title: Markers associated with heading and aftermath heading in perennial ryegrass full-sib families.
abstract: Heading and aftermath heading are important traits in perennial ryegrass because they impact forage quality. So far, genome-wide association analyses in this major forage species have only identified a small number of genetic variants associated with heading date that overall explained little of the variation. Some possible reasons include rare alleles with large phenotypic affects, allelic heterogeneity, or insufficient marker density. We established a genome-wide association panel with multiple genotypes from multiple full-sib families. This ensured alleles were present at the frequency needed to have sufficient statistical power to identify associations. We genotyped the panel via partial genome sequencing and performed genome-wide association analyses with multi-year phenotype data collected for heading date, and aftermath heading.
  
  
  
  Genome wide association using a mixed linear model failed to identify any variants significantly associated with heading date or aftermath heading. Our failure to identify associations for these traits is likely due to the extremely low linkage disequilibrium we observed in this population. However, using single marker analysis within each full-sib family we could identify markers and genomic regions associated with heading and aftermath heading. Using the ryegrass genome we identified putative orthologs of key heading genes, some of which were located in regions of marker-trait associations.
  
  
  
  Given the very low levels of LD, genome wide association studies in perennial ryegrass populations are going to require very high SNP densities. Single marker analysis within full-sibs enabled us to identify significant marker-trait associations. One of these markers anchored proximal to a putative ortholog of TFL1, homologues of which have been shown to play a key role in continuous heading of some members of the rose family, Rosaceae.
authors.affiliation: Teagasc, Crop Science Department, Oak Park, Carlow, Ireland.|Department of Botany, Trinity College Dublin, Dublin 2, Dublin, Ireland.
authors.forename: Sai Krishna
authors.initials: SK
authors.lastname: Arojju
authors.affiliation: Teagasc, Crop Science Department, Oak Park, Carlow, Ireland.
authors.forename: Susanne
authors.initials: S
authors.lastname: Barth
authors.affiliation: Teagasc, Crop Science Department, Oak Park, Carlow, Ireland.
authors.forename: Dan
authors.initials: D
authors.lastname: Milbourne
authors.affiliation: Teagasc, Grassland Science Research Department, Animal and Grassland Research and Innovation Centre, Oak Park, Carlow, Ireland.
authors.forename: Patrick
authors.initials: P
authors.lastname: Conaghan
authors.affiliation: Teagasc, Crop Science Department, Oak Park, Carlow, Ireland.
authors.forename: Janaki
authors.initials: J
authors.lastname: Velmurugan
authors.affiliation: Department of Botany, Trinity College Dublin, Dublin 2, Dublin, Ireland.
authors.forename: Trevor R
authors.initials: TR
authors.lastname: Hodkinson
authors.affiliation: Teagasc, Crop Science Department, Oak Park, Carlow, Ireland. stephen.byrne@teagasc.ie.
authors.forename: Stephen L
authors.identifier: 0000-0002-1179-2272
authors.initials: SL
authors.lastname: Byrne
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D005819:Genetic Markers; D014644:Genetic Variation; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics; D005838:Genotype; D008129:Lolium / Q000145:classification / Q000235:genetics*; D010802:Phylogeny
chemical_list: D005819:Genetic Markers
keywords: Aftermath heading; Flowering; Genome wide association; Heading; Lolium perenne; Perennial ryegrass; Single marker analysis