Articles tagged with Rice Genomes
Researchers developed a strategy to predict multiple traits at once based on the whole genome, increasing predictive ability by 2-10 times. This method, called multi-trait genomic selection (MT-GS), combines genetic markers with known trait links for more accurate predictions, making it a promising tool for efficient and cost-effective...
A recent study has revealed that the diploidization process in plants can be both episodic and gradual, depending on the type of mutation. The researchers used population genomics to uncover a nuanced picture of this process, including gene fractionation, transposable element accumulation, and homoeologous expression bias.
A two-year study found that fluridone is effective in controlling Palmer pigweed in rice, but its use can cause injury to some cultivars. Rice farmers should apply the herbicide before the three-leaf stage and follow the label instructions to minimize risk.
Researchers at King Abdullah University of Science & Technology (KAUST) have discovered genes that can strengthen rice crops against environmental stresses such as heat, drought, and salinity. The study also identified a comprehensive framework for developing robust rice crops that can thrive in challenging environments.
A pangenome study has constructed an unprecedented map of wild and cultivated rice, decoding the genetic architecture and diversity of rice. The researchers found 3.87 billion base pairs of novel genetic sequences absent from the single acknowledged reference genome, as well as 69,531 genes spanning the pangenome.
The Phytovirome Focus Issue addresses fundamental and translational aspects of phytovirome science, highlighting the transformative role of high-throughput sequencing technologies. Researchers discovered a remarkable diversity of viruses in plants, with complex communities interacting with hosts in both pathogenic and beneficial ways.
Scientists have identified chemical compounds released by rice roots that determine how much methane the plants emit. A new strain of rice was bred using traditional breeding methods, resulting in yields of 8.96 tons/hectare while emitting up to 70% less methane.
A new study found that over half of weedy rice sampled in the southeastern US has become resistant to certain herbicides, including imidazolinone and a newer class of herbicides. The researchers also discovered that individual fields have distinct compositions of weedy rice strains, making management harder.
Researchers found that a regulatory level change enabled C4 plants to photosynthesize more efficiently. By studying this shift, they believe it could be applied to make C3 crops like rice and wheat more resilient to climate change.
Ling Li's groundbreaking research improves global nutrition and sustainability by increasing protein content in rice and soybean crops. The gene-edited approach boosts nutritional value while promoting sustainable agricultural practices.
A new study by Salk scientists reveals a key gene that enhances plants' zinc tolerance, allowing them to thrive in toxic conditions. The discovery enables the development of crops more resilient to soil contamination, a major goal of Salk's Harnessing Plants Initiative.
Ratoon rice cultivation has seen significant advancements in China, thanks to improved breeding methods and technology. The research highlights the need for precise rhizosphere regulation to boost regeneration capacity and yields.
A study using hyperspectral data and DCGANs improves the estimation of rice grain protein content, achieving high validation accuracy and identifying genetic loci related to GPC. This approach demonstrates the potential for combining hyperspectral technology and DCGANs for efficient genetic analysis and selection of high-quality rice v...
Researchers from the University of Illinois have used CRISPR/Cas9 to alter the upstream regulatory DNA of a food crop, increasing gene expression and improving downstream photosynthesis. This approach, which does not require adding foreign DNA, has shown promising results in increasing photosynthetic activity in rice.
Researchers identified an ideal small-grain gene, GSE3, and used CRISPR-Cas9 technology to edit it in male sterile lines, achieving fully mechanized hybrid seed production. This breakthrough enables significant yield improvements and enhances food security.
A research team has achieved a groundbreaking improvement in the haplotype-resolved genome sequence of japonica rice cultivar Nipponbare, revealing over 3,000 new genes. The enhanced genome assembly provides a robust framework for further rice genetic studies and breeding programs.
Researchers developed four plant-based A-to-K base editors, rAKBEs, that enable simultaneous adenine transition and transversion base editing in rice. The rAKBEs, including rAKBE03 and rAKBE04, showed improved efficiency and capacity for different editing products.
The KAUST team developed an open-source platform to detect small DNA differences, revealing over 2 million previously overlooked genetic variants in rice and other crops. This tool will accelerate the discovery of genetic variations for developing crops with improved resilience and yield.
A study found that weedy rice's promiscuity allows it to crossbreed with wild rice, enabling it to adapt and outcompete cultivated rice. This process, called adaptive introgression, has contributed to the evolution of Southeast Asian weedy rice.
A research team has developed rice lines resistant to Rice Yellow Mottle Virus (RYMV) using genome editing, offering hope for African small-scale farmers. The resistant varieties were created by inserting a resistance gene into Asian rice, which can be easily transferred to local elite varieties.
