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1.
Epigenomic features of DNA G-quadruplexes and their roles in regulating rice gene transcription.
Feng, Y, Tao, S, Zhang, P, Sperti, FR, Liu, G, Cheng, X, Zhang, T, Yu, H, Wang, XE, Chen, C, et al
Plant physiology. 2022;(3):1632-1648
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Abstract
A DNA G-quadruplex (G4) is a non-canonical four-stranded nucleic acid structure involved in many biological processes in mammals. The current knowledge on plant DNA G4s, however, is limited; whether and how DNA G4s impact gene expression in plants is still largely unknown. Here, we applied a protocol referred to as BG4-DNA-IP-seq followed by a comprehensive characterization of DNA G4s in rice (Oryza sativa L.); we next integrated dG4s (experimentally detectable G4s) with existing omics data and found that dG4s exhibited differential DNA methylation between transposable element (TE) and non-TE genes. dG4 regions displayed genic-dependent enrichment of epigenomic signatures; finally, we showed that these sites displayed a positive association with expression of DNA G4-containing genes when located at promoters, and a negative association when located in the gene body, suggesting localization-dependent promotional/repressive roles of DNA G4s in regulating gene transcription. This study reveals interrelations between DNA G4s and epigenomic signatures, as well as implicates DNA G4s in modulating gene transcription in rice. Our study provides valuable resources for the functional characterization or bioengineering of some of key DNA G4s in rice.
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2.
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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3.
Epigenetic regulation of salinity stress responses in cereals.
Rashid, MM, Vaishnav, A, Verma, RK, Sharma, P, Suprasanna, P, Gaur, RK
Molecular biology reports. 2022;(1):761-772
Abstract
Cereals are important crops and are exposed to various types of environmental stresses that affect the overall growth and yield. Among the various abiotic stresses, salt stress is a major environmental factor that influences the genetic, physiological, and biochemical responses of cereal crops. Epigenetic regulation which includes DNA methylation, histone modification, and chromatin remodelling plays an important role in salt stress tolerance. Recent studies in rice genomics have highlighted that the epigenetic changes are heritable and therefore can be considered as molecular signatures. An epigenetic mechanism under salinity induces phenotypic responses involving modulations in gene expression. Association between histone modification and altered DNA methylation patterns and differential gene expression has been evidenced for salt sensitivity in rice and other cereal crops. In addition, epigenetics also creates stress memory that helps the plant to better combat future stress exposure. In the present review, we have discussed epigenetic influences in stress tolerance, adaptation, and evolution processes. Understanding the epigenetic regulation of salinity could help for designing salt-tolerant varieties leading to improved crop productivity.
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Combination treatment of bamboo shoot dietary fiber and dynamic high-pressure microfluidization on rice starch: Influence on physicochemical, structural, and in vitro digestion properties.
Wang, N, Wu, L, Huang, S, Zhang, Y, Zhang, F, Zheng, J
Food chemistry. 2021;:128724
Abstract
The physicochemical, structural properties and digestibility of rice starch treated by bamboo shoot dietary fiber (BSDF) combined with dynamic high-pressure microfluidization (DHPM) were investigated. Compared with starch modified by BSDF alone, the combination treatment decreased the pasting viscosity and viscoelasticity of starch. Furthermore, the pasting viscosity and viscoelasticity showed an increase from 50 to 100 MPa and then decreased after increasing the pressure to 150 and 200 MPa. The enthalpy of gelatinization and relative crystallinity of starch treated by BSDF and 100 MPa DHPM significantly increased by 17% and 63%, respectively. Scanning electron microscopy images demonstrated that flaky BSDF coated on starch granules to form a protective layer. As a result, the fractions of resistant starch increased and the starch hydrolysis extent and rate decreased under 100 MPa DHPM. This study highlights an innovative and promising strategy for improving the properties of starch and facilitating its utilization.
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Investigating the cell and developmental biology of plant infection by the rice blast fungus Magnaporthe oryzae.
Eseola, AB, Ryder, LS, Osés-Ruiz, M, Findlay, K, Yan, X, Cruz-Mireles, N, Molinari, C, Garduño-Rosales, M, Talbot, NJ
Fungal genetics and biology : FG & B. 2021;:103562
Abstract
Magnaporthe oryzae is the causal agent of rice blast disease, the most widespread and serious disease of cultivated rice. Live cell imaging and quantitative 4D image analysis have provided new insight into the mechanisms by which the fungus infects host cells and spreads rapidly in plant tissue. In this video review article, we apply live cell imaging approaches to understanding the cell and developmental biology of rice blast disease. To gain entry to host plants, M. oryzae develops a specialised infection structure called an appressorium, a unicellular dome-shaped cell which generates enormous turgor, translated into mechanical force to rupture the leaf cuticle. Appressorium development is induced by perception of the hydrophobic leaf surface and nutrient deprivation. Cargo-independent autophagy in the three-celled conidium, controlled by cell cycle regulation, is essential for appressorium morphogenesis. Appressorium maturation involves turgor generation and melanin pigment deposition in the appressorial cell wall. Once a threshold of turgor has been reached, this triggers re-polarisation which requires regulated generation of reactive oxygen species, to facilitate septin GTPase-dependent cytoskeletal re-organisation and re-polarisation of the appressorium to form a narrow, rigid penetration peg. Infection of host tissue requires a further morphogenetic transition to a pseudohyphal-type of growth within colonised rice cells. At the same time the fungus secretes an arsenal of effector proteins to suppress plant immunity. Many effectors are secreted into host cells directly, which involves a specific secretory pathway and a specialised structure called the biotrophic interfacial complex. Cell-to-cell spread of the fungus then requires development of a specialised structure, the transpressorium, that is used to traverse pit field sites, allowing the fungus to maintain host cell membrane integrity as new living plant cells are invaded. Thereafter, the fungus rapidly moves through plant tissue and host cells begin to die, as the fungus switches to necrotrophic growth and disease symptoms develop. These morphogenetic transitions are reviewed in the context of live cell imaging studies.
