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Biotechnology and Biological Transformations

Transcriptomic Analysis of Red-fleshed Apples Reveals the Novel Role of MdWRKY11 in Flavonoid and Anthocyanin Biosynthesis Nan Wang, Wenjun Liu, Tianliang Zhang, Shenghui Jiang, Haifeng Xu, Yicheng Wang, Zongying Zhang, Chuanzeng Wang, and Xuesen Chen J. Agric. Food Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jafc.8b01273 • Publication Date (Web): 18 Jun 2018 Downloaded from http://pubs.acs.org on June 18, 2018

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Journal of Agricultural and Food Chemistry

Transcriptomic Analysis of Red-fleshed Apples Reveals the Novel Role of MdWRKY11 in Flavonoid and Anthocyanin Biosynthesis

Nan Wang, † ‡ Wenjun Liu, † ‡ Tianliang Zhang, † Shenghui Jiang, † Haifeng Xu, † Yicheng Wang,† Zongying Zhang,† Chuanzeng Wang,§ Xuesen Chen,*,†



State Key Laboratory of Crop Biology, College of Horticulture Science and

Engineering, Shandong Agricultural University, Tai’an, Shandong 271018, China §



Shandong Institute of Pomology, Tai’an, Shandong 271000, China

Nan Wang and Wenjun Liu are co-first authors.

*Corresponding author: Tel: +86-538-8249338. E-mail: [email protected]

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ABSTRACT: In plants, flavonoids are important secondary metabolites that

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contribute to the nutritional quality of many foods. Apple is a popular and frequently

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consumed food because of its high flavonoid content. In this study, flavonoid

4

composition and content were detected and compared between the red- and

5

white-fleshed apples in a BC1 hybrid populations using ultra-performance liquid

6

chromatography/quadrupole

7

analysis of the red- and white-fleshed apples was then performed using RNA-seq

8

technology. By screening differentially expressed genes encoding transcription factors

9

we unearthed a WRKY family transcription factor designated MdWRKY11.

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Overexpression of MdWRKY11 promoted the expression of F3H, FLS, DFR, ANS and

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UFGT and increased the accumulation of flavonoids and anthocyanin in apple calli.

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Our findings explored novel role of MdWRKY11 in flavonoid biosynthesis and

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suggest several other genes that may be also potentially involved. This provides

14

valuable information on flavonoid synthesis for the breeding of elite red-fleshed

15

apples.

time-of-flight

mass

spectrometry.

Transcriptomic

16 17

KEYWORDS: plant secondary metabolites, flavonoids,

18

transcriptome analysis, WRKY

red-fleshed

apple,

19 20 21 22 2

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INTRODUCTION

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In plants, flavonoids are important secondary metabolites that provide protection

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against ultraviolet radiation, prevent pathogenic microorganism invasion, regulate

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auxin transport, act as signaling molecules in plant–bacteria interactions, and promote

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pollen germination and fertility.1–4 Moreover, flavonoids are natural antioxidants that

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reduce myocardial oxygen consumption, prevent vascular sclerosis, enhance

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immunity, and have anti-aging and anti-cancer effects.5–8 Evidence suggests that

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flavonoids taken from various fruits and vegetables play a key role in reducing

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disease risk.9,10

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Apple (Malus domestica Borkh.), one of the most widely produced and

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economically important fruit crops in temperate regions,11 is a significant source of

34

flavonoids in people's diet and is one of the top nutritionally rated and consumed fruit

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worldwide.12–14 Boyer and Liu found that apples had the second highest level of

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antioxidant activity when compared to many other commonly consumed fruits in the

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United States.15 More importantly, apple contains high levels of free flavonoid, which

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are not bound to other compounds and may be more available for eventual absorption

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into the human bloodstream.15,16 For example, apples rich in flavonoids can

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independently enhance endothelial function and acutely lower blood pressure,

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benefitting cardiovascular health.17 The effects of apples on specific enzymes related

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to cancer etiology have also been examined, with studies showing that apple juice

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extracts rich in flavonoids reduced the growth of cancer cells and increased the

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expression of several genes, including phase 2 enzymes associated with 3

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chemoprevention.18 Studies have also shown that proanthocyanidins have significant

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effects on plasma antioxidant activity, whereas quercetin has slight effects on plasma

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antioxidant biomarkers in vivo but can affect some carcinogenesis markers.19

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Eberhardt found that 100 g of fresh apples had the same antioxidant activity as 1500

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mg VC and that apple extracts inhibit the growth of colon and liver cancer cells in

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vitro in a dose-dependent manner.20 According to these epidemiological studies,

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apples appear to play a significant role in the intake of flavonoids and the

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maintenance of human health.

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In apple, studies on flavonoid biosynthesis and regulation first focused on

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anthocyanin. Members of three TF families (MYB, bHLH, and WD40) function

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together in a ternary MYB-bHLH-WD40 (MBW) protein complex to participate in

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the anthocyanidin pathway, a role that is widely conserved among plant species.21–24

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Among these, the MdMYB1 and MdMYBA genes encoding TFs were initially isolated

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and observed to regulate anthocyanin biosynthesis in apple skin.25,26 MdMYB10, an

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allele of MdMYB1/MYBA, determines the red pigmentation of red-fleshed apple. The

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red-fleshed apple has a minisatellite-like structure comprising six tandem repeats in

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the promoter of MdMYB10 (R6:MdMYB10), whereas the white-fleshed apple has only

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one (R1:MdMYB10).27 Subsequently, MdMYB3, MdMYB9, MdMYB11, MdMYB12,

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MdMYB22, and other genes regulating flavanol and flavanol biosynthesis have also

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been cloned and identified.28–30 In addition to MYB TFs, MdbHLH3 reportedly binds

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to the promoters of MdDFR and MdUFGT to promote the anthocyanin synthesis.31

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Conversely, MdTTG1 of class WD40 cannot bind to the promoters of MdDFR and 4

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MdUFGT nor interact with MdMYB1. The regulation of anthocyanin by MdTTG1

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may be achieved by interaction with MdbHLH3 and MdbHLH33.32

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Many studies have examined flavonoid synthesis in apples. However,

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considerable inbreeding has narrowed the hereditary basis of cultivated apple varieties

71

and resulted in fruit with poor nutritional quality and low flavonoid content. Thus, the

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breeding of red-fleshed apples with a high flavonoid content is of great interest to

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apple breeder worldwide.33–35 Since 2006, we have used wild red-fleshed apple

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germplasm resources, Malus. sieversii f. niedzwetzkyana, to breed red-fleshed apple

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and expand the genetic basis and diversity of cultivated apple. Although M. sieversii f.

