Skin Color in Apple Fruit (Malus × domestica): Genetic and Epigenetic Insights
and François Laurens 1,*Round 1
Reviewer 1 Report
This is a review of the manuscript submitted by Wang et al. to Epigenomes. In this review, the authors summarize the importance of genetic and epigenetic events on skin color in apple fruit. The manuscript was prepared in a very solid way and would bring a big impact for researchers interested in this topic. In my opinion, the review can be published in the current form with minor improvements.
I have the following suggestions:
Lines 26: Please add “transcriptome factor” as a key world
Lines 32: Please add the abbreviation after “DUS”
Figure 2: Please try to improve the quality of this Figure.
Author Response
Response to Reviewer 1 Comments
Point 1: Lines 26: Please add “transcriptome factor” as a key word
Response 1: Lines 26, I added “transcriptome factor” as a key word.
Point 2: Lines 32: Please add the abbreviation after “DUS”
Response 2: Lines 32, I added the definition of DUS (Distinctness, Uniformity and Stability)
Point 3: Figure 2: Please try to improve the quality of this Figure.
Response 3: Line 156, Figure 2, to change the quality of figure, firstly I thought it needs to change with high pixel, so I changed the figure quality with a high pixel.
Secondly, I thought the quality of figure could change the format (use different color to highlight different genes), in that case I also made a new format of the Figure below, if you think the new format is better, please use this figure.
For details, please see the attachment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
This was a delightful review to read. Wang and co-authors provide a comprehensive and insightful survey of research on the genetic and epigenetic factors affecting apple fruit coloration and pigment regulation. Overall, the manuscript is well written and well referenced; and an engaging read.
Minor questions:
- Line 32 define DUS
- Do most studies directly profile apple skin (metabolites, gene expression, epigenetics)? How important or relevant are signals (or metabolite biosynthesis) coming from other tissues?
- Likewise how relevant is the root stock?
- In the epigenetics sections, there was no discussion of the stability of epialleles? Is this relevant, they can be less stable right? Are there examples of unstable fruit color phenotypes that might be due to unstable epialleles (within a tree or within an orchard or from year to year)?
Author Response
Please see the attachment (Figure and References).
Response to Reviewer 2 Comments
Point 1: Line 32 define DUS
Response 1:
Lines 32, I added the definition of DUS (Distinctness, Uniformity and Stability)
Point 2: Do most studies directly profile apple skin (metabolites, gene expression, epigenetics)? How important or relevant are signals (or metabolite biosynthesis) coming from other tissues?
Response 2:
Yes, most of the studies directly profile apple skin in genetic field, to find the genes which could control the apple skin color, to do the gene expression and validation, or to examine gene interaction through molecular hybridization.
Anthocyanins could accumulate in leaves, roots, stocks [1], the enzymes involved in the flavonoid biosynthesis pathway are localized in the cytosol. After biosynthesis, flavonoids are transported to vacuoles or cell walls [2].
Anthocyanins upregulated by maturity, formation of flavonoids, especially anthocyanin and chlorogenic acid in ‘Jonagold’ apple skin, which influences of growth regulators and fruit maturity [3]. The signals or metabolite biosynthesis which could influence the maturity of fruits also could influence the anthocyanins. For example, plant hormones (abscisic acid, ethylene, jasmonates, auxin, gibberellin) have a crucial role in the regulation of fruit development and ripening. They interact with MYB–bHLH–WD40 complexes at either the transcriptional or the post-transcriptional level to control the anthocyanin composite [4]. Espley, et al. (2013) [1] reported that the increased flux in the anthocyanin pathway was also associated with increases in metabolite concentrations of other polyphenols, including up to a 10-fold increase in quercetin-3-galactoside.
Anthocyanins in the vacuole are degraded by peroxidases, the possible involvement of vacuolar peroxidases in anthocyanin degradation may be a component of the adaptation of plants to changing environmental conditions such as decreased light intensities, but may also be a component of the plant developmental program [5].
Point 3: Likewise how relevant is the rootstock?
Response 3:
For the link between rootstock and apple color is an interesting question, from the 20th century, there were many people doing the research for it. Apple color may be influenced by rootstock. In a study using seven rootstocks, Rogers (1926) [6] observed the best color on fruit from 'Bramley' trees grafted on ‘M9’. Tukey and Brase (1941) [7]and Blair (1938) observed that red-colored cultivars developed higher color on ‘M9’. Hewetson (1944) [8] and Upshall (1943) [9] found that the increase in red fruit color intensity found on some Malling rootstocks was due to earlier maturity date [10].
The amount of total phenolic compounds and flavonoids increased, which may be due to the influence of different rootstocks and the incompatibility between the rootstock and the scion or grafting wound. Generally in a study ‘Bud 9’ rootstock had a negative effect on the amount of anthocyanin while ‘M9’ increased the amount of anthocyanin [11]. Grafting of ‘Bekran’ on ‘Bekran’ rootstock and ‘Red Delicious’ cultivar on ‘Bekran’ decreased anthocyanin in scion leaves but when ‘Bastam’ cultivar was grafted on this rootstock it increased the amount of anthocyanin [11].
Point 4: In the epigenetics sections, there was no discussion of the stability of epialleles? Is this relevant, they can be less stable right? Are there examples of unstable fruit color phenotypes that might be due to unstable epialleles (within a tree or within an orchard or from year to year)?
Epigenetic levels are different in different organizations and in different developmental stages in plants [12]. It is inherited, but it is less stable, and depending upon the environment, the methylation level could be change [12]. For example, chestnut methylation level will decrease with the age of the tree [13].
Epialleles or epimutations, can generate stable and heritable changes of fruit phenotypes [14]. But in some situation, epialleles could be less stable, apple mutant skin color could come back to original apple color. For example, one mutant of Pink lady has the yellow skin in the orchard, but there is one branch of apple is in red skin color, this case really exists in the orchard (please see the figure below). The changes are unstable, depending upon the environment. But for the reasons of whether genetic reason or epigenetic reason caused this change is still unknown (not published).
Author Response File: Author Response.pdf
Round 2
Reviewer 2 Report
Superlative work.
The response to reviewers was great - the authors might consider adding some of this info to the manuscript (at their discretion), I'm sure readers would be interested too!
