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Gigascience. 2019 Jan 31. doi: 10.1093/gigascience/giz012. [Epub ahead of print]

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

Author information

1
Department of Horticulture, Michigan State University, East Lansing, MI, USA.
2
Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
3
Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, USA.
4
Department of Biochemistry, Purdue University, West Lafayette, IN, USA.
5
Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA.
6
Human Longevity Inc: San Diego, CA.
7
Key Laboratory of Herbage and Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
8
NRGene, Ness Ziona, 7403648 Israel.
9
Dovetail Genomics, Santa Cruz, CA, USA.
10
Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, MI, USA.
11
Mass Spectrometry & Metabolomics Core Facility, Michigan State University, East Lansing, MI, USA.
12
Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA.
13
Philip E. Marucci Center for Blueberry and Cranberry Research and Extension, Rutgers University, Chatsworth, NJ, USA.
14
Plant Resilience Institute, Michigan State University, East Lansing, MI, USA.

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 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 seventy-one cultivars and thirteen 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.

PMID:
30715294
DOI:
10.1093/gigascience/giz012

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