Protein quantification and enzyme activity estimation of Pakistani wheat landraces

Transcriptomic analysis reveals the regulatory mechanisms of messenger RNA (mRNA) and long non-coding RNA (lncRNA) in response to waterlogging stress in rye (Secale cereale L.)

BACKGROUND

Waterlogging stress (WS) negatively impacts crop growth and productivity, making it important to understand crop resistance processes and discover useful WS resistance genes. In this study, rye cultivars and wild rye species were subjected to 12-day WS treatment, and the cultivar Secale cereale L. Imperil showed higher tolerance. Whole transcriptome sequencing was performed on this cultivar to identify differentially expressed (DE) messenger RNAs (DE-mRNAs) and long non-coding RNAs (DE-lncRNAs) involved in WS response.

RESULTS

Among the 6 species, Secale cereale L. Imperil showed higher tolerance than wild rye species against WS. The cultivar effectively mitigated oxidative stress, and regulated hydrogen peroxide and superoxide anion. A total of 728 DE-mRNAs and 60 DE-lncRNAs were discovered. Among these, 318 DE-mRNAs and 32 DE-lncRNAs were upregulated, and 410 DE-mRNAs and 28 DE-lncRNAs were downregulated. GO enrichment analysis discovered metabolic processes, cellular processes, and single-organism processes as enriched biological processes (BP). For cellular components (CC), the enriched terms were membrane, membrane part, cell, and cell part. Enriched molecular functions (MF) terms were catalytic activity, binding, and transporter activity. LncRNA and mRNA regulatory processes were mainly related to MAPK signaling pathway-plant, plant hormone signal transduction, phenylpropanoid biosynthesis, anthocyanin biosynthesis, glutathione metabolism, ubiquitin-mediated proteolysis, ABC transporter, Cytochrome b6/f complex, secondary metabolite biosynthesis, and carotenoid biosynthesis pathways. The signalling of ethylene-related pathways was not mainly dependent on AP2/ERF and WRKY transcription factors (TF), but on other factors. Photosynthetic activity was active, and carotenoid levels increased in rye under WS. Sphingolipids, the cytochrome b6/f complex, and glutamate are involved in rye WS response. Sucrose transportation was not significantly inhibited, and sucrose breakdown occurs in rye under WS.

CONCLUSIONS

This study investigated the expression levels and regulatory functions of mRNAs and lncRNAs in 12-day waterlogged rye seedlings. The findings shed light on the genes that play a significant role in rye ability to withstand WS. The findings from this study will serve as a foundation for further investigations into the mRNA and lncRNA WS responses in rye.

The Over-Expression of Two R2R3-MYB Genes, PdMYB2R089 and PdMYB2R151, Increases the Drought-Resistant Capacity of Transgenic Arabidopsis

The R2R3-MYB genes in plants play an essential role in the drought-responsive signaling pathway. Plenty of R2R3-MYB S21 and S22 subgroup genes in Arabidopsis have been implicated in dehydration conditions, yet few have been covered in terms of the role of the S21 and S22 subgroup genes in poplar under drought. PdMYB2R089 and PdMYB2R151 genes, respectively belonging to the S21 and S22 subgroups of NL895 (Populus deltoides × P. euramericana cv. 'Nanlin895'), were selected based on the previous expression analysis of poplar R2R3-MYB genes that are responsive to dehydration. The regulatory functions of two target genes in plant responses to drought stress were studied and speculated through the genetic transformation of Arabidopsis thaliana. PdMYB2R089 and PdMYB2R151 could promote the closure of stomata in leaves, lessen the production of malondialdehyde (MDA), enhance the activity of the peroxidase (POD) enzyme, and shorten the life cycle of transgenic plants, in part owing to their similar conserved domains. Moreover, PdMYB2R089 could strengthen root length and lateral root growth. These results suggest that PdMYB2R089 and PdMYB2R151 genes might have the potential to improve drought adaptability in plants. In addition, PdMYB2R151 could significantly improve the seed germination rate of transgenic Arabidopsis, but PdMYB2R089 could not. This finding provides a clue for the subsequent functional dissection of S21 and S22 subgroup genes in poplar that is responsive to drought.

