A5065127576- Genetic Mapping and Diversity in Plants and Animals
- Genetics and Plant Breeding
- Genetic and phenotypic traits in livestock
- Remote Sensing in Agriculture
- Crop Yield and Soil Fertility
- Smart Agriculture and AI
- Leaf Properties and Growth Measurement
- Wheat and Barley Genetics and Pathology
- Genomics and Phylogenetic Studies
- Plant Disease Resistance and Genetics
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Chromosomal and Genetic Variations
- Remote Sensing and LiDAR Applications
- Ecology and Vegetation Dynamics Studies
- Plant Pathogens and Resistance
- Rice Cultivation and Yield Improvement
- Gene expression and cancer classification
- Banana Cultivation and Research
- Species Distribution and Climate Change
- RNA modifications and cancer
North Carolina State University
2022-2024
Cornell University
2013-2023
North Central State College
2023
Ithaca College
2019-2020
Agricultural Research Service
2020
University of Wisconsin–Madison
2017-2019
Remarkable productivity has been achieved in crop species through artificial selection and adaptation to modern agronomic practices. Whether intensive changed the ability of improved cultivars maintain high across variable environments is unknown. Understanding genetic control phenotypic plasticity genotype by environment (G × E) interaction will enhance performance predictions diverse environments. Here we use data generated from Genomes Fields (G2F) Maize G E project assess effect on...
Maize stover is an important source of crop residues and a promising sustainable energy in the United States. Stalk main component stover, representing about half dry weight. Characterization genetic determinants stalk traits provide foundation to optimize maize as biofuel feedstock. We investigated natural variation genome-wide association studies (GWAS) detect candidate genes associated with related biomass (stalk diameter plant height) anatomy (rind thickness, vascular bundle density...
Abstract Accurate prediction of the phenotypic outcomes produced by different combinations genotypes, environments, and management interventions remains a key goal in biology with direct applications to agriculture, research, conservation. The past decades have seen an expansion new methods applied toward this goal. Here we predict maize yield using deep neural networks, compare efficacy 2 model development methods, contextualize performance conventional linear machine learning models. We...
The maize male inflorescence (tassel) produces pollen necessary for reproduction and commercial grain production of maize. size the tassel has been linked to factors affecting yield, so understanding genetic control architecture is an important goal. Tassels are fragile deform easily after removal from plant, necessitating rapid measurement any shape characteristics that cannot be retained during storage. Some morphological tassels such as curvature compactness difficult quantify using...
Abstract Objectives Advanced tools and resources are needed to efficiently sustainably produce food for an increasing world population in the context of variable environmental conditions. The maize genomes fields (G2F) initiative is a multi-institutional effort that seeks approach this challenge by developing flexible distributed infrastructure addressing emerging problems. G2F has generated large-scale phenotypic, genotypic, datasets using publicly available inbred lines hybrids evaluated...
Inflorescence capacity plays a crucial role in reproductive fitness plants, and production of hybrid crops. Maize is monoecious species bearing separate male female flowers (tassel ear, respectively). The switch from open-pollinated populations maize to hybrid-based breeding schemes the early 20th century was accompanied by dramatic reduction tassel size, trend has continued with modern over recent decades. goal this study identify selection signatures genes that may underlie transformation....
Use of a single reference genome for genome-wide association studies (GWAS) limits the gene space represented to that accession. This limitation can complicate identification and characterization genes located within presence-absence variations (PAVs). In this study, we present draft de novo assembly 'PHJ89', an 'Oh43'-type inbred line maize ( L.). From three separate assemblies ('B73', 'PH207', PHJ89) represent predominant germplasm groups maize, generated whole-seedling expression profiles...
The Genomes to Fields (G2F) 2022 Maize Genotype by Environment (GxE) Prediction Competition aimed develop models for predicting grain yield the GxE project field trials, leveraging datasets previously generated this and other publicly available data.This resource used data from within G2F Initiative [1]. dataset included phenotypic genotypic of hybrids evaluated in 45 locations 2014 2022. Also, soil, weather, environmental covariates metadata information all environments (combination year...
Core Ideas Subcanopy rovers enabled 3D characterization of thousands hybrid maize plots. Machine learning produces heritable latent traits that describe plant architecture. Rover‐based phenotyping is far more efficient than manual phenotyping. Latent phenotypes from are ready for application to biology and breeding. Collecting useful, interpretable, biologically relevant in a resource‐efficient manner bottleneck breeding, genetic mapping, genomic prediction. Autonomous affordable subcanopy...
