Ecological and evolutionary drivers of phenotypic and genetic variation in the European crabapple (Malus sylvestris (L.) Mill.), a wild relative of the cultivated apple

Authors: CHEN, X - Inrae; AVIA, K - Inrae; FORLER, A - Inrae; REMOUÉ, C - Inrae; VENON, A - Inrae; ROUSSELET, A - Inrae; LUCAS, G - Institute Of Forest Entomology, Forest Pathology And Forest Protection (IFFF); KWARTENG, A - Inrae; ROVER, R - Inrae; LE GUILLOUX, M - Inrae; BELCRAM, H - Inrae; COMBES, V - Inrae; CORTI, H - Inrae; OLVERÀ-VAZQUEZ, S - Inrae; FALQUE, M - Inrae; ALINS, G - Institute De Recerca I Tecnologia Agroalimentaries (IRTA); KIRISITS, T - Institute Of Forest Entomology, Forest Pathology And Forest Protection (IFFF); URSU, T - Institute Of Biological Research; ROMAN, A - Institute Of Biological Research; Volk, Gayle; BAZOT, S - Centre National De La Recherche Scientifique; CORNILLE, A - Inrae

Submitted to: Annals of Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/3/2023
Publication Date: 5/3/2023
Citation: 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., Olverà-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.
DOI: https://doi.org/10.1093/aob/mcad061

Interpretive Summary: Malus sylvestris is a progenitor of the cultivated apple, Malus domestica, that is native across Europe. This research combines genotypic (microsatellite) and phenotypic (seedling traits) to identify locations that have high levels of M. sylvestris and M. domestica admixture and to describe differentiation among populations. Inclusion of climatic variables into the analyses revealed that geographic distance and past climate during the last glacial maximum were primary drivers of the genetic variation that is observed. This information informs future species collection trips to target wild populations that are not introgressed to ensure that genebank materials are true-to-type.

Technical Abstract: Characterizing phenotypic and genetic variation among populations of crop wild relatives is an important step for understanding ecological and evolutionary processes involved in population divergence, and to mobilize crop wild relatives’ diversity to mitigate the impact of climate change. Population genetic structure and differentiation of seedlings of Malus sylvestris, a main contributor to the cultivated apple genome (Malus domestica), were assessed using 13 microsatellite loci. Seedling early-fitness traits including growth rates and carbon-uptake traits were measured in a common garden. Additionally, we tested for the occurrence of any patterns of isolation by distance, isolation by climate, and isolation by adaptation that might have caused genetic and phenotypic differentiation among M. sylvestris populations. Bayesian clustering revealed that seedlings belonged to seven M. sylvestris populations in Europe, and 11.6% of the seedlings were introgressed by M. domestica. Significant trait variation among populations of M. sylvestris was observed; which for some was of moderate to high heritability. Lack of association between trait and genetic divergences suggests that this significant phenotypic variation was mainly achieved by genetic drift alone. Our results also provide strong evidence that geographic distance and past climate during the last glacial maximum, but not current climate, are the main drivers of genetic variation in M. sylvestris. This study provides a first insight of the ecological and evolutionary drivers of phenotypic and genetic differentiation among populations of a wild apple species relative to cultivated apples, which is a starting point for future breeding programs.