Genome-wide association study identifies genetic loci for soybean herbicide resistance in maize

Maize-soybean strip relay intercropping has become a key strategy for ensuring national grain and oil security and promoting sustainable agricultural development. However, weed control in this system remains challenging, and there is a severe shortage of maize germplasm resistant to herbicides commonly applied in soybean fields, which hinders the efficient implementation of this cropping model. In this work, a panel of 170 elite inbred lines and 735 landraces were evaluated for their responses to five soybean herbicides applied at the seedling stage. Chlorophyll content and injury rate were assessed after treatment.

The results revealed significant differences in herbicide-induced injury: chloransulam and lactofen caused relatively mild damage, while imazamox and clomazone resulted in the most severe injury. Population structure analysis classified the materials into nine inbred line subgroups and 12 landrace subgroups, indicating rich genetic diversity. Genome-wide association study identified 271 quantitative trait nucleotides (QTNs) associated with herbicide tolerance. A meta-analysis of QTNs further detected 10 consensus loci. Finally, a functional validation was performed for the chloransulam tolerance locus PZE-104,050,858, located at Chr4_S_87070067 on chromosome 4, where the G allele was significantly associated with tolerance.

This study provides important genetic insights into maize tolerance to soybean herbicides and establishes a practical foundation for germplasm screening and marker-assisted breeding, thereby supporting the sustainable advancement of maize-soybean strip intercropping system.