Dataset Information

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.

SUBMITTER: Yocca AE

PROVIDER: S-EPMC10418200 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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

Yocca Alan E AE Platts Adrian A Alger Elizabeth E Teresi Scott S Mengist Molla F MF Benevenuto Juliana J Ferrão Luis Felipe V LFV Jacobs MacKenzie M Babinski Michal M Magallanes-Lundback Maria M Bayer Philipp P Golicz Agnieszka A Humann Jodi L JL Main Dorrie D Espley Richard V RV Chagné David D Albert Nick W NW Montanari Sara S Vorsa Nicholi N Polashock James J Díaz-Garcia Luis L Zalapa Juan J Bassil Nahla V NV Munoz Patricio R PR Iorizzo Massimo M Edger Patrick P PP

bioRxiv : the preprint server for biology 20230802

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 ...[more]

PMID: 37577683

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Project description:Blueberry is well recognized as a rich source of health promoting phytochemicals such as flavonoids and phenolic acids. Multiple studies in blueberry and other crops indicated that flavonoids and phenolic acids function as bioactive compounds in the human body promoting multiple health effects. Despite their importance, information is limited about the levels of variation in bioactive compounds within and between ploidy level and species, and their association with fruit quality traits. Such information is crucial to define a strategy to study the genetic mechanisms controlling these traits and to select for these traits in blueberry breeding programs. Here we evaluated 33 health related phytochemicals belonging to four major groups of flavonoids and phenolic acids across 128 blueberry accessions over two years together with fruit quality traits, including fruit weight, titratable acidity, total soluble acids and pH. Highly significant variation between accessions, years, and accession by year interaction were identified for most of the traits. Cluster analysis grouped phytochemicals by their functional structure (e.g., anthocyanins, flavanols, flavonols, and phenolic acids). Multivariate analysis of the traits resulted in separation of diploid, tetraploid and hexaploid accessions. Broad sense heritability of the traits estimated in 100 tetraploid accessions, ranged from 20 to 90%, with most traits revealing moderate to high broad sense heritability (H2 > 40%), suggesting that strong genetic factors control these traits. Fruit size can be estimated as a proxy of fruit weight or volume and vice versa, and it was negatively correlated with content of most of phytochemicals evaluated here. However, size-independent variation for anthocyanin content and profile (e.g., acylated vs. non-acylated anthocyanin) exists in the tetraploid accessions and can be explored to identify other factors such as genes related to the biosynthetic pathway that control this trait. This result also suggests that metabolite concentrations and fruit size, to a certain degree can be improved simultaneously in breeding programs. Overall, the results of this study provide a framework to uncover the genetic basis of bioactive compounds and fruit quality traits and will be useful to advance blueberry-breeding programs focusing on integrating these traits.

Dataset Information

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

Publications

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

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