Rapid improvement of grain appearance in three-line hybrid rice via CRISPR/Cas9 editing of grain size genes.

Genetic editing of grain size genes quickly improves three-line hybrid rice parents to increase the appearance quality and yield of hybrid rice. Grain size affects rice yield and quality. In this study, we used CRISPR/Cas9 to edit the grain size gene GW8 in the maintainer line WaitaiB (WTB) and restorer line Guanghui998 (GH998).

Functional characterization of D-type cyclins involved in cell division in rice.

Background: D-type cyclins (CYCD) regulate the cell cycle G/S transition and are thus closely involved in cell cycle progression. However, little is known about their functions in rice.

Results: We identified 14 CYCD genes in the rice genome and confirmed the presence of characteristic cyclin domains in each.

Stacking Multiple Genes Improves Resistance to , , and in Transgenic Rice.

The ability of various pests and diseases to adapt to a single plant resistance gene over time leads to loss of resistance in transgenic rice. Therefore, introduction of different pest and disease resistance genes is critical for successful cultivation of transgenic rice strains with broad-spectrum resistance to multiple pathogens. Here, we produced resistance rice lines with multiple, stacked resistance genes by stacking breeding and comprehensively evaluated their resistance to (striped rice stemborer), (rice blast), and (brown planthopper) in a pesticide-free environment.

Analysis of the Genetic Stability of Insect and Herbicide Resistance Genes in Transgenic Rice Lines: A Laboratory and Field Experiment.

A lack of stability in the expression of Bacillus thuringiensis genes (CRY) and the dialaninophosphate resistance gene (BAR) in transgenic rice plants can lead to the loss of important characters. The genetic stability of transgenic expression in high-generation lines is thus critically important for ensuring the success of molecular breeding efforts. Here, we studied the genetic stability of resistance to insect pests and herbicides in transgenic rice lines at the molecular and phenotypic levels in a pesticide-free environment.

Comparison of the Phenotypic Performance, Molecular Diversity, and Proteomics in Transgenic Rice.

The extent of molecular diversity and differentially expressed proteins (DEPs) in transgenic lines provide valuable information to understand the phenotypic performance of transgenic crops compared with their parents. Here, we compared the differences in the phenotypic variation of twelve agronomic and end-use quality traits, the extent of microsatellite diversity, and DEPs of a recurrent parent line with three transgenic rice restorer lines carrying either gene on chromosome 11 or gene on chromosome 12 or both genes. The three transgenic lines had significantly smaller stem borer infestation than the recurrent parent without showing significant differences among most agronomic traits, yield components, and end-use quality traits.

A base substitution in OsphyC disturbs its Interaction with OsphyB and affects flowering time and chlorophyll synthesis in rice.

Background: Phytochromes are important photoreceptors in plants, and play essential roles in photomorphogenesis. The functions of PhyA and PhyB in plants have been fully analyzed, while those of PhyC in plant are not well understood.

Results: A rice mutant, late heading date 3 (lhd3), was characterized, and the gene LHD3 was identified with a map-based cloning strategy.

Rice microtubule-associated protein OsMAP65-3.1, but not OsMAP65-3.2, plays a critical role in phragmoplast microtubule organization in cytokinesis.

In plants, MAP65 preferentially cross-links the anti-parallel microtubules (MTs) and plays an important role for cytokinesis. However, the functions of MAP65 isoforms in rice ( L) are largely unknown. Here, we identified two MAP65-3 homologs in rice, OsMAP65-3.

The genetic editing of via CRISPR/Cas9 accelerates the breeding of three-line hybrid rice with superior yield and grain quality.

Unlabelled: Grain size is one of the major traits that determine rice grain yield and quality. The gene is the first major quantitative trait locus (QTL) that was identified in regulating rice grain length and weight. It was reported that the allele with a mutation in the organ size regulation (OSR) domain of the protein produced longer grains.

Detection of QTLs for panicle-related traits using an × recombinant inbred line population in rice.

Background: The panicle is the most important organ in rice, and all the panicle-related traits are correlated with rice grain yield. Understanding the underlying genetic mechanisms controlling panicle development is very important for improving rice production.

