scholarly journals OsmiR396/Growth Regulating Factor modulate rice grain size through direct regulation of embryo-specific miR408

2021 ◽  
Author(s):  
Xiaofang Yang ◽  
Xiaoling Zhao ◽  
Zhengyan Dai ◽  
Feilong Ma ◽  
Xuexia Miao ◽  
...  
Keyword(s):  
Grain Size ◽  
Regulatory Networks ◽  
Oryza Sativa L ◽  
Indica Rice ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Genetic Regulatory Networks ◽  
Rice Grain ◽  
Rice Varieties ◽  
Size Regulation

Abstract microRNAs (miRNAs) are promising targets for crop improvement of complex agricultural traits. Coordinated activity between/among different miRNAs may fine-tune specific developmental processes in diverse organisms. Grain size is a main factor determining rice (Oryza sativa L.) crop yield, but the network of miRNAs influencing this trait remains uncharacterized. Here we show that sequestering OsmiR396 through target mimicry (MIM396) can substantially increase grain size in several japonica and indica rice subspecies and in plants with excessive tillers and a high panicle density. Thus, OsmiR396 has a major role related to the regulation of rice grain size. The grain shape of Growth Regulating Factor8 (OsGRF8)-overexpressing transgenic plants was most similar to that of MIM396 plants, suggesting OsGRF8 is a major mediator of OsmiR396 in grain size regulation. A miRNA microarray analysis revealed changes to the expression of many miRNAs, including OsmiR408, in the MIM396 plants. Analyses of gene expression patterns and functions indicated OsmiR408 is an embryo-specific miRNA that positively regulates grain size. Silencing OsmiR408 expression (miR408KO) using CRISPR technology resulted in small grains. Moreover, we revealed the direct regulatory effects of OsGRF8 on OsMIR408 expression. A genetic analysis further showed that the large-grain phenotype of MIM396 plants could be complemented by miR408KO. Also, several hormone signaling pathways might be involved in the OsmiR396/GRF-meditated grain size regulation. Our findings suggest that genetic regulatory networks comprising various miRNAs, such as OsmiR396 and OsmiR408, may be crucial for controlling rice grain size. Furthermore, the OsmiR396/GRF module may be important for breeding new high-yielding rice varieties.

scholarly journals Joint profiling of gene expression and chromatin accessibility of amphioxus development at single cell resolution

2021 ◽  
Author(s):  
Pengcheng Ma ◽  
Xingyan Liu ◽  
Huimin Liu ◽  
Zaoxu Xu ◽  
Xiangning Ding ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cell Fate ◽  
Regulatory Networks ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Genetic Regulatory Networks ◽  
Public Access ◽  
Origin And Evolution ◽  
Key Species

Abstract Vertebrate evolution was accompanied with two rounds of whole genome duplication followed by functional divergence in terms of regulatory circuits and gene expression patterns. As a basal and slow-evolving chordate species, amphioxus is an ideal paradigm for exploring the origin and evolution of vertebrates. Single cell sequencing has been widely employed to construct the developmental cell atlas of several key species of vertebrates (human, mouse, zebrafish and frog) and tunicate (sea squirts). Here, we performed single-nucleus RNA sequencing (snRNA-seq) and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) for different stages of amphioxus (covering embryogenesis and adult tissues). With the datasets generated we constructed the developmental tree for amphioxus cell fate commitment and lineage specification, and revealed the underlying key regulators and genetic regulatory networks. The generated data were integrated into an online platform, AmphioxusAtlas, for public access at http://120.79.46.200:81/AmphioxusAtlas.

scholarly journals Mechanical and Processing Properties of Rice Grains

2020 ◽  
Vol 12 (2) ◽  
pp. 552 ◽  
Author(s):  
Weronika Kruszelnicka ◽  
Andrzej Marczuk ◽  
Robert Kasner ◽  
Patrycja Bałdowska-Witos ◽  
Katarzyna Piotrowska ◽  
...  
Keyword(s):  
Grain Size ◽  
Oryza Sativa ◽  
Negative Correlation ◽  
Oryza Sativa L ◽  
Strength Properties ◽  
Rice Grain ◽  
Static Compression ◽  
Positive Correlation ◽  
Rice Grains ◽  
Processing Properties

