Genomic selection, a lever for faster varietal improvement

Accelerating varietal innovation in the face of agricultural challenges

Varietal improvement aims to develop higher-performing plants, capable of resisting parasites and pests, better adapting to climate change, and offering improved quality of harvested products. It is a key lever for sustainable, productive, and resilient agriculture.
In West Africa, several strategic sectors rely on perennial species such as cocoa, rubber (Hevea brasiliensis), oil palm, cashew, and shea. These crops play a major economic and social role, particularly in Côte d'Ivoire.

However, the genetic improvement of perennial plants presents significant constraints:

• Long life cycles;
• Late entry into production;
• Prolonged evaluation periods;
• High field trial costs.

These characteristics considerably slow down the development of new varieties.

Paradoxically, these are also the species that stand to benefit most from recent scientific and technological advances:

• Next-generation sequencing and high-throughput multi-omics data acquisition;
• High-throughput phenotyping (infrared imaging, microscopy, digital sensors);
• Development of high-performance computing infrastructure;
• Methods for analysing massive datasets and artificial intelligence.

Genomic selection: a paradigm shift

Genomic selection relies on the systematic search for regions of the genome that control traits of interest and on the early, large-scale prediction of the genetic performance of individuals within breeding populations. Theorized in 2001 by Meuwissen et al., this approach involves using markers distributed throughout the genome to predict an individual's genetic value, without waiting for the full expression of traits in the field. Already widely applied in animal breeding, particularly for complex traits such as milk production, it is gradually transforming plant breeding strategies.

In perennial plants, the initial results are promising:

• Eucalyptus: commercial plantations have been established using elite clones obtained more rapidly through genomic selection (Nippon Paper Industries, 2023).
• Hevea: recent work has confirmed the ability of predictive models to distinguish, even at the nursery stage, high-yielding clones from lower-performing ones (Kouassi, 2026).

These advances make it possible to significantly reduce the duration of breeding cycles while increasing the accuracy of varietal selection.

CIRAD's expertise in tropical genetics and genomics

CIRAD has recognized expertise in the genetics and genomics of perennial tropical crops, as well as in optimizing breeding strategies (Ahmadi & Bartholomé, 2022; Seyum et al., 2022).

In Côte d’Ivoire, genetic improvement programs have been conducted for many years by public research institutions and private partners on various species, particularly perennials. Integrating genomic selection into these programs represents a strategic development to enhance the effectiveness of existing breeding schemes.

A scientific mission to three Ivorian universities

In this context, a scientific mission was conducted in Côte d'Ivoire from January 13 to 23, 2026. An intervention entitled "Genomic Selection and its Application to Perennial Plants" was carried out at three universities:

• Nangui-Abrogoua University (UNA, Abidjan)
• Jean Lorougnon Guédé University (UJLoG, Daloa)
• Péléforo Gon Coulibaly University (UPGC, Korhogo)

The sessions were aimed at Master's and doctoral students as well as researchers. These sessions, led by David Cros, Research Director at the AGAP Joint Research Unit, covered:

• The theoretical foundations of genomic selection;
• The statistical and genomic tools used; and
• The practical application of genomic selection through concrete examples of genetic improvement in oil palm, rubber, and eucalyptus.

This mission is part of an ongoing effort to structure future research and training projects on genomic selection, in partnership with Ivorian universities and the National Centre for Agronomic Research (CNRA). The objective is to:

• Strengthen local scientific capacities;
• Support the progressive integration of genomic selection into existing breeding programs;
• Accelerate the development of varieties adapted to the agroecological conditions and needs of agricultural sectors in West Africa.

References

Ahmadi N., Bartholomé J. (éd.). Genomic Prediction of Complex Traits: Methods and Protocols [En ligne]. New York, NY : Springer US, 2022. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-0716-2205-6 (consulté le 11 janvier 2023)ISBN : 978-1-0716-2204-9.

Georges M., Charlier C., Hayes B. Harnessing genomic information for livestock improvement. Nat Rev Genet. 2019. Vol. 20, n°3, p. 135‑156. https://doi.org/10.1038/s41576-018-0082-2

Kouassi D. K. Optimisation de l’amélioration génétique de l’hévéa (Hevea brasiliensis Müll. Arg) à l’aide de la sélection génomique. Thèse de Doctorat. Daloa : Université Jean Lorougnon Guédé, 2026.

Meuwissen T. H. E., Hayes B. J., Goddard M. E. Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps. Genetics. 2001. Vol. 157, n°4, p. 1819‑1829. https://doi.org/10.1093/genetics/157.4.1819

Nippon Paper Industries Co., Ltd. Nippon Paper Announces the Development of Commercial Clones through Selective Breeding Technology using Genomic Information (Genomic Selection). [s.l.] : [s.n.], 2023. Disponible sur :  Nippon Paper annonce le développement de clones commerciaux grâce à une technologie de sélection utilisant l'information génomique (sélection génomique)(consulté le 16 février 2026)

Seyum E. G., Bille N. H., Abtew W. G., Munyengwa N., Bell J. M., Cros D. Genomic selection in tropical perennial crops and plantation trees: a review. Molecular Breeding. 2022. Vol. 42, n°10, p. 58. https://doi.org/10.1007/s11032-022-01326-4