Heritability in Plant Breeding on a Genotype-Difference Basis

In plant breeding, heritability is often calculated (i) as a measure of precision of trials and/or (ii) to compute the response to selection. It is usually estimated on an entry-mean basis, since the phenotype is usually an aggregated value, as genotypes are replicated in trials, which stands in contrast with animal breeding and human genetics. When this was first proposed, assumptions such as balanced data and independent genotypic effects were made that are often violated in modern plant breeding trials/analyses. Due to this, multiple alternative methods have been proposed, aiming to generalize heritability on an entry-mean basis. In this study, we propose an extension of the concept for heritability on an entry-mean to an entry-difference basis, which allows for more detailed insight and is more meaningful in the context of selection in plant breeding, because the correlation among entry means can be accounted for. We show that under certain circumstances our method reduces to other popular generalized methods for heritability estimation on an entry-mean basis. The approach is exemplified via four examples that show different levels of complexity, where we compare six methods for heritability estimation on an entry-mean basis to our approach (example codes: https://github.com/PaulSchmidtGit/Heritability). Results suggest that heritability on an entry-difference basis is a well-suited alternative for obtaining an overall heritability estimate, and in addition provides one heritability per genotype as well as one per difference between genotypes.