G2H: A Precise Block-Scanning Strategy for Genetic Background Assessment in Maize Backcross Breeding

(1) Background: Backcross (BC) breeding is a key technology of crop improvement, yet its efficiency largely depends on the precise assessment of the genetic background recovery. Conventional molecular marker-assisted techniques suffer from inadequate genomic coverage or an inability to resolve true chromosomal structure. (2) Methods: To address major issues in maize BC breeding, we devised a G2H block-scanning strategy. This approach converts high-density point markers into haplotype blocks, enabling precise evaluation of the genetic background in backcross progenies. A key innovation is the CFDI, which quantifies the distribution of unrecovered fragments, allowing for visual tracking of chromosomal recombination and identification of ideal individuals with both a high genetic background recovery rate and few small fragments retention. (3) Results: We validated the accuracy and effectiveness of the G2H strategy across multiple backcross generations. Through enabling a precise “point-to-line-to-area” panoramic assessment of genetic background, G2H provides a powerful tool for developing ideal breeding materials with pure genetic background and minimized linkage drag. (4) Conclusions: Notably, this strategy significantly shortens the breeding cycle by 2–3 generations compared to conventional background assessment methods, thereby accelerating precision molecular design breeding in crops.