Strength properties of grains have a significant impact on the energy demand of grinding mills. This paper presents the results of tests of strength and energy needed the for destruction of rice grains. The research aim was to experimentally determine mechanical and processing properties of the rice grains. The research problem was formulated in the form of questions: (1) what force and energy are needed to induce a rupture of rice grain of the Oryza sativa L. of long-grain variety? (2) what is the relationship between grain size and strength parameters and the energy of grinding rice grain of the species Oryza sativa L. long-grain variety? In order to find the answer to the problems posed, a static compression test of rice grains was done. The results indicate that the average forces needed to crush rice grain are 174.99 kg m·s−2, and the average energy is 28.03 mJ. There was no statistically significant relationship between the grain volume calculated based on the volumetric mass density Vρ and the crushing energy, nor between the volume Vρ and other strength properties of rice grains. In the case of Vs, a low negative correlation between strength σmin and a low positive correlation between the power inducing the first crack were found for the grain size related volume. A low negative correlation between the grain thickness a3, stresses σmin and work WFmax was found as well as a low positive correlation between thickness a3 and the force inducing the first crack Fmin.

ON CONSTRUCTION OF STOCHASTIC GENETIC NETWORKS BASED ON GENE EXPRESSION SEQUENCES

2005 ◽  
Vol 15 (04) ◽  
pp. 297-310 ◽  
Author(s):  
WAI-KI CHING ◽  
MICHAEL M. NG ◽  
ERIC S. FUNG ◽  
TATSUYA AKUTSU
Keyword(s):  
Gene Expression ◽  
Regulatory Networks ◽  
Expression Patterns ◽  
Boolean Networks ◽  
Genetic Regulatory Networks ◽  
Efficient Estimation ◽  
Estimation Methods ◽  
Series Data ◽  
Model Parameters ◽  
Proposed Model

Reconstruction of genetic regulatory networks from time series data of gene expression patterns is an important research topic in bioinformatics. Probabilistic Boolean Networks (PBNs) have been proposed as an effective model for gene regulatory networks. PBNs are able to cope with uncertainty, corporate rule-based dependencies between genes and discover the sensitivity of genes in their interactions with other genes. However, PBNs are unlikely to use directly in practice because of huge amount of computational cost for obtaining predictors and their corresponding probabilities. In this paper, we propose a multivariate Markov model for approximating PBNs and describing the dynamics of a genetic network for gene expression sequences. The main contribution of the new model is to preserve the strength of PBNs and reduce the complexity of the networks. The number of parameters of our proposed model is O(n2) where n is the number of genes involved. We also develop efficient estimation methods for solving the model parameters. Numerical examples on synthetic data sets and practical yeast data sequences are given to demonstrate the effectiveness of the proposed model.

scholarly journals Effect of tidal submergence on potassium nutrition and yield of rice (Oryza sativa L.)

2012 ◽  
Vol 37 (3) ◽  
pp. 433-439
Author(s):  
MA Haque
Keyword(s):  
Ground Water ◽  
Field Experiments ◽  
Oryza Sativa L ◽  
Growth Yield ◽  
Rice Grain ◽  
K Uptake ◽  
Rice Varieties ◽  
Potassium Nutrition ◽  
Tidal Water ◽  
Absolute Control

Field experiments were conducted at Patuakhali Science and Technology University research farm during 2009 T. Aman season to investigate the effect of tidal submergence on potassium nutrition and yield of rice. The experiment included two levels of irrigation water source- i) tidal water and ii) ground water, and three levels of fertilizers- i) absolute control (no fertilizer), ii) NP (K omission), and iii) NPK (K addition). The rice varieties were BR23 (HYV) and Lalmota (traditional variety). A general increase in growth, yield and yield contributing parameters were found due to irrigation with tidal water. Tidal water contributed about 19% (BR23) and 11% (Lalmota) higher grain yield in Aman season 2009 compared to that grown with ground water. Potassium contents of rice grain and straw were always higher when plants are irrigated with tidal water. In general, tidal submergence increased K uptake of rice. The K uptake by BR23 under tidal water was about 47, 43 and 8 kg/ha more than those recorded with ground water irrigation under absolute control, K omission and K addition treatments, respectively whereas it was 31, 21, and 68 kg/ha, in Lalmota. The results indicated that whether fertilizers were applied or not plants absorb considerable amount of K from tidal water. Bangladesh J. Agril. Res. 37(3): 433-439, September 2012 DOI: http://dx.doi.org/10.3329/bjar.v37i3.12086

scholarly journals Variability in Nutraceutical Lipid Content of Selected Rice (Oryza sativa L. spp. indica) Germplasms

