Seed vigor is one of the key determinants of seed quality in maize, directly influencing emergence rate, seedling growth, and stand uniformity, thereby affecting final yield formation. This study aimed to identify high-vigor inbred lines and hybrids, uncover key genes involved in regulating seed germination, and provide a theoretical basis for breeding high-vigor maize varieties.

Twenty-two maize inbred lines from two heterotic groups, Shaan A Group and Shaan B Group, were used to produce 104 F₁ hybrids following an NC-Ⅱ mating design. Seed vigor was evaluated under both the standard germination test and the cold soaking germination test. Nine traits were recorded, including germination energy (GE), germination percentage (GP), germination index (GI), seedling length (SL), root length (RL), dry weight (DW), vigor index I (VIⅠ), vigor index Ⅱ (VIⅡ), and vigor index Ⅲ (VIⅢ). Genotypic and phenotypic data were combined to perform a genome-wide association study (GWAS) for major traits. Quantitative trait nucleotides (QTNs) significantly associated with seed vigor were identified. Public transcriptome data were further used to screen potential candidate genes and to predict their possible functions.

Significant genetic variation was observed for seed vigor–related traits in both inbred lines and hybrids. Compared with the standard germination test, cold soaking treatment reduced GE, GP, and GI, and increased the range of phenotypic variation among genotypes. Most traits showed significant effects of genotype, treatment, and their interaction, indicating that seed vigor is mainly controlled by genetic factors. Germination traits were positively correlated with seedling growth traits and vigor indices. Several materials showed stable performance under different germination conditions and low sensitivity to cold soaking. Hybrids derived from KA105, KA088, KA085, and KA205 of the Shaan A Group, and KB088, KB060, KB168, KB076, and KB021 of the Shaan B Group maintained relatively high seed vigor under cold soaking conditions. Some inbred lines with moderate seed vigor were able to improve hybrid performance in specific combinations. GWAS detected 43 QTNs significantly associated with seed vigor, including seven loci that were shared by two or more traits under cold soaking conditions. Based on transcriptome data, 11 candidate genes were identified, of which eight had functional annotation and were mainly related to stress response and transcription regulation.

Maize seed vigor is a quantitative trait under genetic control, and genetic variation is the main source of phenotypic differences. Seed vigor is regulated by multiple loci, with key genomic regions involved under low-temperature conditions. The accumulation of favorable alleles can improve seed vigor in hybrids, and hybrid performance is also influenced by specific genetic interactions between parents.

By analyzing the yield of the hybrids from the inbred lines bred from the Shaan A and Shaan B group, the combining ability of the inbred lines were evaluated, genome-wide association analysis, and mining associated loci for yield and its combining ability conducted. It will provide references for improving maize inbred lines selected from Shaan A group and Shaan B group and applying them in varieties breeding.

Based on NCⅡ genetic design, 85 excellent inbred lines from Shaan A group and Shaan B group were used to construct a hybrid population containing 246 F₁. Then, the yield of the hybrid population was tested in three environments to evaluate their general combining ability (GCA) and special combining ability (SCA). Using the 6H90K maize array to detect the parental genotypes, 63 879 high-quality SNPs were obtained, which were used to analyze the genetic characteristics of parental lines. According to the parental genotypes, 55 951 high-quality SNPs were inferred in the hybrid population for genome-wide association analysis of hybrid yield, GCA, and SCA using additive model and non-additive model. Meanwhile, candidate genes around the significant SNPs were screened and annotated based on the maize B73 reference genome.

The yield in the three environments accorded to the normal distribution with wide variation, the broad-sense heritability of yield was 59.04%, and the environmental effect was significant. There was significant positive correlation between hybrid yield and combining ability, and the correlation between hybrid yield and SCA (r=0.95) was higher than that between hybrid yield and GCA (r=0.62). The genetic characteristic of Shaan A group and Shaan B group was different, and inbred lines from Shaan A group have higher general combining ability. Totally, five, seven and nine significant SNPs were detected (-log₁₀(P)>3.86) for GCA, hybrid yield and SCA, respectively. Among them, four SNPs were co-located in hybrid yield and SCA. Ultimately, 17 associated SNPs were anchored. Dominant allele analysis of different trait-associated loci showed that four GCA-associated SNPs were controlled by additive effects, and the F₁ BLUE-associated loci could be divided into 4 types mainly by the dominant effect, and the heterozygous genotype is the favorite allele or sub-optimal allele for yield in F₁. Through functional annotation, the candidate genes were specifically expressed in maize growth and kernel establishment, for example, GRMZM2G165828 and GRMZM2G057557 were related to maize kernel development.

Based on this study, we consider that GCA and SCA jointly affect the yield of hybrids, and the effect of SCA is greater. Moreover, GCA and SCA may have different genetic basis, and GCA can be increased with the accumulation of favorable alleles. Using the genome-wide association analysis in the F₁ hybrid population can carry out genetic analysis related to combining ability, mine the genetic loci related to yield and combining ability, and accelerated the application of the associated loci in molecular breeding.