Genetic architecture of rhizome development in diploid perennial sorghum reveals exploratory genomic signals with heterogeneous complementary support

Abstract

Background The genetic architecture of perenniality in sorghum remains incompletely understood, particularly following interspecific hybridization and recovery of diploid progeny. Rhizome development and overwinter regrowth are components of perennial persistence but may differ genetically and environmentally. Characterizing their genomic association patterns in diploid Sorghum bicolor × S. halepense material could identify candidate genomic regions for subsequent validation and breeding. Results We investigated perenniality in S3011, a diploid-derived interspecific population from Sorghum bicolor × S. halepense . A structured F₄ panel was phenotyped under field conditions, and accession-level best linear unbi - ased predictors (BLUPs) were used for genome-wide association analyses. No association exceeded the Bonfer-roni-adjusted genome-wide significance threshold ( P ≤ 1.15 × 10⁻⁶; 43,317 SNPs tested), and none remained sig - nificant after Benjamini–Hochberg false discovery rate correction (q < 0.05). A predefined suggestive threshold ( P < 1 × 10⁻⁴; −log₁₀(P) > 4) identified 13 SNPs, which were consolidated into seven spatially distinct exploratory rhizome-number signals. Complementary characterization using high–low allele-dosage contrasts, local linkage disequilibrium, historical positional correspondence, candidate-gene annotation, and a descriptive marker-based genome scan revealed heterogeneous regional evidence. The strongest