An Integrated Transcriptome and Proteome Analysis Reveals New Insights into Russeting of Bagging and Non-Bagging “Golden Delicious” Apple

Abstract

Apple skin russeting naturally occurs in many varieties, particularly in “Golden Delicious” and its pedigree, and is regarded as a non-invasive physiological disorder partly caused by excessive deposition of lignin. However, the understanding of its molecular mechanism is still limited. In this study, we used iTRAQ (isobaric tags for relative and absolute quantitation) and RNA-seq to detect the changes in the expression levels of genes and proteins in three developmental stages of russeting formation, in russeted (non-bagging) and non-russeted (bagging) skin of “Golden Delicious” apple. 2856 differentially expressed genes and 942 differentially expressed proteins in the comparison groups were detected at the transcript level and protein level, respectively. A correlation analysis of the transcriptomics and proteomics data revealed that four genes (MD03G1059200, MD08G1009200, MD17G1092400, and MD17G1225100) involved in lignin biosynthesis are significant changed during apple russeting formation. Additionally, 92 transcription factors, including 4 LIM transcription factors, may be involved in apple russeting formation. Among them, one LIM transcription factor (MD15G1068200) was capable of binding to the PAL-box like (CCACTTGAGTAC) element, which indicated it was potentially involved in lignin biosynthesis. This study will provide further views on the molecular mechanisms controlling apple russeting formation.

Differential regulation of triterpene biosynthesis induced by an early failure in cuticle formation in apple

“…S 3 ). This unusual trend has previously been described in russeted apple tissue 21 , 34 , where the suberin pathway has been activated. A total of 758 DEGS were consistently differentially expressed among the three stages and were used to highlight the most affected pathways.…”

“…On the basis of candidate genes presented in previous reports 16 , 34 , 35 and KEGG pathways, a schematic heatmap reconstituting cutin, wax, suberin, phenylpropanoid and tri(terpenoid) pathways and their associated gene expression was built, providing a unique tool to identify cuticle-related candidate genes in apple (Fig. S 4 ).…”

Major Latex Protein MdMLP423 Negatively Regulates Defense against Fungal Infections in Apple

“…The BGISEQ-500 System (BGI-Shenzhen, China) was used for cDNA libraries sequencing. The read length of the BGISEQ-500 system was 100 bp [65].…”

“…At least three biological replicates for each gene was performed, all of the primers were listed in Table S5. We used Actin 18S rRNA as the reference genes [65]. SPSS 18.0 software was used for significance analysis.…”

Integrated Transcriptome and Proteome Analysis Provides Insights into Anthocyanin Accumulation in the Leaves of Red-Leaved Poplars

“…Genes are the main directors of life activities, and proteins are the main executor of life activities (Song and Yu, 2019). With the continuous development and improvement of sequencing technology, transcriptome and proteomics have been widely used in biological research, but a single transcriptome or proteomics analysis only provides unilateral information at the transcriptional level or translation level (Yuan et al, 2019;Wang et al, 2019d;Dong et al, 2018). Therefore, the integrated analysis between transcriptome and proteomics is beneficial to the study of multi-level regulation of gene expression process, which is an effective way to study the molecular mechanisms underlying many biological traits (Vogel and Marcotte, 2012).…”