Agronomy ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 823 ◽  
Author(s):  
Bhornchai Harakotr ◽  
Kasidid Prompoh ◽  
Supakorn Boonyuen ◽  
Bhalang Suriharn ◽  
Kamol Lertrat
Keyword(s):  
Oryza Sativa ◽  
Lipid Content ◽  
Oryza Sativa L ◽  
Indica Rice ◽  
Block Design ◽  
Added Value ◽  
Rice Varieties ◽  
Breeding Programs ◽  
Lipid Contents ◽  
Lipid Compounds

Rice (Oryza sativa L.) contains many high-value nutritional compounds, including nutraceutical lipid compounds that offer health benefits. An understanding of the genetic variability in the lipid contents of different rice germplasms is necessary to support breeding programs. The goals of this study were: i) to investigate varietal differences in levels of the nutraceutical lipid α-tocopherol, γ-oryzanol, campesterol, β-sitosterol, octacosanol, and squalene and ii) to identify clusters of rice germplasms based on their lipid contents. Eighty-three indica rice subspecies were evaluated using a randomized complete block design with three replications. Research was conducted in Thailand during the 2016 rice-growing season. Significant differences were found among genotypes across all traits. The largest variation was found for β-sitosterol, followed by campesterol, octacosanol, and α-tocopherol. Variation in squalene content was small. Four principal components were found that accounted for 93.47% of overall variability. β-sitosterol, campesterol, and squalene were the principal discriminatory constituents. No significant correlation was found between color parameters and levels of these compounds, suggesting that former are of little use as an indirect marker for selection of fat-soluble nutraceuticals. Cluster analysis sorted the germplasm into nine clusters, based on their nutraceutical lipid content. TU-010, TU-027, TU-093, and TU-244 genotypes had the highest levels, making them a potentially useful genetic resource in breeding programs for nutraceutically-improved rice. The findings of this study can support the introduction of novel rice varieties with high added-value bioactive properties.

scholarly journals Identification and Validation a Major QTL from “Sea Rice 86” Seedlings Conferred Salt Tolerance

Agronomy ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 410 ◽  
Author(s):  
Fengling Wu ◽  
Jun Yang ◽  
Diqiu Yu ◽  
Peng Xu
Keyword(s):  
Salt Tolerance ◽  
Oryza Sativa L ◽  
Bulked Segregant Analysis ◽  
Indica Rice ◽  
Chromosome 1 ◽  
Saline Stress ◽  
Salt Tolerant ◽  
Rice Varieties ◽  
Target Region ◽  
High Salt Tolerance

Saline stress severely affects rice (Oryza sativa L.) growth and development and reduces crop yield. Therefore, developing salt-tolerant and high-yielding rice using quantitative trait loci (QTLs) and linkage markers is a priority for molecular breeding. Here, the indica rice Sea Rice 86 (SR86) seedlings showed higher tolerance than ordinary rice varieties in saline soil, and a dominant effect on salinity sensitivity was demonstrated by genetic analysis. We constructed bulked segregant analysis pools using F2 populations from parents Dianjingyou 1 as the recipient and SR86 as the donor. We identified a 2.78 Mb region on chromosome 1 as the candidate region. Using simple sequence repeat markers and substitution analysis, we mapped the target region within 5.49 cM in the vicinity of markers RM8904–RM493. We speculated that this QTL, named qST1.1, might contribute significantly to the salt tolerance of SR86. The high salt tolerance of introgression lines obtained by marker assistant selection (MAS) confirmed that the qST1.1 region was associated with salinity tolerance. This newly-discovered QTL will be helpful for the analysis of the salt-tolerant mechanism of rice and breeding high-quality rice varieties using MAS.

scholarly journals Agro-Morphological and Genetic Diversity Studies in Rice (Oryza Sativa L.) Germplasm Using Microsatellite Markers

