Abstract
<title>Abstract</title> <p>Breeding programs for the tropical forage grass Urochloa require the evaluation of interspecific hybrids derived from crosses between apomictic and sexual tetraploid species within the same agamic complex. We evaluated 45,937 genotyping-by-sequencing (GBS)-derived single-nucleotide polymorphism (SNP) markers via dosage-aware calls and a genomic relationship matrix (G) to refine the pedigrees of 245 putative hybrids and 14 parents. Genome-wide association studies (GWASs) based on realized kinship coefficients were conducted to dissect labor-intensive and low-throughput traits, specifically spittlebug (Notozulia entreriana) resistance and reproduction modes. Classification via the G-matrix identified 23.0% of the progeny as true hybrids, 48.5% as U. brizantha pollen contaminants, and 19.3% as apomictic clones. Pedigree correction combined with a permissive minor allele frequency threshold (MAF ≥ 0.05) enabled the detection of two dominant loci associated with damage resistance (qDam-dom1 and qDam-dom2, explaining ~48% of the genetic variance) and one additive locus (qSur-add1) associated with nymph survival. Additionally, three loci associated with apomixis (qApom-dom1, qApom-dom2, and qApom-dom3) mapped independently of the resistance loci. These findings demonstrate that dosage-aware genomic matrix filtering, combined with polyploid-specific association models and permissive MAF thresholds, is essential for dissecting complex traits and accelerating genomic-assisted selection in polyploid Urochloa breeding programs.</p>