title: Genomic dissection and prediction of heading date in perennial ryegrass.
abstract: BACKGROUND
  Genomic selection (GS) has become a commonly used technology in animal breeding. In crops, it is expected to significantly improve the genetic gains per unit of time. So far, its implementation in plant breeding has been mainly investigated in species farmed as homogeneous varieties. Concerning crops farmed in family pools, only a few theoretical studies are currently available. Here, we test the opportunity to implement GS in breeding of perennial ryegrass, using real data from a forage breeding program. Heading date was chosen as a model trait, due to its high heritability and ease of assessment. Genome Wide Association analysis was performed to uncover the genetic architecture of the trait. Then, Genomic Prediction (GP) models were tested and prediction accuracy was compared to the one obtained in traditional Marker Assisted Selection (MAS) methods.
  
  
  RESULTS
  Several markers were significantly associated with heading date, some locating within or proximal to genes with a well-established role in floral regulation. GP models gave very high accuracies, which were significantly better than those obtained through traditional MAS. Accuracies were higher when predictions were made from related families and from larger training populations, whereas predicting from unrelated families caused the variance of the estimated breeding values to be biased downwards.
  
  
  CONCLUSIONS
  We have demonstrated that there are good perspectives for GS implementation in perennial ryegrass breeding, and that problems resulting from low linkage disequilibrium (LD) can be reduced by the presence of structure and related families in the breeding population. While comprehensive Genome Wide Association analysis is difficult in species with extremely low LD, we did identify variants proximal to genes with a known role in flowering time (e.g. CONSTANS and Phytochrome C).
authors.affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé 20, 8830, Tjele, Denmark. dfe@dlf.com.|DLF A/S, Research Division, Højerupvej 31, 4660, Store Heddinge, Denmark. dfe@dlf.com.
authors.forename: Dario
authors.initials: D
authors.lastname: Fè
authors.affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé 20, 8830, Tjele, Denmark. fabio.cericola@mbg.au.dk.
authors.forename: Fabio
authors.initials: F
authors.lastname: Cericola
authors.affiliation: Department of Molecular Biology and Genetics, Crop Genetics and Biotechnology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark. stephen.byrne@mbg.au.dk.
authors.forename: Stephen
authors.initials: S
authors.lastname: Byrne
authors.affiliation: DLF A/S, Research Division, Højerupvej 31, 4660, Store Heddinge, Denmark. il@dlf.dk.
authors.forename: Ingo
authors.initials: I
authors.lastname: Lenk
authors.affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé 20, 8830, Tjele, Denmark. bilal.ashraf@mbg.au.dk.
authors.forename: Bilal Hassan
authors.initials: BH
authors.lastname: Ashraf
authors.affiliation: DLF A/S, Research Division, Højerupvej 31, 4660, Store Heddinge, Denmark. mg@dlf.dk.
authors.forename: Morten Greve
authors.initials: MG
authors.lastname: Pedersen
authors.affiliation: DLF A/S, Research Division, Højerupvej 31, 4660, Store Heddinge, Denmark. nr@dlf.dk.
authors.forename: Niels
authors.initials: N
authors.lastname: Roulund
authors.affiliation: Department of Molecular Biology and Genetics, Crop Genetics and Biotechnology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark. torben.asp@mbg.au.dk.
authors.forename: Torben
authors.initials: T
authors.lastname: Asp
authors.affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé 20, 8830, Tjele, Denmark. luc.janss@mbg.au.dk.
authors.forename: Luc
authors.initials: L
authors.lastname: Janss
authors.affiliation: DLF A/S, Research Division, Højerupvej 31, 4660, Store Heddinge, Denmark. csj@dlf.com.
authors.forename: Christian Sig
authors.initials: CS
authors.lastname: Jensen
authors.affiliation: Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé 20, 8830, Tjele, Denmark. just.jensen@mbg.au.dk.
authors.forename: Just
authors.initials: J
authors.lastname: Jensen
mesh_terms: D001947:Breeding; D005828:Genetics, Population; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D015810:Linkage Disequilibrium; D008129:Lolium / Q000235:genetics*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable; D015203:Reproducibility of Results; D012641:Selection, Genetic