An NGS approach for the identification of precise homoeologous recombination sites between A and C genomes in genus.

The introgression of heterologous genomes through interspecific hybridization offers a great opportunity to expand the gene pool of crops, thereby broadening the traits that can be targeted for improvement. The introgression of C genomic regions carrying desirable traits from (AACC) into the diploid (AA) via homoeologous recombination (HR) has been commonly used. However, the precise identification of HR sites remains a significant challenge, limiting the practical application of genome introgression via HR in breeding programs. Here, we developed an indicator named 'Dosage-score' from the coverage depth of next-generation sequencing reads. Then, Dosage-score analysis applied to both in BCF individuals obtained by backcrossing to F progeny ( × ) and in the parental lines, and successfully identified the precise HR sites resulting from F meiosis as well as those that were native in the parental genome. Additionally, we introgressed the C6 segment from HR identified by Dosage-score analysis into genome background, revealing gene expression on the added segment without noticeable phenotypic change. The identification of HR by Dosage-score analysis will contribute to the expansion of the gene pool for breeding by introgression of heterologous genomes in crops.