title: Implementation of Genomic Prediction in Lolium perenne (L.) Breeding Populations.
abstract: Perennial ryegrass (Lolium perenne L.) is one of the most widely grown forage grasses in temperate agriculture. In order to maintain and increase its usage as forage in livestock agriculture, there is a continued need for improvement in biomass yield, quality, disease resistance, and seed yield. Genetic gain for traits such as biomass yield has been relatively modest. This has been attributed to its long breeding cycle, and the necessity to use population based breeding methods. Thanks to recent advances in genotyping techniques there is increasing interest in genomic selection from which genomically estimated breeding values are derived. In this paper we compare the classical RRBLUP model with state-of-the-art machine learning techniques that should yield themselves easily to use in GS and demonstrate their application to predicting quantitative traits in a breeding population of L. perenne. Prediction accuracies varied from 0 to 0.59 depending on trait, prediction model and composition of the training population. The BLUP model produced the highest prediction accuracies for most traits and training populations. Forage quality traits had the highest accuracies compared to yield related traits. There appeared to be no clear pattern to the effect of the training population composition on the prediction accuracies. The heritability of the forage quality traits was generally higher than for the yield related traits, and could partly explain the difference in accuracy. Some population structure was evident in the breeding populations, and probably contributed to the varying effects of training population on the predictions. The average linkage disequilibrium between adjacent markers ranged from 0.121 to 0.215. Higher marker density and larger training population closely related with the test population are likely to improve the prediction accuracy.
authors.affiliation: Manchester Institute of Biotechnology, University of Manchester Manchester, UK.
authors.forename: Nastasiya F
authors.initials: NF
authors.lastname: Grinberg
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK.
authors.forename: Alan
authors.initials: A
authors.lastname: Lovatt
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK.
authors.forename: Matt
authors.initials: M
authors.lastname: Hegarty
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK.
authors.forename: Andi
authors.initials: A
authors.lastname: Lovatt
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK.
authors.forename: Kirsten P
authors.initials: KP
authors.lastname: Skøt
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK.
authors.forename: Rhys
authors.initials: R
authors.lastname: Kelly
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK.
authors.forename: Tina
authors.initials: T
authors.lastname: Blackmore
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK.
authors.forename: Danny
authors.initials: D
authors.lastname: Thorogood
authors.affiliation: Manchester Institute of Biotechnology, University of Manchester Manchester, UK.
authors.forename: Ross D
authors.initials: RD
authors.lastname: King
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK.
authors.forename: Ian
authors.initials: I
authors.lastname: Armstead
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK; CGIAR Consortium, CGIAR Consortium OfficeMontpellier, France.
authors.forename: Wayne
authors.initials: W
authors.lastname: Powell
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK.
authors.forename: Leif
authors.initials: L
authors.lastname: Skøt
keywords: BLUP; forage crop; genomic selection; machine learning; perennial ryegrass