Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts
Alan E. Yocca1,2 , Adrian Platts1,2, , Elizabeth Alger1 , Scott Teresi1,3 , Molla F. Mengist4 , Juliana Benevenuto5 , Luis Felipe V. Ferrão5 , MacKenzie Jacobs1,6 , Michal Babinski1 , Maria Magallanes-Lundback1 , Philipp Bayer7 , Agnieszka Golicz8 , Jodi L. Humann9 , Dorrie Main9 , Richard V. Espley10 , David Chagné11 , Nick W. Albert11 , Sara Montanari12 , Nicholi Vorsa13 , James Polashock13 , Luis Díaz-Garcia14 and Juan Zalapa14 , Nahla V. Bassil15 , Patricio R. Munoz5 , Massimo Iorizzo4,16 , Patrick P. Edger,1,3,17,
1Department of Horticulture, Michigan State University, East Lansing, MI, 48824, United States 2Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, United States 3Genetics and Genome Sciences, Michigan State University, East Lansing, MI, 48824, United States 4Plants for Human Health Institute, North Carolina State University, Kannapolis, NC United States 5Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, United States 6Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, United States 7University of Western Australia, Perth 6009 Australia 8Justus Liebig University, Giessen, 35390 Germany 9Department of Horticulture, Washington State University, Pullman, WA, 99163, United States 10The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand 11The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston, New Zealand 12The New Zealand Institute for Plant and Food Research Limited (PFR), Motueka, New Zealand 13SEBS, Plant Biology, Rutgers University, New Brunswick NJ 01019 United States 14Department of Viticulture and Enology, University of California, Davis, Davis, CA 95616, United States 15National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR 97333, United States 16Department of Horticulture, North Carolina State University, Kannapolis, NC United States 17MSU AgBioResearch, Michigan State University, East Lansing, MI, 48824, United States *Corresponding author. E-mail: aeyap42@gmail.com,edgerpat@msu.edu
Received: 26 Jul 2023 Accepted: 01 Oct 2023 Published online: 10 Oct 2023
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.