Genetic characterization of commercial spring maize germplasm in Northern China for hybrid breeding and trait improvement

Abstract

Introduction Commercial spring maize germplasm in northern China has been shaped by five decades of intensive breeding and the continual incorporation of elite domestic and introduced germplasm, but its genetic diversity, pedigree structure, and genomic signatures of selection remain incompletely characterized. Methods We re-sequenced 108 representative inbred lines from China’s commercial spring maize germplasm and combined them with 14 previously published key inbred lines. Population structure, genetic diversity, identity-by-descent, selective sweeps, and haplotype-trait associations were analyzed across seven heterotic groups. Results The 122 inbred lines represented nearly five decades of elite maize germplasm in northern China. Modern breeding materials showed reduced nucleotide diversity, with π decreasing from 1.58 × 10−3 to 1.34 × 10−3, and an increased deleterious mutation burden. We identified 275 Mb of high-impact IBD regions shared among elite germplasm, containing genes associated with flowering, plant architecture, photosynthesis, and grain quality. Selective sweep analyses detected genomic regions associated with agronomic traits including grain quality and floral organ development. Haplotype analyses further revealed natural alleles related to tassel structure, with differential allele frequencies between the SS and TSPT heterotic groups. Discussion These findings provide a genomic resource for northern Chinese commercial maize germplasm and support future heterotic group optimization, marker-assisted breeding, and genomic selection.