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niedzwetzkyana (R6R1) has red-fleshed phenotype, its flesh is soft and sour.

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Therefore, M. domestica (R6R1) with crisp and sweet flesh was chosen to cross with

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it. In the crossed F1 hybrid populations, we identified a red-fleshed mutant was

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homozygous for the R6R6 genotype, in conflict with the parent R6R1 and R1R1

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genotypes.30 In the BC1 hybrid populations of the R6R6 homozygous mutant crossed

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with M. domestica, all progeny had the R6R1 genotype, but the flavonoid and

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anthocyanin content of their flesh differed significantly. This genetic diversity reflects

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the combined effect of the R6:MdMYB10 and other unknown regulation factors that

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have not previously been reported. Therefore, RNA-seq was used in this study to

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compare the transcriptomes of red- and white-fleshed apple strains in the BC1

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populations. Focusing on screening TFs differentially expressed between the red- and

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white-fleshed apples unearthed a WRKY family TF designated MdWRKY11. Its role

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in flavonoid biosynthesis was identified through overexpression studies in ‘Orin’ calli. 5

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We aimed to identify flavonoid-related functional genes useful for providing a

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valuable perspective on flavonoid synthesis and breeding elite red-fleshed apples with

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a high flavonoid content.

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MATERIAL AND METHODS

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Plant materials. The BC1 hybrid populations obtained by crossing the R6R6

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red-fleshed mutant and M. domestica were grown in the Guanxian Fruit Tree

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Breeding Base (36°580’N, 115°420’E). Five strain lines with different degree red

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flesh were selected. Three individual strains were selected from each line for

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biological repetition and their fruits were harvested at the ripe stage, and then frozen

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in liquid nitrogen and stored at −80°C. Among them, three individual strains with

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extremely red flesh (RF) and three individual strains with white flesh (WF) fruit were

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selected for UPLC-ESI-TOF/MS analysis and RNA-seq.

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The ‘Orin’ calli were induced and cultured based as described previously.36 The

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regenerated tissues were placed on a callus-induction medium consisting of

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Murashige

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2,4-dichlorophenoxyacetic acid, 0.5 mg·l−1 thidiazuron, 30 g·l−1 sugar, and 7.5 g·l−1

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agar. The pH was adjusted to 5.8 ± 0.1. The calli were cultured at 24°C and

107

subcultured every 15 d.

and

Skoog

(MS)

medium

supplemented

with

2.5

mg·l−1

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R6:MYB10 Genotype identification. For genotype identification, the total DNA

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of each sample was isolated using the Plant Genomic DNA Kit (TianGen, Beijing,

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China). The R6 and/or R1 repetitive sequences were amplified by the forward primer 6

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proMYB10-F (5ʹ-GGTGGTCAAAGATGTGTGTTGT-3ʹ) and the reverse primer

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proMYB10-R (5ʹ-TTTGCCTGCTACCCACTTCA-3ʹ) that were designed from the

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MdMYB10 promoter. Genotypes were then identified by agarose gel electrophoresis.

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Flavonoid extraction and UPLC-ESI-TOF/MS analysis. Total flavonoids were

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extracted from 0.3 g powdered apple flesh incubated in 5 ml 1% (v/v) HCl methanol

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for 2 h at 4°C in darkness. Then, the extract was centrifuged at 10,000 g for 15 min.

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The obtained flavonoid extract was used for UPLC-ESI-TOF/MS analysis. The upper

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aqueous phase was saved and filtered using an organic filter membrane (0.2 µm). The

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UPLC-ESI-TOF/MS (MALDI SYNAPT MS, Waters, http://www.waters.com/) was

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performed using the ACQUITY UPLC system (Waters), and the chromatographic

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column was a Waters BEH C18 column (100 mm × 2.1 mm, 1.7 µm particle size,

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25°C column temperature). Samples were eluted at a 0.4 ml·min-1 flow rate. The

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mobile phase: solvent A (acetonitrile) and solvent B (2% formic acid aqueous solution,

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v/v). The gradient: 0–0.1 min with 5% A, 20 min with 20% A, 22 min with 80% A, 21

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min with 5% A, and 25 min with 5% A. MS was performed using a XEVO G2-S

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Q-TOF (Waters) with electrospray ionization (ESI+ for anthocyanin and ESI− for

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others). The following conditions were used: sweep range: 100–150 m/z, capillary

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voltage: 3.5 kV, cone voltage: 30 V, source temperature: 100°C, desolvation

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temperature: 300°C, and desolvation gas flow: 500 L·h-1.

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RNA isolation and RNA-Seq. Total RNA was extracted using the RNAprep Pure

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Plant kit (Tiangen, Beijing, China). The quality of the purified RNA was determined

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using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA). The 7

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mRNA with poly(A) tails were enriched by magnetic beads with oligo (dT). Interrupt

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buffer was used to fragment the obtained RNA. The random N6 primers were used for

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reverse transcription and then double-stranded cDNA was synthesized. After

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amplification and denaturation, a single-strand circular DNA library was obtained and

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sequenced using the BGISEQ-500 system (The Beijing Genomics Institute, Shenzhen,

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China).

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RNA-Seq data analysis. Raw RNA-seq reads were filtered by removing low

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quality reads containing the connectors and more than 10% unknown base N. The

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filtered clean reads were compared with the apple genome reference sequence using

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HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts).37 The

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expression levels of genes and transcripts were calculated using RSEM.38 Raw counts

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for each gene were derived and normalized to fragments per kilobase per million

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mapped fragments (FPKM). The differentially expressed genes (DEGs) were screened

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using the DEseq2 algorithm39 with adjusted P-value ≤ 0.05 and fold change ≥ 2 as the

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significance cutoffs. The red-fleshed strains (RF) were used as control. The stratified

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cluster analysis of gene expression was based on the Cluster software to calculate the

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common formula with Euclidean distance as matrix.40 According to the GO

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annotation results41, KEGG annotation results42, and the official classification, the

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DEGs were grouped into different functional and biological pathways and the Phyper

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function of R software was used for further enrichment and analysis. FDR correction

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was performed on the P-value, with FDR ≤ 0.01 generally regarded as significant

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enrichment. 8

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Real-time RT-PCR analysis. First-strand cDNA was synthesized from 1 µg total

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RNA using a First-strand cDNA Synthesis kit (TianGen, Beijing, China). The

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synthesized cDNA samples were stored at −20°C for qRT-PCR. Primers were

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designed using the Beacon Designer 7 program and synthesized by Sangon Biotech

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(Shanghai, China). The qRT-PCR analysis was conducted using SYBR Green PCR

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Master Mix (TransGen Biotech, Beijing, China) and the iCycler iQ5 system (Bio-Rad,

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Hercules, CA). The MdActin gene served as an internal control and the relative

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quantities of mRNAs were calculated using the 2−∆∆Ct method of the IQ5 2.0

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program.43 The primers are shown in Table 1 in the Supporting Information.

