Abstract
BackgroundAcidity is a major contributor to fruit quality. Several organic acids are present in apple fruit, but malic acid is predominant and determines fruit acidity. The trait is largely controlled by the Malic acid (Ma) locus, underpinning which Ma1 that putatively encodes a vacuolar aluminum-activated malate transporter1 (ALMT1)-like protein is a strong candidate gene. We hypothesize that fruit acidity is governed by a gene network in which Ma1 is key member. The goal of this study is to identify the gene network and the potential mechanisms through which the network operates.ResultsGuided by Ma1, we analyzed the transcriptomes of mature fruit of contrasting acidity from six apple accessions of genotype Ma_ (MaMa or Mama) and four of mama using RNA-seq and identified 1301 fruit acidity associated genes, among which 18 were most significant acidity genes (MSAGs). Network inferring using weighted gene co-expression network analysis (WGCNA) revealed five co-expression gene network modules of significant (P < 0.001) correlation with malate. Of these, the Ma1 containing module (Turquoise) of 336 genes showed the highest correlation (0.79). We also identified 12 intramodular hub genes from each of the five modules and 18 enriched gene ontology (GO) terms and MapMan sub-bines, including two GO terms (GO:0015979 and GO:0009765) and two MapMap sub-bins (1.3.4 and 1.1.1.1) related to photosynthesis in module Turquoise. Using Lemon-Tree algorithms, we identified 12 regulator genes of probabilistic scores 35.5–81.0, including MDP0000525602 (a LLR receptor kinase), MDP0000319170 (an IQD2-like CaM binding protein) and MDP0000190273 (an EIN3-like transcription factor) of greater interest for being one of the 18 MSAGs or one of the 12 intramodular hub genes in Turquoise, and/or a regulator to the cluster containing Ma1.ConclusionsThe most relevant finding of this study is the identification of the MSAGs, intramodular hub genes, enriched photosynthesis related processes, and regulator genes in a WGCNA module Turquoise that not only encompasses Ma1 but also shows the highest modular correlation with acidity. Overall, this study provides important insight into the Ma1-mediated gene network controlling acidity in mature apple fruit of diverse genetic background.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1816-6) contains supplementary material, which is available to authorized users.
Highlights
Acidity is a major contributor to fruit quality
The trend of fruit juice titratable acidity (TA) was similar to that of malate in the ten varieties (Fig. 1a, b) while an expected reverse trend was observed for fruit juice pH (Fig. 1d)
Transcriptional regulation of fruit acidity mediated by Malic acid1 (Ma1) In an ongoing survey of the USDA Malus repository at Geneva, New York, we identified 40 diverse apple accessions of genotype ma1ma1 using marker CAPS1455 that can detect the stop codon leading SNP in ma1 [10] and found that each of them had fruit pH >4.0 (Xu, unpublished data), a typical low fruit acidity characteristic in genotype group mama
Summary
Several organic acids are present in apple fruit, but malic acid is predominant and determines fruit acidity. It has been shown that several organic acids are present in mature apple fruit, including malic acid, quinic acid, citric acid and others, but malic acid consists of more than 90 % of the total [1,2,3], thereby largely determining fruit acidity. Apple fruit acidity is primarily controlled by the major gene or QTL on chromosome 16, called Malic acid (Ma) alongside a significant QTL on chromosome 8 and a few other QTLs with relatively smaller effects [4,5,6,7,8,9].
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