Abstract
Genomic selection (GS) can substantially reduce breeding cycle times in forest trees compared to traditional breeding cycles. Practical implementation of GS in tree breeding requires an assessment of significant drivers of genetic gains over time, which may differ among species and breeding objectives. We present results of a GS study of growth and wood quality traits in an operational Eucalyptus grandis breeding program in South Africa. The training population consisted of 1575 full and half-sib individuals, genotyped with the Eucalyptus (EUChip60K) SNP chip resulting in 15,040 informative SNP markers. The accuracy of the GS models ranged from 0.47 (diameter) to 0.67 (fibre width). We compared a 4-year GS breeding cycle equivalent to half of a traditional 8-year E. grandis breeding cycle and obtained GS efficiencies ranging from 1.20 (wood density) to 1.62 (fibre length). Simulated over 17 years, the ratio of the accumulated genetic gains between three GS cycles and two traditional breeding cycles ranged from 1.53 (diameter) to 3.35 (wood density). To realise these genetic gains per unit time in E. grandis breeding, we show that significant adjustments have to be made to integrate GS into operational breeding steps.
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Acknowledgements
We thank Mondi South Africa for the use of their E. grandis breeding population as well as the use of facilities and technical support to generate phenotypic data. The authors acknowledge North Carolina State University for training on R and ASReml analysis.
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The full SNPs, pedigree, and phenotypic data are provided in the supplementary materials as supporting data.
Funding
SNP genotyping, wet chemistry data generation used to develop the NIR models and pedigree reconstruction was supported through funding from Mondi South Africa for the Forest Molecular Genetics (FMG) Programme at the University of Pretoria. We further thank the financial support from the funding organisation Mondi South Africa (Pty) Ltd: Forests: Research and Development, National Research Foundation (NRF), Department of Science and Technology: Bioinformatics and Functional Genomics Programme (BFG) Grant UID 86936 and 97911 and Department Trade and Industry South Africa: Technology and Human Resource Industry Programme (THRIP) Grant 80118 and 964134.
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M.M. carried out the experimental design, data collection, data analysis, and drafting of this paper as part of his PhD thesis. F.I. assisted with the modelling and scripts of the data analysis tools. F.I., G.H. and A.A.M. supervised the study and helped with data interpretation and the drafting of the manuscript. M.O. assisted with SNP data analysis and M.R. assisted with DNA extraction and pedigree reconstruction. All authors have read and approved the final manuscript.
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The authors declare that they have no conflict of interest. The author M.M. is an employee of Mondi South Africa (Pty) Ltd.
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Mphahlele, M.M., Isik, F., Mostert-O’Neill, M.M. et al. Expected benefits of genomic selection for growth and wood quality traits in Eucalyptus grandis. Tree Genetics & Genomes 16, 49 (2020). https://doi.org/10.1007/s11295-020-01443-1
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DOI: https://doi.org/10.1007/s11295-020-01443-1