A5103076451- Genetic Mapping and Diversity in Plants and Animals
- Rice Cultivation and Yield Improvement
- Genomics and Phylogenetic Studies
- Genetic and phenotypic traits in livestock
- Gene expression and cancer classification
- Genetics and Plant Breeding
- Plant Pathogenic Bacteria Studies
- Plant-Microbe Interactions and Immunity
- Wheat and Barley Genetics and Pathology
- Climate change impacts on agriculture
- Plant Pathogens and Fungal Diseases
- Plant Taxonomy and Phylogenetics
- Chromosomal and Genetic Variations
- Plant Disease Resistance and Genetics
- GABA and Rice Research
- Plant nutrient uptake and metabolism
International Rice Research Institute
2017-2021
Inari Agriculture (United States)
2018
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...
Rice (Oryza sativa L.) not only provides insurance covering global food security but also works as a model for plant research. Currently, with overwhelmingly accumulated sequencing data, various databases were constructed different target users, including the Genome Variation Map (Song et al., 2018), RiceVarMap (Zhao 2015), SNP-Seek database (Alexandrov RPAN (Sun 2017) and MBK V1 (Institute of Genetics Developmental Biology, C.A.S., 2018). However, none them is designed to meet increasing...
Abstract As sequencing and genotyping technologies evolve, crop genetics researchers accumulate increasing numbers of genomic data sets from various platforms on different germplasm panels. Imputation is an effective approach to increase marker density existing toward the goal integrating resources for downstream applications. While a number imputation software packages are available, limitations utilization rice community include high computational demand lack reference panel. To address...
Abstract Crop improvement efforts aiming at increasing crop production (quantity, quality) and adapting to climate change have been subject of active research over the past years. But, question remains ‘to what extent can breeding gains be achieved under a changing climate, pace sufficient usefully contribute adaptation, mitigation food security?’. Here, we address this by critically reviewing how model‐based approaches used assist activities, with particular focus on all CGIAR (formerly...
In this study, we used 2.9 million single nucleotide polymorphisms (SNP) and 393,429 indels derived from whole genome sequences of 591 rice landraces to determine the genetic basis cooked raw grain length, width shape using genome-wide association study (GWAS). We identified a unique fine-mapped region GWi7.1 significantly associated with width. Additionally, GWi7.2 that harbors GL7/GW7 cloned gene for dimension was found. Novel regions in chromosomes 10 11 were also found be width,...
Rice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies high-density genotyping platforms for genome variation analysis gene discovery. Germplasm collections representing rice improved varieties, elite breeding materials are accessible through banks use in with many having sequences genotype data available. Combining phenotypic genotypic information on these accessions enables genome-wide association...
Plant disease resistance that is durable and effective against diverse pathogens (broad-spectrum) essential to stabilize crop production. Such frequently controlled by Quantitative Trait Loci (QTL), often involves differential regulation of Defense Response (DR) genes. In this study, we sought understand how expression DR genes orchestrated, with the long-term goal enabling genome-wide breeding for more resistance. We identified short sequence motifs in rice promoters are shared across...
Abstract The features in some machine learning datasets can naturally be divided into groups. This is the case with genomic data, where grouped by chromosome. In many applications it common for these groupings to ignored, as interactions may exist between belonging different However, including a group that does not influence response introduces noise when fitting model, leading suboptimal predictive accuracy. Here we present two general frameworks generation and combination of meta-features...
Abstract Background Rice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies high density genotyping platforms for genome variation analysis gene discovery. Germplasm collections representing rice improved varieties elite breeding materials are accessible through banks use in with many having sequences genotype data available. Combining phenotypic genotypic information on these accessions enables...
Abstract To secure the world’s food supply it is essential that we improve our knowledge of genetic underpinnings complex agronomic traits. In this paper, report findings from performing trait prediction and association mapping using marker stability in diverse rice landraces. We used least absolute shrinkage selection operator as algorithm, considered twelve real traits a hundred simulated population with approximately thousand markers. For prediction, several statistical/machine learning...