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  • Perspective
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Potential approaches to create ultimate genotypes in crops and livestock

Nature Genetics volume 56, pages 2310–2317 (2024)Cite this article

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Abstract

Many thousands and, in some cases, millions of individuals from the major crop and livestock species have been genotyped and phenotyped for the purpose of genomic selection. ‘Ultimate genotypes’, in which the marker allele haplotypes with the most favorable effects on a target trait or traits in the population are combined together in silico, can be constructed from these datasets. Ultimate genotypes display up to six times the performance of the current best individuals in the population, as demonstrated for net profit in dairy cattle (incorporating a range of economic traits), yield in wheat and 100-seed weight in chickpea. However, current breeding strategies that aim to assemble ultimate genotypes through conventional crossing take many generations. As a hypothetical thought piece, here, we contemplate three future pathways for rapidly achieving ultimate genotypes: accelerated recombination with gene editing, direct editing of whole-genome haplotype sequences and synthetic biology.

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Fig. 1: Gene pyramiding and ‘ultimate genotypes’.
Fig. 2: Use of synthetic biology.

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Acknowledgements

We acknowledge M. Goddard and M. Morell for useful discussions. We thank the ARC Training Centre in Predictive Breeding for Agricultural for funding (IC230100016).

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Authors and Affiliations

  1. Queensland Alliance for Agriculture and Food Innovation, the University of Queensland, St Lucia, Queensland, Australia

    Ben J. Hayes, Timothy J. Mahony, Kira Villiers, Christie Warburton, Eric Dinglasan, Owen Powell, Ian D. Godwin & Lee T. Hickey

  2. Institute for Molecular Biology, the University of Queensland, St Lucia, Queensland, Australia

    Kathryn E. Kemper

  3. Department of Plant Breeding, Hochschule Geisenheim University, Geisenheim, Germany

    Hannah Robinson & Kai Voss-Fels

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Contributions

B.J.H., I.D.G., T.J.M., K.V.-F., K.E.K. and L.T.H. conceived the main ideas presented in this Perspective and drafted the manuscript. K.V., C.W., E.D., H.R. and O.P. contributed to sections of the manuscript and helped draft the overall content.

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Correspondence to Ben J. Hayes.

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Hayes, B.J., Mahony, T.J., Villiers, K. et al. Potential approaches to create ultimate genotypes in crops and livestock. Nat Genet 56, 2310–2317 (2024). https://doi.org/10.1038/s41588-024-01942-0

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