Fine mapping of two stable QTL related to plant architecture traits in peanut (Arachis hypogaea L.)

Optimizing plant architecture is essential for improving mechanized harvesting and yield potential in peanut (Arachis hypogaea L.), yet its genetic basis remains unclear. This study aimed to identify stable major-effect QTL associated with main stem length, basal branch length, and the main stem length to basal branch length ratio, and to predict candidate genes using gene expression data and genome sequencing. A previously constructed population of recombinant inbred lines (RIL) derived from a cross between erect-type JH5 and bunch-type KX01-6 was evaluated across three field environments. Statistical analysis identified six QTL with LOD scores ranging from 3.27 to 9.77, explaining 6.14%–24.14% of the phenotypic variation. Among them, qMSL_B09, qBBL_B09, qBBL_B05, and qMBR_B05 were identified in at least two environments. By integrating QTL analysis based on Best Linear Unbiased Prediction (BLUP) values, we narrowed these four stable QTL to two loci, Rpa1 (Regulating plant architecture 1) and Rph1 (Regulating plant height 1) that were delimited to a ~6.840 Mb region (B05: 154.040 Mb to the end) and a ~400 kb physical interval (B09: 158.05–158.45 Mb), respectively. Phenotypic validation using near-isogenic lines (NILs) demonstrated that Rpa1 increased basal branch length by 27.22% and branch angle by 140.08%, while reducing the main stem-to-branch ratio by 22.91%. In contrast, Rph1 decreased main stem length by 42.31% and basal branch length by 46.84%. Map-based cloning of Rph1 identified an 1816-bp deletion in parental line JH5 that influenced the expression of two candidate genes: Ah19g561300 (encoding a bifunctional inhibitor/lipid-transfer protein) and Ah19g561500 (encoding a proteasome subunit). A diagnostic InDel marker to facilitate marker-assisted selection for ideal plant height in breeding programs was developed to track the deletion. Haplotype analysis of 241 accessions confirmed the association of Rph1 with plant architecture, and accessions carrying Hap^rph1 exhibited significantly higher main stem and basal branch lengths (by ~10%; P < 0.01). These findings provide novel genetic insights and molecular tools for improving plant architecture and enhancing yield potential in peanut.