Ancestral and modern wheat genotypes
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ABSTRACT:
PROVIDER: PRJNA643787 | ENA |
REPOSITORIES: ENA
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Project description:Wheat represents one of the most important cereals for mankind. However, since wheat proteins are also the causative agent of several adverse reactions, during the last decades, consumers have shown an increasing interest in the old wheat genotypes, which are generally perceived as more “natural” and healthier than the modern ones. Comparison of nutritional value for modern and old wheat genotypes is still controversial, and to evaluate the real impact of these foods on human health comparative experiments involving old and modern genotypes are desirable. The nutritional quality of grain is correlated with its proteomic composition that depends on the interplay between the genetic characteristics of the plant and external factors related to the environment. We report here the label-free shotgun quantitative comparison of the metabolic protein fractions of two old Sicilian landraces (Russello and Timilia) and the modern variety Simeto, from the 2010-11 and 2011-12 growing seasons. The overall results show that Timilia presents the major differences with respect to the other two genotypes investigated. These differences may be related to different defense mechanisms and some other peculiar properties of these genotypes. On the other hand, our results confirm previous results leading to the conclusion that with respect to a nutritional value evaluation, there is a substantial equivalence between old and modern wheat genotypes.
2021-05-13 | PXD024204 | Pride
Project description:The close relationship between diet and health is generally recognized and the growing wellness and consciousness, especially in developed countries, have led to increasing interest for old wheat genotypes, based on perceived health benefits. Although nutritional comparison between old and modern wheat varieties is still controversial, it is generally accepted that old wheat genotypes remained unchanged over the last hundred years. By contrast, modern wheat genotypes are derived by modification of old wheats during the so-called “Green-Revolution” in the second half of the 20th century focusing on obtaining properties in terms of higher grain yield. The present work reports the first comprehensive proteomic profiling and qualitative comparison at the molecular level of metabolic and Chloroform-Methanol (CM)-like protein fractions extracted from mature kernels of two old Sicilian durum wheat landraces, Russello and Timilia Reste Bianche, and Simeto, an improved durum wheat variety widespread in Italy and other Mediterranean countries and chosen as representative of the most widely commercial cultivars. The results obtained reveal that metabolic and CM-like protein fractions of old and modern genotypes present remarkably high similarity with only minor differences. This leads to the conclusion that from a food and nutritional perspective there is a substantial equivalence of the protein composition of the old and modern cultivars.
2019-10-25 | PXD014449 | Pride
Project description:Bread wheat (Triticum aestivum L.) is one of the most valuable cereal crops for the human consumption. Its grain storage proteins greatly impact bread quality, though may cause food intolerances or allergies in susceptible individuals. Consequently, the investigation of a proteome polymorphism among wheat varieties is important to spot the genotypes, which would be promising donors for the breeding of hypoallergenic cereals. Herein, we discovered diversity of grain proteins in three Ukrainian wheat cultivars: ‘Sotnytsia’, ‘Panna’ (both modern selection) and ‘Ukrainka’ (old landrace). Firstly, proteins were isolated with a SDS-containing buffer that allowed extraction of various groups of storage proteins (glutenins, gliadins, globulins and albumins). Secondly, the proteome was profiled by the two-dimensional gel electrophoresis, revealing 810 clearly-separated gel spots. Software-assisted analysis of gel images, showed 66 differentially abundant proteins. Using multi-enzymatic digestion, followed by the tandem mass spectrometry, we identified 49 differentially accumulated proteins. Parallel ultrahigh-performance liquid chromatography profiling and direct mass spectrometry quantification complemented the results. With this approach we quantified 127 proteins, 12 being differentially abundant. Principal component analysis confirmed genotype as a major source of variation in both cases. Non-gluten fraction was the most diverse among investigated bread wheat cultivars. Information from public databases of clinically relevant plant proteins highlighted variable groups of wheat allergens/toxins. Data suggested that one of the modern cultivars contained less health affecting proteins in grain. Finally, we proposed set of genetic landmarks for the development of DNA marker system, which will enable fast and efficient assessment of medical safety of multiple wheat genotypes to facilitate breeding programs.
