Quantitative trait loci associated with apple endophytes during pathogen infection

Amanda Karlström; Matevz Papp-Rupar; Tom A J Passey; Greg Deakin; Xiangming Xu

doi:10.3389/fpls.2023.1054914

Quantitative trait loci associated with apple endophytes during pathogen infection

Front Plant Sci. 2023 Mar 28:14:1054914. doi: 10.3389/fpls.2023.1054914. eCollection 2023.

Authors

Amanda Karlström¹, Matevz Papp-Rupar¹, Tom A J Passey¹, Greg Deakin¹, Xiangming Xu¹

Affiliation

¹ NIAB East Malling, East Malling, United Kingdom.

Abstract

The plant phyllosphere is colonized by microbial communities that can influence the fitness and growth of their host, including the host's resilience to plant pathogens.There are multiple factors involved in shaping the assemblages of bacterial and fungal endophytes within the phyllosphere, including host genetics and environment. In this work, the role of host genetics in plant-microbiome assembly was studied in a full-sibling family of apple (Malus x domestica) trees infected with the fungal pathogen Neonectria ditissima. A Quantitative Trait Loci (QTL) analysis showed that there are multiple loci which influence the abundance of individual endophytic taxa, with the majority of QTL having a moderate to large effect (20-40%) on endophyte abundance. QTL regions on LG 1, 3, 4, 5, 10, 12, 13, 14 and 15 were shown to affect multiple taxa. Only a small proportion of the variation in overall taxonomic composition was affected by host genotype, with significant QTL hits for principal components explaining <8% and <7.4% of the total variance in bacterial and fungal composition, respectively. Four of the identified QTL colocalised with previously identified regions associated with tolerance to Neonectria ditissima. These results suggest that there is a genetic basis shaping apple endophyte composition and that microbe-host associations in apple could be tailored through breeding.

Keywords: European canker; Malus x domestica; Neonectria ditissima; apple; microbiome; phyllosphere.

Grants and funding

This study received funding from the UK Biotechnology and Biological Science Research Council (BBSRC) and the industry organisations listed above. The funders were not involved in the study design, collection, analysis, interpretation of data, the writing of this article or the decision to submit it for publication. All authors declare no other competing interests. This work was supported by the UK Biotechnology and Biological Science Research Council (BBSRC) [grant number: BB/P007899/1 and BB/P000851/1] and several industry organisations (Agriculture and Horticulture Development Board [AHDB], Adrian Scripps Limited, Avalon Produce Limited, T&G Global, Frank P Matthews Limited, and Worldwide Fruit Limited).