Comparative Small RNA Profiling and Functional Exploration on Wheat With High- and Low-Cadmium Accumulation.
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ABSTRACT:
SUBMITTER: Liu Y
PROVIDER: S-EPMC8084923 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Cadmium (Cd) is a heavy metal that has no known biological function and is toxic for many living organisms. The maximum level of Cd concentration allowed in the international market for wheat grain is 0.2 mg kg-1 Because phenotyping for Cd uptake is expensive and time consuming, molecular markers associated with genes conferring low Cd uptake would expedite selection and lead to the development of durum cultivars with reduced Cd concentrations. Here, we identified single nucleotide polymorphisms (SNPs) associated with a novel low Cd uptake locus in the durum experimental line D041735, which has hexaploid common wheat in its pedigree. Genetic analysis revealed a single major QTL for Cd uptake on chromosome arm 5BL within a 0.3 cM interval flanked by SNP markers. Analysis of the intervening sequence revealed a gene with homology to an aluminum-induced protein as a candidate gene. Validation and allelism tests revealed that the low Cd uptake gene identified in this study is different from the closely linked Cdu1-B gene, which also resides on 5BL. This study therefore showed that the durum experimental line D041735 contains a novel low Cd uptake gene that was likely acquired from hexaploid wheat.
| S-EPMC5844312 | biostudies-literature
Project description:Soybean is a valuable crop, used in animal feed and for human consumption. Selecting soybean cultivars with low seed cadmium (Cd) concentration is important for the purpose of minimizing the transfer of Cd into the human body. To ensure international trade, farmers need to produce soybean that meets the European Union (EU) Cd limit of 0.2 mg kg-1. In this study, we evaluated two populations of recombinant inbred lines (RILs), X5154 and X4050, for seed Cd accumulation. Linkage maps were constructed with 325 and 280 polymorphic simple sequence repeat (SSR) markers, respectively, and used to identify a novel minor quantitative trait locus (QTL) on chromosome 13 in the X4050 population between SSR markers Satt522 and Satt218. Based on a gene ontology search within the QTL region, seven genes were identified as candidates responsible for low seed Cd accumulation, including Glyma.13G308700 and Glyma.13G309100. In addition, we confirmed the known major gene, Cda1, in the X5154 population and developed KASP and CAPS/dCAPS allele-specific markers for efficient marker-assisted breeding for Cda1.
| S-EPMC9102923 | biostudies-literature
Project description:The contamination of food crops by cadmium (Cd) is a major concern in food production because it can reduce crop yields and threaten human health. In this study, knockout rice plants (Oryza sativa) tagged with the gene trap vector pGA2707 were screened for Cd tolerance, and the tolerant line lcd was obtained. The lcd mutant showed tolerance to Cd on agar plates and in hydroponic culture during early plant development. Metal concentration measurements in hydroponically grown plants revealed significantly less Cd in the shoots of lcd plants compared with wild-type (WT) shoots. When cultured in the field in soil artificially contaminated with low levels of Cd, lcd showed no significant difference in the Cd content of its leaf blades; however, the Cd concentration in the grains was 55% lower in 2009 and 43% lower in 2010. There were no significant differences in plant dry weight or seed yield between lcd and wild-type plants. LCD, a novel gene, is not homologous to any other known gene. LCD localized to the cytoplasm and nucleus, and was expressed mainly in the vascular tissues in the roots and phloem companion cells in the leaves. These data indicate that lcd may be useful for understanding Cd transport mechanisms and is a promising candidate rice line for use in combating the threat of Cd to human health.
| S-EPMC3223062 | biostudies-literature
Project description:BACKGROUND:Cadmium (Cd) is a widespread toxic heavy metal pollutant in agricultural soil, and Cd accumulation in rice grains is a major intake source of Cd for Asian populations that adversely affect human health. However, the molecular mechanism underlying Cd uptake, translocation and accumulation has not been fully understood in rice plants. RESULTS:In this study, a mutant displaying extremely low Cd accumulation (lcd1) in rice plant and grain was generated by EMS mutagenesis from indica rice cultivar 9311 seeds. The candidate SNPs associated with low Cd accumulation phenotype in the lcd1 mutant were identified by MutMap and the transcriptome changes between lcd1 and WT under Cd exposure were analyzed by RNA-seq. The lcd1 mutant had lower Cd uptake and accumulation in rice root and shoot, as well as less growth inhibition compared with WT in the presence of 5 μM Cd. Genetic analysis showed that lcd1 was a single locus recessive mutation. The SNP responsible for low Cd accumulation in the lcd1 mutant located at position 8,887,787 on chromosome 7, corresponding to the seventh exon of OsNRAMP5. This SNP led to a Pro236Leu amino acid substitution in the highly conserved region of OsNRAMP5 in the lcd1 mutant. A total of 1208 genes were differentially expressed between lcd1 and WT roots under Cd exposure, and DEGs were enriched in transmembrane transport process GO term. Increased OsHMA3 expression probably adds to the effect of OsNRAMP5 mutation to account for the significant decreases in Cd accumulation in rice plant and grain of the lcd1 mutant. CONCLUSIONS:An extremely low Cd mutant lcd1 was isolated and identified using MutMap and RNA-seq. A Pro236Leu amino acid substitution in the highly conserved region of OsNRAMP5 is likely responsible for low Cd accumulation in the lcd1 mutant. This work provides more insight into the mechanism of Cd uptake and accumulation in rice, and will be helpful for developing low Cd accumulation rice by marker-assisted breeding.
