A5083094488- Genetic Mapping and Diversity in Plants and Animals
- Rice Cultivation and Yield Improvement
- Genomics and Phylogenetic Studies
- Plant-Microbe Interactions and Immunity
- Plant Disease Resistance and Genetics
- Chromosomal and Genetic Variations
- GABA and Rice Research
- Plant Virus Research Studies
- Banana Cultivation and Research
- Plant Genetic and Mutation Studies
- Cystic Fibrosis Research Advances
- Plant tissue culture and regeneration
- Cannabis and Cannabinoid Research
- Genetics and Plant Breeding
- Gut microbiota and health
- Plant Pathogens and Fungal Diseases
- Plant biochemistry and biosynthesis
- Plant Stress Responses and Tolerance
- Plant Pathogenic Bacteria Studies
- Legume Nitrogen Fixing Symbiosis
- Polyamine Metabolism and Applications
- Plant responses to water stress
- Gene expression and cancer classification
- Child Nutrition and Feeding Issues
- Plant Micronutrient Interactions and Effects
Southern Cross University
2019-2025
International Rice Research Institute
2015-2025
University of Southern Mindanao
2023
Institute of Agrobiological Sciences
2012
Ghent University
2012
Colorado State University
2010
Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with five major groups previously recognized, but also suggest several unreported subpopulations that correlate geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 small indels over 90,000 structural variations contribute to within- between-population variation....
The genus Oryza is a model system for the study of molecular evolution over time scales ranging from few thousand to 15 million years. Using 13 reference genomes spanning species tree, we show that despite large-scale chromosomal rearrangements rapid diversification mirrored by lineage-specific emergence and turnover many novel elements, including transposons, potential new coding noncoding genes. Our resolves controversial areas phylogeny, showing complex history introgression among...
This article describes the development of Multi-parent Advanced Generation Inter-Cross populations (MAGIC) in rice and discusses potential applications for mapping quantitative trait loci (QTLs) varietal development. We have developed 4 multi-parent populations: indica MAGIC (8 parents); plus parents with two additional rounds 8-way F1 inter-crossing); japonica Global (16 - 8 japonica). The used creating these are improved varieties desirable traits biotic abiotic stress tolerance, yield,...
We have identified about 20 million rice SNPs by aligning reads from the 3000 genomes project with Nipponbare genome.The and allele information are organized into a SNP-Seek system (http://www.oryzasnp.org/iric-portal/),which consists of Oracle database having total number rows SNP genotypes close to 60 billion (20 M × 3 K lines) web interface for convenient querying.The allows quick retrieving alleles all varieties in given genome region, finding different predefined querying basic passport...
We describe updates to the Rice SNP-Seek Database since its first release. ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides Nipponbare reference genome, was run on genome assemblies of IR 64, 93-11, DJ 123 Kasalath. New genotype query display features are added for assemblies, datasets indels. JBrowse now displays BAM, VCF other annotation tracks, additional an embedded VISTA comparison viewer. Middleware is...
Abstract Brassinosteroids (BRs) are a unique class of plant steroid hormones that orchestrate myriad growth and developmental processes. Although BRs have long been known to protect plants from suite biotic abiotic stresses, our understanding the underlying molecular mechanisms is still rudimentary. Aiming further decipher logic BR-modulated immunity, we examined dynamics impact during infection rice (Oryza sativa) with root oomycete Pythium graminicola. Challenging prevailing view...
Heat and drought stress are projected to become major challenges sustain rice (Oryza sativa L.) yields with global climate change. Both stresses lead yield losses when they coincide flowering. A significant knowledge gap exists in the mechanistic understanding of responses floral organs that determine reproductive success under stress. Our work connects metabolomic transcriptomic changes anthers, pistils before pollination pollinated a heat-tolerant (N22) heat-sensitive (Moroberekan)...
Investigation of large structural variants (SVs) is a challenging yet important task in understanding trait differences highly repetitive genomes. Combining different bioinformatic approaches for SV detection, we analyzed whole-genome sequencing data from 3000 rice genomes and identified 63 million individual calls that grouped into 1.5 allelic variants. We found enrichment long SVs promoters an excess shorter 5′ UTRs. Across the genomes, regions high frequency enriched stress response...