Singh A, Kumar A. Unlocking the potential of ancient hexaploid Indian dwarf wheat, Tritium sphaerococcum for grain quality improvement

Wild and ancient wheat are considered to be a rich source of nutrients and better stress tolerant, hence being re-considered for mainstreaming its cultivation by the farmers and bringing it back to the food basket. In the present study, thirty-four diverse accessions of Indian dwarf wheat, Triticum sphaerococcum conserved in the Indian National Genebank were evaluated for thirteen-grain quality parameters namely thousand-grain weight (TGW), hectolitre weight (HW), sedimentation value (Sed), grain hardness index (HI), protein (Pro), albumin (Alb), globulin (Glo), gliadin (Gli), glutenin (Glu), gluten, lysine (Lys), Fe²⁺ and Zn²⁺ content, and four antioxidant enzymes activities. Substantial variations were recorded for studied traits. TGW, HW, Sed, HI, Pro, Alb, Glo, Gli, Glu, Gluten, Lys, Fe²⁺, and Zn²⁺ varied from 26.50-45.55 g, 70.50-86.00 kg/hl, 24.00-38.00 ml, 40.49-104.90, 15.34-19.35%, 17.60-40.31 mg/g, 10.75-16.56 mg/g, 26.35-44.94 mg/g, 24.47-39.56 mg/g, 55.33-75.06 mg/g, 0.04-0.29%, 42.72-90.72 ppm, and 11.45-25.70 ppm, respectively. Among antioxidants, peroxidase (POX), catalase (CAT), glutathione reductase (GR), and superoxide dismutase (SOD) activity ranged from 0.06-0.60 unit/ml, 0.02-0.61 unit/ml, 0.11-2.26 unit/ml, and 0.14-0.97 unit/ml, respectively. Hardness Index was positively associated with Pro and Zn²⁺ content whereas Lys was negatively associated with gluten content. Likewise, gluten and Fe²⁺ content had a positive association with the major protein fraction i.e., Gli and Glu. Hierarchical cluster analysis grouped 34 accessions into four clusters and the major group had nine indigenous and eight exotic accessions. We also validated high GPC accessions and EC182958 (17.16%), EC187176 and EC182945 (16.16%), EC613057 (15.79%), IC634028 (15.72%) and IC533826 (15.01%) were confirmed with more than 15% GPC. Also, superior trait-specific accessions namely, EC187167, IC534021, EC613055, EC180066, and EC182959 for low gluten content and IC384530, EC313761, EC180063, IC397363, EC10494 for high iron content (>76.51) were identified that may be used in wheat quality improvement for nutritional security of mankind.

Genome-wide characterization of the U-box gene in Camellia sinensis and functional analysis in transgenic tobacco under abiotic stresses

Plants U-box genes are crucial for plant survival, and they extensively regulate plant growth, reproduction and development as well as coping with stress and other processes. In this study, we identified 92 CsU-box genes through genome-wide analysis in the tea plant (Camellia sinensis), all of them contained the conserved U-box domain and were divided into 5 groups, which supported by the further genes structure analysis. The expression profiles in eight tea plant tissues and under abiotic and hormone stresses were analyzed using the TPIA database. 7 CsU-box genes (CsU-box27/28/39/46/63/70/91) were selected to verify and analyze expression patterns under PEG-induced drought and heat stress in tea plant respectively, the qRT-PCR results showed consistent with transcriptome datasets; and the CsU-box39 were further heterologous expressed in tobacco to perform gene function analysis. Phenotypic analyses of overexpression transgenic tobacco seedlings and physiological experiments revealed that CsU-box39 positively regulated the plant response to drought stress. These results lay a solid foundation for studying the biological function of CsU-box, and will provide breeding strategy basis for tea plant breeders.

Coupled online sequential extreme learning machine model with ant colony optimization algorithm for wheat yield prediction

Inadequate agricultural planning compounded by inaccurate predictions results in an inflated local market rate and prompts higher importation of wheat. To tackle this problem, this research has designed two-phase universal machine learning (ML) model to predict wheat yield (W_pred), utilizing 27 agricultural counties’ data within the Agro-ecological zone. The universal model, online sequential extreme learning machines coupled with ant colony optimization (ACO-OSELM) is developed, by incorporating the significant annual yield data lagged at (t − 1) as the model’s predictor to generate future yield at 6 test stations. In the first phase, ACO is adopted to search for suitable, statistically relevant data stations for model training, and the corresponding test station by virtue of a feature selection strategy. An annual wheat yield time-series input dataset is constructed utilizing data from each selected training station (1981–2013) and applied against 6 test stations (with each case modelled with 26 station data as the input) to evaluate the hybrid ACO-OSELM model. The partial autocorrelation function is implemented to deduce statistically significant lagged data, and OSELM is applied to generate W_pred. The two-phase hybrid ACO-OSELM model is tested within the 6 agricultural districts (represented as stations) of Punjab province, Pakistan and the results are benchmarked with extreme learning machine (ELM) and random forest (RF) integrated with ACO (i.e., hybrid ACO-ELM and hybrid ACO-RF models, respectively). The performance of the ACO-OSELM model was proven to be good in comparison to ACO-ELM and ACO-RF models. The hybrid ACO-OSELM model revealed its potential to be implemented as a decision-making system for crop yield prediction in areas where a significant association with the historical agricultural crop is well-established.

