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Komlan AVIA
AVIA Komlan
komlan.avia@inrae.fr
+33 (0) 3 89 22 49 83
GAV Team
Research scientist

Research Project: Integrative biology and genomic selection in grapevine

As part of INRAE's ongoing efforts to promote high-performance, environmentally respectful agriculture that anticipates the impacts of climate change, the development of new grapevine varieties resistant to major diseases such as downy and powdery mildew is a strategic priority. To accelerate and diversify varietal creation, with the goal of producing cultivars that are not only disease-resistant but also suitable for high-quality wine production, my project primarily focuses on integrating genomics into breeding cycles. This is achieved through a genomic selection strategy aimed at optimizing the prediction of trait expression based on gene combinations present in selected populations. The project is structured around several key objectives:

  • Deepen our understanding of the genetic determinism underlying traits of interest in grapevine, leveraging this knowledge to drive varietal innovation.
  • Shorten breeding cycles while increasing the number of genotypes evaluated, thereby enhancing genetic gain.
  • Diversify grapevine ideotypes to adapt to various viticultural regions by optimizing the combination of traits incorporated into breeding schemes.

The optimal integration of diverse datasets (genomic, transcriptomic, metabolomic, etc.) through an integrative biology approach allows for the strategic use of available resources to successfully advance this work.

Research Projects / Coordination

GrapeBreed4IPM (2024–2028, €5.6M): Developing sustainable solutions for viticulture through multi-actor innovation targeting breeding for integrated pest management. This Horizon Europe project supports the EU's ambition to reduce the use of phytosanitary products by 50% by 2030, with a focus on viticulture, a major user of these products. It involves 19 partners and 2 associate partners, and aims to develop and promote the adoption of disease-resistant grapevine varieties to minimize chemical treatments. GrapeBreed4IPM employs a multi-actor approach to advance varietal research, overcome adoption barriers, and deliver decision-support tools for sustainable vineyard management. The project is organized into seven work packages, ranging from varietal innovation to training and knowledge dissemination to foster sustainable practices in viticulture.

PhD Project (2022–2025): Optimization of the selection of disease-resistant grapevine varieties through genomic and phenomic predictions. Co-funded by INRAE's BAP department (50%) and the International Organisation of Vine and Wine (OIV) (50%). This thesis builds on the plant material developed during the INRAE-ResDur breeding program to establish and optimize trait prediction models, and evaluate their accuracy relative to conventional phenotypic selection.

MetabOptimum (2023–2024, €18K): Predictions in varietal innovation in grapevine: optimizing sampling for metabolomic and phenomic analyses. Funded by INRAE’s BAP department.

SelGenVit (2020–2024, €170K): Genomic selection to support grapevine improvement for the diversification and deployment of disease-resistant varieties with high oenological potential. This ANR Ecophyto Maturation project aims to establish a reference panel for genomic selection in grapevine. Carefully designed to include strategic genotypes for breeding, this panel is planted at four sites across France to simultaneously assess environmental effects. The project fosters collaboration with regional partners, offering genomic selection as a decision-support tool within their breeding programs to develop resistant varieties tailored to their specific regions. Key partners include the Colmar Experimental Unit, INRAE Montpellier’s DAAV team, and the IFV.

