Comparison of localGEBV and Optimal Haplotype Stacking Fitness Functions using a Novel R Package: HapSelect

Abstract

Haplotype-based breeding strategies have emerged as promising approaches to maximize long-term genetic gain by identifying complementary parental combinations while maintaining genetic diversity. However, these methods typically require phased genotypes and more intensive workflow pipelines and skillsets. We developed a novel local genomic estimated breeding value (localGEBV) fitness function with similar intent to the optimal haplotype stacking (OHS) framework fitness function and implemented both in the novel R package, HapSelect. Our aim was to evaluate whether phased haplotypes provide additional benefit over the more easily available dosage-based unphased genotypes in highly inbred crops. A subset of bread wheat nested association mapping (NAM) population comprising 444 lines genotyped with 6,054 DArT-Seq markers was analysed. Marker effects were estimated using rrBLUP, localGEBV and haplotype effects were calculated across linkage disequilibrium-defined haploblocks, and genetic algorithms (GA) were used to identify optimal sets of 30 founders using either a localGEBV derived fitness function with unphased, dosage inputs or the OHS fitness function with phased inputs. Selected parental sets were compared with conventional truncation selection (TS) through 150 generations of forward simulation. The OHS fitness function achieved a marginally greater optimized ultimate GEBV than the localGEBV fitness function during GA optimization, with only 18 of the 30 selected founders overlapped between the two methods. Despite these differences, forward simulations demonstrated nearly identical long-term genetic gain for localGEBV and OHS-selected founders, with both approaches outperforming conventional truncation selection by maintaining greater genetic diversity and delaying the genetic plateau. The minimal difference between localGEBV and OHS is likely attributable to the high homozygosity of the population, where localGEBV and haplotype effects are nearly confounded. These results demonstrate that dosage-based localGEBV provides a practical alternative to phased haplotype approaches for parent selection in inbred crops, substantially simplifying genomic workflows while maintaining long-term breeding performance. Future work should evaluate these methods in more diverse inbred populations and outbred species, where great haplotypic diversity may increase the advantage of true haplotype-based optimizations.