High-Density Genetic Mapping Identifies QTL and Candidate Genes for Plant Architecture and Kernel Traits in Cultivated Peanut

Background/Objectives: Plant architecture and kernel-related traits are important determinants of yield potential and breeding value in peanut (Arachis hypogaea L.). This study aimed to construct a high-density genetic linkage map, identify quantitative trait loci (QTL) associated with these traits, and prioritize candidate genes underlying key genomic regions in cultivated peanut. Methods: A recombinant inbred line population derived from Luojiangjiwo, a sprawling large-pod line, and Fuhuasheng, an erect small-pod line, was used to construct a high-density genetic linkage map and identify QTL associated with plant architecture and kernel traits. Results: Specific-locus amplified fragment sequencing generated 1,295,490,603 clean reads, with an average Q30 of 93.67%. After SNP discovery, filtering, and linkage analysis, 2646 SNP markers were mapped to 20 linkage groups, spanning 1338.86 cM with an average marker interval of 0.51 cM. Phenotypic evaluation of 16 traits revealed broad variation among 200 recombinant inbred lines, with strong positive correlations among pod-size traits and among kernel-size traits. Composite interval mapping detected eight QTL distributed on chr04, chr05, chr13, and chr15, including five QTL for plant architecture traits and three QTL for kernel-related traits. qLBL13 for lateral branch length explained the highest phenotypic variation, whereas qMKL05 for mean kernel length was delimited to a 0.151 Mb interval containing only nine genes. Candidate-gene analysis prioritized AH05G29360, encoding a knotted-1-like homeobox protein; AH05G29380, encoding mitogen-activated protein kinase kinase 9; AH05G29350, encoding COP1-interacting protein 7; and AH05G29410, encoding a pentatricopeptide repeat-containing protein. Additional candidates included AH15G16520, AH15G16460, AH15G16630, and AH15G16770 in the shared qHKW15/qMKW15 interval. Conclusions: This study identified genomic regions and biologically relevant candidate genes associated with plant architecture and kernel-related traits in peanut. These findings provide valuable genomic resources for future functional validation and facilitate marker-assisted breeding for improved plant architecture and kernel characteristics.