Maize (Zea mays L.) is the most extensively cultivated food crop in China, and current studies on maize general combining ability (GCA) focus primarily on the genetic basis of traits. However, the dynamic trends and underlying genetic loci associated with GCA for yield-related traits during breeding remain underexplored. This study was designed to investigate the changing trends of the general combining ability (GCA) and the frequency of elite alleles among 218 major maize inbred lines from Northeast China, spanning the 1970s to the 2010s. PH6WC and PH4CV were used as testers to develop 436 hybrid combinations via the North Carolina design II (NCII) method, and these combinations were evaluated across three environments. We further analyzed the combining ability (particularly the GCA) of 16 yield-related traits and their dynamic trends during breeding, grouped into three age periods (AGE1: 1960s–1970s; AGE2: 1980s–1990s; AGE3: 2000s–2010s). We also screened for genetic loci associated with the GCA effects of these traits. Results show that breeding selection significantly affected the GCA of six yield-related traits (ear length (EL), tassel branch number (TBN), tassel main axis length (TL), kernel length (KL), stem diameter (SDR), and hundred kernel weight (HKW)). Specifically, the mean TBN_GCA value decreased from 2.51 in AGE1 to −1.28 in AGE3, and the mean HKW_GCA increased from −1.58 in AGE1 to 0.36 in AGE3. Yield per plant GCA (YPP_GCA) was positively correlated with the GCA values of EL, ear diameter (ED), kernel row number (KRN), kernel number per row (KNPR), and HKW. Association analysis identified 38 single nucleotide polymorphisms (SNP_S) related to GCA. The T/T alleles for TBN were absent in AGE1, emerged in AGE2 (1980s–1990s), and persisted in AGE3—consistent with the decreasing trend of TBN_GCA from AGE1 to AGE3. For HKW, the A/A alleles not only exhibited higher GCA (effectively improving the HKW_GCA of inbred lines) but also showed an 11% increase in allelic frequency from AGE1 to AGE3. Taken together, these results suggest that the accumulation of elite alleles is the primary factor driving the GCA improvement during maize breeding in Northeast China.

Single-replicate field trials are common in early-stage maize hybrid screening, but raw plot observations contain field noise that can weaken genomic prediction. We evaluated whether pedigree and spatial adjustment improve the predictability of phenotypic targets and Top-N recovery, whether joint pedigree-spatial adjustment provides complementary gains, and whether target construction has a larger influence than baseline model choice. Across four sites, five agronomic traits, four phenotypic inputs, and six genomic prediction models, pedigree-corrected phenotypes (Ped) increased mean predictive ability from 0.465 ± 0.157 for raw observations (Raw) to 0.573 ± 0.131 and increased upper-tail Top-20 recall from 0.558 ± 0.146 to 0.656 ± 0.146 under a 20% predicted retention window. Spatial correction alone (Spa) was less predictable than Raw, whereas joint pedigree-spatial correction (Ped+Spa) improved over Raw but did not exceed Ped. Phenotypic input explained substantially more variation in predictive ability than model choice, whose main effect was not significant (F5428 = 1.59, p = 0.161). These results support pedigree correction as a useful target-construction strategy in the evaluated single-replicate trials while showing that spatial adjustment is conditional on model adequacy and trial structure. Top-N recall directly represents favorable direction recovery for grain yield; for grain moisture, plant height, ear height, and silking date, the archived upper-tail metric is interpreted as rank consistency because the favorable direction or ideotype is breeding-program-dependent.