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Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach.
Mirdar Mansuri, R, Shobbar, ZS, Babaeian Jelodar, N, Ghaffari, M, Mohammadi, SM, Daryani, P
BMC plant biology. 2020;(1):452
Abstract
BACKGROUND Salinity, as one of the main abiotic stresses, critically threatens growth and fertility of main food crops including rice in the world. To get insight into the molecular mechanisms by which tolerant genotypes responds to the salinity stress, we propose an integrative meta-analysis approach to find the key genes involved in salinity tolerance. Herein, a genome-wide meta-analysis, using microarray and RNA-seq data was conducted which resulted in the identification of differentially expressed genes (DEGs) under salinity stress at tolerant rice genotypes. DEGs were then confirmed by meta-QTL analysis and literature review. RESULTS A total of 3449 DEGs were detected in 46 meta-QTL positions, among which 1286, 86, 1729 and 348 DEGs were observed in root, shoot, seedling, and leaves tissues, respectively. Moreover, functional annotation of DEGs located in the meta-QTLs suggested some involved biological processes (e.g., ion transport, regulation of transcription, cell wall organization and modification as well as response to stress) and molecular function terms (e.g., transporter activity, transcription factor activity and oxidoreductase activity). Remarkably, 23 potential candidate genes were detected in Saltol and hotspot-regions overlying original QTLs for both yield components and ion homeostasis traits; among which, there were many unreported salinity-responsive genes. Some promising candidate genes were detected such as pectinesterase, peroxidase, transcription regulator, high-affinity potassium transporter, cell wall organization, protein serine/threonine phosphatase, and CBS domain cotaining protein. CONCLUSIONS The obtained results indicated that, the salt tolerant genotypes use qualified mechanisms particularly in sensing and signalling of the salt stress, regulation of transcription, ionic homeostasis, and Reactive Oxygen Species (ROS) scavenging in response to the salt stress.
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Meta-analysis of grain iron and zinc associated QTLs identified hotspot chromosomal regions and positional candidate genes for breeding biofortified rice.
Raza, Q, Riaz, A, Sabar, M, Atif, RM, Bashir, K
Plant science : an international journal of experimental plant biology. 2019;:110214
Abstract
Biofortification of staple crops with essential micronutrients is the sustainable way to overcome the hidden hunger. A large number of quantitative trait loci (QTL) linked with grain micronutrient contents have been reported in different mapping studies. Identification of consistent QTLs across diverse genetic backgrounds is useful for candidate gene analysis and marker assisted selection of target traits. In this study, an up to date meta-analysis of grain iron and zinc associated QTLs was performed and 48 meta-QTLs (MQTLs) distributed across 12 rice chromosomes were identified. The 95% confidence intervals of identified genomic regions were significantly narrower than the average of their corresponding original QTLs. A total of 9308 genes/transcripts physically located within or near MQTL regions were retrieved and through prioritization of candidate genes (CGs) 663 non-redundant iron and zinc CGs were selected and studied in detailed. Several functionally characterized iron and zinc homoeostasis related genes e.g OsATM3, OsDMAS1, OsFRO2, OsNAS1-3, OsVIT2, OsYSL16, OsZIP3 and OsZIP7 were also included in our MQTL analysis. More than 64% genes were enriched with zinc and iron binding gene ontology terms and were involved in oxidation reduction process, carbohydrate metabolic process, regulation of transcription, trans-membrane transport, response to oxidative stress, cell redox homeostasis and proteolysis etc. In-silico transcriptomic analysis of rice identified 260 CGs which were regulated in response to iron and zinc stresses. We also identified at least 37 genes which were differentially expressed under both stress conditions and majority of these have not been studied in detailed before. Our results strongly indicate that majority of the MQTLs identified in this study are hotspots for grain iron and zinc concentration and are worth of intensive functional studies in near future.
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Concentrations of arsenic and lead in rice (Oryza sativa L.) in Iran: A systematic review and carcinogenic risk assessment.
