Identification of QTLs for plant height and branching-related traits in cultivated peanut

• Five pleiotropic unique QTLs for peanut plant height and branching-related traits were discovered and their genetic bases were mathematically estimated. • Three major and stable unique QTLs were identified and their candidate genes were further mined. • SNPs linking to these stable QTLs have great potentials to improve plant architectural traits in peanut. Plant height (PH), primary lateral branch length (PBL), and branch number (BN) are architectural components impacting peanut pod yield, biomass production, and adaptivity to mechanical harvesting. In this study, a recombinant inbred population consisting of 181 individual lines was used to determine genetic controls of PH, PBL, and BN across three environments. Phenotypic data collected from the population demonstrated continuous distributions and transgressive segregation patterns. Broad-sense heritability of PH, PBL, and BN was found to be 0.87, 0.88, and 0.92, respectively. Unconditional individual environmental analysis revealed 35 additive QTLs with phenotypic variation explained (PVE) ranging from 4.57 to 21.68%. A two-round meta-analysis resulted in 24 consensus and 19 unique QTLs. Five unique QTLs exhibited pleiotropic effects and their genetic bases (pleiotropy or tight linkage) were evaluated. A joint analysis was performed to estimate the QTL by environment interaction (QEI) effects on PH, PBL, and BN, collectively explaining phenotypic variations of 10.80, 11.02, and 7.89%, respectively. We identified 3 major and stable QTL regions ( uq9-3 , uq10-2 , and uq16-1 ) on chromosomes 9, 10, and 16, spanning 1.43–1.53 Mb genomic regions. Candidate genes involved in phytohormones biosynthesis, signaling, and cell wall development were proposed to regulate these morphological traits. These results provide valuable information for further genetic studies and the development of molecular markers applicable to peanut architecture improvement.