Meiotic recombination assembles complementary parental alleles in an elite soybean line

Crop hybrid breeding relies on homologous recombination to generate novel allele combinations that facilitate the assembly of superior agronomic traits. However, the extent to which recombination shapes elite phenotypes at the genomic and transcriptomic levels remains insufficiently understood. In this study, we investigated the genetic architecture underlying elite trait formation in soybean using an integrative parent–offspring trio strategy. We performed whole-genome resequencing and transcriptome profiling of two parental cultivars and their elite offspring line, HX3, which exhibits improved performance in plant height, flowering time, and yield-related traits. High-density single-nucleotide polymorphism markers enabled reconstruction of the recombination landscape and delineation of the mosaic genomic structure of HX3, revealing extensive reshuffling of parental haplotypes through meiotic crossovers. By integrating genotype, phenotype, and gene expression data, we traced the parental origins of loci associated with key traits and identified candidate genes linked to elite performance. Genes regulating plant architecture and flowering time were predominantly inherited from the paternal parent, whereas those associated with photosynthesis, grain quality, disease resistance, and abiotic stress tolerance were mainly derived from the maternal parent. Together, our results provide insight into how meiotic recombination assembles complementary parental alleles that contribute to elite phenotypes and demonstrate the value of trio-based approaches for dissecting trait formation in crop breeding.