DataSheet_1_Transcriptome and metabolome analyses reveal phenotype formation differences between russet and non-russet apples.xlsx

The apple is an economically important fruit, and fruit russeting is not conducive to its appearance. Although studies have examined fruit russeting, its mechanism remains unclear. Two apple strains of the F1 hybrid population derived from ‘Fuji’ and ‘Golden Delicious’ were used in this study. We found that the skin of russet apples was rough and fissured, while that of non-russet apples was smooth and waxy. Chemical staining, LC- and GC-MS showed that both lignin and suberin were increased in russet apple skin. Meanwhile, genes involved in lignin and suberin synthetic pathways were upregulated in russet apple skin. Additionally, we found many differentially expressed genes (DEGs1) involved in hormone biosynthesis and signaling and stress responses in the two apple strains. We found that WRKY13 may influence russeting by regulating lignin synthesis. Our study identified several candidate metabolites and genes, which will provide a good foundation for further research.</p

DataSheet_2_Transcriptome and metabolome analyses reveal phenotype formation differences between russet and non-russet apples.docx

The apple is an economically important fruit, and fruit russeting is not conducive to its appearance. Although studies have examined fruit russeting, its mechanism remains unclear. Two apple strains of the F1 hybrid population derived from ‘Fuji’ and ‘Golden Delicious’ were used in this study. We found that the skin of russet apples was rough and fissured, while that of non-russet apples was smooth and waxy. Chemical staining, LC- and GC-MS showed that both lignin and suberin were increased in russet apple skin. Meanwhile, genes involved in lignin and suberin synthetic pathways were upregulated in russet apple skin. Additionally, we found many differentially expressed genes (DEGs1) involved in hormone biosynthesis and signaling and stress responses in the two apple strains. We found that WRKY13 may influence russeting by regulating lignin synthesis. Our study identified several candidate metabolites and genes, which will provide a good foundation for further research.</p

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

In plants, flavonoids are important secondary metabolites that contribute to the nutritional quality of many foods. Apple is a popular and frequently consumed food because of its high flavonoid content. In this study, flavonoid composition and content were detected and compared between red- and white-fleshed apples in a BC₁ hybrid population using ultraperformance liquid chromatography–quadrupole time-of-flight mass spectrometry. Transcriptomic analysis of the red- and white-fleshed apples was then performed using RNA-seq technology. By screening differentially expressed genes encoding transcription factors, we unearthed a WRKY-family transcription factor designated MdWRKY11. Overexpression of MdWRKY11 promoted the expression of <i>F3H</i>, <i>FLS</i>, <i>DFR</i>, <i>ANS</i>, and <i>UFGT</i> and increased the accumulation of flavonoids and anthocyanin in apple calli. Our findings explored the novel role of MdWRKY11 in flavonoid biosynthesis and suggest several other genes that may also be potentially involved. This provides valuable information on flavonoid synthesis for the breeding of elite red-fleshed apples

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

In plants, flavonoids are important secondary metabolites that contribute to the nutritional quality of many foods. Apple is a popular and frequently consumed food because of its high flavonoid content. In this study, flavonoid composition and content were detected and compared between red- and white-fleshed apples in a BC₁ hybrid population using ultraperformance liquid chromatography–quadrupole time-of-flight mass spectrometry. Transcriptomic analysis of the red- and white-fleshed apples was then performed using RNA-seq technology. By screening differentially expressed genes encoding transcription factors, we unearthed a WRKY-family transcription factor designated MdWRKY11. Overexpression of MdWRKY11 promoted the expression of <i>F3H</i>, <i>FLS</i>, <i>DFR</i>, <i>ANS</i>, and <i>UFGT</i> and increased the accumulation of flavonoids and anthocyanin in apple calli. Our findings explored the novel role of MdWRKY11 in flavonoid biosynthesis and suggest several other genes that may also be potentially involved. This provides valuable information on flavonoid synthesis for the breeding of elite red-fleshed apples

GO terms enriched in differentially expressed genes between red- and white-fleshed apples.

<p>(A) GO terms enriched in up-regulated genes in red-fleshed apple. (B) GO terms enriched in down-regulated genes in red-fleshed apple.</p

Up-regulated genes involved in both the flavonoid biosynthetic process and stress response in red-fleshed apples.

<p>Up-regulated genes involved in both the flavonoid biosynthetic process and stress response in red-fleshed apples.</p

Up-regulated genes involved in flavonoid biosynthetic processes in red-fleshed apples.

<p>Up-regulated genes involved in flavonoid biosynthetic processes in red-fleshed apples.</p

Functional categories of genes with changed expression between red- and white-fleshed apples.

<p>Functional categories of genes with changed expression between red- and white-fleshed apples.</p

Model of the regulatory network involved in flavonoid metabolism and stress responses.

<p>Model of the regulatory network involved in flavonoid metabolism and stress responses.</p

Red- and white-fleshed apples at the ripe stage used for RNA-Seq.

<p>(A)Red-fleshed apples in the F₁ population. Scale bar = 1cm. (B) White-fleshed apples in the F₁ population. Scale bar = 1cm. (C) Flavonoid content in red- and white-fleshed apples. (D) Anthocyanin content in red- and white-fleshed apples.</p