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Transformation of apple calli with MdWRKY11. For gene transformation, the

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coding sequences of MdWRKY11 were recombined into the pRI101-AN vector

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containing the cauliflower mosaic virus (CaMV) 35S promoter and a GFP tag. This

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vector was transformed into Agrobacterium tumefaciens LBA4404 that were then

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used to infect ‘Orin’ calli for 20 min and followed by co-culturing on MS solid

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medium in the dark for 24–48 h at 24°C. The co-cultured calli were then transferred to

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screening medium containing 250 mg·l−1 carbenicillin (Solarbio) and 50 mg·l−1

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kanamycin (Solarbio, Beijing, China) for selection. The amplification primers are

172

shown in Table 1 in the Supporting Information.

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Determination of flavonoid and anthocyanin content. For spectrophotometric

174

quantification, flavonoids were extracted from 1 g powdered apple flesh and then

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incubated in 10 ml 1% (v/v) HCl methanol for 4 h at 4°C in darkness. The extract was

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centrifuged at 12,000 g for 15 min before 0.5 ml of the upper aqueous phase was 9

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removed and added to 1 ml of 5% NaNO2, 1 ml of 10% Al(NO3)3, and 4 ml of 2

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mol·l−1 NaOH. Samples were incubated at room temperature for 15 min before

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spectrophotometric quantification was performed at 510 nm using a UV–vis

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spectrophotometer (Shimadzu UV-2450, Kyoto, Japan). Rutin (Sigma Chemicals,

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Saint Louis, MI) was used as the master standard.

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Anthocyanin was extracted from 1 g powdered apple flesh and was incubated in 10

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mL 1% (v/v) HCl-methanol for 24 h at 4°C in darkness. Then, the extract was

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centrifuged at 10,000 g for 10 min before 1 ml supernatant was mixed with 4 ml KCl

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buffer (pH 1.0) and 4 ml NaAc buffer (pH 4.5). After 15 min incubation at 4°C,

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spectrophotometric quantification was performed at 510 nm and 700 nm using a UV–

187

vis spectrophotometer. Anthocyanin content was calculated using the pH differential

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method.44

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RESULTS

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Genotype determination of BC1 hybrid populations and flavonoid composition

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and content analyses between red- and white-fleshed apples. In previous studies,

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we obtained an R6R6 homozygous F1 hybrid plant.30 Using the R6R6 individual plant

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as the parent, we further constructed a BC1 backcross population. In the BC1 hybrid

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populations, the degree of redness of the fruit flesh varied widely (Figure 1A). The

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genotypes of five strain lines with different red flesh degree were identified (Figure

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1B) with all five strains having both a 497-bp and a 396-bp fragment, indicating the

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R6R1 heterozygous genotype. This demonstrates that the presence of R6:MdMYB10

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cannot completely determine the red phenotype of red-fleshed apples and that other 10

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factors are involved.

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To observably determine the differences in flavonoid content among these R6R1

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individuals, the red-fleshed (RF) and white-fleshed (WF) strains that displayed

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extremely different degrees of red flesh were selected for UPLC-ESI-TOF/MS

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analysis. A total of 10 flavonoids, including four flavanols, three flavonols, one

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dihydrochalcone, and two anthocyanins were detected (Figure 1C, D). Two

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anthocyanins were detected under the positive ion signal and the others were detected

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under the negative ion signal. The chromatogram map showed that there were

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significant differences in the peak areas between the two apple cultivars. The levels of

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the four flavanols in red-fleshed apples were 2.4–3.3 times higher than in the

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white-fleshed

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3-O-α-L-arabinoside, and phlorizin content of red-fleshed apples was 14.5, 3.7, 5.2,

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and 8.6 times higher than that of white-fleshed apples, respectively. Significantly, the

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cyanidin 3-O-galactoside and cyanidin 3-arabinoside content of red-fleshed apples

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were 128.9 and 150.5 times higher than of white-fleshed apples, respectively (Table

214

1).

apples.

The

rutin,

quercetin

3-β-D-glucoside,

quercetin

215

Analysis of differentially expressed genes between red- and white-fleshed

216

apples by RNA-seq. To systematically study the phenotypic differences in

217

red-fleshed apples and explore the differentially expressed genes related to flavonoid

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synthesis, transcriptome profiles of the red-fleshed (RF) and white-fleshed (WF)

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apples were generated using RNA-seq technology and then compared. A total of 412

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DEGs were obtained using Padj (adjusted P value) ≤ 0.05 and fold change ≥2 as the 11

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cutoffs. A total of 164 genes were up-regulated in WF and 248 genes were

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down-regulated compared with RF apples (Figure 2A). Of these, the gene encoding a

223

cyclin-dependent kinase F-4 had the greatest differential expression in RF than in WF

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apples (Table 2 in the Supporting Information). Then, based on the results of DEGs

225

detection, we used the pheatmap function for hierarchical clustering analysis. The

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result included three biological repeats in two groups of samples and showed that

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there was a high reproducibility between the biological repeats. In both RF and WF

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apples, some DEGs were poorly expressed or not expressed at all, suggesting that

229

they may be associated with certain phenotypic deletions in corresponding apple

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samples (Figure 2B). Raw reads data were deposited in the NCBI sequence read

231

archive under accession number SRP134054.

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GO functional classification and KEGG pathway enrichment analyses.

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According to the DEG results, we classified the Gene Ontology (GO) function and

234

analyzed its enrichment. GO terms were divided into three functional categories:

235

molecular function, cellular component, and biological process. In the molecular

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function category, both up- and down-regulated DEGs were most enriched in

237

metabolic process. In the cellular component category, both up- and down-regulated

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DEGs were most enriched in cell and cell part. In the biological process category, the

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up-regulated DEGs in WF were most enriched in catalytic activity, while the

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down-regulated DEGs were most enriched in binding activity (Figure 3). Significantly,

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only down-regulated DEGs were enriched in developmental process, reproduction,

242

reproductive process, cytoskeleton, extracellular region, membrane-enclosed lumen, 12

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nucleic acid binding transcription factor activity, transporter activity, and molecular

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transducer activity.

