Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry

Marivi Colle, Courtney P. Leisner, Ching Man Wai, Shujun Ou, Kevin A. Bird, Jie Wang, Jennifer H. Wisecaver, Alan E. Yocca, Elizabeth I. Alger, Haibao Tang, Zhiyong Xiong, Pete Callow, Gil Ben-Zvi, Avital Brodt, Kobi Baruch, Thomas Swale, Lily Shiue, Guo Qing Song, Kevin L. Childs, Anthony SchilmillerNicholi Vorsa, C. Robin Buell, Robert Vanburen, Ning Jiang, Patrick P. Edger*

*Corresponding author for this work

Research output: Contribution to journalArticle

16 Scopus citations

Abstract

Background Highbush blueberry (Vaccinium corymbosum) has long been consumed for its unique flavor and composition of health-promoting phytonutrients. However, breeding efforts to improve fruit quality in blueberry have been greatly hampered by the lack of adequate genomic resources and a limited understanding of the underlying genetics encoding key traits. The genome of highbush blueberry has been particularly challenging to assemble due, in large part, to its polyploid nature and genome size. Findings Here, we present a chromosome-scale and haplotype-phased genome assembly of the cultivar "Draper," which has the highest antioxidant levels among a diversity panel of 71 cultivars and 13 wild Vaccinium species. We leveraged this genome, combined with gene expression and metabolite data measured across fruit development, to identify candidate genes involved in the biosynthesis of important phytonutrients among other metabolites associated with superior fruit quality. Genome-wide analyses revealed that both polyploidy and tandem gene duplications modified various pathways involved in the biosynthesis of key phytonutrients. Furthermore, gene expression analyses hint at the presence of a spatial-temporal specific dominantly expressed subgenome including during fruit development. Conclusions These findings and the reference genome will serve as a valuable resource to guide future genome-enabled breeding of important agronomic traits in highbush blueberry.

Original languageEnglish (US)
JournalGigaScience
Volume8
Issue number3
DOIs
StatePublished - Jan 31 2019
Externally publishedYes

Keywords

  • Blueberry
  • Genome
  • Haplotype-phased
  • Phytonutrients
  • Polyploid
  • Subgenome Dominance
  • Tetraploid
  • Vaccinium

ASJC Scopus subject areas

  • Computer Science Applications
  • Health Informatics

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    Colle, M., Leisner, C. P., Wai, C. M., Ou, S., Bird, K. A., Wang, J., Wisecaver, J. H., Yocca, A. E., Alger, E. I., Tang, H., Xiong, Z., Callow, P., Ben-Zvi, G., Brodt, A., Baruch, K., Swale, T., Shiue, L., Song, G. Q., Childs, K. L., ... Edger, P. P. (2019). Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. GigaScience, 8(3). https://doi.org/10.1093/gigascience/giz012