Characterizing the genomic consequence of diploid‐to‐haploid induction in potato using large‐scale whole‐genome sequencing

SUMMARY Reinventing the tetraploid potato as an inbred‐line‐based diploid crop has become an increasingly attractive strategy to accelerate genetic gain in potato breeding. During this process, haploid induction holds great potential, as it enables the rapid production of homozygous inbred lines. However, the genomic consequences of haploid induction remain largely unclear and controversial. Here, we systematically investigated the genomic outcomes of one diploid‐to‐haploid induction in potato using large‐scale whole‐genome sequencing. Starting from a heterozygous diploid genotype (YS1), we generated 779 haploid progeny and sequenced each genome to an average depth of ~15×. Leveraging these genomic data, we identified a rare aneuploid individual carrying an additional paternal genomic segment, constructed a high‐resolution recombination map at the individual gamete level, and assessed the associated de novo mutation burden arising during haploid induction. More importantly, we discovered and experimentally validated the introgression of genomic segments from haploid inducer (HI) into haploid progeny. Overall, our findings provide new insights into the genomic consequences of haploid induction in potato and shed light on the mechanisms underlying HI genome elimination. These results offer valuable guidance for optimizing haploid‐based breeding strategies and advancing the development of homozygous diploid inbred lines in this important crop.