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Research Project: Conservation and Utilization of Temperate-Adapted Fruit, Nut, and Other Specialty Crop Genetic Resources

Location: National Clonal Germplasm Repository

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

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