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TRANS-ACTING SIRNA3-derived short interfering RNAs confer cleavage of mRNAs in rice.
Luo, L, Yang, X, Guo, M, Lan, T, Yu, Y, Mo, B, Chen, X, Gao, L, Liu, L
Plant physiology. 2022;(1):347-362
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Abstract
Plant TRANS-ACTING SIRNA3 (TAS3)-derived short interfering RNAs (siRNAs) include tasiR-AUXIN RESPONSE FACTORs (ARFs), which are functionally conserved in targeting ARF genes, and a set of non-tasiR-ARF siRNAs, which have rarely been studied. In this study, TAS3 siRNAs were systematically characterized in rice (Oryza sativa). Small RNA sequencing results showed that an overwhelming majority of TAS3 siRNAs belong to the non-tasiR-ARF group, while tasiR-ARFs occupy a diminutive fraction. Phylogenetic analysis of TAS3 genes across dicot and monocot plants revealed that the siRNA-generating regions were highly conserved in grass species, especially in the Oryzoideae. Target genes were identified for not only tasiR-ARFs but also non-tasiR-ARF siRNAs by analyzing rice Parallel Analysis of RNA Ends datasets, and some of these siRNA-target interactions were experimentally confirmed using tas3 mutants generated by genome editing. Consistent with the de-repression of target genes, phenotypic alterations were observed for mutants in three TAS3 loci in comparison to wild-type rice. The regulatory role of ribosomes in the TAS3 siRNA-target interactions was further revealed by the fact that TAS3 siRNA-mediated target cleavage, in particular tasiR-ARFs targeting ARF2/3/14/15, occurred extensively in rice polysome samples. Altogether, our study sheds light into TAS3 genes in plants and expands our knowledge about rice TAS3 siRNA-target interactions.
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A quick journey into the diversity of iron uptake strategies in photosynthetic organisms.
Martín-Barranco, A, Thomine, S, Vert, G, Zelazny, E
Plant signaling & behavior. 2021;(11):1975088
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Abstract
Iron (Fe) is involved in multiple processes that contribute to the maintenance of the cellular homeostasis of all living beings. In photosynthetic organisms, Fe is notably required for photosynthesis. Although iron is generally abundant in the environment, it is frequently poorly bioavailable. This review focuses on the molecular strategies that photosynthetic organisms have evolved to optimize iron acquisition, using Arabidopsis thaliana, rice (Oryza sativa), and some unicellular algae as models. Non-graminaceous plants, including Arabidopsis, take up iron from the soil by an acidification-reduction-transport process (strategy I) requiring specific proteins that were recently shown to associate in a dedicated complex. On the other hand, graminaceous plants, such as rice, use the so-called strategy II to acquire iron, which relies on the uptake of Fe3+ chelated by phytosiderophores that are secreted by the plant into the rhizosphere. However, apart these main strategies, accessory mechanisms contribute to robust iron uptake in both Arabidopsis and rice. Unicellular algae combine reductive and non-reductive mechanisms for iron uptake and present important specificities compared to land plants. Since the majority of the molecular actors required for iron acquisition in algae are not conserved in land plants, questions arise about the evolution of the Fe uptake processes upon land colonization.
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Genome-wide association studies of ionomic and agronomic traits in USDA mini core collection of rice and comparative analyses of different mapping methods.
Liu, S, Zhong, H, Meng, X, Sun, T, Li, Y, Pinson, SRM, Chang, SKC, Peng, Z
BMC plant biology. 2020;(1):441
Abstract
BACKGROUND Rice is an important human staple food vulnerable to heavy metal contamination leading to serious concerns. High yield with low heavy metal contamination is a common but highly challenging goal for rice breeders worldwide due to lack of genetic knowledge and markers. RESULTS To identify candidate QTLs and develop molecular markers for rice yield and heavy metal content, a total of 191 accessions from the USDA Rice mini-core collection with over 3.2 million SNPs were employed to investigate the QTLs. Sixteen ionomic and thirteen agronomic traits were analyzed utilizing two univariate (GLM and MLM) and two multivariate (MLMM and FarmCPU) GWAS methods. 106, 47, and 97 QTLs were identified for ionomics flooded, ionomics unflooded, and agronomic traits, respectively, with the criterium of p-value < 1.53 × 10- 8, which was determined by the Bonferroni correction for p-value of 0.05. While 49 (~ 20%) of the 250 QTLs were coinciding with previously reported QTLs/genes, about 201 (~ 80%) were new. In addition, several new candidate genes involved in ionomic and agronomic traits control were identified by analyzing the DNA sequence, gene expression, and the homologs of the QTL regions. Our results further showed that each of the four GWAS methods can identify unique as well as common QTLs, suggesting that using multiple GWAS methods can complement each other in QTL identification, especially by combining univariate and multivariate methods. CONCLUSIONS While 49 previously reported QTLs/genes were rediscovered, over 200 new QTLs for ionomic and agronomic traits were found in the rice genome. Moreover, multiple new candidate genes for agronomic and ionomic traits were identified. This research provides novel insights into the genetic basis of both ionomic and agronomic variations in rice, establishing the foundation for marker development in breeding and further investigation on reducing heavy-metal contamination and improving crop yields. Finally, the comparative analysis of the GWAS methods showed that each method has unique features and different methods can complement each other.
