Multi-Year Dynamics of Single-Step Genomic Prediction in an Applied Wheat Breeding Program

Abstract

The availability of cost-efficient genotyping technologies has facilitated the implementation of genomic selection into numerous breeding programs. However, some studies reported a superiority of pedigree over genomic selection in line breeding, and as, aside from systematic record keeping, no additional costs are incurring in pedigree-based prediction, the question about the actual benefit of fingerprinting several hundred lines each year might suggest itself. This study aimed thus on shedding some light on this question by comparing pedigree, genomic, and single-step prediction models using phenotypic and genotypic data that has been collected during a time period of ten years in an applied wheat breeding program. The mentioned models were for this purpose empirically tested in a multi-year forward prediction as well as a supporting simulation study. Given the availability of deep pedigree records, pedigree prediction performed similar to genomic prediction for some of the investigated traits if preexisting information of the selection candidates was available. Notwithstanding, blending both information sources increased the prediction accuracy and thus the selection gain substantially, especially for low heritable traits. Nevertheless, the largest advantage of genomic predictions can be seen for breeding scenarios where such preexisting information is not systemically available or difficult and costly to obtain.

Genomic selection of parents and crosses beyond the native gene pool of a breeding program

“…Aside from enlarging training populations, the interest of testing germplasm coming from other regions and plant breeding programs lies in the opportunity to estimate the breeding value of potential elite parents developed outside a given breeding program. Although some studies reported similar accuracies for the prediction of genomic-based and pedigree-based breeding values if phenotypic information is already available (Juliana et al, 2020;Michel et al, 2020a), producing such information would require a reallocation of resources, which are usually reserved for testing a breeder's own cultivar candidates. Furthermore, pedigree information for plant material from other programs is in most cases scarce and not systematically available, rendering the genomic selection of potential crossing parents and combinations an interesting strategy.…”

Accuracy of Selection in Early Generations of Field Pea Breeding Increases by Exploiting the Information Contained in Correlated Traits

“…Genomic relationship information is expected to improve accuracy of PBV especially when combined with pedigree information [52,56,58,59]. It will be relatively simple to combine genomic analysis (GBLUP) and pedigree analysis (ABLUP) in single-step or hybrid BLUP (HBLUP) analysis [60][61][62][63]. GBLUP was used for selection of non-inbred progeny of wheat by Bonnett et al [64], and we expect that accuracy of PBV on non-inbred progeny will be improved further when pedigree and genomic information are combined in HBLUP.…”

Improving the efficiency of multi-location field trials with complete and incomplete relationship information

“…Although the estimated experimental efficiency and accuracy was highest with complete genomic relationship information in the study at hand, a marked advantage was likewise observed when utilizing pedigree records for modelling relationship. The latter resulted in lower accuracies in comparison to a genomic prediction of non-phenotyped individuals (Auinger et al 2016;Cericola et al 2017) as the Mendelian sampling term i.e., segregation within families cannot be addressed in such a case, but pedigree best linear unbiased predictions can readily distinguish between family members if phenotypic observations are already available for them (Michel et al 2020).…”