Genome-wide association studies revealed partial genetic links between early vigour and precocity in macadamia

Abstract

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.

Consent for publication

All authors approve the manuscript and consent to publication of the work.

Acknowledgement

This work has been supported by the National Macadamia Breeding and Evaluation Program (MC19000, MC14000), funded by Hort Innovation Australia, using the Macadamia research and development levy and contributions from the Australian Government. Hort Innovation is the grower-owned, not-for-profit research and development corporation for Australian horticulture. Research funding was also provided by Queensland Government-supported Advance Queensland Industry Research Mid-Career Fellowship grant (AQIRF073-2022RD5; RM 2022002724). The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript. The funders had no role in the conceptualization, design, data collection, analysis, decision to publish, or preparation of the manuscript. The University of Queensland provided a higher degree research scholarship to P.D.P.

Author contributions

B.T. and M.A. acquired the funding and resources. P.D.P. wrote the paper, performed analyses, and made final edits. P.D.P., J.D.F., and M.A. developed the analytical models. J.D.F., B.T., and M.A. assisted in interpretation of results and revised the manuscript. All authors read and approved the final manuscript.

Data availability

The datasets used and/or analysed during the current study are available from the corresponding author/s on reasonable request.

Conflict of interest statement

The authors declare that they have no competing interests.

Supplementary data

Supplementary data is available at Hortre Journal online.

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