A Similarity Matrix for Preserving Haplotype Diversity Amongst Parents in Genomic Selection

In genomic selection, balancing genetic gain with the preservation of genetic diversity is a critical challenge, requiring innovative approaches to parent selection. Traditional methods risk losing valuable genetic diversity by not fully accounting for the complex patterns of haplotype distribution. To address this, we developed a novel haplotype similarity measure that estimates the genetic similarity amongst offspring from parent pairs by analysing segregating marker patterns and the covariance of additive genetic effects between potential parental gametes. This measure is encapsulated in a novel similarity matrix that quantifies parental genetic relationships and their Mendelian sampling variance, facilitating the selection of parents with diverse haplotypes to maintain genetic diversity. Our method was evaluated through simulation studies and empirical data analysis, indicating that the similarity matrix can help preserve haplotype diversity and potentially improve long-term genetic gains compared to traditional selection methods. These results suggest that the similarity matrix could contribute to more efficient and sustainable genomic selection programs, although further research is necessary to fully understand its impact.