Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices

Abstract

Diverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomic mate selection criteria suitable for organisms of arbitrary homozygosity level where the full-sibling progeny are of direct interest as future parents and/or cultivars. We extended cross variance and covariance variance prediction to include dominance effects and predicted the multivariate selection index genetic variance of crosses based on haplotypes of proposed parents, marker effects and recombination frequencies. We combined the predicted mean and variance into usefulness criteria for parent and variety development. We present an empirical study of cassava (Manihot esculenta), a staple tropical root crop. We assessed the potential to predict the multivariate genetic distribution (means, variances and trait covariances) of 462 cassava families in terms of additive and total value using cross-validation. Most variance (89%) and covariance (70%) prediction accuracy estimates were greater than zero. The usefulness of crosses were accurately predicted with good correspondence between the predicted and the actual mean performance of family members breeders selected for advancement as new parents and candidate varieties. We also used a directional dominance model to quantify significant inbreeding depression for most traits. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with top breeding values) and varieties (progeny with top own performance).

The potential of genome-wide prediction to support parental selection, evaluated with data from a commercial barley breeding program

“…The results presented in the underlying study largely correspond to ndings obtained from a cassava breeding program (Wolfe et al 2021). In cassava, median prediction abilities for the usefulness criterion predicted by the UFC ranged from 0.1 to 0.83 in a cross-validated scenario and 95% of the prediction abilities were greater than zero, assuming a heritability of h 2 = 1 and varying selection intensities per family.…”

“…In cassava, median prediction abilities for the usefulness criterion predicted by the UFC ranged from 0.1 to 0.83 in a cross-validated scenario and 95% of the prediction abilities were greater than zero, assuming a heritability of h 2 = 1 and varying selection intensities per family. Wolfe et al (2021) similarly described low differences between the prediction abilities for the family mean and the UFC and reported a high correlation of both.…”

“…Besides the mean, the genetic variance of the family resulting from a cross is the most important factor for its superiority and is therefore considered in the UFC. Despite an increasing number of publications proposing to predict the family mean and variance for a speci c cross based on marker effects, proof of concepts using large-scale data from breeding programs are scarce (Wolfe et al 2021). The data set presented in our study was generated in the course of commercial winter barley breeding and was used to examine the potential and limitations of predicting the UFC to identify optimal parent combinations.…”

The Potential of Genome-Wide Prediction to Support Parental Selection, Evaluated with Data from a Commercial Barley Breeding Program

“…Despite an increasing number of publications proposing to predict the family mean and variance for a specific cross based on marker effects, proof of concepts based on comprehensive data sets are scarce. A recent attempt used a dataset from a cassava breeding program and yielded disappointing results [ 18 ]. In our study, we investigated the potential and limitations of predicting the UFC to identify optimal parent combinations using a data set generated in the course of commercial winter barley breeding.…”

“…All the aforementioned studies showed very promising results but assumed that marker effects were known [ 10 , 11 , 12 , 14 , 15 , 16 ] or estimated marker effects considering genomic and phenotypic data of the populations whose UFC should be predicted [ 17 ]. In a study on cassava [ 18 ], marker effects and UFC were estimated in separate training and testing populations, yielding disappointing results.…”