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

Authors: YOCCA, ALAN - Michigan State University; PLATTS, ADRIAN - Michigan State University; ALGER, ELIZABETH - Michigan State University; TERESI, SCOTT - Michigan State University; MENGIST, MOLLA - North Carolina State University; FERRAO, LUIS FELIPE - University Of Florida; BENEVENUTO, JULIANA - University Of Florida; JACOBS, MACKENZIE - Michigan State University; BABINSKI, MICHAL - Michigan State University; BAYER, PHILIP - University Of Western Australia; GOLICZ, AGNIESZKA - Justus-Liebig University; HUMANN, JODI - Washington State University; MAIN, DORRIE - Washington State University; ESPLEY, RICHARD - Plant And Food Research; CHAGNE, DAVID - Plant And Food Research; ALBERT, NICK - Plant And Food Research; MONTANARI, SARA - Plant And Food Research; VORSA, NICHOLI - Rutgers University; Polashock, James; Zalapa, Juan; Bassil, Nahla; MUNOZ, PATRICIO - University Of Florida; IORIZZO, MASSIMO - North Carolina State University; EDGER, PATRICK - Michigan State University

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/6/2023
Publication Date: 10/10/2023
Citation: Yocca, A., Platts, A., Alger, E., Teresi, S., Mengist, M., Ferrao, L., Benevenuto, J., Jacobs, M., Babinski, M., Bayer, P., Golicz, A., Humann, J., Main, D., Espley, R., Chagne, D., Albert, N., Montanari, S., Vorsa, N., Polashock, J.J., Zalapa, J.E., Bassil, N.V., Munoz, P., Iorizzo, M., Edger, P. 2023. Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts. Horticulture Research. https://doi.org/10.1093/hr/uhad202.
DOI: https://doi.org/10.1093/hr/uhad202

Interpretive Summary: Domestication of cranberry and blueberry began in the northern United States in the early 1800s and 1900s, respectively. Due to their delicious flavors and health promoting benefits, these fruit crops are now cultivated and consumed worldwide. Although consumption of these valuable fruit crops has steadily increased over the past several decades, 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 to other high-value crops. This article describes the construction and analysis of the first almost complete set of genes or 'pangenome' for both blueberry and cranberry. Our analysis of these pangenomes revealed that both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Genes that are not shared by all cultivars (auxillary), are significantly enriched with 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 genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. These pangenomes and associated sequences are publicly available for analysis on the Genome Database of for Vaccinium - a curated and integrated web-based relational database. Sequences from these pangenomes will serve to develop a community genotyping platform to guide future molecular breeding efforts across the family.

Technical Abstract: Domestication of cranberry and blueberry began in the northern United States in the early 1800s and 1900s, respectively, and in part due to their delicious flavors and health promoting benefits are now cultivated and consumed worldwide. Although consumption of these valuable fruit crops has steadily increased over the past several decades, 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 to 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 that 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 Genome Database of 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.