Combination Genome-wide Association Study and Bulked Segregant Analysis Reveals the Loci Controlling Stalk Fiber Traits Related to Stalk Rot in Maize

Stalk rot is a widespread soil-borne disease that severely impacts both the yield and quality of maize. The occurrence of stalk rot is closely related to the structure and composition of the stalk. Microstructure analysis revealed that the disease-resistant inbred line (QM1) presented a more organized and tidy arrangement of vascular bundles, along with an increased area and greater cortex thickness than did the susceptible inbred line (HZ4). To explore the regulatory loci of stalk rot-associated stalk fiber components, genome-wide association studies (GWASs), bulk segregation analysis (BSA), and localization approaches were used to explore the regulatory loci of maize stalk rot-associated stalk fiber components. A total of 20 SNPs appeared to be connected in controlling maize’s disease defense response. PZE-105083600 at Chr5, and PZE-107034235 at Chr7 were identified as candidate loci for regulating lignin content. The fluorescence quantification results revealed that the expression of two genes, PZE-105083600 and PZE-107034235, was significantly greater in the disease-resistant lines than in the disease-susceptible materials. The results revealed that the expression of these two genes was significantly greater in the disease-resistant lines than in the disease-susceptible materials. This study is highly important for further investigations of regulatory genes related to the fiber composition of maize rot-associated stalks and the selection and breeding of disease-resistant varieties.