Selected Publications

  • Denoeud, F., Godfroy, O., Cruaud, C., Heesch, S., Nehr, Z., Tadrent, N., ... Avia, K., … & Cock, J. M. (2024). Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems. Cell, 187(24), 6943-6965. https://doi.org/10.1016/j.cell.2024.10.049
  • Chedid E., Avia K., Dumas V., Ley L., Reibel N., Butterlin G., Soma M., Lopez-Lozano, R., Baret F., Merdinoglu D. & Duchêne, É. (2023). LiDAR Is Effective in Characterizing Vine Growth and Detecting Associated Genetic Loci. Plant Phenomics, 5, 0116. https://doi.org/10.34133/plantphenomics.0116
  • Avia K., Schneider C., Onimus C., Arnold G., Dumas V., Umar-Faruk A., Butterlin G., Dorne M.-A., Alais A., Jaegli N., Lacombe M.-C., Piron M.-C., Prado E., Wiedemann-Merdinoglu S., Mestre P., Duchêne É., Merdinoglu D. (2023). The French grapevine breeding program ResDur: state of the art and perspectives. IVES Conference Series. https://hal.inrae.fr/hal-04231604
  • Trapp O., Avia K., Eibach R., Töpfer R. (2023). How to deal with the Green Deal – Resistant grapevine varieties to reduce the use of pesticides in the EU. IVES Conference Series. https://hal.inrae.fr/hal-04231667
  • Kujala S. T., Avia K., Kumpula T. A., Kärkkäinen H., Heikkinen J., Kärkkäinen K., Savolainen O. (2023). Within and between population comparisons suggest independently acting selection maintaining parallel clines in Scots pine (Pinus sylvestris). Evolution Letters. DOI: 10.1093/evlett/qrad054
  • Shi X., Cao S., Wang X., Huang S., Wang Y., Liu Z., Liu W., Leng X., Peng Y., Wang N., Wang Y., Ma Z., Xu X., Zhang F., Xue H., Zhong H., Wang Y., Zhang K., Velt A., Avia K., Holtgräwe D., Grimplet J., Matus J.T., Ware D., Wu X., Wang H., Liu C., Fang Y., Rustenholz C., Cheng Z., Xiao H., Zhou Y. (2023). The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding. Hortic Res. 10(5). https://doi.org/10.1093/hr/uhad061
  • Chen X., Avia K., Forler A., Remoué C., Venon A., Rousselet A., Lucas G., Kwarteng A.O., Rover R., Le Guilloux M., Belcram H., Combes V., Corti H., Vazquez S., Falque M., Alins G., Kirisits T., Ursu T.M., Roman A., Volk G.M., Bazot S., Cornille A. (2023). Ecological and evolutionary drivers of phenotypic and genetic variation in the European crabapple (Malus sylvestris (L.) Mill.), a wild relative of the cultivated apple. Annals of Botany, 131(6), 1025–1037. https://doi.org/10.1093/aob/mcad061
  • Kastally C., Niskanen A., Perry A., Kujala S., Avia K., Cervantes S., Haapanen M., Kesälahti R., Kumpula T., Mattila T. et al. (2022). Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research. Plant Journal, 109(5), 1337–1350. https://dx.doi.org/10.1111/tpj.15628
  • Mignerot L., Avia K., Luthringer R., Lipinska A.P., Peters A.F., Cock J.M., Coelho S.M. (2019). A key role for sex chromosomes in the regulation of parthenogenesis in the brown alga Ectocarpus. PLOS Genetics, 15(6). https://doi.org/10.1371/journal.pgen.1008211
  • Arun A., Coelho S.M., Peters A.F., Bourdareau S., Peres L., Scornet D., Strittmatter M., Lipinska A.P., Yao H., Godfroy O., Montecinos G.J., Avia K., Macaisne N., Troadec C., Bendahmane A., Cock J.M. (2019). Convergent recruitment of TALE homeodomain life cycle regulators to direct sporophyte development in land plants and brown algae. eLife, 8. https://doi.org/10.7554/eLife.43101
  • Avia K., Lipinska A.P., Mignerot L., Montecinos A.E., Jamy M., Ahmed S., Valero M., Peters A.E., Cock J.M., Roze D., Coelho S.M. (2018). Genetic Diversity in the UV Sex Chromosomes of the Brown Alga Ectocarpus. Genes, 9(6). https://doi.org/10.3390/genes9060286
  • Avia K., Coelho S.M., Montecinos G.J., Cormier A., Lerck F., Mauger S., Faugeron S., Valero M., Cock J.M., Boudry P. (2017). High-density genetic map and identification of QTLs for responses to temperature and salinity stresses in the model brown alga Ectocarpus. Scientific Reports, 7, 43241. https://doi.org/10.1038/srep43241

Academic Background

  • September 2023: Habilitation to Supervise Research (HDR), University of Strasbourg. Title: From understanding the genetic determinism of traits of interest in plants to developing predictive approaches for varietal innovation in grapevine.
  • January 2019: Research Scientist at INRAE.
  • 2018: Postdoctoral Researcher at the Agroecology Joint Research Unit in Dijon, in the 'Espèces Cibles Protéagineux' team led by Judith Burstin. Conducted association genetics analyses and developed genomic selection methods in pea.
  • 2014–2017: Postdoctoral Researcher at the CNRS-Sorbonne University Marine Biology Station in Roscoff, in the 'Algal Genetics' team (led by Susana Coelho and Mark Cock) and the 'Evolutionary Biology and Ecology of Algae' team (led by Myriam Valéro). Research focused on the genetic basis of growth under high temperature and low salinity stress in the model brown alga Ectocarpus sp., phylogenetic analyses of the Ectocarpus species complex, and sex determination genetics in algae.
  • 2009–2013: Postdoctoral Researcher at the University of Oulu, Finland, in the 'Plant Genetics' group led by Prof. Outi Savolainen. Investigated the genetic basis of adaptation to photoperiod and frost stress in Scots pine (Pinus sylvestris).
  • 2005–2008: PhD at INRA Estrées-Mons, supervised by Isabelle Lejeune-Hénaut. Research on co-localization of positional candidate genes with QTLs for frost tolerance in Medicago truncatula.

Collaborations