Implications of using genomic prediction within a high-density SNP dataset to predict DUS traits in barley

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Huw Jones, Ian Mackay

Abstract

Alternative methods for genomic prediction of traits and trait differences are compared and recommendations made. We make recommendations for implementing methods in the context of DUS testing. High-throughput genotyping provides an opportunity to explore the application of genotypes in predicting plant phenotypes. We use a genome-wide prediction model to estimate the contribution of all loci and sum over multiple minor effects to predict traits. A potential use is in plant variety protection to discriminate among varieties on distinctness. We investigate this use with alternate scenarios in a set of 431 winter and spring barley varieties, with trait data from UK DUS trials comprising 28 characteristics, together with SNP genotype data. Firstly, each trait is predicted from genotypes by ridge regression with discrimination among varieties using predicted traits. Secondly, squared trait differences between each pair of varieties are regressed on genetic distances between each variety by ridge regression, with discrimination among varieties using the predicted squared trait differences directly. This latter approach is analogous to the use of phenotype and marker differences introduced to human genetic linkage analysis by Haseman...Continue Reading

References

Mar 1, 1972·Behavior Genetics·J K Haseman, R C Elston
Aug 6, 2002·American Journal of Human Genetics·Eleanor Feingold
Jul 25, 2009·Genetic Epidemiology·Yun J YooUNKNOWN Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications Research Group
Dec 8, 2009·BMC Genomics·Timothy J CloseRobbie Waugh
Dec 1, 2010·Proceedings of the National Academy of Sciences of the United States of America·James CockramDonal M O'Sullivan
Dec 13, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Huw JonesIan Mackay

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Citations

May 3, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Seyed Hossein JamaliLee T Hickey

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