Genome-Wide Analysis to Identify SNP Markers Associated with Plant Height in Sorghum bicolor

Understanding the genetic basis of plant height (PH) in sorghum is essential for improving crop performance and breeding efficiency. This study analyzed 309 sorghum accessions using genome-wide association studies (GWAS) to identify significant single nucleotide polymorphism (SNP) markers associated with PH. Genotyping was conducted using SeqSNP with 5000 markers, of which 3143 high-quality SNPs were selected for analysis. Principal component analysis (PCA) and kinship analysis revealed two distinct genetic clusters. GWAS was performed using seven models: GLM, MLM, MLMM, CMLM, ECMLM, SUPER, FarmCPU, and BLINK. While GLM and SUPER identified a large number of significant SNPs, their Manhattan and QQ plots indicated high false-positive rates. FarmCPU and BLINK proved to be the most reliable models, detecting 10 and 8 significant SNPs, respectively, with four SNPs shared between both models. The most influential SNPs were located on chromosomes 1 and 8, in genes Sobic.001G017500 and Sobic.008G050800, known for their roles in plant growth and development. These findings demonstrate the advantage of multi-locus GWAS models in reducing false positives and enhancing SNP detection accuracy. The identified markers provide valuable insights for sorghum breeding programs, enabling the selection of desirable traits to optimize plant height and improve overall yield potential.