David Vanavermaete, Jan Fostier, Steven Maenhout & Bernard De Baets

Theoretical and Applied Genetics December 2021; vol. 134: 3845–3861

Key message

The deep scoping method incorporates the use of a gene bank together with different population layers to reintroduce genetic variation into the breeding population, thus maximizing the long-term genetic gain without reducing the short-term genetic gain or increasing the total financial cost.

Abstract

Genomic prediction is often combined with truncation selection to identify superior parental individuals that can pass on favorable quantitative trait locus (QTL) alleles to their offspring. However, truncation selection reduces genetic variation within the breeding population, causing a premature convergence to a sub-optimal genetic value. In order to also increase genetic gain in the long term, different methods have been proposed that better preserve genetic variation. However, when the genetic variation of the breeding population has already been reduced as a result of prior intensive selection, even those methods will not be able to avert such premature convergence. Pre-breeding provides a solution for this problem by reintroducing genetic variation into the breeding population. Unfortunately, as pre-breeding often relies on a separate breeding population to increase the genetic value of wild specimens before introducing them in the elite population, it comes with an increased financial cost. In this paper, on the basis of a simulation study, we propose a new method that reintroduces genetic variation in the breeding population on a continuous basis without the need for a separate pre-breeding program or a larger population size. This way, we are able to introduce favorable QTL alleles into an elite population and maximize the genetic gain in the short as well as in the long term without increasing the financial cost.

See https://link.springer.com/article/10.1007/s00122-021-03932-w

Fig.1: Mean genetic value (GV) of the top-10 individuals in the breeding population using the population merit method (left) and the scoping method (right) after first applying 0, 5, or 20 breeding cycles (BC) of truncation selection (black line). When the genetic variation of the breeding population is already reduced by means of truncation selection, both the population merit method and the scoping method result in a lower genetic value