Mining the Wheat Grain Proteome

Bread wheat is the most widely cultivated crop worldwide, used in the production of food products and a feed source for animals. Selection tools that can be applied early in the breeding cycle are needed to accelerate genetic gain for increased wheat production while maintaining or improving grain quality if demand from human population growth is to be fulfilled. Proteomics screening assays of wheat flour can assist breeders to select the best performing breeding lines and discard the worst lines. In this study, we optimised a robust LC–MS shotgun quantitative proteomics method to screen thousands of wheat genotypes. Using 6 cultivars and 4 replicates, we tested 3 resuspension ratios (50, 25, and 17 µL/mg), 2 extraction buffers (with urea or guanidine-hydrochloride), 3 sets of proteases (chymotrypsin, Glu-C, and trypsin/Lys-C), and multiple LC settings. Protein identifications by LC–MS/MS were used to select the best parameters. A total 8738 wheat proteins were identified. The best method was validated on an independent set of 96 cultivars and peptides quantities were normalised using sample weights, an internal standard, and quality controls. Data mining tools found particularly useful to explore the flour proteome are presented (UniProt Retrieve/ID mapping tool, KEGG, AgriGO, REVIGO, and Pathway Tools).

The Variability for the Biochemical Indicators at the Winter Wheat Assortment and Identifying the Sources with a High Antioxidant Activity

This study presents the variability of some biochemical indicators in the winter wheat assortments tested in south-western Oltenia (Romania) and identification of the sources showing a high antioxidant activity. The peroxidase activity has intensified as the stress induced by treatment with PEG of different concentrations and in different doses increased. Regarding the peroxidase content, among the varieties treated with PEG 10,000 25%, the majority of the Romanian varieties tested showed higher values of the PEG/control treatment ratio, which suggests tolerance to drought. In reverse, the activity of ascorbate peroxidase is lower in tolerant varieties. The varieties with a subunit report have been noted. Among them are the Izvor variety, known as the drought-tolerant variety, as well as other Romanian varieties: Alex, Delabrad, Lovrin 34, etc. An increased activity of catalase was present in most varieties, so there is the possibility of drought tolerance. Among the varieties highlighted are Romanian varieties (Dropia, Trivale, Nikifor, etc.) but also foreign varieties (Kristina, GH Hattyu, Karlygash, etc.). However, the correlation between yield index in the limited assortment and the antioxidant enzyme content ratios between PEG and control treatments does not exist, suggesting that none of these biochemical indicators are a selective indicator for drought tolerance under the experimental condition.

Assessment of Four Portuguese Wheat Landrace Diversity to Cope With Global Warming

Wheat is a dietary staple consumed worldwide strongly responsible for proteins and carbohydrate population intake. However, wheat production and quality will scarcely fulfill forward demands, which are compounded by high-temperature (HT) events as heatwaves, increasingly common in Portugal. Thus, landraces assume crucial importance as potential reservoirs of useful traits for wheat breeding and may be pre-adapted to extreme environmental conditions. This work evaluates four Portuguese landrace yield and grain composition through attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy, particularly protein content, and their responses to HT treatment mimicking a heatwave. Landraces showed distinct yield traits, especially plant height and first spike grain number, and a similar pattern in FTIR spectra, although revealing differences in grain components' proportions. Comparison between spectra band intensity indicates that Ardito has the highest protein-related peaks, contrary to Magueija, which appears to be the landrace with higher lipid content. In plants submitted to 1 week of HT treatment 10 days after anthesis, the first spike grain size and weight were markedly reduced in all landraces. Additionally, it was observed that a general increase in grain protein content in the four landraces, being the increment observed in Ardito and Grécia, is statistically significant. The comparative assessment of control and HT average FTIR spectra denoted also the occurrence of alterations in grain polysaccharide composition. An integrated assessment of the evaluations performed revealed that Ardito and Magueija landraces presented diverse yield-related characteristics and distinct responses to cope with HT. In fact, the former landrace revealed considerable grain yield diminution along with an increase in grain protein proportion after HT, while the latter showed a significant increase in spikes and grain number, with grain quality detriment. These results reinforce the relevance of scrutinizing old genotype diversity seeking for useful characteristics, particularly considering HT impact on grain production and quality.