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Comparative study on cytogenetics and transcriptome between diploid and autotetraploid rice hybrids harboring double neutral genes.
Chen, L, Guo, H, Chen, S, Yang, H, Ghouri, F, Shahid, MQ
PloS one. 2020;(9):e0239377
Abstract
Double pollen fertility neutral genes, San and Sbn, can control pollen sterility in intersubspecific (indica × japonica) rice hybrids, which has excellent potential to increase rice yield. Previous studies showed that polyploidy could increase the interaction of three pollen sterility loci, i.e. Sa, Sb and Sc, which cause pollen sterility in autotetraploid rice hybrids, and hybrid fertility could be improved by double neutral genes, San and Sbn, in autotetraploid rice hybrids. We compared cytological and transcriptome data between autotetraploid and diploid rice hybrid during meiosis and single microspore stages to understand the molecular mechanism of neutral genes for overcoming pollen sterility in autotetraploid rice hybrids, which harbored double neutral genes. Cytological results revealed that the double neutral genes resulted in higher pollen fertility (76.74%) and lower chromosomal abnormalities in autotetraploid hybrid than in parents during metaphase I, metaphase II, anaphase I and anaphase II. Moreover, autotetraploid rice hybrid displayed stronger heterosis than a diploid hybrid. Compared with diploid rice hybrid, a total of 904 and 68 differently expressed genes (DEGs) were identified explicitly in autotetraploid hybrid at meiosis and single microspore stages, respectively. Of these, 133 and 41 genes were detected in higher-parent dominance and transgressive up-regulation dominance, respectively, which were considered autotetraploid potential heterosis genes, including a meiosis-related gene (Os01g0917500, MSP1) and two meiosis specific-genes (Os07g0624900 and Os04g0208600). Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genomes pathway (KEGG) analysis revealed that DEGs significantly enriched in amino acid metabolism and photosynthesis metabolism. These results indicated that meiosis-specific and meiosis-related genes, and amino acids and photosynthesis metabolism-related genes contribute to higher yield and pollen fertility in autotetraploid rice hybrid. This study provides a theoretical basis for molecular mechanisms of heterosis in autotetraploid rice harboring double neutral genes for pollen fertility.
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Effects of supplementation with rice husk powder and rice bran on inflammatory factors in overweight and obese adults following an energy-restricted diet: a randomized controlled trial.
Edrisi, F, Salehi, M, Ahmadi, A, Fararoei, M, Rusta, F, Mahmoodianfard, S
European journal of nutrition. 2018;(2):833-843
Abstract
PURPOSE Overweight and obesity are major public health concerns worldwide which are associated with a low-grade chronic inflammation. Dietary fiber as an important component of diet could be effective in controlling weight and inflammatory factors. The present study aimed to compare the effects of rice husk powder and rice bran on inflammatory factors along with an energy-restricted diet in overweight and obese adults. METHODS In this randomized trial, 105 eligible individuals were assigned to one of the three energy-restricted diet groups receiving; rice bran (n = 35), rice husk powder (n = 35), and control group (n = 35) for 12 weeks. Demographic data, dietary intake, anthropometric indices and inflammatory factors (serum levels of IL-6 and hs-CRP) were measured at baseline and at the end of the study. RESULTS Weight, BMI and waist circumference reduced significantly in all groups after 12 weeks of study (P < 0.01 for all). However, pre- and post-measure differences between groups were not significant. Moreover, serum levels of hs-CRP and IL-6 were not significantly different between participants in the rice bran or rice husk groups. However, the reduction in serum levels of hs-CRP in rice husk (mean change = - 0.14 ± 0.05 µg/ml) and rice bran (mean change = - 0.13 ± 0.03 µg/ml) was significantly higher when compared to the control group (mean change = - 0.03 ± 0.02 µg/ml) (P < 0.05 for both groups). The same pattern was found when changes in IL-6 serum levels of participants in rice husk (mean change = - 0.48 ± 0.11 pg/ml) and rice bran (mean change = - 0.57 ± 0.13 pg/ml) groups were compared to the control group (mean change= - 0.19 ± 0.07 pg/ml) (P < 0.05 for both groups). CONCLUSION The results of this study showed positive effects of rice bran and rice husk powder supplementation, combined with an energy-restricted diet, on inflammatory markers among overweight and obese adults.