2021 ◽  
Author(s):  
Shiraz Mehmood ◽  
Israr Ud Din ◽  
Izhar Ullah ◽  
Heba I. Mohamed ◽  
Abdul Basit ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Oryza Sativa L ◽  
Crop Improvement ◽  
Biodiversity Loss ◽  
Cadmium Content ◽  
Rice Varieties ◽  
Morphological Variations ◽  
Germplasm Collections ◽  
Rice Genotypes

Abstract Knowledge of the genetic diversity and population structure of germplasm collections is an important foundation for crop improvement. Rice production across a broad range of rice-growing environments results in a diverse array of local rice varieties. Many rice varieties have been lost as a result of biodiversity loss and are now grown in Pakistan. To protect the biodiversity of rice varieties, an experiment was carried out to check the genetic and morphological variations between 8 exotic and 7 local rice genotypes, using 5 different SSR markers, i.e, RM3, RM259, RM341, RM520, and RM11943. The analysis of morphological and quality traits of rice observed significant variation across genotypes. The results revealed that genotype Irri-Pak attained the highest plant height and primary branch plant-1, while genotype Mushkan produced a higher number of productive tillers and obtained a higher fertility factor (%). Similarly, the highest value for panicle length was observed for genotype Faker-e-Malakand, 1000-grains weight in genotype Calmochi, and maximum days to maturity was noticed in genotype Swati-2014. Moreover, the genotype Brio attained the highest value of stem diameter, while maximum seed length was noted in genotype Sug Dasi. The highest number of primary branches plant-1 in genotype Ibge-I and secondary branches plant-1 in genotype Calmochi were noticed. A higher concentration of sodium and potassium was observed for the genotype Marte, while the genotype Muskan attained the maximum content of copper. Moreover, the highest concentration of iron in genotype Originario, zinc in genotype JP-5, and cadmium content were noticed in genotype Ibge. Similarly, the dendrogram analysis for quantitative parameters showed three clusters at 74.13 % similarities. Whereas all the genotypes of European origin formed a separate cluster. A set of 5 SSR primers, covering four chromosomes, amplified a total of 14 alleles and showed 100% polymorphism with an average PIC value ranging from 0.39 to 0.91. The UPGMA cluster analysis separated the 15 rice genotypes into 3 main groups based on 32.5% similarities and the highest genetic distance (45.1%) was observed between two genotypes (Fakher-e-malakand and Musa), having different geographical origins. There was no genetic distance between genotype Marte and Brio, irrespective of having the same origin.

Geographic pattern of variation among Asian native rice cultivars (Oryza sativa L.) based on fifteen isozyme loci

Genome ◽  
1988 ◽  
Vol 30 (5) ◽  
pp. 782-792 ◽  
Author(s):  
J. C. Glaszmann
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Indian Subcontinent ◽  
Indica Rice ◽  
Japonica Rice ◽  
Geographic Pattern ◽  
Cultivated Rice ◽  
Rice Varieties ◽  
Himalayan Foothills

The geographic pattern of isozyme variation among rice varieties (Oryza sativa L.) in Asia is described based on an electrophoretic survey of 1688 accessions for 15 loci. The distribution patterns are strongly determined by the existence of several varietal groups that are characterized by contrasting multilocus types with dissimilar environmental and macrogeographic distributions. The two main groups correspond to the indica and japonica subspecies. Other types are frequently found in the Indian subcontinent, especially along the Himalayan foothills. These types are predominant in the Indus River basin. They are differentiated into four groups in the eastern part of the Himalayan foothills. There is variation within the groups. Non-random allele distributions are observed, such as regional clines and narrow localization of alleles. Diversity among indica rice is evenly distributed in whole tropical Asia. Variation among japonica rice shows the hilly part of continental Southeast Asia to be the region of highest genetic diversity and its probable area of origin. All this information provides a guide for further analysis aimed at elucidating the history of cultivated rice in Asia and, subsequently, in other continents.Key words: Asian rice, genetic diversity, isozymes, geographic distributions.

scholarly journals Nitrogen sources affected the biosynthesis of 2-acetyl-1-pyrroline, cooked rice elongation and amylose content in rice

