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

## TL;DR

This study examines how the genetic potential for maize yield traits has changed in Northeast China over decades of breeding.

## Contribution

The study identifies specific genetic loci and allele frequency shifts that correlate with improved general combining ability in maize breeding.

## Key findings

- Six yield-related traits showed significant changes in general combining ability (GCA) over three breeding periods.
- Allele frequencies for tassel branch number and hundred kernel weight changed notably, aligning with GCA trends.
- Thirty-eight SNPs were associated with GCA effects, highlighting the role of elite allele accumulation in breeding improvements.

## Abstract

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 TBNGCA value decreased from 2.51 in AGE1 to −1.28 in AGE3, and the mean HKWGCA increased from −1.58 in AGE1 to 0.36 in AGE3. Yield per plant GCA (YPPGCA) 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 (SNPS) 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 TBNGCA from AGE1 to AGE3. For HKW, the A/A alleles not only exhibited higher GCA (effectively improving the HKWGCA 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.