Fakhri, Y, Bjørklund, G, Bandpei, AM, Chirumbolo, S, Keramati, H, Hosseini Pouya, R, Asadi, A, Amanidaz, N, Sarafraz, M, Sheikhmohammad, A, et al
Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association. 2018;:267-277
Abstract
Exposure to heavy metals such as arsenic (As), lead (Pb), and cadmium (Cd) in either the short or the long term can cause cancers in humans. Dietary intake and consumption of rice (Oryza sativa L.) is increasing in Iran, and several studies on the concentration of heavy metals in rice have been carried out in this country in recent years. In this perspective, the main objective of the present study was to investigate, even via a meta-analysis of the existing literature, the presence of As and Pb in rice from many geographical areas in Iran, as well as to estimate the carcinogenic risk of these heavy metals in rice consumers. The results of the present ten years-spanning systematic review indicate that 21 reports, collecting a total of 2088 samples, were performed between 2008 and October 2017. The minimum and maximum concentration of As was observed in the Golestan area (0.01 ± 0.01 mg/kg d.w) and the Gillan region (3 mg/kg d.w); and Pb in the Shahrekord (0.07 ± 0.02 mg/kg d.w) and Mazandaran (35 mg/kg d.w). The meta-analysis of data showed that pooled concentration of As in the rice was 0.04 (95%CI: 0.02-0.06 mg/kg d.w), which resulted lower than the National Standard (NS) limits. However, the pooled concentration of Pb in the rice was 0.38 (95%CI: 0.25-0.5 mg/kg d.w), i.e., higher than NS limits. The heterogeneity was significant between As (I2 = 63%, P value = .003) and Pb (I2 = 96%, P value < .001) studies. The carcinogenic risk assessment showed that minimum and maximum incremental lifetime cancer risk (ILCR) of As was in the 45-54 (4.53 × 10-2) and 15-24 (5.50 × 10-2) year age groups consumers; and Pb, 45-54 (2.442 × 10-3) and 15-24 (2.96 × 10-3), respectively. The overall carcinogenesis risk of As (4.864 × 10-2) was 18.5 times higher than Pb (2.623 × 10-3). All age groups consumers of rice content of As and Pb are at considerable carcinogenesis risk (ILCR > 10-3). Therefore a decreased level of heavy metals in rice cultivation should be encouraged and performed in next planning.
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The socioeconomics of genetically modified biofortified crops: a systematic review and meta-analysis.
De Steur, H, Wesana, J, Blancquaert, D, Van Der Straeten, D, Gellynck, X
Annals of the New York Academy of Sciences. 2017;(1):14-33
Abstract
Building upon the growing interest and research on genetically modified (GM) biofortification, its socioeconomic potential has been increasingly examined. We conducted two systematic reviews and meta-analyses to provide comprehensive evidence of consumers' willingness to pay (11 economic valuation studies, 64 estimates) and cost-effectiveness/benefits (five economic evaluation studies, 30 estimates). Worldwide, consumers were willing to pay 23.9% more for GM biofortified food crops. Aside from crop and design-related differences, information provision was deemed crucial. Positive information (nutrition and GM benefits) is associated with the highest consumer willingness to pay, compared with negative, objective, and conflicting GM information, especially when negative information was mentioned last. This health intervention would reduce the aggregated micronutrient deficiency burden in Asia (15.6 million disability-adjusted life years (DALYs)) by 12.5-51.4%, at a low cost of USD 7.9-27.8 per DALY in a pessimistic and optimistic scenario, respectively. Given that GM biofortified crops could tackle hidden hunger in a cost-effective and well-accepted way, its implementation is worth pursuing. A case study on folate biofortification further elaborates on the importance of socioeconomic research and the determinants of their market potential.
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Rice consumption, incidence of chronic diseases and risk of mortality: meta-analysis of cohort studies.
