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Genomic selection in tropical perennial crops and plantation trees: a review

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Abstract

To overcome the multiple challenges currently faced by agriculture, such as climate change and soil deterioration, more efficient plant breeding strategies are required. Genomic selection (GS) is crucial for the genetic improvement of quantitative traits, as it can increase selection intensity, shorten the generation interval, and improve selection accuracy for traits that are difficult to phenotype. Tropical perennial crops and plantation trees are of major economic importance and have consequently been the subject of many GS articles. In this review, we discuss the factors that affect GS accuracy (statistical models, linkage disequilibrium, information concerning markers, relatedness between training and target populations, the size of the training population, and trait heritability) and the genetic gain expected in these species. The impact of GS will be particularly strong in tropical perennial crops and plantation trees as they have long breeding cycles and constrained selection intensity. Future GS prospects are also discussed. High-throughput phenotyping will allow constructing of large training populations and implementing of phenomic selection. Optimized modeling is needed for longitudinal traits and multi-environment trials. The use of multi-omics, haploblocks, and structural variants will enable going beyond single-locus genotype data. Innovative statistical approaches, like artificial neural networks, are expected to efficiently handle the increasing amounts of heterogeneous multi-scale data. Targeted recombinations on sites identified from profiles of marker effects have the potential to further increase genetic gain. GS can also aid re-domestication and introgression breeding. Finally, GS consortia will play an important role in making the best of these opportunities.

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Abbreviations

BLUP:

Best linear unbiased prediction

CGM:

Crop growth model

CNV:

Copy number variation

GBLUP:

Genomic BLUP

GEBV:

Genomic estimated breeding value

GEGV:

Genomic estimated genetic value

GEI:

Genotype-by-environment interactions

GS:

Genomic selection

GWAS:

Genome-wide association study

HTP:

High-throughput phenotyping

LD:

Linkage disequilibrium

MAS:

Marker-assisted selection

NIRS:

Near-infrared spectroscopy

NGS:

Next-generation sequencing

QTL:

Quantitative trait locus

RKHS:

Reproducing kernel Hilbert spaces

rrBLUP:

Random regression BLUP

SNP:

Single nucleotide polymorphism

SV:

Structural variants

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Acknowledgements

The authors acknowledge the GENES program of the Intra-Africa Academic Mobility Scheme of the European Union for financial support (EU-GENES:2017-2552/001-001). The authors also thank Marie Denis, Gilles Trouche, André Clément-Demange, Angélique D’Hont, Dominique Dessauw, and Xavier Argout for discussions that improved the manuscript.

Funding

This study was funded by the GENES Intra-Africa Academic Mobility Scheme of the European Union (EU-GENES:2017–2552/001–001) program, by CIRAD, and by a grant from PalmElit SAS.

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Authors and Affiliations

  1. Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon

    Essubalew Getachew Seyum, Ngalle Hermine Bille & Joseph Martin Bell

  2. Department of Horticulture and Plant Sciences, College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia

    Essubalew Getachew Seyum & Wosene Gebreselassie Abtew

  3. Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia

    Norman Munyengwa

  4. CIRAD, UMR AGAP Institut, 34398, Montpellier, France

    David Cros

  5. UMR AGAP Institut, CIRAD, INRAE, Univ. Montpellier, Institut Agro, 34398, Montpellier, France

    David Cros

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  1. Essubalew Getachew Seyum
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  2. Ngalle Hermine Bille
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  4. Norman Munyengwa
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  5. Joseph Martin Bell
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  6. David Cros
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Contributions

EGS and DC carried out the literature review and wrote the manuscript, with help from WGA, NHB, NM, and JMB. All authors read and approved the final manuscript.

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Correspondence to David Cros.

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Seyum, E.G., Bille, N.H., Abtew, W.G. et al. Genomic selection in tropical perennial crops and plantation trees: a review. Mol Breeding 42, 58 (2022). https://doi.org/10.1007/s11032-022-01326-4

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