Genome-wide identification of quantitative trait nucleotides for plant architecture-related traits in peanut

Peanut (Arachis hypogaea L.) is globally recognized as an important oilseed crop. Traits related to plant architecture are closely associated with yield in peanut. In this study, we focused on four specific traits related to plant architecture-first branch length (FBL), main stem height (MSH), stem diameter (SD), and the number of nodes on the main stem (NSK)-across three locations. Using whole-genome resequencing data from a genetically diverse collection of peanut landraces, we conducted a genome-wide association study analysis to identify genetic variants associated with these traits. Notably, a novel genomic region on Arahy.03:39916768-42652757 was associated with SD for the first time. Homology analysis suggested that two annotated genes within this region may contribute to stem elongation and seed development. For MSH, NSK, and FBL, more than half of the significantly associated single-nucleotide polymorphisms (SNPs) were localized on chromosome Arahy.05. Two SNPs at Arahy.09:112028951 and Arahy.09:112272948 were identified as the potential diagnostic markers for MSH and FBL: one homologous gene near these SNPs encoded an E3 ubiquitin-protein ligase, while the other encodes cinnamyl alcohol dehydrogenase. Additionally, one SNP at Arahy.05:53493734 was identified as a potential diagnostic marker for MSH, FBL, and NSK and validated using the penta-primer amplification refractory mutation system and quantitative real-time polymerase chain reaction. A gene near this SNP belongs to the protein kinase superfamily. Enzymes are known to regulate diverse cellular and biological processes, including plant development. These findings advance our understanding of the genetic basis of peanut architecture and provide valuable markers for future yield improvement efforts.