A Pseudohaploid-Based Imputation Strategy for Interspecific F₁ Hybrids and Its Application in Genetic Analyses of...

Hybrid breeding is widely applied in agriculture and aquaculture. However, high-throughput genome-wide genotyping for interspecific hybrids remains challenging, limiting the further utilization of these hybrid resources. Here, we present a genotyping and imputation strategy for interspecific F₁ hybrids, which treats F₁ hybrids as pseudohaploids, aligns reads to a pseudogenome constructed by concatenating the genome assemblies of the two parental species, and retains reliable sites for imputation by filtering heterozygous sites and masking regions prone to interspecific misalignment. Subsequently, by using reference panels from the two parental species to separately impute corresponding intervals, the genotype information for these filtered sites can be recovered, ultimately achieving comprehensive and highly accurate haploid genotypes even at low sequencing depth. Based on the haploid genotypes and integrating transcriptome data, we successfully identified a growth-associated QTL and candidate genes, as well as a copy number variation that may affect growth in the hybrid scallops. Overall, this study provides a low-cost method for obtaining highly accurate interspecific F₁ hybrid genotypes with broad applicability and demonstrates its utility in practical interspecific analyses. It enables advanced genotype-based analytical methods and breeding approaches to be reasonably applied to interspecific F₁ hybrids and holds significant importance for promoting the further development of interspecific hybrid breeding as well as related ecological research.