Genotyping crossing parents and family bulks can facilitate cost-efficient genomic prediction strategies in small-scale line breeding programs

KEY MESSAGE: Genomic relationship matrices based on mid-parent and family bulk genotypes represent cost-efficient alternatives to full genomic prediction approaches with individually genotyped early generation selection candidates. ABSTRACT: The routine usage of genomic selection for improving line varieties has gained an increasing popularity in recent years. Harnessing the benefits of this approach can, however, be too costly for many small-scale breeding programs, as in most genomic breeding strategies several hundred or even thousands of lines have to be genotyped each year. The aim of this study was thus to compare a full genomic prediction strategy using individually genotyped selection candidates with genomic predictions based on genotypes obtained from pooled DNA of progeny families as well as genotypes inferred from crossing parents. A population of 722 wheat lines representing 63 families tested in more than 100 multi-environment trials during 2010–2019 was for this purpose employed to conduct an empirical study, which was supplemented by a simulation with genotypic data from further 3855 lines. A similar or higher prediction ability was achieved for grain yield, protein yield, and the protein content when using mid-parent or family bulk genotypes in comparison with pedigree selection in the empirical across family prediction scenario. The difference of these methods with a full genomic prediction strategy became furthermore marginal if pre-existing phenotypic data of the selection candidates was already available. Similar observations were made in the simulation, where the usage of individually genotyped lines or family bulks was generally preferable with smaller family sizes. The proposed methods can thus be regarded as alternatives to full genomic or pedigree selection strategies, especially when pedigree information is limited like in the exchange of germplasm between breeding programs. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00122-021-03794-2.