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Likewise, KEGG pathway enrichment analyses were performed according to the

246

DEGs. The pathway enrichment results showed that the highest number of DEGs

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were enriched in metabolic pathways, followed by biosynthesis of secondary

248

metabolites (Figure 4A). Furthermore, there were eight DEGs enriched in flavonoid

249

biosynthesis and two in anthocyanin biosynthesis, including cytochrome P450,

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polyketide synthase 5, leucoanthocyanidin reductase, naringenin, 2-oxoglutarate

251

3-dioxygenase,

252

anthocyanidin 3-O-glucosyltransferase. Both up- and down-regulated DEGs in WF

253

were most enriched in metabolic process. Only down-regulated DEGs were enriched

254

in

255

monoterpenoid biosynthesis, and taurine and hypotaurine metabolism, indicating that

256

they had high metabolic activity in RF apples (Figure 4B).

citrate

chalcone-flavonone

cycle,

anthocyanin

isomerase,

biosynthesis,

UDP-glycosyltransferase,

arachidonic

acid

and

metabolism,

257

The screening of DEGs encoding transcriptional factors and qRT-PCR

258

validation. To further investigate the transcriptional pattern differences between RF

259

and WF apples, the DEGs encoding TFs were analyzed further. A total of 22 DEGs

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that were found to encode members of 14 TF families, including 17 up-regulated and

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five down-regulated genes, were found in RF apples compared with WF apples (Table

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3 in the Supporting Information). Notably, the DEGs encoding MADS TF family

263

members such as MADS24 and AGL24 differed most significantly higher expression,

264

respectively, in RF than in WF apples. The expression of MYB10 in RF apples was 22 13

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times higher than in WF apples. Additionally, genes with similar expression patterns

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are usually functionally related. Cluster analysis shows that DEGs encoding WLIM1,

267

WRKY11, and ETC1 had the closest cluster relationship with MYB10 (Figure 5A).

268

Next, real-time RT-PCR was performed to validate the expression of these 22 DEGs

269

encoding TFs obtained from RNA-Seq. The qRT-PCR results showed that most of the

270

differences in expression were consistent with the expression levels obtained by

271

RNA-seq. The qRT-PCR data for TCP8 and SCL14, however, did not differ

272

significantly between RF and WF apples. Additionally, the differential expression

273

levels of WRKY11 and NAC62 were much higher in the qRT-PCR data compared with

274

the RNA-seq data, reaching 8-fold, and 7.5-fold, respectively (Figure 5B).

275

Furthermore, the expressions of MdWRKY11, MdMYB10, NAC62, WLIM1,

276

MADS24 and AGL24 with significant differences of more than five times were further

277

compared in different red-fleshed phenotypes (Figure 6A). The results showed that

278

MdWRKY11 and MdMYB10 had similar expression patterns in different red-fleshed

279

phenotype strains, which increased their expression with the increase of red flesh

280

degree. However, the expression patterns of MADS24, NAC62 and WLIM1 did not

281

appear to be related to the different red-fleshed phenotypes (Figure 6B). Thus, to

282

explore whether there was some genetic difference of MdWRKY11 in the red-fleshed

283

apple with different red degree, we compared the coding region and promoter

284

sequence of MdWRKY11 and found that there was no difference, indicating that

285

MdWRKY11 is not an additional ‘genetic’ factor for red coloration.

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Overexpression of MdWRKY11 promotes flavonoid and anthocyanin 14

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accumulation in apple calli. Among the 17 up-regulated DEGs, no genes other than

288

MdMYB10 have been reported to be involved in flavonoid synthesis. A small number

289

of the WRKY TFs are, however, known to participate in flavonoid synthesis.45, 46 To

290

determine whether MdWRKY11 was involved in flavonoid synthesis, the flavonoid

291

and anthocyanin contents in the selected R6R1 hybrid individual plants were

292

measured, as well as the relative expression of MdWRKY11. Correlation analysis

293

showed that MdWRKY11 was positively correlated with the flavonoid and

294

anthocyanin content, with correlation coefficients of 0.72 and 0.835, respectively

295

(Figure 7A).

296

To further confirm the function of MdWRKY11 in flavonoid and/or anthocyanin

297

synthesis, we transferred MdWRKY11 into ‘Orin’ apple calli under the control of the

298

CaMV 35S promoter. Three independent transgenic calli lines of 35S:MdWRKY11

299

(OE1, OE2. and OE3) turned red, while the wild-type (WT) calli and control calli

300

(CK) with empty vectors did not change color (Figure 7B). The presence of the

301

transgene in OE calli was confirmed by PCR amplification (Figure 7C) and western

302

blotting (Figure 7D). Next, flavonoid and anthocyanin content were determined. The

303

results showed that OE calli produced 5.3–8.5 times more flavonoid and 2.9–5.2 times

304

more anthocyanin than the WT and CK calli (Figure 7E). Finally, the expression of

305

flavonoid pathway genes was analyzed by qRT-PCR. The transcript levels of F3H,

306

FLS, DFR, ANS and UFGT increased significantly in the OE calli, while other genes

307

remained unchanged (Figure 7F). These results demonstrate that MdWRKY11 is a

308

positive regulator for anthocyanin biosynthesis and lay a foundation for further study 15

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on the metabolic mechanism of flavonoids.

310 311

DISCUSSION

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The crop and fruit tree industry is challenged by a serious inbreeding problem that

313

has narrowed the hereditary basis of the plants, resulting in lines with poor nutritional

314

quality. Using wild germplasm resources to improve the genetic diversity of cultivated

315

varieties has become an important method of counteracting this.47, 48 In apple, with the

316

completion of the apple genome sequence and the resequencing of the apple

317

germplasm resources, M. sieversii has been clarified and confirmed to be the ancestor

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of cultivated apples.11, 49 In this study, we made full use of M. sieversii and its red

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variety M. sieversii f. niedzwetzkyana to conduct extensive cross-breeding

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experiments. In the F1 hybrid populations, we previously performed a transcriptomic

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analysis comparing red- and white-fleshed apples that had the R6R1 and R1R1

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genotypes, respectively.50 Here, in the BC1 hybrid populations, we found that while

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the selected individual plants were all R6R1 heterozygotes, the degree of red

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coloration of fruit flesh varied widely. Therefore, high throughput RNA-seq was

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performed between red- and white-fleshed fruit strains to study the mechanism

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underlying differences in flavonoid content in plants with the same genotypes in more

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depth.

