Ensembl Plant Populations: integrating trait analyses and population-based sequence variants into a browsable genomic context
Lead Research Organisation:
National Institute of Agricultural Botany
Department Name: Genetics and Breeding
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
Ensembl Plants contains community-generated high-quality annotated reference genome assemblies for >100 model and crop species. Numerous plant genetic resources and populations have been generated to capture and exploit genetic diversity, e.g. association mapping/diversity panels and experimental populations, many of which now come with founder genome assemblies and extensive variant data on the progeny. However significant bioinformatic, genetic, statistical and technical expertise from users is required to use these genetic resources and analyse the results in the context of the genes, genetic variants and appropriate reference genomes.
We will establish the 'Ensembl Plant Populations' platform - a web-tool containing existing population-based sequence and variant data, supporting users to run statistically sound genetic analyses. We will focus on seven plant/crop species of high relevance to UK researchers: wheat, barley, rice, brassica, arabidopsis, tomato and oat. The tool will provide users with an integrated pipeline to undertake genetic analyses from start to finish, including: (i) upfront investigation of the predicted power of the selected population to detect genetic loci, (ii) adjustable forward genetic analysis settings, including selection of co-factors, significance threshold type/level, and appropriate corrections for varying levels of relatedness between genotypes, (iii) interactive genome-wide view of the results allowing users to move to identified genomic locations of interest in Ensembl Plants, (iv) presentation of useful information linked to genes and variants within those identified regions to help users identify candidate genes for further study.
We will work with the UK plant research community to select appropriate populations for inclusion, a process which has already started, and attend community meetings throughout the project to raise awareness and gather feedback, including hosting a dedicated stakeholder workshop.
We will establish the 'Ensembl Plant Populations' platform - a web-tool containing existing population-based sequence and variant data, supporting users to run statistically sound genetic analyses. We will focus on seven plant/crop species of high relevance to UK researchers: wheat, barley, rice, brassica, arabidopsis, tomato and oat. The tool will provide users with an integrated pipeline to undertake genetic analyses from start to finish, including: (i) upfront investigation of the predicted power of the selected population to detect genetic loci, (ii) adjustable forward genetic analysis settings, including selection of co-factors, significance threshold type/level, and appropriate corrections for varying levels of relatedness between genotypes, (iii) interactive genome-wide view of the results allowing users to move to identified genomic locations of interest in Ensembl Plants, (iv) presentation of useful information linked to genes and variants within those identified regions to help users identify candidate genes for further study.
We will work with the UK plant research community to select appropriate populations for inclusion, a process which has already started, and attend community meetings throughout the project to raise awareness and gather feedback, including hosting a dedicated stakeholder workshop.
