Transcriptome analysis identifies genes associated with the waxy coating on blueberry fruit in two northern-adapted rabbiteye hybrid breeding populations

Authors: QI, XINPENG - Orise Fellow; Ogden, Elizabeth; DIE, JOSE - University Of Cordoba; Ehlenfeldt, Mark; Polashock, James; DARWISH, OMAR - Towson University; ALKHAROUF, NADIM - Towson University; Rowland, Lisa

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/11/2019
Publication Date: 10/31/2019
Citation: Qi, X., Ogden, E.L., Die, J.V., Ehlenfeldt, M.K., Polashock, J.J., Darwish, O., Alkharouf, N., Rowland, L.J. 2019. Transcriptome analysis identifies genes associated with the waxy coating on blueberry fruit in two northern-adapted rabbiteye hybrid breeding populations. Biomed Central (BMC) Plant Biology. https://doi.org/10.1186/s12870-019-2073-7.
DOI: https://doi.org/10.1186/s12870-019-2073-7

Interpretive Summary: Light blue colored fruit is preferred for the blueberry fresh market. Black colored fruit is generally considered unacceptable for the fresh market but usable for processing. The difference between blueberries with a light blue color versus black color is the presence of a waxy coating on the fruit. Besides giving fruit the light, dusty blue color, this layer helps protect fruit from disease and water loss. In this study, we attempted to identify the gene(s) responsible for the waxy coating by using two related blueberry breeding populations comprised of individual plants with both light blue and black-colored fruit. When comparing genes among the waxy and non-waxy, we identified a ‘waxy’ gene that had much higher expression in the waxy plants than the non-waxy plants. This gene encodes an enzyme that plays a role in supplying fatty acids for wax biosynthesis. This gene may prove useful to breeders as a marker for selecting plants with the waxy coating even before they are old enough to set fruit.

Technical Abstract: Blueberry varieties selected for the fresh market have a light blue coating on the fruit, which is due to a heavy epicuticular wax layer. We attempted to identify the gene(s) responsible utilizing two unique germplasm populations that segregate for the waxy layer. We bulked RNA from waxy and non-waxy progenies from these populations and generated 316.85 million RNA-seq reads. We de novo assembled the data set, integrated with other publicly available RNA-seq data, trimmed the assembly into 91,861 unigenes, and functionally annotated them. By comparing the transcriptome from waxy and non-waxy progenies, we identified genes with at least a two-fold expression difference. After validating expression by RT-qPCR, a candidate gene encoding acyl-[acyl-carrier-protein] hydrolase emerged as likely being responsible for the waxy coating in our populations. This gene was expressed in waxy plants at more than five times the level in non-waxy plants. We amplified and sequenced the cDNA for this gene from three waxy plants of each population, but were unable to amplify the cDNA from non-waxy plants. In addition to helping us achieve a greater understanding of epicuticular wax biosynthesis in blueberry, the unigene collection from this study should facilitate functional annotation of the forthcoming chromosome-level blueberry genome assembly.