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The complexity of the regulation mechanism underlying flavonoid biosynthesis

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embodies the diversity of red-fleshed apple germplasm resources. In terms of

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flavonoid metabolism, extensive research has been conducted on the cause of 16

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differences in red-fleshed coloration. The overexpression of MdMYB10 in transgenic

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‘Royal Gala’ results in a red-fleshed apple phenotype.51 Interestingly, although

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MdMYB10 was highly expressed in type 1 red-fleshed apples, it was not expressed in

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type 2 red-fleshed apples. Conversely, another MYB transcription factor close to

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MdMYB10, designated MdMYB110a, is associated with the red pigmentation

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phenotype in type 2 red-fleshed apples but is not expressed in type 1 red-fleshed

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apples.52 In this study, the RNA-seq and qRT-PCR results showed that the expression

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of MdMYB10 was significantly up-regulated in red-fleshed apples, proving that it was

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associated with type 1 red-fleshed apples. No MdMYB110a was found in the screened

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DEGs, suggesting that MdMYB110a was not the cause of the difference in red flesh

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coloration between red- and white-fleshed apples with the same R6R1 genotype in the

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BC1 populations. MADS family TFs have been widely reported to be closely related

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to pollen development and flower formation.53,54 Likewise, flavonoids have also been

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shown to be closely related to pollen development in plants.55 There are, however, no

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reports of MADS family transcription factors being related to flavonoid or

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anthocyanin synthesis. In this study, we found two MADS family genes that had the

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most significant up-regulation of expression in RF. Whether MADS TFs are involved

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in flavonoid metabolism requires further study. In terms of negative regulatory factors,

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it has been reported that the expression of AtLOB37, AtLOB38, and AtLOB39 can be

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induced by nitrate and can negatively regulate anthocyanin biosynthesis.56

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Furthermore, it has been shown that overexpression of MdLOB52 can inhibit the

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synthesis of anthocyanin in apple.57 Here, the results of our RNA-seq also showed 17

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that the expression of MdLOB37 was significantly up-regulated in WF to a level 11.41

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times higher than that in RF; this may be one of the reasons why the WF apples were

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not red.

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Flavonoids play important roles in the protection of plants against biotic and

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abiotic stress through their ability to inhibit reactive oxygen species formation.58

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Under oxidative and drought stress, the overaccumulation of anthocyanin can

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effectively mitigate the accumulation of reactive oxygen species in vivo.59 In carrot

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cells cultivated in vitro, the ability of specific anthocyanins and other

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phenylpropanoids to protect cells from heat stress was investigated.60 Moreover,

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flavonoids were identified to have anti-fungal activity in the defense against Fusarium

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species and Pyricularia oryzae.61 In this study, we screened several transcription

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factors related to biotic and abiotic stress responses using the RNA-seq data,

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including SPL12, AP2, NAC62, MYB44, and WRKY11. They were all found to be

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significantly up-regulated in RF but their role in flavonoid synthesis is unknown. In

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both Arabidopsis and tobacco, overexpression of SPL1 or SPL12 can enhance

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thermotolerance at the reproductive stage.62 In tobacco, overexpression of an AP2 TF

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enhanced resistance to pathogen attack and osmotic stress.63 In Arabidopsis, the

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expression of the RD26 gene encoding a NAC TF could be induced by drought,

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abscisic acid, and high salinity.64 The MYB family TF MYB44 has been characterized

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as a phosphorylation-dependent positive regulator in salt stress signaling.65 Among

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these screened TFs, the WRKY family has been widely studied in plant stress

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resistance pathways. In rice, for example, OsWRKY11 was suggested to be induced by 18

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pathogens, drought, and heat stress.66 Ectopic expression of the grapevine VvWRKY11

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in Arabidopsis seedlings resulted in higher tolerance to water stress induced by

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mannitol than in wild-type plants.67 While sporadic, reports on the involvement of

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WRKY family TFs in flavonoid synthesis are slowly emerging. Ectopic

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overexpression of the Brassica napus WRKY41-1 in Arabidopsis showed its role in

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negative regulating anthocyanin biosynthesis.45 In grape, VvWRKY26 involvement in

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the flavonoid pathway was shown to possibly be restricted to the control of

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proanthocyanidin biosynthesis.46 In this study, MdWRKY11 expression was found to

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be significantly up-regulated in RF apples. However, the promoter and coding regions

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of MdWRKY11 are identical in all red-fleshed apples with different colors, indicating

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that MdWRKY11 is not an additional ‘genetic’ factor for red coloration. MdWRKY11

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may promote anthocyanin synthesis through the regulation of other factors rather than

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the ‘genetic’ factor. The overexpression of MdWRKY11 promoted the expression of

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F3H, FLS, DFR, ANS and UFGT genes and increased the accumulation of flavonoids

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and anthocyanin in apple calli, confirming the role of MdWRKY11 in flavonoid

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biosynthesis.

391 392

ASSOCIATED CONTENT

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Supporting Information

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Primers used for RT-qPCR and the plasmids construction, differentially expressed

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genes between red- and white-fleshed apples, and differentially expressed genes

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encoding transcription factors. 19

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AUTHOR INFORMATION

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Corresponding Author

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*Tel: +86-538-8249338. E-mail: [email protected]

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ORCID

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Nan Wang: 0000-0002-8648-3941

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Notes

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The authors declare no competing financial interest.

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N.W. and W.L. are co-first authors.

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Funding

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This work was supported by the National Key Research Project (2016YFC0501505)

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and the National Natural Science Foundation of China (CN) (31572091, 31730080).

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ACKNOWLEDGMENTS

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We thank the Luntai National Fruit Germplasm Resources Garden for providing

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germplasm resources, and the Shujing Wu and Yujin Hao Laboratories for providing

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the vectors. We thank Emma Tacken, PhD, from Liwen Bianji, Edanz Group China

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for editing the English text of a draft of this manuscript.