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254182
Author(s):  
Pouwedeou Mouloumdema Potcho ◽  
Nnaemeka Emmanuel Okpala ◽  
Tchalla Korohou ◽  
Muhammad Imran ◽  
Nabieu Kamara ◽  
...  
Keyword(s):  
Grain Yield ◽  
Amylose Content ◽  
Indica Rice ◽  
Grain Weight ◽  
Rice Grain ◽  
Rice Varieties ◽  
Cooked Rice ◽  
N Sources ◽  
Significant Difference ◽  
1000 Grain Weight

Many studies have been carried out on N sources effect on fragrant rice; however, their impact on rice grain quality is largely unclear. In this study, we evaluated the effects of different types of N sources on rice growth, yield, 2-acetyl-1-pyrroline (2AP), amylose and cooked rice elongation. Two indica rice cultivars, Basmati 385 (B385), Xiangyaxiangzhan (XYXZ) and two japonica cultivars, Yunjingyou (YJY), Daohuaxiang (DHX) were grown in experimental pots with six replications under four N sources: Potassium nitrate (KNO3), ammonium bicarbonate (NH4HCO3), urea (H2NCONH2) and sodium nitrate (NaNO3) in 2019 and 2020 early seasons. Our results showed that N dynamics regulated the number of panicles, 1000-grain weight, grain yield, 2-acetyl-1-pyrroline, amylose and cooked rice elongation across all the four treatments. The NH4HCO3 treatment significantly increased the number of panicles and grain yield across the four rice varieties compared with KNO3, H2NCONH2 and NaNO3 N sources in both 2019 and 2020 early season, The KNO3 treatment significantly showed higher 1000-grain weight in B-385, YJY, XYXZ and DHX compared to other N sources. Compared with other N sources treatment, the NH4HCO3 treatments significantly increased the 2AP contents in heading stage leaves, matured leaves and grains of B-385, YJY, XYXZ and DHX respectively. Cooked rice elongation percentage also showed significant difference in all treatments studied with KNO3 recorded the highest across the four varieties. Analysis of major enzymes and compounds such as P5C, P5CS, PDH, Pyrroline, proline and Methylglyoxal showed remarkable differences in each cultivar at heading and maturity stages with higher activity in NH4HCO3 and H2NCONH2 treatments. Similarly, in all treatments, we also observed significant increase in amylose content percentage, with NH4HCO3 having greater percentage of amylose.

scholarly journals Improving the Rice Photosynthetic Efficiency and Yield by Editing OsHXK1 via CRISPR/Cas9 System

2021 ◽  
Vol 22 (17) ◽  
pp. 9554
Author(s):  
Shaoyan Zheng ◽  
Chanjuan Ye ◽  
Jingqin Lu ◽  
Jiamin Liufu ◽  
Lin Lin ◽  
...  
Keyword(s):  
Photosynthetic Efficiency ◽  
Gene Editing ◽  
Molecular Breeding ◽  
Oryza Sativa L ◽  
Indica Rice ◽  
Rice Breeding ◽  
Phenotypic Analysis ◽  
Rice Varieties ◽  
Crop Species ◽  
Rice Yields

Rice (Oryza sativa L.) is an important food crop species in China. Cultivating high-yielding rice varieties that have a high photosynthetic efficiency is an important goal of rice breeding in China. In recent years, due to the continual innovation of molecular breeding methods, many excellent genes have been applied in rice breeding, which is highly important for increasing rice yields. In this paper, the hexokinase gene OsHXK1 was knocked out via the CRISPR/Cas9 gene-editing method in the indica rice varieties Huanghuazhan, Meixiangzhan, and Wushansimiao, and OsHXK1-CRISPR/Cas9 lines were obtained. According to the results of a phenotypic analysis and agronomic trait statistics, the OsHXK1-CRISPR/Cas9 plants presented increased light saturation points, stomatal conductance, light tolerance, photosynthetic products, and rice yields. Moreover, transcriptome analysis showed that the expression of photosynthesis-related genes significantly increased. Taken together, our results revealed that knocking out OsHXK1 via the CRISPR/Cas9 gene-editing method could effectively lead to the cultivation of high-photosynthetic efficiency and high-yielding rice varieties. They also revealed the important roles of OsHXK1 in the regulation of rice yield and photosynthesis.

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