| S-EPMC6560816 | biostudies-other
Project description:BACKGROUND:Sequencing-based analyses of low-biomass samples are known to be prone to misinterpretation due to the potential presence of contaminating molecules derived from laboratory reagents and environments. DNA contamination has been previously reported, yet contamination with RNA is usually considered to be very unlikely due to its inherent instability. Small RNAs (sRNAs) identified in tissues and bodily fluids, such as blood plasma, have implications for physiology and pathology, and therefore the potential to act as disease biomarkers. Thus, the possibility for RNA contaminants demands careful evaluation. RESULTS:Herein, we report on the presence of small RNA (sRNA) contaminants in widely used microRNA extraction kits and propose an approach for their depletion. We sequenced sRNAs extracted from human plasma samples and detected important levels of non-human (exogenous) sequences whose source could be traced to the microRNA extraction columns through a careful qPCR-based analysis of several laboratory reagents. Furthermore, we also detected the presence of artefactual sequences related to these contaminants in a range of published datasets, thereby arguing in particular for a re-evaluation of reports suggesting the presence of exogenous RNAs of microbial and dietary origin in blood plasma. To avoid artefacts in future experiments, we also devise several protocols for the removal of contaminant RNAs, define minimal amounts of starting material for artefact-free analyses, and confirm the reduction of contaminant levels for identification of bona fide sequences using 'ultra-clean' extraction kits. CONCLUSION:This is the first report on the presence of RNA molecules as contaminants in RNA extraction kits. The described protocols should be applied in the future to avoid confounding sRNA studies.
| S-EPMC5952572 | biostudies-literature
Project description:Light is an important factor that affects the synthesis of functional metabolites in longan embryogenic calli (ECs). However, analysis of the effect of light on functional metabolites in longan ECs via RNA sequencing has rarely been reported and their light regulation network is unclear. The contents of various functional metabolites as well as the enzymatic activities of superoxide dismutase and peroxidase and the level of H₂O₂ in longan ECs were significantly higher under blue light treatment than under the other treatments (dark, white). In this study, we sequenced three mRNA libraries constructed from longan ECs subjected to different treatments. A total of 4463, 1639 and 1806 genes were differentially expressed in the dark versus blue (DB), dark versus white (DW) and white versus blue (WB) combinations, respectively. According to GO and KEGG analyses, most of the differentially expressed genes (DEGs) identified were involved in transmembrane transport, taurine and hypotaurine metabolism, calcium transport and so forth. Mapman analysis revealed that more DEGs were identified in each DB combination pathway than in DW combination pathways, indicating that blue light exerts a significantly stronger regulatory effect on longan EC metabolism than the other treatments. Based on previous research and transcriptome data mining, a blue light signaling network of genes that affect longan functional metabolites was constructed and HY5, PIF4 and MYC2 were shown to be the key regulatory genes in the network. The results of this study demonstrate that the expression levels of phase-specific genes vary with changes in longan EC functional metabolites.
| S-EPMC6359358 | biostudies-literature
Project description:BackgroundAll the reports on insect small RNAs come from holometabolous insects whose genome sequence data are available. Therefore, study of hemimetabolous insect small RNAs could provide more insights into evolution and function of small RNAs in insects. The locust is an important, economically harmful hemimetabolous insect. Its phase changes, as a phenotypic plasticity, result from differential gene expression potentially regulated at both the post-transcriptional level, mediated by small RNAs, and the transcriptional level.ResultsHere, using high-throughput sequencing, we characterize the small RNA transcriptome in the locust. We identified 50 conserved microRNA families by similarity searching against miRBase, and a maximum of 185 potential locust-specific microRNA family candidates were identified using our newly developed method independent of locust genome sequence. We also demonstrate conservation of microRNA*, and evolutionary analysis of locust microRNAs indicates that the generation of miRNAs in locusts is concentrated along three phylogenetic tree branches: bilaterians, coelomates, and insects. Our study identified thousands of endogenous small interfering RNAs, some of which were of transposon origin, and also detected many Piwi-interacting RNA-like small RNAs. Comparison of small RNA expression patterns of the two phases showed that longer small RNAs were expressed more abundantly in the solitary phase and that each category of small RNAs exhibited different expression profiles between the two phases.ConclusionsThe abundance of small RNAs in the locust might indicate a long evolutionary history of post-transcriptional gene expression regulation, and differential expression of small RNAs between the two phases might further disclose the molecular mechanism of phase changes.