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Commercially available gluten-free pastas elevate postprandial glycemia in comparison to conventional wheat pasta in healthy adults: a double-blind randomized crossover trial.
Johnston, CS, Snyder, D, Smith, C
Food & function. 2017;(9):3139-3144
Abstract
Given the popularity of gluten-free diets, research regarding the health implications of gluten-free (GF) products is necessary. This study compared the postprandial glycemic responses to three GF pastas commonly available in the U.S. market to that of wheat pasta in healthy adults. Thirteen healthy non-smoking men and women from a university campus population were enrolled in this randomized 4 × 4 block crossover study and completed all four treatments. Participants followed a standardized diet and activity protocol the day prior to testing, and one week separated testing periods. The test meal (a macaroni and cheese dish prepared with conventional wheat pasta or with GF pasta composed of either brown rice, rice and corn, or corn and quinoa flours) was consumed under observation, and blood was sampled in the fasted state and at one-half hour intervals for the first 2 hours following meal ingestion. A significant pasta × time interaction was observed for the incremental postprandial glycemia curves (p = 0.036, repeated measures ANOVA; effect size [partial eta squared], 0.943). Post-hoc analysis revealed a significant difference for the 30-minute postprandial blood glucose concentrations: the plasma glucose concentration was 57% higher for the GF rice and corn pasta compared to traditional wheat pasta (p = 0.011). Since postprandial glycemia was higher for GF pasta composed of rice and corn flours compared to wheat pasta, more research is needed to understand how the substitute ingredients for GF pastas impact health parameters and disease risk.
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Evaluating Crossbred Red Rice Variants for Postprandial Glucometabolic Responses: A Comparison with Commercial Varieties.
Se, CH, Chuah, KA, Mishra, A, Wickneswari, R, Karupaiah, T
Nutrients. 2016;(5)
Abstract
Consumption of white rice predisposes some Asian populations to increased risk of type 2 diabetes. We compared the postprandial glucometabolic responses to three newly-developed crossbred red rice variants (UKMRC9, UKMRC10, UKMRC11) against three selected commercial rice types (Thai red, Basmati white, Jasmine white) using 50-g carbohydrate equivalents provided to 12 normoglycaemic adults in a crossover design. Venous blood was drawn fasted and postprandially for three hours. Glycaemic (GI) and insulin (II) indices, incremental areas-under-the-curves for glucose and insulin (IAUCins), indices of insulin sensitivity and secretion, lactate and peptide hormones (motilin, neuropeptide-Y, orexin-A) were analyzed. The lowest to highest trends for GI and II were similar i.e., UKMRC9 < Basmati < Thai red < UKMRC10 < UKMRC11 < Jasmine. Postprandial insulinaemia and IAUCins of only UKMRC9 were significantly the lowest compared to Jasmine. Crude protein and fiber content correlated negatively with the GI values of the test rice. Although peptide hormones were not associated with GI and II characteristics of test rice, early and late phases of prandial neuropeptide-Y changes were negatively correlated with postprandial insulinaemia. This study indicated that only UKMRC9 among the new rice crossbreeds could serve as an alternative cereal option to improve diet quality of Asians with its lowest glycaemic and insulinaemic burden.
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A BAC physical map of aus rice cultivar 'Kasalath', and the map-based genomic sequence of 'Kasalath' chromosome 1.