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6.
Base editing in rice: current progress, advances, limitations, and future perspectives.
Yarra, R, Sahoo, L
Plant cell reports. 2021;(4):595-604
Abstract
Base editing is one of the promising genome editing tools for generating single-nucleotide changes in rice genome. Rice (Oryza sativa L.) is an important staple food crop, feeding half of the population around the globe. Developing new rice varieties with desirable agronomic traits is necessary for sustaining global food security. The use of genome editing technologies for developing rice varieties is pre-requisite in the present scenario. Among the genome editing technologies developed for rice crop improvement, base editing technology has emerged as an efficient and reliable tool for precise genome editing in rice plants. Base editing technology utilizes either adenosine or cytidine base editor for precise editing at the target region. A base editor (adenosine or cytidine) is a fusion of catalytically inactive CRISPR/Cas9 domain and adenosine or cytidine deaminase domain. In this review, authors have discussed the different adenine and cytosine base editors developed so far for precise genome editing of rice via base editing technology. We address the current progress, advances, limitations, as well as future perspectives of the base editing technology for rice crop improvement.
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In vitro digestion and structural properties of rice starch modified by high methoxyl pectin and dynamic high-pressure microfluidization.
Zheng, J, Wang, N, Huang, S, Kan, J, Zhang, F
Carbohydrate polymers. 2021;:118649
Abstract
The rheological, structural properties and in vitro digestibility of starch with high methoxyl pectin (HMP) and further modified by dynamic high-pressure microfluidization (DHPM) were investigated. The viscosity and elasticity increased on addition of HMP and were more pronouncedly affected by 10% HMP. However, after DHPM treatment, the viscosity and elasticity decreased with increasing DHPM pressure. After 100 MPa DHPM treatment, the ordered and crystalline structures were further increased compared with starch-HMP mixtures. A compact and dense surface of starch paste was formed under 100 MPa DHPM and 10% HMP treatment, thus significantly slowing down the digestibility. In contrast, the crystalline and semicrystalline structure of starch were disrupted by intense shear force under 200 MPa DHPM. This study provides theoretical information regarding starch-HMP interaction and improves their functional and physicochemical properties through a promising strategy for better applications in food formulation.
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8.
Arms race between rice and viruses: a review of viral and host factors.
Zhao, S, Wu, Y, Wu, J
Current opinion in virology. 2021;:38-44
Abstract
Much is known about the molecular interactions between positive-strand RNA viruses and dicotyledon plants. However, many important viral pathogens of the monocotyledon rice crop contain negative-strand or double-strand RNA genomes. Recent studies have shown that virus-derived small-interfering RNAs (siRNAs), host microRNAs and phytohormones regulate antiviral responses in rice plants and that rice-infecting RNA viruses encode a diverse repertoire of multifunctional proteins with counter-defensive activities. Moreover, the interactions between viral virulence proteins and host susceptibility factors also shape the virus-rice arms race. This review will focus on these recent advances and discuss strategies and challenges in the translation of discoveries made on molecular virus-rice interactions into practical virus control measures.
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9.
Application of γ-aminobutyric acid under low light conditions: Effects on yield, aroma, element status, and physiological attributes of fragrant rice.
Xie, W, Li, Y, Li, Y, Ma, L, Ashraf, U, Tang, X, Pan, S, Tian, H, Mo, Z
Ecotoxicology and environmental safety. 2021;:111941
Abstract
Cloudy weather with low light is more common during rice growing season of South China which often leads reduced yield and aroma formations in fragrant rice. However, exogenous γ-aminobutyric acid (GABA) application could enhance the 2-acetyl-1-pyrroline (2AP) accumulations and yield of fragrant rice under low light conditions. Field and pot experiments were conducted with three fragrant rice cultivars i.e., Basmati and Yuxiangyouzhan (indica), and Yungengyou 14 (japonica) that were grown under three different treatments i.e., normal light + GABA 0 mg L-1 (CK), low light + GABA 0 mg L-1 (T1), and low light + GABA 250 mg L-1 (T2). The results revealed that the grain 2AP contents were increased by 14.67-34.83% and up to 29.34% under T1 and T2 treatments in pot and field experiments, respectively, as compared with CK. The T1 and T2 treatments improved aroma owing to regulation in the accumulation of micronutrients i.e., Na, Mn, and Fe and enzyme activities involved in 2AP biosynthesis. The grain yield was substantially reduced in T1 as compared with T2 treatment for all rice cultivars. On the other hand, GABA application improved the grain yield under low light conditions by regulating the plant growth, and related physiological and biochemical attributes in all rice cultivars. Thus, GABA could balance low light-induced 2AP content and grain yield by modulating morphological and yield related attributes as well as physio-biochemical responses of fragrant rice.
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10.
Gene Mapping, Cloning and Association Analysis for Salt Tolerance in Rice.
Fan, X, Jiang, H, Meng, L, Chen, J
International journal of molecular sciences. 2021;(21)
Abstract
Soil salinization caused by the accumulation of sodium can decrease rice yield and quality. Identification of rice salt tolerance genes and their molecular mechanisms could help breeders genetically improve salt tolerance. We studied QTL mapping of populations for rice salt tolerance, period and method of salt tolerance identification, salt tolerance evaluation parameters, identification of salt tolerance QTLs, and fine-mapping and map cloning of salt tolerance QTLs. We discuss our findings as they relate to other genetic studies of salt tolerance association.