Integrated transcriptomic and metabolomic analysis provides insight into the pollen development of CMS-D1 rice.

Background: Cytoplasmic male sterility (CMS) has greatly improved the utilization of heterosis in crops due to the absence of functional male gametophyte. The newly developed sporophytic D1 type CMS (CMS-D1) rice exhibits unique characteristics compared to the well-known sporophytic CMS-WA line, making it a valuable resource for rice breeding.

Results: In this research, a novel CMS-D1 line named Xingye A (XYA) was established, characterized by small, transparent, and shriveled anthers.

DNAL7, a new allele of NAL11, has major pleiotropic effects on rice architecture.

dnal7, a novel allelic variant of the OsHSP40, affects rice plant architecture and grain yield by coordinating auxins, cytokinins, and gibberellic acids. Plant height and leaf morphology are the most important traits of the ideal plant architecture (IPA), and discovering related genes is critical for breeding high-yield rice. Here, a dwarf and narrow leaf 7 (dnal7) mutant was identified from a γ-ray treated mutant population, which exhibits pleiotropic effects, including dwarfing, narrow leaves, small seeds, and low grain yield per plant compared to the wild type (WT).

OsCBL1 modulates rice nitrogen use efficiency via negative regulation of OsNRT2.2 by OsCCA1.

Background: For cereal crop breeding, it is meaningful to improve utilization efficiency (NUE) under low nitrogen (LN) levels while maintaining crop yield. OsCBL1-knockdown (OsCBL1-KD) plants exhibited increased nitrogen accumulation and NUE in the field of low N level.

Results: OsCBL1-knockdown (OsCBL1-KD) in rice increased the expression of a nitrate transporter gene OsNRT2.

Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome.

Background: The assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions.

Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing.

Oryza sativa ssp. javanica rice varieties exhibit a wide variation in the phenotypes of several important agronomic traits, including grain quality, grain shape, plant architecture, disease resistance, and high adaption to an unfavorable environment, indicating a great potential for rice improvement. DNA molecular markers are basic and critical tools in genetic analysis and gene mining.

Whole Genome Resequencing of 20 Accessions of Rice Landraces Reveals Javanica Genomic Structure Variation and Allelic Genotypes of a Grain Weight Gene TGW2.

The landraces preserved by indigenous worldwide exhibited larger variation in the phenotypes and adaption to different environments, which suggests that they comprise rich resources and can be served as a gene pool for rice improvement. Despite extensive studies on cultivated rice, the variations and relationships between landraces and modern cultivated rice remain unclear. In this study, a total of 20 varieties that include 10 javanica collected from different countries worldwide and 10 indica from China were genotyped and yielded a sum of 99.

Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication.

Microbial communities from rhizosphere (rhizomicrobiomes) have been significantly impacted by domestication as evidenced by a comparison of the rhizomicrobiomes of wild and related cultivated rice accessions. While there have been many published studies focusing on the structure of the rhizomicrobiome, studies comparing the functional traits of the microbial communities in the rhizospheres of wild rice and cultivated rice accessions are not yet available. In this study, we used metagenomic data from experimental rice plots to analyze the potential functional traits of the microbial communities in the rhizospheres of wild rice accessions originated from Africa and Asia in comparison with their related cultivated rice accessions.

Strategies and Structure Feature of the Aboveground and Belowground Microbial Community Respond to Drought in Wild Rice (Oryza longistaminata).

Background: Drought is global environmental stress that limits crop yields. Plant-associated microbiomes play a crucial role in determining plant fitness in response to drought, yet the fundamental mechanisms for maintaining microbial community stability under drought disturbances in wild rice are poorly understood. We make explicit comparisons of leaf, stem, root and rhizosphere microbiomes from the drought-tolerant wild rice (Oryza longistaminata) in response to drought stress.

Comparison of wild rice (Oryza longistaminata) tissues identifies rhizome-specific bacterial and archaeal endophytic microbiomes communities and network structures.

Compared with root-associated habitats, little is known about the role of microbiota inside other rice organs, especially the rhizome of perennial wild rice, and this information may be of importance for agriculture. Oryza longistaminata is perennial wild rice with various agronomically valuable traits, including large biomass on poor soils, high nitrogen use efficiency, and resistance to insect pests and disease. Here, we compared the endophytic bacterial and archaeal communities and network structures of the rhizome to other compartments of O.

Effects of external Mn activities on OsNRAMP5 expression level and Cd accumulation in indica rice.