Abstract As a result of millions years transposon activity, multiple rounds ancient polyploidization, and large populations that preserve diversity, maize has an extremely structurally diverse genome, evidenced by high-quality genome assemblies capture substantial levels both tropical temperate diversity. We generated pangenome representation (the Practical Haplotype Graph, PHG) these in database, representing the haplotype diversity providing initial estimate structural leveraged to...
Significance Proteins are the machinery which execute essential cellular functions. However, measuring their abundance within an organism can be difficult and resource-intensive. Cells use a variety of mechanisms to control protein synthesis from mRNA, including short open reading frames (uORFs) that lie upstream main coding sequence. Ribosomes preferentially translate uORFs instead sequence, leading reduced translation protein. In this study, we show uORF sequence variation between...
Abstract Objectives This report provides information about the public release of 2018–2019 Maize G X E project Genomes to Fields (G2F) Initiative datasets. G2F is an umbrella initiative that evaluates maize hybrids and inbred lines across multiple environments makes available phenotypic, genotypic, environmental, metadata information. The understands necessity characterize deploy sources genetic diversity face challenges for more sustainable agriculture in context variable environmental...
This release note describes the Maize GxE project datasets within Genomes to Fields (G2F) Initiative. The aims understand genotype by environment (GxE) interactions and use information collected improve resource allocation efficiency increase predictability stability, particularly in scenarios of variable environmental patterns. Hybrids inbreds are evaluated across multiple environments phenotypic, genotypic, environmental, metadata made publicly available.The include phenotypic data hybrids...
Abstract Marand et al. use a high-resolution recombination map to dissect the genetic components of yield in diploid potato. Regions recalcitrant heterozygosity inbred parent co-localized with elevated rates, signatures selection, and tissue-specific gene expression... Deconvolution architecture underlying is critical for understanding bases gain species agronomic importance. To potato, we adopted reference-based composed four segregating alleles from an interspecific pseudotestcross F1...
Abstract Increasing popularity of high-throughput phenotyping technologies, such as image-based phenotyping, offer novel ways for quantifying plant growth and morphology. These new methods can be more or less accurate precise than traditional, manual measurements. Many large-scale efforts are conducted to enable genome-wide association studies (GWAS), but it is unclear exactly how alternative will affect GWAS results. In this study we simulate phenotypes that controlled by the same set...
Abstract Predicting phenotypes from a combination of genetic and environmental factors is grand challenge modern biology. Slight improvements in this area have the potential to save lives, improve food fuel security, permit better care planet, create other positive outcomes. In 2022 2023 first open-to-the-public Genomes Fields (G2F) initiative Genotype by Environment (GxE) prediction competition was held using large dataset including genomic variation, phenotype weather measurements field...
Abstract Predicting phenotypes from a combination of genetic and environmental factors is grand challenge modern biology. Slight improvements in this area have the potential to save lives, improve food fuel security, permit better care planet, create other positive outcomes. In 2022 2023, first open-to-the-public Genomes Fields initiative Genotype by Environment prediction competition was held using large dataset including genomic variation, phenotype weather measurements, field management...
Abstract Understanding the genetic basis of plant traits requires comprehensive and quantitative descriptions phenotypic variation that exists within populations. Cameras other sensors have made high‐throughput phenotyping possible, but image‐based procedures involve a step where researcher selects to be measured. This feature selection is inherently prone human biases. Recently, set approaches, which are referred collectively as latent techniques, arisen in literature. Latent techniques...
Abstract Collecting useful, interpretable, and biologically relevant phenotypes in a resource-efficient manner is bottleneck to plant breeding, genetic mapping, genomic prediction. Autonomous affordable sub-canopy rovers are an efficient scalable way generate sensor-based datasets of in-field crop plants. Rovers equipped with light detection ranging (LiDar) can produce three-dimensional reconstructions entire hybrid maize fields. In this study, we collected 2,103 LiDar scans field plots...
<b><sc>Abstract.</sc></b> Maize is the most productive grain crop in world terms of total production and yield. Leaf azimuth angle an important characteristic that affects efficiency sunlight reception photosynthesis maize canopies. To study plant architecture, previous studies have been focusing on leaf characterization due to inherent difficulty measuring accurately. Achieving accurate efficient measurement for yield improvement. Traditionally, measured manually, which time-consuming,...
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Circadian entrainment and external cues can cause gene transcript abundance to oscillate throughout the day, these patterns of diel oscillation vary across genes plant species. Less is known about within-species allelic variation for oscillation, or how regulatory sequence influences transcription patterns. In this study, we evaluated 24 diverse maize inbred lines. We observed extensive natural in patterns, with two-fold number that over course day. A convolutional neural network trained...