A5020150778- Genetic Mapping and Diversity in Plants and Animals
- Genetics and Plant Breeding
- Genetic and phenotypic traits in livestock
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Wheat and Barley Genetics and Pathology
- Genetic diversity and population structure
- Plant Disease Resistance and Genetics
- Plant Molecular Biology Research
- Crop Yield and Soil Fertility
- RNA and protein synthesis mechanisms
- Bioenergy crop production and management
- Plant Taxonomy and Phylogenetics
- Plant Virus Research Studies
- CRISPR and Genetic Engineering
- Machine Learning in Bioinformatics
- Horticultural and Viticultural Research
- Antioxidant Activity and Oxidative Stress
- Plant Micronutrient Interactions and Effects
- Plant Gene Expression Analysis
- Advances in Cucurbitaceae Research
- Agriculture Sustainability and Environmental Impact
- Gene expression and cancer classification
- Plant nutrient uptake and metabolism
- Cassava research and cyanide
Agricultural Research Service
2016-2025
Cornell University
2016-2025
United States Department of Agriculture
2016-2025
Ithaca College
2015-2024
Robert W. Holley Center for Agriculture & Health
2015-2024
Center for Genomic Science
2008-2024
Agricultural Research Service - Northeast Area
2022
University of California, Davis
2011-2019
Institute of Crop Science
2019
University of Illinois Urbana-Champaign
2009-2019
Association analyses that exploit the natural diversity of a genome to map at very high resolutions are becoming increasingly important. In most studies, however, researchers must contend with confounding effects both population and family structure. TASSEL (Trait Analysis by aSSociation, Evolution Linkage) implements general linear model mixed approaches for controlling For result interpretation, program allows linkage disequilibrium statistics be calculated visualized graphically. Database...
Advances in next generation technologies have driven the costs of DNA sequencing down to point that genotyping-by-sequencing (GBS) is now feasible for high diversity, large genome species. Here, we report a procedure constructing GBS libraries based on reducing complexity with restriction enzymes (REs). This approach simple, quick, extremely specific, highly reproducible, and may reach important regions are inaccessible sequence capture approaches. By using methylation-sensitive REs,...
Abstract Summary: Software programs that conduct genome-wide association studies and genomic prediction selection need to use methodologies maximize statistical power, provide high accuracy run in a computationally efficient manner. We developed an R package called Genome Association Prediction Integrated Tool (GAPIT) implements advanced methods including the compressed mixed linear model (CMLM) CMLM-based selection. The GAPIT can handle large datasets excess of 10 000 individuals 1 million...
The rhizosphere is a critical interface supporting the exchange of resources between plants and their associated soil environment. Rhizosphere microbial diversity influenced by physical chemical properties rhizosphere, some which are determined genetics host plant. However, within plant species, impact genetic variation on composition microbiota poorly understood. Here, we characterized bacterial 27 modern maize inbreds possessing exceptional grown under field conditions. Randomized...
Genotyping by sequencing (GBS) is a next generation based method that takes advantage of reduced representation to enable high throughput genotyping large numbers individuals at number SNP markers. The relatively straightforward, robust, and cost-effective GBS protocol currently being applied in numerous species researchers. Herein we describe bioinformatics pipeline, tassel-gbs, designed for the efficient processing raw sequence data into genotypes. tassel-gbs pipeline successfully fulfills...
Flowering time is a complex trait that controls adaptation of plants to their local environment in the outcrossing species Zea mays (maize). We dissected variation for flowering with set 5000 recombinant inbred lines (maize Nested Association Mapping population, NAM). Nearly million were assayed eight environments but showed no evidence any single large-effect quantitative loci (QTLs). Instead, we identified numerous small-effect QTLs shared among families; however, allelic effects differ...
There exists extraordinary morphological and genetic diversity among the maize landraces that have been developed by pre-Columbian cultivators. To explain this high level of in maize, several authors proposed were products multiple independent domestications from their wild relative (teosinte). We present phylogenetic analyses based on 264 individual plants, each genotyped at 99 microsatellites, challenge multiple-origins hypothesis. Instead, our results indicate all arose a single...
There is tremendous interest in using association mapping to identify genes responsible for quantitative variation of complex traits with agricultural and evolutionary importance. Recent advances genomic technology, impetus exploit natural diversity, development robust statistical analysis methods make appealing affordable plant research programs. Association identifies trait loci (QTLs) by examining the marker‐trait associations that can be attributed strength linkage disequilibrium between...
False positives in a Genome-Wide Association Study (GWAS) can be effectively controlled by fixed effect and random Mixed Linear Model (MLM) that incorporates population structure kinship among individuals to adjust association tests on markers; however, the adjustment also compromises true positives. The modified MLM method, Multiple Loci (MLMM), multiple markers simultaneously as covariates stepwise partially remove confounding between testing kinship. To completely eliminate confounding,...
Association studies based on linkage disequilibrium (LD) can provide high resolution for identifying genes that may contribute to phenotypic variation. We report patterns of local and genome-wide LD in 102 maize inbred lines representing much the worldwide genetic diversity used breeding, address its implications association maize. In a survey six genes, we found intragenic generally declined rapidly with distance ( r 2 < 0.1 within 1500 bp), but rates decline were highly variable among...
Abstract We investigated the genetic and statistical properties of nested association mapping (NAM) design currently being implemented in maize (26 diverse founders 5000 distinct immortal genotypes) to dissect basis complex quantitative traits. The NAM simultaneously exploits advantages both linkage analysis mapping. demonstrated power for high-power cost-effective genome scans through computer simulations based on empirical marker data simulated traits with different complexities. With...
Maize genetic diversity has been used to understand the molecular basis of phenotypic variation and improve agricultural efficiency sustainability. We crossed 25 diverse inbred maize lines B73 reference line, capturing a total 136,000 recombination events. Variation for frequencies was observed among families, influenced by local (cis) variation. identified evidence numerous minor single-locus effects but little two-locus linkage disequilibrium or segregation distortion, which indicated...
Crop improvement and the dissection of complex genetic traits require germplasm diversity. Although this necessary phenotypic variability exists in diverse maize, most research is conducted using a small subset inbred lines. An association population 302 lines now available--a valuable tool that captures large proportion alleles cultivated maize. Provided appropriate statistical models correcting for structure are included, can be used analyses to provide high-resolution evaluation multiple...
Accelerating crop improvement in sorghum, a staple food for people semiarid regions across the developing world, is key to ensuring global security context of climate change. To facilitate gene discovery and molecular breeding we have characterized ∼265,000 single nucleotide polymorphisms (SNPs) 971 worldwide accessions that adapted diverse agroclimatic conditions. Using this genome-wide SNP map, population structure with respect geographic origin morphological type identified patterns...
Maize is an important crop species of high genetic diversity. We identified and genotyped several million sequence polymorphisms among 27 diverse maize inbred lines discovered that the genome was characterized by highly divergent haplotypes showed 10- to 30-fold variation in recombination rates. Most chromosomes have pericentromeric regions with suppressed appear influenced effectiveness selection during development may be a major component heterosis. found hundreds selective sweeps...