Early vigour (EV) and precocity are important traits for orchard establishment and profitability in macadamia. EV determines tree growth and adaptation, while precocity facilitates early yield, offering economic benefits. Although, a positive relationship between these traits has been observed in other tree crops, their association in macadamia remains unclear. This study aimed to identify genetic links between EV and precocity by assessing genetic variability, heritability, and correlations in a 5-year-old macadamia breeding population. The population comprised 904 progenies planted across six sites in Queensland, Australia. Genome-wide association studies (GWAS) were conducted on a subset of 220 accessions genotyped with 7401 SNP markers. A linear mixed model incorporating a kinship matrix and principal components to account for population structure was used to perform association analysis in TASSEL. Phenotypic analyses in ASReml-R revealed that precocity had higher broad- (H2 = 0.25–0.84) and narrow-sense (h2 = 0.10–0.77) heritability compared to EV (H2 = 0–0.61, h2 = 0–0.49). EV and precocity showed positive phenotypic (0.25–0.42) and genetic (0.21–0.31) correlations. GWAS identified 11 significant markers (false discovery rate < 0.05), including two pleiotropic markers (Mint10079 and Mint4004) associated with both EV and precocity. Putative genes linked to these markers were involved in cell wall modelling, pathogen defence, abiotic stress tolerance, flowering, overall growth, and development in other tree species. These significant markers, postvalidation, hold substantial promise for utilization in marker-assisted selection (MAS). Integrating putative pleiotropic markers into MAS can enhance genetic gain by reducing the selection time for and enabling simultaneous selection for EV and precocity.

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