Kanamori, H, Fujisawa, M, Katagiri, S, Oono, Y, Fujisawa, H, Karasawa, W, Kurita, K, Sasaki, H, Mori, S, Hamada, M, et al
The Plant journal : for cell and molecular biology. 2013;(4):699-708
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Abstract
Comparative analysis using available genomic resources within closely related species is an effective way to investigate genomic sequence and structural diversity. Rice (Oryza sativa L.) has undergone significant physiological and morphological changes during its domestication and local adaptation. We present a complete bacterial artificial chromosome (BAC) physical map for the aus rice cultivar 'Kasalath', which covers 90% of the sequence of temperate japonica rice cultivar 'Nipponbare'. Examination of physical distances between computational and experimental measurements of 'Kasalath' BAC insert size revealed the presence of more than 500 genomic regions that appear to have significant chromosome structural changes between the two cultivars. In particular, a genomic region on the long arm of 'Kasalath' chromosome 11 carrying a disease-resistance gene cluster was greatly expanded relative to the 'Nipponbare' genome. We also decoded 41.37 Mb of high-quality genomic sequence from 'Kasalath' chromosome 1. Extensive comparisons of chromosome 1 between 'Kasalath' and 'Nipponbare' led to the discovery of 317,843 single-nucleotide polymorphisms (SNPs) and 66,331 insertion/deletion (indel) sites. Nearly two-thirds of the expressed genes on rice chromosome 1 carried natural variations involving SNPs and/or indels that resulted in substitutions, insertions or deletions of amino acids in one cultivar relative to the other. We also observed gain and loss of genes caused by large indels. This study provides an important framework and an invaluable dataset for further understanding of the molecular mechanisms underlying the evolution and functions of the rice genome.
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The effect of apparent amylose content and dietary fibre on the glycemic response of different varieties of cooked milled and brown rice.
Trinidad, TP, Mallillin, AC, Encabo, RR, Sagum, RS, Felix, AD, Juliano, BO
International journal of food sciences and nutrition. 2013;(1):89-93
Abstract
Brown rice is a good source of dietary fibre (DF) and contains higher vitamins/minerals than milled rice. The study determined the effect of amylose content (AC) and DF on glucose response (GR) from different varieties of milled and brown rice. Milled and brown rice were used as test foods. They were fed to 9-10 human volunteers containing 50 g available carbohydrate after an overnight fast. GR and the glycemic index (GI) were determined. Results found that Sinandomeng with the lowest AC had a high GI = 75, while PSBRc10 with the highest AC had a low GI = 50. Sinandomeng with a low DF had GI = 75, while its brown rice had GI = 55. Brown rice (IR64) with 23% AC and DF of 2.5 g/100 g had low GI = 51. In conclusion, the GR and GI of the different varieties of cooked milled and brown rice varied depending on its AC and DF contents.
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Bean and rice meals reduce postprandial glycemic response in adults with type 2 diabetes: a cross-over study.
Thompson, SV, Winham, DM, Hutchins, AM
Nutrition journal. 2012;:23
Abstract
BACKGROUND Around the world, beans and rice are commonly consumed together as a meal. With type 2 diabetes increasing, the effect of this traditional diet pattern on glycemic response has not been studied fully. METHODS We evaluated the glycemic response of bean and rice traditional meals compared to rice alone in adults with type 2 diabetes. Seventeen men and women with type 2 diabetes controlled by metformin (n = 14) or diet/exercise (n = 3) aged 35-70 years participated in the randomized 4 × 4 crossover trial. The white long grain rice control, pinto beans/rice, black beans/rice, red kidney beans/rice test meals, matched for 50 grams of available carbohydrate, were consumed at breakfast after a 12 hour fast. Capillary blood glucose concentrations at baseline and at 30 minute intervals up to 180 minutes postprandial were collected. MANOVA for repeated measures established glucose differences between treatments. Paired t tests identified differences between bean types and the rice control following a significant MANOVA. RESULTS Postprandial net glucose values were significantly lower for the three bean/rice treatments in contrast to the rice control at 90, 120 and 150 minutes. Incremental area under the curve values were significantly lower for the pinto and black bean/rice meals compared to rice alone, but not for kidney beans. CONCLUSIONS Pinto, dark red kidney and black beans with rice attenuate the glycemic response compared to rice alone. Promotion of traditional foods may provide non-pharmaceutical management of type 2 diabetes and improve dietary adherence with cultural groups.