Researchers found evidence of separate domestication events for Asian rice in different areas, with wild rice species O. rufipogon and O. nivara contributing to the genetic pool. The study provides a new framework for understanding the evolutionary history of domesticated rice.
A new technique using DNA barcoding can identify the plant matter in human feces, improving clinical trials, nutrition studies and historical research. The method detected specific plant species and their relative amounts consumed, varying according to diet, age, and household income.
A new gene variant, RBL1, has been identified in a type of rice that can be modified to improve performance without yield penalties. This breakthrough could lead to more disease-resistant rice crops with high yields, addressing a major threat to the industry and meeting growing global demand.
A team of scientists used CRISPR-Cas genome editing to create a disease-resistant rice variety, which showed high yields and resistance to the fungus that causes rice blast. The new rice variety produced five times more yield than the control rice in small-scale field trials.
International researchers have identified nutrient-rich black rice varieties with improved agronomic traits, including shorter stem length and early maturity. These findings provide important resources for crop bioengineers to improve pigmented rice for human health and sustainable agriculture.
A review of gene editing techniques suggests that the CRISPR/Cas method could be a game-changer for rice crops threatened by climate change and high food demand. The study highlights its efficiency in improving yield, tolerance to biotic and abiotic stresses, and grain quality.
Researchers at Rice University have developed a multiplex base-editing platform that significantly improves the pace of new drug discovery by inducing fungi to produce more bioactive compounds. The technique has been deployed as a tool for mining fungal genomes for medically useful compounds, reducing research timeline by over 80%.
A recent study has revealed a novel cold domesticated repair mechanism for DNA damage in rice, providing elite modules for improving chilling tolerance. The discovery of GCG codon repeats in the first exon of COLD11, a DNA repair protein, has opened the way for fine regulation of rice chilling tolerance with a single site.
A new report showcases perennial rice strains that can thrive in various climate conditions, offering labor and cost savings for farmers. The research emphasizes the need for large-scale localization of perennial rice to tailor it to local climates, with potential applications in Africa and other regions.
Researchers have identified a cork-like substance called suberin that helps protect rice roots from floods and drought. By understanding how suberin is produced, they hope to use gene editing or selective breeding to make the crop more resilient to climate change.
New research enables regionally relevant eating-quality traits to be selected early in breeding programs, saving time and effort. Genetic markers associated with 10 grain-quality traits have been identified, which can now be used by rice breeders in Latin America and potentially worldwide.
A team of scientists led by Assistant Professor Lae-Hyeon Cho identified a single mutation in the gene that codes for cytidine triphosphate synthase (CTPS), an enzyme crucial for early endosperm development. The study showed that overexpressing CTPS in genetically modified rice plants results in a larger endosperm, opening up opportuni...
Researchers found that prime editors have extremely low off-target effects in plant cells, with editing rates of 0.00%~0.23%. The study suggests designing pegRNAs to minimize off-target sites and eliminates concerns about nonspecific effects from M-MLV RT.
A new bioinformatics tool called PlasmidHawk has been developed by Rice University researchers to track the origin of synthetic genetic code. The tool uses a sequence alignment-based approach and was found to outperform recent deep learning approaches in lab-of-origin prediction, achieving 76% accuracy.
Two distinct maternal lineages have been identified in rice through a study of over 3000 genotypes. This discovery sheds light on how rice adapted to its environment and could help improve breeding for climate change adaptation and food security.
A recent study found that genomic adaptations to a rice-based diet may mitigate the risk of obesity and diabetes in some east-Asian populations. The researchers analyzed the genomes of over 2,000 subjects and identified genetic modifications associated with lower BMI and reduced insulin resistance.
Researchers have developed novel APOBEC-Cas9 fusion-induced deletion systems (AFIDs) that induce precise, predictable multi-nucleotide deletions in rice and wheat genomes. The AFID system has been shown to confer enhanced resistance to rice bacterial blight.
Researchers identified a specific non-coding genomic region essential for proper development of male and female reproductive organs in rice. The discovery highlights the importance of non-coding RNAs in plant reproduction and could lead to increased productivity and stable yields of rice.
A global cooling event 4,200 years ago may have led to the evolution of new rice varieties and the spread of rice into northern and southern Asia. The study used genomics, archeology, and climate data to reconstruct the history of rice.
A new study reveals the extent to which high-yielding rice varieties favored in the Green Revolution have evolved into weedy populations worldwide, outcompeting cultivated varieties. The scientists found that over a third of Asian weed strains originated from elite cultivars developed during this era.
