Abstract

Background. Maize is a crucial crop for global food security, and plant height is a key agronomic trait influencing growth, yield, and resistance to lodging. The genetic factors controlling plant height are complex and involve multiple genes and environmental interactions. Improving maize plant height has been a significant goal in breeding programs, as it directly affects yield potential and the efficiency of mechanized farming. In this study, we aimed to identify genetic loci associated with plant height variation across different maize breeding eras using a genome-wide association study (GWAS).
Methods. A GWAS was performed using a large panel of maize inbred lines representing three distinct breeding eras: the 1960s–1970s (CN1960&70s), 1980s–1990s (CN1980&90s), and 2000s–2010s (CN2000&10s). Shoot height data were collected from a controlled-environment greenhouse. . The dataset consisted of 380 maize inbred lines, and genotyping was performed using a 507-SNP panel to conduct the GWAS. In addition, selective sweep analysis was conducted to identify genes that might have been selected during different breeding periods. Functional validation of key candidate genes was performed using CRISPR-Cas9 gene editing technology .
Results. The study identified significant variation in shoot height across the different breeding eras. Modern breeding lines (CN2000&10s) exhibited notably taller plants compared to those from the 1960s–1970s (CN1960&70s) and 1980s–1990s (CN1980&90s). The selective sweep analysis revealed several key genes associated with plant height regulation, including ZmBR2, ZmLIL1, ZmNA1, ZmTE1, ZmSPL12, ZmBV1, ZmDIL1, ZmKN1, and ZmACS7, which influence traits like cell elongation, shoot apical meristem activity, and hormonal regulation. Furthermore, GWAS identified 3 significant SNPs on chromosome 1, 38 on chromosome 8, and 2 on chromosome 10, corresponding to 12 candidate genes. The functional validation of ZmGDCL, a gene identified on chromosome 8, confirmed its critical role in regulating shoot height through CRISPR-Cas9 knockout.
Conclusions. This study identifies several key genetic loci associated with plant height in maize and provides valuable insights into the genetic mechanisms that have shaped plant height variation across different breeding eras. The identified candidate genes, including ZmGDCL, offer promising targets for future maize breeding programs aimed at improving plant height and enhancing productivity. These findings contribute to our understanding of the genetic control of maize plant height and could aid in the development of more efficient breeding strategies for improved maize performance.