2020-05-20 | PXD012940 | Pride
Project description:Fusarium Head Blight (FHB) is a disease of wheat and other cereal crops, where Fusarium graminearum and related species infects the wheat inflorescence during and post-anthesis. The fungus produces trichothecene toxins that accumulate in the grain of infected head, and are required for disease spread. Microarrays were used to observe differential gene expression in the uninoculated spikelets of FHB-challenged wheat spikes in three wheat genotypes. A summary of our findings will be published in Plant Pathology.
2011-09-01 | GSE28973 | GEO
Project description:The transcriptome profile was examined in four wheat genotypes in roots and shoots under nitrogen stressed condition which indicates genotype specific transcript data-set apart from the common transcripts. Unique genes was identified for nitrogen uptake and utilization process. We used microarrays to detail the gene expression and identify the candidate genes related to uptake and utilization of nitrogen in root and shoot tissues of wheat genotypes.
2020-06-30 | GSE116473 | GEO
Project description:Hi-C data of 16 wheat genotypes
| PRJEB38974 | ENA
Project description:We report differentially expressed genes in four wheat genotypes, Nyubai, Wuhan 1 and their progeny line HC374, shaw associated with resistance and susceptibility against Fusarium Head Blight (FHB). Our result indicates an early up-regulation of LRR-RKs distinct between susceptible and resistant genotypes; subsequently, different sets of genes associated with defense response were up-regulated. Differences in expression profiles among the resistant genotypes indicate genotype specific defense mechanisms. This study also showed a greater resemblance in transcriptomics of HC374 to Nyubai, consistent with their sharing of two type II FHB resistant QTLs on 3BS and 5AS, than to Wuhan 1 which carries one QTL on 2DL in common with HC374.
2018-08-09 | GSE113128 | GEO
Project description:Fusarium graminearum is responsible for Fusarium head blight (FHB), which is a destructive disease of wheat that makes its quality unsuitable for end use. To understand the temporal molecular response against this pathogen, microarray gene expression analysis was carried out at two time points on three wheat genotypes, the spikes of which were infected by Fusarium graminearum. The greatest number of genes was upregulated in Nobeokabouzu-komugi followed by Sumai 3, whereas the minimum expression in Gamenya was at three days after inoculation (dai). In Nobeokabouzu-komugi, high expression of detoxification genes, such as multidrug-resistant protein, multidrug resistance-associated protein, UDP-glycosyltransferase and ABC transporters, in addition to systemic defense-related genes, were identified at the early stage of infection. This early response of the highly-resistant genotype implies a different resistance response from the other resistant genotype, Sumai 3, primarily containing local defense-related genes, such as cell wall defense genes. In Gamenya, the expression of all three functional groups was minimal. The differences in these molecular responses with respect to the time points confirmed the variation in the genotypes. For the first time, we report the nature of gene expression in the FHB-highly resistant cv. Nobeokabouzu-komugi during the disease establishment stage and the possible underlying molecular response.
2015-01-30 | GSE59721 | GEO
Project description:Three wheat genotypes were exposed to water stress and root tissue collected for expression analysis
2013-05-03 | GSE42214 | GEO
Project description:The use of statistical tools established for the genetic analysis of quantitative traits can be applied to gene expression data. Quantitative trait loci (QTL) analysis can associate expression of genes or groups of genes with particular genomic regions and thereby identify regions that play a role in the regulation of gene expression. A segregating population of 41 doubled haploid (DH) lines from the hard red spring wheat cross RL4452 x AC Domain was used. This population had previously been mapped with microsatellites and includes a full QTL analysis for agronomic and seed quality traits. Expression analysis from 5 day post anthesis developing seed was conducted on 39 of the 41 DH lines using the Affymetrix wheat array. Expression analysis of developing seeds from field grown material identified 1,327 sequences represented by Affymetrix probe sets whose expression varied significantly between genotypes of the population. A sub-set of 378 transcripts were identified that each mapped to a single chromosome interval illustrating that major expression QTLs can be found in wheat. Genomic regions corresponding to multiple expression QTLs were identified that were coincident with previous identified seed quality trait QTL. These regions may be important regulatory regions governing economically important traits. Comparison of expression mapping data with physical mapping for a sub-set of sequences showed that both cis and trans acting expression QTLs were present. Keywords: genetic differences, expression QTL
2007-03-25 | GSE4935 | GEO