Maize breeding germplasm used in Southwest China has high complexity because of the diverse ecological features of this area. In this study, the population structure, genetic diversity, and linkage disequilibrium decay distance of 362 important inbred lines collected from the breeding program of Southwest China were characterized using the MaizeSNP50 BeadChip with 56,110 single nucleotide polymorphisms (SNPs). With respect to population structure, two (Tropical and Temperate), three (Tropical, Stiff Stalk and non-Stiff Stalk), four [Tropical, group A germplasm derived from modern U.S. hybrids (PA), group B germplasm derived from modern U.S. hybrids (PB) and Reid] and six (Tropical, PB, Reid, Iowa Stiff Stalk Synthetic, PA and North) subgroups were identified. With increasing K value, the Temperate group showed pronounced hierarchical structure with division into further subgroups. The Genetic Diversity of each group was also estimated, and the Tropical group was more diverse than the Temperate group. Seven low-genetic-diversity and one high-genetic-diversity regions were collectively identified in the Temperate, Tropical groups, and the entire panel. SNPs with significant variation in allele frequency between the Tropical and Temperate groups were also evaluated. Among them, a region located at 130 Mb on Chromosome 2 showed the highest genetic diversity, including both number of SNPs with significant variation and the ratio of significant SNPs to total SNPs. Linkage disequilibrium decay distance in the Temperate group was greater (2.5–3 Mb) than that in the entire panel (0.5–0.75 Mb) and the Tropical group (0.25–0.5 Mb). A large region at 30–120 Mb of Chromosome 7 was concluded to be a region conserved during the breeding process by comparison between S37, which was considered a representative tropical line in Southwest China, and its 30 most similar derived lines. For the panel covered most of widely used inbred lines in Southwest China, this work representatively not only illustrates the foundation and evolution trend of maize breeding resource as a theoretical reference for the improvement of heterosis, but also provides plenty of information for genetic researches such as genome-wide association study and marker-assisted selection in the future.

When genomic prediction is implemented in breeding maize (Zea mays L.), it can accelerate the breeding process and reduce cost to a large extent. In this study, 11 yield-related traits of maize were used to evaluate four genomic prediction methods including rrBLUP, HEBLP|A, RF, and LightGBM. In all the 11 traits, rrBLUP had similar predictive accuracy to HEBLP|A, and so did RF to LightGBM, but rrBLUP and HEBLP|A outperformed RF and LightGBM in 8 traits. Furthermore, genomic prediction-based heterotic pattern of yield was established based on 64620 crosses of maize in Southwest China, and the result showed that one of the parent lines of the top 5% crosses came from temp-tropic or tropic germplasm, which is highly consistent with the actual situation in breeding, and that heterotic pattern (Reid+ × Suwan+) will be a major heterotic pattern of Southwest China in the future.