Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

Abstract

Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures), as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence–absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium-a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.

Acknowledgements

This work was supported by Michigan State University AgBioResearch, Michigan State University Institute for Cyber-Enabled Research, NIH 5T32GM110523-10, NSF NRT-HDR 1828149 USDA-NIFA HATCH MICL02742, USDA-NIFA AFRI 1015241, and USDA-NIFA SCRI award 2019-51181-30015. This work is supported in part by the National Science Foundation Research Traineeship Program (DGE-1828149) to M.J.

Conflict of interest statement

The authors declare no conflict of interest.

Data availability

Custom scripts for analyses performed throughout this manuscript are available on Github (https://github.com/Aeyocca/VaccPan). Raw sequencing data are available on the NCBI SRA under project code PRJNA687008. Genome assemblies, pangenome alignments and annotations are available on the Genome Database for Vaccinium [47].

Supplementary data

Supplementary data is available at Horticulture Research online.

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