Population genetics of Chinese maize landraces reveals local adaptation and underutilized breeding potential

Seven distinct genetic groups in Chinese maize landraces are shaped by local adaptation. Genomic contributions from landraces to inbred lines are enriched for genes associated with stress resistance and flowering regulation. Landraces harbor unique, untapped favorable alleles for key traits, offering resources to diversify modern breeding. Maize landraces, shaped by long-term adaptation to diverse environments, represent an invaluable but underexplored resource for modern breeding. Despite their potential, the genetic architecture and breeding value of Chinese maize landraces remain poorly characterized. In this study, we established a global diversity panel comprising 3,187 maize landraces, including 2,042 accessions from China, and integrated genomic data from teosintes and modern inbred lines to trace the evolutionary and breeding history of maize. We delineated Chinese landraces into seven distinct genetic groups, whose spatial distribution closely aligns with major agro-ecological zones in China, revealing a genetic structure profoundly influenced by local adaptation. Notably, TreeMix and f d analyses revealed significant gene flow between the Chinese landrace group CL3, which primarily distributed in the Huang-Huai-Hai plain, and the Sipingtou (SPT) inbred lines. Furthermore, XP-CLR analysis indicated that the selected regions encompass genes associated with abiotic stress response, flowering and photoperiod regulation, and growth processes, highlighting the functional relevance of landrace-derived alleles. Through genome-wide association studies (GWAS), we identified numerous candidate genes for key traits, including known flowering regulator ZCN8 and disease resistance gene OPR8. Although modern breeding has efficiently accumulated favorable alleles for desired traits, landraces retain unique favorable alleles, particularly in flowering time and disease resistance, which are largely untapped. This study provides a comprehensive genetic resource and unveils the evolutionary and breeding dynamics of Chinese maize landraces. Our findings underscore the necessity of targeted utilization of landrace diversity to broaden the genetic base and enhance resilience in future maize breeding.