Abstract Detail

Conference Wide

Cobo-Simon, Irene [1], Wegrzyn, Jill [1], Almsaeed, Abdullah [2], Staton, Margaret [2], Ramnath, Risharde  [1].

Data Collection to Analysis: Landscape Genomics with CartograPlant and WildType.

All aspects of biology are interfacing with high resolution data due to the emergence of new and affordable technologies, such as high throughput sequencing, remote sensing, phenomics, and machine-guided data integration. These technologies allow us to address a plethora of adaptive questions in a wide range of plant systems. One of these questions is the identification of loci controlling traits of interest (e.g. abiotic/biotic stress resilience). This is particularly relevant to plant health and productivity in the context of a changing climate, since these loci can be used to inform conservation and management strategies. This can be accomplished through genome-wide association analysis (GWAS). GWAS uses statistical inference to identify genomic variants throughout the genome associated with phenotypic variants (traits) or environmental metrics of interest among large populations of individuals. These analyses require high-performance computing bioinformatic platforms and multiple software tools for data preprocessing and analysis. CartograPlant (https://treegenesdb.org/ct) is a web application that integrates, visualizes, and analyzes genotypic, phenotypic, environmental data from georeferenced plants. The map-based interface integrates regional and global layers related to key metrics such as climate, or precipitation. The genotype and phenotype metrics are collected through direct submission of studies at the time of publication via the Tripal Plant PopGen Submit (TPPS) pipeline (https://tpps.readthedocs.io/en/latest/) or the biocuration efforts of affiliated databases (TreeGenes, Hardwood Genomics Web, Genome Database for Rosaceae, Dryad). TPPS provides a mechanism for plant biologists to obtain a DOI for their data submission and have their data available in a FAIR (Findable, accessible, interoperable, reusable) format. Georeferenced trait data can be also submitted to CartograPlant using the WildType application (https://wildtypeapp.org/), a mobile app for field-based data and sample collection. Data analysis is enabled by accessing the metadata associated with the public studies and providing workflows through Galaxy (https://usegalaxy.org/), a user-friendly interface which allows the performance of bioinformatic analysis without the need of coding skills. This workshop will introduce the integrated suite of CartograPlant, TPPS, and WildType applications. Together, they provide functionality to collect and integrate a diversity of high-throughput data types, and to perform user-friendly but accurate data analysis, suitable for publication. We will provide the basic user guidelines for these softwares, including a brief introduction of CartograPlant, georeferenced and mobile phone enabled data collection using WildType, FAIR genotype, phenotype, and environment data submission via TPPS, and reproducible data analysis. To this end, we will also provide background and best practices for landscape genomics/GWAS in CartograPlant.

Related Links:

1 - University Of Connecticut EEB Dept., Ecology & Evolutionary Biology, 75 N Eagleville Rd Unit 3043, Storrs, CT, 06269, United States
2 - University of Tennessee, Department of Entomology and Plant Pathology, Institute of Agriculture

none specified

Presentation Type: Workshop
Abstract ID:1106
Candidate for Awards:None

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