Transcriptome analysis identifies genes related to the waxy coating on blueberry fruit in two northern-adapted rabbiteye breeding populations

Abstract

BackgroundBlueberry is of high economic value. Most blueberry varieties selected for the fresh market have an appealing light blue coating or “bloom” on the fruit due to the presence of a visible heavy epicuticular wax layer. This waxy layer also serves as natural defense against fruit desiccation and deterioration.ResultsIn this study, we attempted to identify gene(s) whose expression is related to the protective waxy coating on blueberry fruit utilizing two unique germplasm populations that segregate for the waxy layer. We bulked RNA from waxy and non-waxy blueberry progenies from the two northern-adapted rabbiteye hybrid breeding populations (‘Nocturne’ x T 300 and ‘Nocturne’ x US 1212), and generated 316.85 million RNA-seq reads. We de novo assembled this data set integrated with other publicly available RNA-seq data and trimmed the assembly into a 91,861 blueberry unigene collection. All unigenes were functionally annotated, resulting in 79 genes potentially related to wax accumulation. We compared the expression pattern of waxy and non-waxy progenies using edgeR and identified overall 1125 genes in the T 300 population and 2864 genes in the US 1212 population with at least a two-fold expression difference. After validating differential expression of several genes by RT-qPCR experiments, a candidate gene, FatB, which encodes acyl-[acyl-carrier-protein] hydrolase, emerged whose expression was closely linked to the segregation of the waxy coating in our populations. This gene was expressed at more than a five-fold higher level in waxy than non-waxy plants of both populations. We amplified and sequenced the cDNA for this gene from three waxy plants of each population, but were unable to amplify the cDNA from three non-waxy plants that were tested from each population. We aligned the Vaccinium deduced FATB protein sequence to FATB protein sequences from other plant species. Within the PF01643 domain, which gives FATB its catalytic function, 80.08% of the amino acids were identical or had conservative replacements between the blueberry and the Cucumis melo sequence (XP_008467164). We then amplified and sequenced a large portion of the FatB gene itself from waxy and non-waxy individuals of both populations. Alignment of the cDNA and gDNA sequences revealed that the blueberry FatB gene consists of six exons and five introns. Although we did not sequence through two very large introns, a comparison of the exon sequences found no significant sequence differences between the waxy and non-waxy plants. This suggests that another gene, which regulates or somehow affects FatB expression, must be segregating in the populations.ConclusionsThis study is helping to achieve a greater understanding of epicuticular wax biosynthesis in blueberry. In addition, the blueberry unigene collection should facilitate functional annotation of the coming chromosomal level blueberry genome.

Phenotypic Evaluation of a Hybrid Diploid Blueberry Population for Plant Development and Fruit Quality Traits

“…Interestingly, Scar exhibited weak negative correlations with Weight and Dia, and a weak positive correlation with 3 mm. 1 Correlation coefficients in bold are significantly different from zero at the p level shown in the following row. 2 NS, not significant (p > 0.05).…”

“…The popularity of blueberry has risen dramatically in recent years. Production in the United States, the largest producer of blueberries, has more than doubled from 2005 to 2015 (United States Department of Agriculture-National Agricultural Statistics Service (USDA-NASS)) and has increased worldwide by 58% from 2009 to 2014 (United Nations Food and Agriculture Organization) [1]. Blueberry consumption has increased as well, by approximately 3-fold from 2000 to 2010 in the U.S., likely due to greater awareness of its high anthocyanin content and its many health benefits [2].…”

Characterization and Analysis of Anthocyanin-Related Genes in Wild-Type Blueberry and the Pink-Fruited Mutant Cultivar ‘Pink Lemonade’: New Insights into Anthocyanin Biosynthesis

“…In 2012, we reported the first next-generation sequencing transcriptome (from 454 sequencing) of the species [19]. More recently, in 2019, we published a transcriptome from an RNA-seq analysis aimed at identifying gene(s) important for wax accumulation on blueberry fruit [44,45]. We also examined the expression levels of the structural genes of the anthocyanin biosynthesis pathway in treated fruits (35S:MYB) and compared them with those from fruits infiltrated with an empty vector (35S) and untreated mutant fruits (control).…”

“…In 2012, we reported the first next-generation sequencing transcriptome (from 454 sequencing) of the species [19]. More recently, in 2019, we published a transcriptome from an RNA-seq analysis aimed at identifying gene(s) important for wax accumulation on blueberry fruit [44,45].…”

Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species

“…Due to global climate change effects, further research involving comprehensive phenotypic, molecular, and genetic characterization of the impact of heat stress on blueberries has become essential. Comparative transcriptome analyses performed in the past few years have revealed molecular and genetic components of several traits, including fruit and color development [ 14 ], flowering pathways [ 15 ], fruit ripening and biosynthesis of bioactive compounds [ 16 ], waxy coating on fruit [ 17 ], anthocyanin synthesis [ 18 ], and cold acclimation pathways [ 19 ] in blueberry. However, no studies have reported the transcriptome analysis of blueberry plants under high-temperature stress.…”