Methods: Nine panicle-related traits including heading date, panicle length, number of primary branches, number of secondary branches, number of grains per panicle, number of panicles per plant, number of filled grains per plant, seed-setting rate, and grain yield per plant were investigated.

Fine Mapping of a Novel Major Quantitative Trait Locus, , That Controls Panicle Apical Abortion in Rice.

The panicle apical abortion (PAA) causes severe yield losses in rice production, but details about its development and molecular basis remain elusive. Here, we detected PAA quantitative trait loci (QTLs) in three environments using a set of chromosome segment substitution lines (CSSLs) that was constructed with Changhui121 as the recurrent parent and Koshihikari as the donor parent. First, we identified a novel major effector quantitative trait locus, , and selected a severe PAA line, CSSL176, which had the highest PAA rate among CSSLs having Koshihikari segments at this locus.

qTGW12a, a naturally varying QTL, regulates grain weight in rice.

A stable QTL associated with rice grain type with a large effect value was found in multiple environments, and its candidate genes were verified by genetic transformation. Rice (Oryza sativa L.) grain size is critical to both yield and appearance quality.

Combined proteomics, metabolomics and physiological analyses of rice growth and grain yield with heavy nitrogen application before and after drought.

Background: Nitrogen application can effectively mitigate the damage to crop growth and yield caused by drought. However, the efficiency of heavy nitrogen application before drought (NBD) and heavy nitrogen application after drought (NAD) to regulate rice response to drought stress remains controversial. In this study, we profiled physiology, proteomics and metabolomics in rice variety Wufengyou 286 of two nitrogen management modes (NBD and NAD) to investigate their yield formation and the mechanism of nitrogen regulation for drought resistance.

Ribosome profiling reveals the effects of nitrogen application translational regulation of yield recovery after abrupt drought-flood alternation in rice.

Abrupt drought-flood alternation is a frequent meteorological disaster during the summer in Southern China. The study of physiological and translation mechanisms of rice yield recovery after abrupt drought-flood alternation has great potential benefits in field production. Our results showed that yield recovery upon nitrogen (N) application after abrupt drought-flood alternation was due to the increase in effective panicle numbers per plant.

Is Involved in Cuticular Wax Biosynthesis and Affects Leaf Senescence in Rice.

Leaf senescence is one of the most common factors that affects the growth and yield of rice. Although numerous genes affecting leaf senescence have been identified, few involved in cuticular wax synthesis have been described for rice premature leaf senescence. Here, we cloned and characterized in rice (), which encodes a putative 3-oxoacyl-reductase in the fatty acid biosynthetic pathway.

Comprehensive metabolomic, proteomic and physiological analyses of grain yield reduction in rice under abrupt drought-flood alternation stress.

Abrupt drought-flood alternation (T1) is a meteorological disaster that frequently occurs during summer in southern China and the Yangtze river basin, often causing a significant loss of rice production. In this study, the response mechanism of yield decline under abrupt drought-flood alternation stress at the panicle differentiation stage was analyzed by looking at the metabolome, proteome as well as yield and physiological and biochemical indexes. The results showed that drought and flood stress caused a decrease in the yield of rice at the panicle differentiation stage, and abrupt drought-flood alternation stress created a synergistic effect for the reduction of yield.

Genetic analysis for the grain number heterosis of a super-hybrid rice WFYT025 combination using RNA-Seq.

Background: Despite the great contributions of utilizing heterosis to crop productivity worldwide, the molecular mechanism of heterosis remains largely unexplored. Thus, the present research is focused on the grain number heterosis of a widely used late-cropping indica super hybrid rice combination in China using a high-throughput next-generation RNA-seq strategy.

Results: Here, we obtained 872 million clean reads, and at least one read could maps 27,917 transcripts out of 35,679 annotations.

Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress.

Background: Long non-coding RNAs (lncRNAs) have been found to play a vital role in several gene regulatory networks involved in the various biological processes in plants related to stress response. However, systematic analyses of lncRNAs expressed in rice Cadmium (Cd) stress are seldom studied. Thus, we presented the characterization and expression of lncRNAs in rice root development at an early stage in response to Cd stress.