413

REFERENCES (1) Koes, R. E.; Quattrocchio, F.; Mol, J. N. M. The flavonoid biosynthetic pathway in plants: function and evolution. Bio Essays. 1994, 16, 123–132. (2) Dixon, R. A.; Paiva, N. L. Stress-induced phenylpropanoid metabolism. Plant Cell. 1995, 7, 1085–1097. (3) Taylor, L. P.; Grotewold, E. Flavonoids as developmental regulators. Curr. Opin. Plant Biol. 2005, 8, 317–323. (4) Treutter, D. Significance of flavonoids in plant resistance and enhancement of their biosynthesis. Plant Biol. 2005, 7, 581–591. 20

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(5) Knekt, P.; Jarvinen, R.; Seppanen, R.; Helibvaara, M.; Teppo, L.; Pukkala, E.; Aromaa, A. Dietary flavonoids and the risk of lung cancer and other malignant neoplasms. Am. J. Epidemiol. 1997, 146, 223–252. (6) Middleton, E. J.; Kandaswami, C.; Theoharides, T. C. The efects of plant flavonoids on mammalian cells: implications for inflammation, heart disease, and cancer. Pharmacol Rev. 2000, 52, 673–751. (7) Winkel-Shirley, B. Flavonoid biosynthesis:a colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiol. 2001, 126, 485–493. (8) Williams, R. J.; Spencer, J. P. E.; Rice-Evans, C. Flavonoids: antioxidants or signalling molecules? Free Radical Bio. Med. 2004, 36, 838–849. (9) Hertog, M. G.; Hollman, P. C. H.; Katan, M. B. Content of potentially anticarcinogenic flavonoids of 28 vegetables and 9 fruits commonly consumed in the Netherlands. J. Agric. Food Chem. 1992, 12, 2379–2383. (10) Knekt, P.; Kumpulainen, J.; Jarvinen, R.; Rissanen, H.; Heliövaara, M.; Reunanen, A.; Hakulinen, T.; Aromaa, A. Flavonoid intake and risk of chronic diseases. Am J Clin Nutr. 2002, 76, 560–568. (11) Duan, N. B.; Bai, Y.; Sun, H. H.; Wang, N.; et al. Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement. Nature communications. 2017, 8, 1. (12) Hertog, M. G.; Feskens, E. J.; Kromhout, D.; Antioxidant flavonols and coronary heart disease risk. Lancet. 1997, 349, 699. (13) Vinson, J.; Su, X.; Zubik, L.; Bose, P. Phenol antioxidant quantity andquality in foods: fruits. J. Agric. Food Chem. 2001, 49, 5315–5321. (14) Zamora-Ros, R.; Andres-Lacueva, C.; Lamuela-Raventós, R. M.; Berenguer, T.; Jakszyn, P.; Barricarte, A.; Ardanaz, E.; Amiano, P.; Dorronsoro, M.; Larrañaga, N.; Martínez, C.; Sánchez, M. J.; Navarro, C.; Chirlaque, M. D.; Tormo, M. J.; Quirós, J. R.; González, C. A. Estimation of Dietary Sources and Flavonoid Intake in a Spanish Adult Population (EPIC-Spain). Journal of the American Dietetic Association. 2010, 110, 390–398. (15) Boyer, J.; Liu, R. H. Apple phytochemicals and their health benefits. Nutrition Journal. 2004, 3, 5. (16) Chu, Y.; Sun, J.; Wu, X.; Liu, R. H. Antioxidant and antiproliferative activities of common fruits. J. Agric. Food Chem. 2002, 50, 7449–7454. (17) Bondonno, C. P.; Yang, X.; Considine, M. J.; Ward, N. C.; Rich, L.; Puddey, I. B.; Swinny, E.; Mubarak, A.; Hodgson, J. M. Flavonoid-rich apples and nitrate-rich spinach augment nitric oxide status and improve endothelial function in healthy men and women: a randomized controlled trial. Free Radical Biology & Medicine. 2012, 52, 95–102. (18) Veeriah, S.; Kautenburger, T.; Habermann, N.; Sauer, J.; Dietrich, H.; Will, F.; Pool-Zobel, B. L. Apple flavonoids inhibit growth of HT29 human colon cancer cells and modulate expression of genes involved in the biotransformation of xenobiotics. Mol Carcinog. 2006, 45, 164–174. (19) Williamson, G.; Manach, C. Bioavailability and bioefficacy of polyphenols in humans. II. Review of 93 intervention studies. Am. J. Clin. Nutr. 2005, 81, 243S–255S. (20) Eberhardt, M. V.; Changyong, L.; Liu, R. H. Antioxidant activity of fresh apples. Nature. 2000, 405, 903–4. 21

ACS Paragon Plus Environment

Journal of Agricultural and Food Chemistry

Page 22 of 36

(21) Nesi, N.; Jond, C.; Debeaujon, I.; Lepiniec, L. The Arabidopsis TT2 gene encodes an R2R3 MYB domain protein that acts as a key determinant for proanthocyanidin accumulation in developing seed. Plant Cell. 2001, 13, 2099–2114. (22) Gonzalez, A.; Zhao, M.; Leavitt, J. M.; Lloyd, A. M. Regulation of the anthocyanin biosynthetic pathway by the ttg1/bhlh/myb transcriptional complex in arabidopsis seedlings. Plant Journal. 2008, 53, 814–827. (23) Schaart, J. G.; Dubos, C.; Romero, D. L.; van Houwelingen, A. M; de Vos, R. C.; Jonker, H. H.; Xu, W.; Routaboul, J. M.; Lepiniec, L.; Bovy, A. G.; Identification and characterization of MYB-bHLH-WD40 regulatory complexes controlling proanthocyanidin biosynthesis in strawberry (Fragaria×ananassa) fruits. New Phytologist. 2013, 197, 454–467. (24) Albert, N. W.; Davies, K. M.; Lewis, D.H.; Zhang, H.; Montefiori, M.; Brendolise, C.; Boase, M. R.; Ngo, H.; Jameson, P. E.; Schwinn, K. E.; A conserved network of transcriptional activators and repressors regulates anthocyanin pigmentation in eudicots. The Plant Cell. 2014, 26, 962–980. (25) Takos, A. M.; Jaffe, F. W.; Jacob, S. R.; Bogs, J.; Robinson, S. P.; Walker, A. R. Light-induced expression of a MYB gene regulates anthocyanin biosynthesis in red apples. Plant Physiol. 2006, 142, 1216–1232. (26) Ban, Y.; Honda, C.; Hatsuyama, Y.; Igarashi, M.; Bessho, H.; Moriguchi, T. Isolation and functional analysis of a MYB transcription factor gene that is a key regulator for the development of red coloration in apple skin. Plant Cell Physiol. 2007, 48, 958–970. (27) Espley, R. V.; Brendolise, C.; Chagne, D.; Kutty-Amma, S.; Green, S.; Volz, R.; Putterill, J.; Schouten, H. J.; Gardiner, S. E.; Hellens, R. P.; Allan, A. C. Multiple repeats of a promoter segment causes transcription factor autoregulation in red apples. Plant Cell. 2009, 21, 168– 183. (28) Vimolmangkang, S.; Han, Y.; Wei, G.; Korban, S. S. An apple myb transcription factor, mdmyb3, is involved in regulation of anthocyanin biosynthesis and flower development. Bmc Plant Biology. 2013, 13, 176. (29) Gesell, A.; Yoshida, K.; Lan, T. T.; Constabel, C. P. Characterization of an apple TT2-type R2R3 MYB transcription factor functionally similar to the poplar proanthocyanidin regulator PtMYB134. Planta. 2014, 240, 497–511. (30) Wang, N.; Xu, H. F.; Jiang, S. H.; Zhang, Z.; Lu, N.; Qiu, H.; Qu, C.; Wang, Y.; Wu, S.; Chen, X. MYB12 and MYB22 play essential roles in proanthocyanidin and flavonol synthesis in red-fleshed apple (Malus sieversii f.niedzwetzkyana). Plant Journal. 2017, 90, 276–292. (31) Xie, X. B.; Li, S.; Zhang, R. F.; Zhao, J.; Chen, Y. C.; Zhao, Q.; Yao, Y. X.; You, C.X.; Zhang, X. S.; Hao, Y. J.; The bHLH transcription factorMdbHLH3 promotes anthocyanin accumulation and fruit colouration in response to low temperature in apples. Plant, Cell and Environment. 2012, 35, 1884–1897. (32) An, X. H.; Tian, Y.; Chen, K. Q.; Wang, X. F.; Hao, Y. J. The apple WD40protein MdTTG1 interacts with bHLH but not MYB proteins to regulate anthocyanin accumulation. Journal of Plant Physiology. 2012, 169, 710–717. (33) Sadilova, E.; Stintzing, F. C.; Carle, R. Chemical quality parameters and anthocyanin pattern of red-fleshed weirouge apples. Journal of Applied Botany & Food Quality Angewandte Botanik. 2006, 80, 82–87. (34) Volz, R. K.; McGhie, T. K.; Kumar, S. Variation and genetic parameters of fruit colour and 22

