Flexible linear mixed models for complex data in horticultural tree breeding

C. Hardner, J. De Faveri
Response to selection and improved confidence in the value of new germplasm from breeding is dependent on objective and accurate prediction of genetic effects from available data. However, data from horticultural tree crop breeding may be complex. Here we review opportunities for implementing linear mixed models (LMM) for several examples of complex data in horticultural tree crop breeding to obtain the best (most accurate) and unbiased predictions (BLUPs) of the genetic effect of candidates. Firstly, LMM theory for a simple field trial is presented. We then extend LMMs for multiple random observations within an experimental unit (level at which genetic treatment is applied) and demonstrate that multiple sampling from a single tree cannot be considered replication of genetic effect and will lead to incorrect estimates of heritability. Many traits exhibit a trend with tree age, and LMMs are presented that allow for heterogenous genetic and residual variances, and correlations, among repeated measures across experimental units. Thirdly, LMMs that account for within trial spatial variation and spatio-temporal correlation are presented. Fourthly, the flexibility of LMM to model complex data from multi-environment trials and to evaluate genotype-by-environment interaction is discussed, and extended to multi-trial, season within trial, and trait data. Lastly, we describe the use of LMM for data generated from complex multi-tier designs. The examples discussed here demonstrate the flexibility of LMMs modelling complex data in horticultural tree crops breeding and biases that can occur with incorrect or simpler models.
Hardner, C. and De Faveri, J. (2023). Flexible linear mixed models for complex data in horticultural tree breeding. Acta Hortic. 1362, 139-146
DOI: 10.17660/ActaHortic.2023.1362.19
unbalanced data, repeatability model, pseudo-replication, repeated measures, spatial analysis, genotype-by-environment interaction

Acta Horticulturae