Untargeted metabolomic genome-wide association study reveals genetic and biochemical insights into polyphenols of apple fruit

Abstract

Apple (Malus × domestica) is one of the most popular fruits grown and consumed worldwide, contributing to human health with significant amounts of polyphenols and other bioactive compounds, and providing positive impacts to the economy and society. Understanding the diversity and inheritance of health-active compounds in apple can provide novel selection criteria for future breeding and cultivar development, as consumers increasingly prioritize the health benefits of their food choices. We therefore conducted an untargeted metabolomic analysis using ultra-high-performance liquid chromatography-mass spectrometry (UPLC-MS) to investigate thousands of semipolar chemicals, mainly phenolic compounds, in 439 diverse apple accessions, and quantified 2066 features in positive ion mode. To identify key areas of genetic control for apple metabolite abundance, we performed a metabolomic genome-wide association study (mGWAS) on the quantified mass features using ~280 000 single nucleotide polymorphisms (SNPs). The mGWAS revealed >630 significant loci with hotspots for various groups of known and unknown phenolic compounds including flavonols on Chromosome 1, dihydrochalcones on Chromosome 5, and flavanols on Chromosomes 15 and 16. The most significant hotspot on Chromosome 16 included bHLH and C2H2 transcription factors that may play a role in controlling the abundance and complexity of phenolic compounds through regulation of the flavonoid biosynthesis pathway. Our analysis links the apple metabolome with candidate genes and biosynthetic mechanisms and establishes a foundation for marker-assisted breeding and gene editing to improve and modify phenolic compounds in apple for marketability and the benefit of human health.

Acknowledgements

This research was supported by A-Base funding (J-00242021) from Agriculture and Agri-Food Canada (J.S.). We thank Drs Zoë Migicovsky and Sean Myles for their published research in genotyping the Apple Biodiversity Collection (ABC) [69], which has been the foundation for mGWAS in this study, as well as their and Dr. Sophie Watts’ collaborations on phenomic and association studies of the same orchard [14,24]. We thank Prof. Arthur Jones III at MSU for the recommendation of the internal standard for this study. We further thank the Farm Services team at AAFC-Kentville for establishing and maintaining the ABC orchard.

Author contributions

J.S. designed the experiment, obtained the funding and supervised the whole experiment, and drafted and revised the manuscript. B.A. guided data analysis and interpretation, created visualizations, and co-wrote the manuscript. L.C. conducted sample collection and LC-MS analysis. M.V. conducted sample collection, sample preparation, and data analysis. K.D. and L.D.R. assisted with data analysis. All authors agree and approve the current version of the manuscript.

Data availability

Supplementary information accompanies the manuscript in the supplemental tables and files provided. This paper makes use of genotypic data that were previously published and are available online [69].

Conflict of interest statement

The authors declare no conflict of interests. The use of trade names in the materials and methods does not imply endorsement of the products named or criticism of similar ones not named.

Supplementary data

Supplementary data is available at Horticulture Research online.

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