Saneei, P, Larijani, B, Esmaillzadeh, A
Public health nutrition. 2017;(2):233-244
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Abstract
OBJECTIVE Findings from cohort studies investigating the association between rice consumption and risk of chronic diseases or mortality have been inconsistent. We performed a comprehensive systematic review and meta-analysis on all published cohort studies examining white rice consumption in relation to incidence of chronic diseases or risk of mortality. DESIGN A systematic literature search of MEDLINE, Embase, Cochrane review, Google Scholar and Scopus databases for relevant cohort studies published until July 2014. For systematic review, we found nineteen studies examining the association between rice intake and risk of chronic diseases (obesity, hypertension, metabolic syndrome, diabetes, CVD and cancers) or mortality. Cohort studies which reported relative risk (RR) or odds ratio for highest v. lowest intake of rice and chronic diseases or mortality were included in the meta-analysis. RESULTS In a meta-analysis on seventeen risk estimates for highest v. lowest category of rice intake, provided from twelve studies, we found a trend towards a positive association (RR; 95 % CI) between rice consumption and risk of all chronic diseases (1·11; 0·96, 1·29); however, significant between-study heterogeneity was found (I 2=70·3 %, P<0·001). Stratified analysis by gender showed a significant positive association between rice consumption and risk of chronic diseases in women (1·40; 1·13, 1·73), but not in men (0·95; 0·72, 1·24). Combining ten effect sizes from five studies showed that high consumption of rice was not significantly associated with mortality (0·97; 0·88, 1·06). Subgroup analysis by gender indicated an inverse association between rice consumption and mortality in men (0·87; 0·81, 0·94), but a trend towards a positive association in women (1·08; 0·97, 1·19). CONCLUSIONS Although white rice consumption was not found to be associated with individual chronic conditions, we observed a positive association between white rice intake and risk of all overall chronic diseases in women. High rice consumption was related to a modest reduction in risk of mortality in men but not in women. Further studies of these relationships, in different populations, are needed.
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White rice consumption and risk of type 2 diabetes: meta-analysis and systematic review.
Hu, EA, Pan, A, Malik, V, Sun, Q
BMJ (Clinical research ed.). 2012;:e1454
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Abstract
OBJECTIVES To summarise evidence on the association between white rice consumption and risk of type 2 diabetes and to quantify the potential dose-response relation. DESIGN Meta-analysis of prospective cohort studies. DATA SOURCES Searches of Medline and Embase databases for articles published up to January 2012 using keywords that included both rice intake and diabetes; further searches of references of included original studies. STUDY SELECTION Included studies were prospective cohort studies that reported risk estimates for type 2 diabetes by rice intake levels. DATA SYNTHESIS Relative risks were pooled using a random effects model; dose-response relations were evaluated using data from all rice intake categories in each study. RESULTS Four articles were identified that included seven distinct prospective cohort analyses in Asian and Western populations for this study. A total of 13,284 incident cases of type 2 diabetes were ascertained among 352,384 participants with follow-up periods ranging from 4 to 22 years. Asian (Chinese and Japanese) populations had much higher white rice consumption levels than did Western populations (average intake levels were three to four servings/day versus one to two servings/week). The pooled relative risk was 1.55 (95% confidence interval 1.20 to 2.01) comparing the highest with the lowest category of white rice intake in Asian populations, whereas the corresponding relative risk was 1.12 (0.94 to 1.33) in Western populations (P for interaction=0.038). In the total population, the dose-response meta-analysis indicated that for each serving per day increment of white rice intake, the relative risk of type 2 diabetes was 1.11 (1.08 to 1.14) (P for linear trend<0.001). CONCLUSION Higher consumption of white rice is associated with a significantly increased risk of type 2 diabetes, especially in Asian (Chinese and Japanese) populations.
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Genevestigator transcriptome meta-analysis and biomarker search using rice and barley gene expression databases.
Zimmermann, P, Laule, O, Schmitz, J, Hruz, T, Bleuler, S, Gruissem, W
Molecular plant. 2008;(5):851-7
Abstract
The wide-spread use of microarray technologies to study plant transcriptomes has led to important discoveries and to an accumulation of profiling data covering a wide range of different tissues, developmental stages, perturbations, and genotypes. Querying a large number of microarray experiments can provide insights that cannot be gained by analyzing single experiments. However, such a meta-analysis poses significant challenges with respect to data comparability and normalization, systematic sample annotation, and analysis tools. Genevestigator addresses these issues using a large curated expression database and a set of specifically developed analysis tools that are accessible over the internet. This combination has already proven to be useful in the area of plant research based on a large set of Arabidopsis data (Grennan, 2006). Here, we present the release of the Genevestigator rice and barley gene expression databases that contain quality-controlled and well annotated microarray experiments using ontologies. The databases currently comprise experiments from pathology, plant nutrition, abiotic stress, hormone treatment, genotype, and spatial or temporal analysis, but are expected to cover a broad variety of research areas as more experimental data become available. The transcriptome meta-analysis of the model species rice and barley is expected to deliver results that can be used for functional genomics and biotechnological applications in cereals.