| S-EPMC2687794 | biostudies-literature
Project description:Staphylococcus aureus contains a repertoire of at least 50 and possibly 500 small RNAs (sRNAs). The functions of most sRNAs are not understood, although some are known to respond to environmental changes, including the presence of antibiotics. Here, in an effort to better understand the roles of sRNAs in the context of antibiotic exposure, we took a clinical methicillin-resistant S. aureus (MRSA) isolate and separately deleted eight sRNAs that were significantly upregulated in response to the last-line antibiotic linezolid as revealed by transcriptome sequencing (RNA-seq) comparisons. We also deleted an additional 10 sRNAs that were either highly expressed or previously found to respond to antibiotic exposure. There were no significant changes for any of the 18 mutants in a variety of phenotypic screens, including MIC screens, growth competition assays in the presence of linezolid, biofilm formation, and resistance to whole-blood killing. These data suggest sRNA functional redundancy, because despite their high expression levels upon antibiotic exposure, individual sRNA genes do not affect readily observable bacterial phenotypes. The sRNA transcriptional changes we measured during antibiotic exposure might also reflect sRNA "indifference," that is, a general stress response not specifically related to sRNA function. These data underscore the need for sensitive assays and new approaches to try and decipher the functions of sRNA genes in S. aureusIMPORTANCE Bacterial small RNAs (sRNAs) are RNA molecules that can have important regulatory roles across gene expression networks. There is a growing understanding of the scope and potential breadth of impact of sRNAs on global gene expression patterns in Staphylococcus aureus, a major human pathogen. Here, transcriptome comparisons were used to examine the roles of sRNA genes with a potential role in the response of S. aureus to antibiotic exposure. Although no measurable impact on key bacterial phenotypes was observed after deleting each of 18 sRNAs identified by these comparisons, this research is significant because it underscores the subtle modes of action of these sometimes abundant molecules within the bacterium.
| S-EPMC6946794 | biostudies-literature
Project description:BackgroundPeanut is one of the most important oil and protein crops, and it exhibits wide cultivar variations in shoot Cd accumulation ability. However, the mechanism of Cd accumulation in peanut shoots has not been well understood. In this study, the root proteomics of two cultivars differing in seed Cd accumulation, Fenghua 1 (F, low Cd cultivar) and Silihong (S, high Cd cultivar), were investigated under 0 (CK) and 2 μM Cd conditions.ResultsA total of 4676 proteins were identified by proteomics screening. Of them, 375, 1762, 1276 and 771 proteins were identified to be differentially expressed proteins (DEPs) for comparison of FCd/FCK, SCd/SCK, FCK/SCK and FCd/SCd, respectively. Silihong is more sensitive to Cd exposure than Fenghua 1 in terms of root proteomics. A total of 30 and 86 DEPs were identified to be related with heavy metal transport and cell wall modification, respectively. The up-regulation of ABCB25, ABCC14, ABCC2, PDR1 and V-ATPases by Cd exposure in Silihong might enhance vacuolar sequestration of Cd and its efflux from symplast to apoplast. The higher Cd accumulation in the root CWs of Silihong might be resulted from its higher capability of CW modification, in which many proteins such as IRX10L, BGLU12-like, BGLU42, EXLB1, XTH30, XTH6, XYL7, PAL3, COMT, CAD1, and CCR1 were involved.ConclusionsThe vacuolar sequestration and efflux of Cd as well as its adsorption in CW might be the principal mechanism of cadmium detoxification in Silihong. The higher capacity of Cd accumulation and translocation of Silihong is an inherent characteristics in which ACA8 and ZIP1 might be involved.
| S-EPMC6458636 | biostudies-literature
Project description:Fusarium graminearum is one of the most devastating diseases of wheat worldwide, and can cause Fusarium head blight (FHB). F. graminearum infection and mycotoxin production mainly present in wheat and can be influenced by environmental factors and wheat cultivars. The objectives of this study were to examine the effect of wheat cultivars and interacting conditions of temperature and water activity (aw) on mycotoxin production by two strains of F. graminearum and investigate the response mechanisms of different wheat cultivars to F. graminearum infection. In this regard, six cultivars of wheat spikes under field conditions and three cultivars of post-harvest wheat grains under three different temperature conditions combined with five water activity (aw) conditions were used for F. graminearum infection in our studies. Liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis showed significant differences in the concentration of Fusarium mycotoxins deoxynivalenol (DON) and its derivative deoxynivalenol-3-glucoside (D3G) resulting from wheat cultivars and environmental factors. Transcriptome profiles of wheat infected with F. graminearum revealed the lower expression of disease defense-factor-related genes, such as mitogen-activated protein kinases (MAPK)-encoding genes and hypersensitivity response (HR)-related genes of infected Annong 0711 grains compared with infected Sumai 3 grains. These findings demonstrated the optimal temperature and air humidity resulting in mycotoxin accumulation, which will be beneficial in determining the conditions of the relative level of risk of contamination with FHB and mycotoxins. More importantly, our transcriptome profiling illustrated differences at the molecular level between wheat cultivars with different FHB resistances, which will lay the foundation for further research on mycotoxin biosynthesis of F. graminearum and regulatory mechanisms of wheat to F. graminearum.
| S-EPMC9318452 | biostudies-literature