Uncovering genetic and metabolite markers associated with resistance against anthracnose fruit rot in northern highbush blueberry

Abstract

Anthracnose fruit rot (AFR), caused by the fungal pathogen Colletotrichum fioriniae, is among the most destructive and widespread fruit disease of blueberry, impacting both yield and overall fruit quality. Blueberry cultivars have highly variable resistance against AFR. To date, this pathogen is largely controlled by applying various fungicides; thus, a more cost-effective and environmentally conscious solution for AFR is needed. Here we report three quantitative trait loci associated with AFR resistance in northern highbush blueberry (Vaccinium corymbosum). Candidate genes within these genomic regions are associated with the biosynthesis of flavonoids (e.g. anthocyanins) and resistance against pathogens. Furthermore, we examined gene expression changes in fruits following inoculation with Colletotrichum in a resistant cultivar, which revealed an enrichment of significantly differentially expressed genes associated with certain specialized metabolic pathways (e.g. flavonol biosynthesis) and pathogen resistance. Using non-targeted metabolite profiling, we identified a flavonol glycoside with properties consistent with a quercetin rhamnoside as a compound exhibiting significant abundance differences among the most resistant and susceptible individuals from the genetic mapping population. Further analysis revealed that this compound exhibits significant abundance differences among the most resistant and susceptible individuals when analyzed as two groups. However, individuals within each group displayed considerable overlapping variation in this compound, suggesting that its abundance may only be partially associated with resistance against C. fioriniae. These findings should serve as a powerful resource that will enable breeding programs to more easily develop new cultivars with superior resistance to AFR and as the basis of future research studies.

Acknowledgements

This work was supported by United States Department of Agriculture - Agriculture and Food Research Initiative (USDA-AFRI) #2018-67013-27592 to G.S., T.M. and P.P.E.; United States Department of Agriculture – Specialty Crop Research Initiative (USDA-SCRI) #2019-51181-30015 to P.P.E.; and National Institute of Health (NIH) Training Grant #T32-GM110523 and National Science Foundation (NSF) Training Grant DGE-1828149 to M.J. and P.P.E. This work was also supported by Michigan State University AgBioResearch and United States Department of Agriculture – HATCH MICL02742 to P.P.E.

Data Availability

The genomic and transcriptomic sequence reported in this paper has been deposited in the National Center for Biotechnology Information BioProject database (#PRJNA1005331). The phenotyping data, metabolite measurement data, and Gene Ontology enrichment results are available in the supplementary materials associated with this manuscript.

Conflict of Interests

The authors have no conflicts of interest to declare.

Supplementary data

Supplementary data is available at Horticulture Research online.

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