ACS Paragon Plus Environment

Page 23 of 36

Journal of Agricultural and Food Chemistry

polyphenol composition in an apple seedling population segregating for red leaf. Tree Genetics Genomes. 2014, 10, 953−964. (35) Barscortina, D.; Macià, A.; Iglesias, I.; Romero, M. P.; Motilvaet, M. J. Phytochemical Profiles of New Red-Fleshed Apple Varieties Compared with Traditional and New White-Fleshed Varieties. J. Agric. Food Chem. 2017, 65, 1684. (36) Wang, N.; Qu, C.; Wang, Y.; Xu, H. F.; Jiang, S. H.; Fang, H. C.; Chen, X. S. Mdmyb4 enhances apple callus salt tolerance by increasing mdnhx1, expression levels. Plant Cell Tissue & Organ Culture. 2017, 4, 1–11. (37) Kim, D.; Langmead, B.; Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods. 2015, 12, 357–360. (38) Li, B.; Dewey, C. N.; RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011, 12, 323. (39) Love, M. I.; Huber, W.; Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014, 15, 550. (40) Eisen, M. B.; Spellman, P. T.; Brown, P. O.; Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA. 1998, 95, 14863–14868. (41) Yong, L.; Roni, R.; Itamar, S.; Nau, G. J.; Ziv, B. J. A probabilistic generative model for go enrichment analysis. Nucleic Acids Research. 2008, 36, 17. (42) Chen, L.; Zhang, Y. H.; Wang, S.; Zhang, Y.; Huang, T.; Cai, Y. D. Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways. Plos One. 2017, 12, 9. (43) Livak, K. J.; Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001, 25, 402–408. (44) Giusti, M. M.; Wrolstad, R. E. Characterization and measurement of anthocyanin by UV-visible spectroscopy. Current Protocols in Food Analytical Chemistry. 2001, 19–31. (45) Duan, S.; Wang, J.; Gao, C.; Jin, C.; Li, D.; Peng, D.; Du, G.; Li, Y.; Chen, M. Functional characterization of a heterologously expressed brassica napus wrky41-1, transcription factor in regulating anthocyanin biosynthesis in arabidopsis thaliana. Plant Science. 2018, 268, 47– 53. (46) Amato, A.; Cavallini, E.; Zenoni, S.; Finezzo, L.; Begheldo, M.; Ruperti, B.; Tornielli, G. B. A grapevine ttg2-like wrky transcription factor is involved in regulating vacuolar transport and flavonoid biosynthesis. Frontiers in Plant Science. 2016, 7. (47) Acostagallegos, J. A.; Kelly, J. D.; Gepts, P. Prebreeding in common bean and use of genetic diversity from wild germplasm. Crop Science. 2007, 47, S44–S59. (48) Moon, H. S.; Nicholson, J. S.; Heineman, A.; Lion, K.; Hoeven, R.; Hayes, A. J.; Lewis, R. S. Changes in genetic diversity of u.s. flue-cured tobacco germplasm over seven decades of cultivar development. Crop Science. 2009, 49, 498–508. (49) Velasco, R.; Zharkikh, A.; Affourtit, J.; et al. The genome of the domesticated apple (malus × domestica borkh.). Nature Genetics. 2010, 42, 833. (50) Wang, N.; Zheng, Y.; Duan, N.; Zhang, Z.; Ji, X.; Jiang, S.; Sun, S.; Yang, L.; Bai, Y.; Fei, Z.; Chen, X. S. Comparative transcriptomes analysis of red- and white-fleshed apples in an f1 population of malus sieversii f. niedzwetzkyana crossed with m. domestica ‘fuji’. Plos One. 2015, 10, 7. (51) Espley, R. V.; Bovy, A.; Bava, C.; Jaeger, S. R.; Tomes, S.; Norling, C.; Crawford, J.; Rowan, 23

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Journal of Agricultural and Food Chemistry

