Genome-Wide Association Study (GWAS) for heading date and crown rust resistance in perennial ryegrass.

Published by: Teagasc

Licensed under: cc-by-nc

Category: Agriculture

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This work aimed to identify Quantitative Trait Loci associated with heading date and crown rust in perennial ryegrass. Full details on the collection and analysis of phenotypic data can be found in https://doi.org/10.1038/s41598-017-03232-8 and https://doi.org/10.1186/s12863-018-0613-z , and associated raw genotyping-by-sequencing (GBS) data is available at the NCBI (BioProject accession PRJNA352789). When those initial studies were carried out a pseudochromosome scale assembly of perennial ryegrass was not yet available. In this work, the GBS data has been re-analysed using the pseudochromosome scale assembly as a reference, a new SNP database established, and used to carry out a GWAS.

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Data Owner	Dr Stephen Byrne
Data Owner Email	stephen.byrne@teagasc.ie
Theme	Agriculture
Rights notes	This license enables reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator. CC BY-NC includes the following elements: BY: credit must be given to the creator. NC: Only noncommercial uses of the work are permitted.
Language	English
Provenance information	+ Heading date Please see https://doi.org/10.1038/s41598-017-03232-8 for full details on data collection and analysis. + Crown rust Please see https://doi.org/10.1186/s12863-018-0613-z for full details on data collection and analysis. + SNPs SNPs were identified by mapping GBS data for each plant back to the reference genome (https://doi.org/10.1186/s12864-022-08697-0) and identifying genetic variation. SNPs are encoded as 0, 1, 2 representing homozygous for reference allele, heterozygous, and homozygous for alternate allele, respectively. + Processing and analysis scripts The GWAS was performed in R and the script outlining the analysis is included. + Figures and tables All figures and tables were created through R. The manhattan plots for each trait are included along with tables of identified QTL. Refer to the R script for detailed information.
High Value Dataset (HVD)	No