Abstract
Key Message
In genomic recurrent selection, the more markers, the better because they buffer the linkage disequilibrium losses caused by recombination over cycles, and consequently, provide higher responses to selection.
Abstract
Reductions of genotyping marker density have been extensively evaluated as potential strategies to reduce the genotyping costs of genomic selection (GS). Low-density marker panels are appealing in GS because they entail lower multicollinearity and computing time and allow more individuals to be genotyped for the same cost. However, statistical models used in GS are usually evaluated with empirical data, using "static" training sets and populations. This may be adequate for making predictions during a breeding program's initial cycles but not for the long-term. Moreover, studies that focus on long selective breeding cycles generally do not consider GS models with the effect of dominance, which is particularly important for breeding outcomes in cross-pollinated crops. Hence, dominance effects are important and unexplored in GS for long-term programs involving allogamous species. To address it, we employed two approaches: analysis of empirical maize datasets and simulations of long-term breeding applying phenotypic and genomic recurrent selection (intrapopulation and reciprocal schemes). In both schemes, we simulated twenty breeding cycles and assessed the effect of marker density reduction on the population mean, the best crosses, additive variance, selective accuracy, and response to selection with models [additive, additive-dominant, general (GCA), and this plus specific combining ability (GCA + SCA)]. Our results indicate that marker reduction based on linkage disequilibrium levels provides useful predictions only within a cycle, as accuracy significantly decreases over cycles. In the long-term, without training set updating, high-marker density provides the best responses to selection. The model to be used depends on the breeding scheme: additive for intrapopulation and additive-dominant or GCA + SCA for reciprocal.
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Codes and supporting data are available in: https://data.mendeley.com/datasets/96p3khhnzj/1.
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To the Queiroz College of Agriculture (University of São Paulo), the Federal University of Ceará, and the National Council for Scientific and Technological Development.
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JCD wrote the manuscript, discussion, contributing to ideas and graphs. HFC and FS contributed to the analysis of empirical data, in writing, mainly discussion. RFN elaborated on the hypothesis, conducted the analysis of the simulated experiments, interpreted the results, and contributed to the writing. All authors read and approved the final manuscript.
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DoVale, J.C., Carvalho, H.F., Sabadin, F. et al. Genotyping marker density and prediction models effects in long-term breeding schemes of cross-pollinated crops. Theor Appl Genet 135, 4523–4539 (2022). https://doi.org/10.1007/s00122-022-04236-3
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DOI: https://doi.org/10.1007/s00122-022-04236-3