Characterization of plant-plant interactions and their genetic basis: the case of the maize-bean association in Europe

Characterization of plant-plant interactions and their genetic basis: the case of the maize-bean association in Europe

Thesis defense
 06/03/2025
 13:30:00
 Noa Vazeux-Blumental, GQE-Le Moulon
 IDEEV - Salles Franklin and Carlson

Jury :

  • Laurent BEDOUSSAC (Professeur, ENSFEA, UMR AGIR) - Examinateur
  • Cécile BERTHOULY (Directrice de recherche, IRD, UMR DIADE), rapportrice et examinatrice
  • Isabelle GOLDRINGER (Directrice de recherche, INRAE, UMR GQE-Le Moulon), examinatrice
  • Anne LAPERCHE (Professeure, Institut Agro Rennes-Angers, UMR IGEPP), rapportrice et examinatrice
  • Germain MONTAZEAUD (Chargé de recherche, INRAE, UMR AGAP) - Examinateur
  • Jacqui SHYKOFF (Directrice de recherche, CNRS, UMR ESE) - Examinatrice

Keywords:

Agroecology – maize-bean intercropping – Plant-Plant Interactions - GWA

Abstract:

The cultivation of maize (Zea mays ssp. mays) and common bean (Phaseolus vulgaris) in association is a key component of the most emblematic multi-cropping subsistence system of Mesoamerica, known as milpa. Its success relies on described benefits such as improved yields and resilience to biotic and abiotic stress, that enable the system to be productive under input-limited conditions. These benefits rely on the mobilization of positive interactions between these species attributed to the complementarity of aerial and root systems, as well as to direct and indirect facilitation processes involving root exudates, bacterial symbioses (through the formation of root nodules), and the mycorrhizal network. While maize-bean intercropping was once common in Europe, it has been replaced by sole maize cropping except for some regions such as Transylvania. Recently, maize-bean intercropping has been reintroduced, using modern varieties in conventional conducts. During my PhD, I aimed to characterize maize-bean interactions and their genetic bases with three specific objectives.

The first objective was to compare sole and intercropped crops in a modern agricultural system in southwestern France, to test the impact of the association on yields, nutritional value, root microbiota, and molecular phenotypes. Results showed an increased bacterial diversity in intercropping compared to sole cropping and significant agronomic differences, with a dominant effect of competition negatively affecting bean yield but increasing seed size and nitrogen and carbon content. Transcriptome analysis confirmed that competition primarily impacted beans, with nearly 30 % of differentially expressed genes detected in beans but none in maize. These findings suggest that potential synergies between the two crops are hindered in modern settings.

The second objective was to evaluate the phenotypic response of beans to different « maize » environments, seeking the genetic basis of the interactions between the two species. We conducted multi-site, multi-year agronomic trials using three maize landraces and 200 bean lines. I found no clear evidence of local adaptation in beans but we were able to distinguish beans grown with each of the three maize indicating that the latter represents distinct environment for beans. I found negative correlations between most maize and bean traits, indicating competition between species; however, a positive correlation between maize flowering time and bean yield was observed for all maize varieties. The best maize-bean partners depended on the year, location, and maize variety. Finally, I combined the genome wide association (GWA) results using meta-GWA that contrasted maize landraces to map the genetic determinants of the maize-bean interaction in the bean genome, and identified loci for 17 out of 18 traits.

The third objective was to investigate how different maize varieties influence bean root architecture, development, and root nodule formation. The experiments conducted for the second objective were used to phenotype root traits on a subset of 38 bean lines in one of the two locations. Although abiotic factors (site, year) strongly influence the root architecture of both species, certain traits related to root surface area and angles differentiated beans grown with different maize varieties—without affecting the abundance of nodules. We discuss the perspectives of our work for the selection of varieties that promote synergies between species in a context of agroecological transition.