hydrolysis of cell wall components, and thus effectively protected the cell wall components, maintained the cellular compartmentation, and prevented the phenolics and flavonoid from degradation by browning-related enzymes. © 2018 Society of Chemical Industry.

Oxidative stability and lipid oxidation flavoring volatiles in antioxidants treated chicken meat patties during storage.

BACKGROUND: Chicken meat contains higher percentage of polyunsaturated fatty acids that are susceptible to oxidative deterioration ultimately leading towards lower consumer acceptability for chicken meat products. Accordingly, meat processing industries are looking for combinations of natural antioxidants to enhance the oxidative stability and consumer acceptability of meat based products. The present study aimed to investigate the influence of directly added quercetin dihydrate in combination with α-tocopherol on oxidative stability, color characteristics, total carbonyls and flavor volatile compounds in chicken meat patties. METHODS: Considering the preliminary studies, 3 levels of quercetin dihdrate @ 25, 50 and 100 mg/kg meat in combination with α-tocopherol at the rate 100 and 200 mg/kg meat were added to develop chicken meat patties and were stored at refrigeration temperature for 7 days. The oxidative stability of the antioxidant treated patties was determined by measuring malonaldehydes using TBARS and total carbonyls assay. The color (Lightness, redness and yellowness) of the patties was determined by using Konica Minolta Color Meter. Moreover, the volatile compounds were measured through gas chromatography at various storage intervals. RESULTS: The results elucidated that quercetin dehydrate inclusion at the rate of 50 mg/kg meat as well as particularly 100 mg/kg meat decreased the oxidation by reducing generation of malonaldehydes and total carbonyls in treated patties. Highest value for TBARS at initiation of storage was reported in (T0) as 1.93 ± 0.02 whereas lowest were reported in T6 and T5 as 0.37 ± 0.01 and 0.38 ± 0.03 that were increased to 3.47 ± 0.14, 0.90 ± 0.05 and 0.94 ± 0.34 at the completion of storage. Moreover, the lowest carbonyls also reported in T6 and the values at various storage intervals (1st, 3rd and 7th) were as 0.59 ± 0.025, 0.77 ± 0.015 and 1.02 ± 0.031, respectively. The antioxidants inclusion also inhibited volatile flavoring compounds particularly aldehydes like hexanal and pentanal in a dose dependent manner (p ≤ 0.05). Lowest hexanal values reported in T6 as 2488 ± 103 followed by T4 (3701 ± 111) at the start of the trial whereas highest in T0 (control) as 54,768 ± 431 that were increased to 9569 ± 607, 112,550 ± 897 and 359,826 ± 1285, correspondingly. The hexanal, as a critical indicator for the determination of volatiles in meat based products, was decreased with the addition of antioxidants and its highest values were reported in control group. CONCLUSIONS: Quercetin dihydrate addition along with alpha tocopherol is a pragmatic choice to improve oxidative storability and volatile flavor compounds in cooked meat patties. The data obtained will help meat processor to better develop antioxidant enriched formulations to augment oxidative stability and quality of processed meat products.