Genome-wide association study identifies novel candidate loci or genes affecting stalk strength in maize

Stalk strength increases resistance to stalk lodging, which causes maize (Zea mays L.) production losses worldwide. The genetic mechanisms regulating stalk strength remain unclear. In this study, three stalk strength-related traits (rind penetrometer resistance, stalk crushing strength, and stalk bending strength) and four plant architecture traits (plant height, ear height, stem diameter, stem length) were measured in three field trials. Substantial phenotypic variation was detected for these traits. A genome-wide association study (GWAS) was conducted using general and mixed linear models and 372,331 single-nucleotide polymorphisms (SNPs). A total of 94 quantitative trait loci including 241 SNPs were detected. By combining the GWAS data with public gene expression data, 56 candidate genes within 50 kb of the significant SNPs were identified, including genes encoding flavonol synthase (GRMZM2G069298, ZmFLS2), nitrate reductase (GRMZM5G878558, ZmNR2), glucose-1-phosphate adenylyltransferase (GRMZM2G027955), and laccase (GRMZM2G447271). Resequencing GRMZM2G069298 and GRMZM5G878558 in all tested lines revealed respectively 47 and 2 variants associated with RPR. Comparison of the RPR of the zmnr2 EMS mutant and the wild-type plant under high- and low-nitrogen conditions verified the GRMZM5G878558 function. These findings may be useful for clarifying the genetic basis of stalk strength. The identified candidate genes and variants may be useful for the genetic improvement of maize lodging resistance.