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Title Genome-Wide Association Study (GWAS) for heading date and crown rust resistance in perennial ryegrass.
License CC-BY-NC
Teagasc Department Crops Research
Teagasc Programme Crops, Environment and Land Use
Description 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.
Language English
Principal Investigator (PI) Dr Stephen Byrne
Principal Investigator (PI) email stephen.byrne@teagasc.ie
Principal Investigator (PI) ORCID http://orcid.org/0000-0002-1179-2272
Digital Object Identifier (DOI) doi.org/10.82253/YKFT-M434
Citation Byrne, S. (2025). Genome-Wide Association Study (GWAS) for heading date and crown rust resistance in perennial ryegrass. [Dataset]. Teagasc - The Irish Agriculture and Food Development Authority. https://doi.org/10.82253/YKFT-M434
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.
Related resources
  1. Byrne, S.L., Conaghan, P., Barth, S., Arojju, S.K., Casler, M., Michel, T., Velmurugan, J. and Milbourne, D. (2017) ‘Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass’, Scientific Reports, 7(1), p.3566. doi:10.1038/s41598-017-03232-8.
  2. Arojju, S., Conaghan, P., Barth, S., Byrne, S.L., Casler, M., Lynn, D. and Milbourne, D. (2018) ‘Genomic prediction of crown rust resistance in Lolium perenne’, BMC Genetics, 19(1), p.35. doi:10.1186/s12863-018-0613-z.
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.