Abstract Background The transcriptional regulatory network involved in low temperature response leading to acclimation has been established Arabidopsis . In japonica rice, which can only withstand transient exposure milder cold stress (10°C), an oxidative-mediated proposed play a key role configuring early responses and short-term defenses. components, hierarchical organization physiological consequences of this were further dissected by systems-level approach. Results Regulatory clusters...
As the human population grows from 7.8 billion to 10 over next 30 years, breeders must do everything possible create crops that are highly productive and nutritious, while simultaneously having less of an environmental footprint. Rice will play a critical role in meeting this demand thus, knowledge full repertoire genetic diversity exists germplasm banks across globe is required. To meet demand, we describe generation, validation preliminary analyses transposable element long-range...
Abstract Aquaporin activity and root anatomy may affect hydraulic properties under drought stress. To better understand the function of aquaporins in rice water fluxes drought, we studied conductivity ( Lp r) sap exudation rate S presence or absence an aquaporin inhibitor (azide) well‐watered conditions following stress six diverse varieties. Varieties varied r both conditions. The contribution to was generally high (up 79% 85% stress) differentially regulated drought. increased most...
Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit "sweet spot" for routine genetics breeding applications rice. Selection informative SNPs across species subpopulations during chip design is essential to obtain useful rates target germplasm groups. This paper summarizes results from large-scale...
The development of rice genotypes with micronutrient-dense grains and disease resistance is one the major priorities in improvement programs. We conducted Genome-wide association studies (GWAS) using a Multi-parent Advanced Generation Inter-Cross (MAGIC) Plus population to identify QTLs SNP markers that could potentially be integrated biofortification breeding. evaluated 144 MAGIC lines for agronomic traits over two locations seasons, while was screened season screen house. X-ray...
A previous Australia-wide pilot study identified pain as a significant burden in people with CF (pwCF). However, the prevalence, frequency and severity have not been evaluated using validated tools. Australian adults, pwCF healthy controls (HC) were invited to complete an online questionnaire from July 2023 - February 2024, consisting of four tools: Brief Pain Inventory, Catastrophising Scale, PAGI-SYM PAC-SYM. The questionnaire, disseminated via Cystic Fibrosis Australia, Together social...
Although quantitative trait loci (QTL) underpin many desirable agronomic traits, their incorporation into crop plants through marker-assisted selection is limited by the low predictive value of markers on phenotypic performance. Here we used candidate defense response (DR) genes to dissect resistance in rice using recombinant inbred (RI) and advanced backcross (BC) populations derived from a blast-resistant cultivar, Sanhuangzhan 2 (SHZ-2). Based DNA profiles DR genes, RI lines were...
Biofuels provide a promising route of producing energy while reducing reliance on petroleum. Developing sustainable liquid fuel production from cellulosic feedstock is major challenge and will require significant breeding efforts to maximize plant biomass production. Our approach elucidating genes genetic pathways that can be targeted for improving exploit the combination genomic tools diversity in rice (Oryza sativa). In this study, we analyzed diverse set 20 recently resequenced varieties...
The identification and introgression of major-effect QTLs for grain yield under drought are some the best well-proven approaches improving tolerance rice varieties. In present study, we characterized Malaysian germplasm yield-related traits identified significant trait marker associations by structured association mapping.The screening was successful in with a reduction up to 60% heritability 78%. There wider phenotypic molecular diversity within panel, indicating suitability population...
Rice is one of the major staple foods in world, especially developing countries Asia. Its consumption as a dietary source also increasing Africa. To meet demand for rice to feed human population, yield essential. Improving genetic potential ideal solution. It imperative introduce identified yield-enhancing gene(s) into modern cultivars rapid improvement through marker-assisted breeding. We report development PCR-gel-based markers eight yield-related functional genes (Gn1a, OsSPL14, SCM2,...
Traditional rice varieties harbour a large store of genetic diversity with potential to accelerate improvement. For long time, this maintained in the International Rice Genebank has not been fully used because lack genome information. The publication first reference Nipponbare by Genome Sequencing Project (IRGSP) marked beginning systematic exploration and use for research breeding. Since then, served as assembly many additional genomes. recently completed 3000 Genomes together public...