Παρασκευή 6 Ιανουαρίου 2017

Persistency of Prediction Accuracy and Genetic Gain in Synthetic Populations Under Recurrent Genomic Selection

Recurrent selection (RS) has been used in plant breeding to successively improve synthetic and other multiparental populations. Synthetics are generated from a limited number of parents (Np), but little is known about how Np affects genomic selection (GS) in RS, especially the persistency of prediction accuracy and genetic gain. Synthetics were simulated by intermating Np= 2 to 32 parent lines from an ancestral population with short- or long-range linkage disequilibrium (LDA) and subjected to multiple cycles of GS. We determined accuracy and genetic gain across 30 cycles for different training set (TS) sizes, marker densities, and generations of recombination before model training. Contributions to accuracy and genetic gain from pedigree relationships as well as from co-segregation and LDA between QTL and markers were analyzed via four scenarios differing in (i) the relatedness between TS and selection candidates and (ii) whether selection was based on markers or pedigree records. Persistency of accuracy was high for small N_p, where predominantly co-segregation contributed to accuracy, but also for large Np, where LDA replaced co-segregation as dominant information source. Together with increasing genetic variance, this compensation resulted in relatively constant long- and short-term genetic gain for increasing Np larger than 4, given long-range LDA in the ancestral population. Although our scenarios suggest that information from pedigree relationships contributed only for very few generations to accuracy in GS, we expect a longer contribution than in pedigree BLUP, because capturing Mendelian sampling by markers reduces selective pressure on pedigree relationships. Larger TS and higher marker density improved persistency of accuracy and hence genetic gain, but additional recombinations could not increase genetic gain.



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