Genetic Trends in General Combining Ability for Maize Yield-Related Traits in Northeast China

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.