Researchers developed a new genome editing strategy using CRISPR to precisely target genes for desirable traits, such as high beta-carotene levels and disease resistance. This approach reduces the need for marker genes and allows for more complex trait clusters.
Researchers at New York University have sequenced the genome of two basmati rice varieties, including one with improved drought tolerance and resistance to bacterial disease. The study provides insights into the evolutionary history of basmati rice and its unique genetic traits.
Researchers found that key changes during rice domestication reflect selection on traits determined by a portion of the genome that does not transcribe proteins. Non-coding RNAs, suspected to play important roles in regulating growth and development, were also implicated.
Scientists decoded the genome of umi-budo, a popular Okinawan seaweed, to understand its unique shape and assist farmers in proper cultivation. The study revealed key genes controlling growth and development, potentially helping ease crop issues and address environmental concerns.
Researchers found that cytosine base editors (BE3 and HF1-BE3) cause unexpected genome-wide off-target mutations in rice, with single-nucleotide variants predominantly occurring in transcribed genic regions. The high frequency of these mutations suggests a need for optimization to increase the specificity of cytosine base editors.
A recent study published in Genome Biology found that the rapid growth of genomic databases is affecting the accuracy of bacterial species identification. The research, led by Rice University scientist Todd Treangen, reveals that the imbalance in database coverage hinders the ability to quickly identify pathogens.
Researchers at Rice University have developed an energy landscape model that details the combination of forces driving nuclear motion in cells. The model, based on a protein folding algorithm, reveals the presence of dynamically associated domains and phase separation in chromatin segments.
Researchers have sequenced the genomes of 13 wild and domesticated rice species, revealing valuable genetic information for developing new, efficient, and sustainable rice varieties. The newly created genetic resource provides insights into disease resistance genes, which could help reduce pesticide use and ensure reliable rice harvests.
Using computer models, researchers analyzed epigenetic marks to predict how chromosomes fold in three dimensions. By training a neural network on these marks, they were able to identify the structural types of chromatin and validate their findings with additional data.
Researchers have created a whole-genome sequenced rice mutant resource to accelerate functional genetic research in plants. The new collection, KitBase, contains 1,504 lines with 45-fold coverage and identified 91,513 mutations affecting 32,307 genes.
Researchers at Hokkaido University discovered that non-autonomous viruses can infect the same plant and exchange DNA to help each other prosper. This 'commensal' partnership with another virus species is crucial in establishing life cycles, with exchanging noncoding regulatory sequences playing a key role.
Scientists have developed a new rice strain that flowers within a certain period after being sprayed with commercial chemicals, enabling farmers to control harvest timing. The research, led by Professor Takeshi Izawa at the University of Tokyo, uses a genetic approach to manipulate flowering time in cereal crops.
A team developed a new way to sequence genomes, assembling the Zika virus mosquito genome for less than $10,000. This allows for rapid creation of reference genomes for all species, including humans, tumors, and patients, enabling better diagnosis and treatment.
A team of researchers has developed a new method, called 3D genome assembly, that can create a human reference genome from scratch for less than $10,000. This technology allows scientists to assemble the genome of Zika virus-carrying mosquitoes at a fraction of the cost and time required by traditional methods.
A team of NYU scientists will investigate how rice adapts to salty soil conditions under a $4 million NSF grant. They aim to identify genes that enable plants to thrive in saline environments, with potential implications for breeding more resilient crops.
The Genome Analysis Centre (TGAC) is training the next generation of rice breeders in Vietnam in advanced bioinformatics and genomics. The programme aims to characterise genetic diversity in Vietnamese native rice lines to accelerate crop breeding and improve yields, addressing climate change threats such as drought and rising sea levels
A Baylor College of Medicine team has reported the first successful genome surgery, changing how the human genome is folded inside the cell nucleus. By manipulating specific DNA motifs, the team was able to destroy, move, and create new loops in the genome.
A new project aims to characterise the genetic diversity of traditional Vietnamese rice varieties using genomic markers for disease resistance and salt tolerance. Bioinformatics capacity will be built in Vietnam through training workshops and data sharing.
A study on the apple maggot pest discovered a massive genome shift in just one generation, with 32,000 genetic changes occurring within a single year. This significant finding highlights the importance of ecological selection at early stages of divergence and calls for further integration of studies on speciation and genome divergence.
Researchers at Rice University have developed a new theory on chromosome folding, which is crucial for understanding gene regulation and other biological processes. The theory predicts the folding mechanisms and resulting structures of chromosomes using statistical tools and energy landscapes.