Page 24 of 36

D.; McGhie, T. K.; Brendolise, C.; Putterill, J.; Schouten, H. J.; Hellens, R. P.; Allan, A. C. Analysis of genetically modified red-fleshed apples reveals effects on growth and consumer attributes. Plant Biotechnol. J. 2013, 11, 408–419. (52) Chagné, D.; Lin-Wang, K.; Espley, R. V.; Volz, R. K.; How, N. M.; Rouse, S.; Brendolise, C.; Carlisle, C. M.; Kumar, S.; De Silva, N.; Micheletti, D.; McGhie, T.; Crowhurst, R. N.; Storey, R. D.; Velasco, R.; Hellens, R. P.; Gardiner, S. E.; Allan, A. C. An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh phenotypes. Plant physiology. 2013, 161, 225. (53) Lee, J.; Oh, M.; Park, H.; Lee, I. Soc1 translocated to the nucleus by interaction with agl24 directly regulates leafy. Plant Journal. 2008, 55, 832–843. (54) Liu, C.; Chen, H.; Er, H.; Soo, H. M.; Kumar, P. P.; Han, J. H.; Liou, Y. C.; Yu, H. Direct interaction of agl24 and soc1 integrates flowering signals in arabidopsis. Development. 2008, 135, 1481–91. (55) Taylor, L. P.; Grotewold, E. Flavonoids as developmental regulators. Current Opinion in Plant Biology. 2005, 8, 317. (56) Rubin, G.; Tohge, T.; Matsuda, F.; Saito, K.; Scheible, W. R. Members of the LOB family of transcription factors repress anthocyanin synthesis and affect additional N responses in Arabidopsis. Plant Cell. 2009, 21, 3567–3584. (57) Wang, Y.; Wang, N.; Xu, H.; Jiang, S. H.; Zhang, T. L.; Su, M. Y.; Xu, L.; Zhang, Z. Y.; Chen, X. S. Nitrogen affects anthocyanin biosynthesis by regulating mdlob52, downstream of mdarf19, in callus cultures of red-fleshed apple (malus sieversii, f. niedzwetzkyana). Journal of Plant Growth Regulation. 2017, 1–11. (58) Mierziak, J.; Kostyn, K.; Kulma, A. Flavonoids as important molecules of plant interactions with the environment. Molecules. 2014, 19, 16240–16265. (59) Nakabayashi, R.; Yonekura-sakakibara, K.; Urano, K.; Suzuki, M.; Yamada, Y.; Nishizawa, T.; Matsuda, F.; Kojima, M.; Sakakibara, H.; Shinozaki, K.; Michael, A. J.; Tohge, T.; Yamazaki, M.; Saito, K. Enhancement of oxidative and drought tolerance in arabidopsis by overaccumulation of antioxidant flavonoids. Plant Journal. 2014, 77, 367. (60) Commisso, M.; Toffali, K.; Strazzer, P.; Stocchero, M.; Ceoldo, S.; Baldan, B.; Levi, M.; Guzzo, F1. Impact of phenylpropanoid compounds on heat stress tolerance in carrot cell cultures. Frontiers in Plant Science. 2016, 7, 273. (61) Liu, Z.; Liu, Y.; Pu, Z.; Wang, J.; Zheng, Y.; Li, Y.; Wei, Y. Regulation, evolution, and functionality of flavonoids in cereal crops. Biotechnology Letters. 2013, 35, 1765–1780. (62) Chao, L. M.; Yao, Q.; Chen, D. Y.; Xue, X. Y.; Mao, Y. B.; Chen, X. Y. Arabidopsis transcription factors spl1 and spl12 confer plant thermotolerance at reproductive stage. Molecular plant. 2017, 10, 735–748. (63) Park, J. M.; Paek, K. H. Overexpression of the tobacco tsi1 gene encoding an erebp/ap2-typetranscription factor enhances resistance against pathogen attack and osmotic stress in tobacco. Plant Cell. 2001, 13, 1035–1046. (64) Fujita, M.; Fujita, Y.; Maruyama, K.; Seki, M.; Hiratsu, K.; Ohme-Takagi, M.; Tran, L. S.; Yamaguchi-Shinozaki, K.; Shinozaki, K. A dehydration-induced nac protein, rd26, is involved in a novel aba-dependent stress-signaling pathway. Plant Journal. 2004, 39, 863– 876. (65) Persak, H.; Pitzschke, A. Dominant repression by arabidopsis transcription factor myb44 24

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causes oxidative damage and hypersensitivity to abiotic stress. International Journal of Molecular Sciences. 2014, 15, 2517. (66) Lee, H.; Cha, J.; Choi, C.; Choi, N.; Ji, H. S.; Park, S. R.; Lee, S.; Hwang, D. J. Rice wrky11 plays a role in pathogen defense and drought tolerance. Rice. 2018, 11, 5. (67) Liu, H. L. Ectopic expression of a grapevine transcription factor vvwrky11 contributes to osmotic stress tolerance in arabidopsis. Molecular Biology Reports. 2011, 38, 417–27.

FIGURE CAPTIONS Figure 1 (A) The establishment of BC1 hybrid populations. BC1 hybrid populations were derived from a cross between an R6R6 homozygous red-fleshed mutant and M. domestica. (B) Both a 497 bp and a 396 bp fragment were present in the selected red-fleshed varieties (a–e). Only a single 396 bp fragment was present in the M. domestica control variety. (C) Flavonoid composition and content analyses and comparisons between red-fleshed (RF) and white-fleshed (WF) apples using UPLC-ESI-TOF/MS. Four flavanols (a–d), three flavonols (e–g), and one dihydrochalcone (h) were detected under the negative ion signal. (D) Two anthocyanins were detected under the positive ion signal (i and j). Figure 2 Analysis of differentially expressed genes (DEGs) between RF and WF. (A) The MA-plot distribution map of all DEGs. The X-axis represents the expression level after conversion of the log2 value. The Y-axis represents the fold-change in expression after conversion of the log2 value. (B) Heatmap cluster analysis of DEGs. The amount of expression after the log10 conversion is represented by different colors. Figure 3 The GO functional classification and enrichment analysis of DEGs. GO terms were divided into three functional categories: molecular function, cellular 25

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component, and biological process. The Y-axis represents the number of DEGs enriched in each GO classification. FDR correction is performed according to P-value, and the function of FDR ≤ 0.01 is generally regarded as significant enrichment. Figure 4 KEGG pathway enrichment analyses of DEGs. (A) The different colors represent different qvalues. The bluer the color, the more significant the enrichment result is. The size of the point represents the number of DEGs enriched in the pathway. (B) According to the KEGG annotation results and the official classification, the top 30 enriched pathways are shown. FDR correction is performed on P-value, and the function of FDR ≤ 0.01 is generally regarded as significant enrichment. Figure 5 The 22 screened DEGs encoding transcription factors and real-time RT-PCR validation. (A) Heatmap cluster analysis of DEGs encoding transcription factors compared between RF and WF. Boxes represent the amount of expression after the log10 conversion. Colors represent Z-score values of normalized expression levels. (B) Real-time RT-PCR was used to validate the transcript levels of 22 selected DEGs. MdActin was used as the internal control gene. Values are means ± SD of three independent biological replicates. Statistical significance: *P