Mapping QTL for Seed Germinability under Low Temperature Using a New High-Density Genetic Map of Rice.

Mapping major quantitative trait loci (QTL) responsible for rice seed germinability under low temperature (GULT) can provide valuable genetic source for improving cold tolerance in rice breeding. In this study, 124 rice backcross recombinant inbred lines (BRILs) derived from a cross cv. Changhui 891 and cv.

Genome-wide identification and phylogenetic analysis of the chalcone synthase gene family in rice.

The enzymes of the chalcone synthase family are also known as type III polyketide synthases (PKS), and produce a series of secondary metabolites in bacteria, fungi and plants. In a number of plants, genes encoding PKS comprise a large multigene family. Currently, detailed reports on rice (Oryza sativa) PKS (OsPKS) family genes and tissue expression profiling are limited.

Using RNA-seq to Profile Gene Expression of Spikelet Development in Response to Temperature and Nitrogen during Meiosis in Rice (Oryza sativa L.).

Rice reproductive development is sensitive to high temperature and soil nitrogen supply, both of which are predicted to be increased threats to rice crop yield. Rice spikelet development is a critical process that determines yield, yet little is known about the transcriptional regulation of rice spikelet development in response to the combination of heat stress and low nitrogen availability. Here, we profiled gene expression of rice spikelet development during meiosis under heat stress and different nitrogen levels using RNA-seq.

RNA-seq reveals differentially expressed genes of rice (Oryza sativa) spikelet in response to temperature interacting with nitrogen at meiosis stage.

Background: Rice (Oryza sativa) is one of the most important cereal crops, providing food for more than half of the world's population. However, grain yields are challenged by various abiotic stresses such as drought, fertilizer, heat, and their interaction. Rice at reproductive stage is much more sensitive to environmental temperatures, and little is known about molecular mechanisms of rice spikelet in response to high temperature interacting with nitrogen (N).

Premature Termination Codons Are Recognized in the Nucleus in A Reading-Frame Dependent Manner.

mRNAs containing premature termination codons (PTCs) are known to be degraded via nonsense-mediated mRNA decay (NMD). Unexpectedly, we found that mRNAs containing any type of PTC (UAA, UAG, UGA) are detained in the nucleus whereas their wild-type counterparts are rapidly exported. This retention is strictly reading-frame dependent.

QTL mapping and correlation analysis for 1000-grain weight and percentage of grains with chalkiness in rice.

The study of 1000-grain weight (TGW) and percentage of grains with chalkiness (PGWC) is very important in rice. In this study, a set of introgression lines (ILs), derived from Sasanishiki/Habataki with Sasanishiki as the recurrent parent, were used to detect correlations and quantitative trait loci (QTL) on TGW and PGWC in two different environments. Phenotypic correlation analysis showed that there was no significant correlation between TGW and PGWC in both environments, which indicated that the linkage of TGW and PGWC traits could be broken via suitable population.

[Low-phosphorus tolerance and related physiological mechanism of Xieqingzao B//Xieqingzao B/Dongxiang wild rice BC1F9 populations].

By the method of water culture, the low-phosphorus tolerance of 221 lines of Xieqingzao B//Xieqingzao B/Dongxiang wild rice BC1 F9 populations was indentified. The morphological indices including plant height, leaf age, yellow leaf number, and shoot dry mass as well as the physiological indices including MDA, soluble sugar, and shoot phosphorus content were measured, also, the phosphorus efficiency was calculated, and the correlations among the indices were analyzed. All the 221 lines had differences in the seven test indices, and the low-phosphorus tolerance lines under low-phosphorus stress had higher values of relative leaf age, relative plant height, relative shoot dry mass, and relative soluble sugar content, but lower values of relative yellow leaf number and relative malondialdehyde content.

Identification and characterization of a novel Waxy allele from a Yunnan rice landrace.

Low amylose content (AC) is a desirable trait for rice (Oryza sativa L.) cooking quality and is selected in soft rice breeding. To gain a better understanding of the molecular mechanism controlling AC formation, we screened 83 Yunnan rice landraces in China and identified a rice variety, Haopi, with low AC.