Manganese (Mn) transporter OsNRAMP5 was widely reported to regulate cadmium (Cd) uptake in rice. However, the relationship between OsNRAMP5 expression level and Cd accumulation, impacts of external ion activities on OsNRAMP5 expression level and Cd accumulation are still unclear. Investigations of the relationship between OsNRAMP5 expression level and Cd accumulation in three indica rice genotypes were conducted under various external Mn activities ranging from Mn deficiency to toxicity in EGTA-buffered nutrient solution.

A -3 Fatty Acid Desaturase Gene, Enhances Cold Tolerance and Seed Germination Rate under Low Temperature in Rice.

Low temperature is an environmental stress factor that is always been applied in research on improving crop growth, productivity, and quality of crops. Polyunsaturated fatty acids (PUFAs) play an important role in cold tolerance, so its genetic manipulation of the PUFA contents in crops has led to the modification of cold sensitivity. In this study, we over-expressed an fatty acid desaturase from () drove by a maize ubiquitin promoter in rice.

Mechanisms and uncertainties of Zn supply on regulating rice Cd uptake.

Application of Zinc (Zn) is considered an effective measure to reduce Cadmium (Cd) uptake and toxicity in Cd-contaminated soils for many plant species. However, interaction between Zn and Cd in rice plant is complex and uncertain. In this study, four indica rice cultivars were selected to evaluate the effect of Zn exposure in an EGTA-buffered nutrient solution under varying Zn activities and a field level of Cd activity to characterize the interaction between Zn and Cd in rice.

Over-expression of a protein disulfide isomerase gene from Methanothermobacter thermautotrophicus, enhances heat stress tolerance in rice.

High temperature (HT) stress is a major environmental stress that limits agricultural production worldwide. Discovery and application of genes promoting high temperature tolerance is essential to enhance crop tolerance to heat stress. Proteins associated with chaperone and protein folding plays an important role in the high temperature stress response of plants.

The E3 Ubiquitin Ligase HAF1 Modulates Circadian Accumulation of EARLY FLOWERING3 to Control Heading Date in Rice under Long-Day Conditions.

The ubiquitin 26S proteasome system (UPS) is critical for enabling plants to alter their proteomes to integrate internal and external signals for the photoperiodic induction of flowering. We previously demonstrated that HAF1, a C3HC4 RING domain-containing E3 ubiquitin ligase, is essential to precisely modulate the timing of Heading Date1 accumulation and to ensure appropriate photoperiodic responses under short-day conditions in rice (). However, how HAF1 mediates flowering under long-day conditions remains unknown.

The chimeric mitochondrial gene orf182 causes non-pollen-type abortion in Dongxiang cytoplasmic male-sterile rice.

D1-cytoplasmic male sterility (CMS) rice is a sporophytic cytoplasmic male-sterile rice developed from Dongxiang wild rice that exhibits a no-pollen-grain phenotype. A mitochondrial chimeric gene (orf182) was detected by mitochondrial genome sequencing and a comparative analysis. Orf182 is composed of three recombinant fragments, the largest of which is homologous to Sorghum bicolor mitochondrial sequences.

Expression of a mitochondrial gene orfH79 from CMS-Honglian rice inhibits Escherichia coli growth via deficient oxygen consumption.

Cytoplasmic male sterility (CMS) has often been associated with abnormal mitochondrial open frames (ORF), orfH79 is a mitochondrial chimeric gene responsible for the CMS trait in Honglian (HL) rice. In this study, the weakly produced ORFH79 protein significantly inhibited the growth of E. coli in an oxygen culture, however, the growth of the transformants producing ORFH79 was indistinguishable from the control under anaerobic incubation conditions.

Regulation of ATRIP protein abundance by RAD9 in the DNA damage repair pathway.

Genotoxic stress activates checkpoint signaling pathways that activate the checkpoint kinases ATM and ATR, halt cell cycle progression, and promote DNA repair. A number of proteins act in concert with ATR to phosphorylate Chk1, including RAD17, the RAD9-RAD1-HUS1 complex, ATR/ATRIP and TopBp1. However, how these proteins involved act in concert with one another to propagate and maintain the checkpoint response is not well understood.

Overexpression of a Vesicle Trafficking Gene, OsRab7, enhances salt tolerance in rice.

High soils salinity is a main factor affecting agricultural production. Studying the function of salt-tolerance-related genes is essential to enhance crop tolerance to stress. Rab7 is a small GTP-binding protein that is distributed widely among eukaryotes.