Novel QTLs/genes affecting single stem elasticity, stem strength, and three lodging indices in bread wheat (Triticum aestivum L.) identified by genome-wide association analysis.

A comprehensive GWAS reveals key QTLs, canditate genes, and networks underlying wheat lodging resistance. Lodging is a complex trait and has implications for wheat grain quality and yield, stem-associated traits are crucial for lodging resistance. Understanding the genetic basis of lodging-associated traits, especially single stem elasticity (SSE), stem strength (SS), and lodging index, is essential for developing effective strategies to enhance lodging resistance in wheat. In this study, 10 lodging-associated traits of 238 diverse wheat varieties were investigated across three diverse growing seasons. The ANOVA revealed significant variations on all traits among wheat genotypes and across three growing seasons. There was significant correlations between SSE, SS, three lodging indices (LI 1, LI 2, LI 3) and stem morphological traits. A total of 126 key candidate quantitative trait loci regions containing at least two marker-trait associations were identified using genome-wide association analysis. By integrating multiple analytical approaches, 84 key candidate genes were screened, including genes encoding enzymes related to stem cell wall synthesis, photosynthesis, hormone synthesis, and root development, which may play an important role in lodging resistance. By using Bayesian ridge regression for genome prediction, the prediction accuracy increased as the number of significant SNPs increased, and high prediction accuracy can also be achieved using only a few top-ranking SNPs. In summary, the results of this study would provide valuable insights for understanding lodging resistance in wheat and its genetic mechanism.