Seedless mutant ‘Wuzi Ougan’ (Citrus suavissima Hort. ex Tanaka ‘seedless’) and the wild type were compared by iTRAQ-based quantitative proteomics and integratedly analyzed with transcriptome to improve understanding of male sterility

Abstract

BackgroundBud mutation is a vital method of citrus. ‘Wuzi Ougan’ (mutant type, MT) as a bud variant of ‘Ougan’ (wild type, WT) was first found in 1996 and has become popular because of its male sterility and seedless character. Previous analysis of its cytological sections and transcriptome revealed that the abnormal microsporogenesis that occurs before the tetrad stage of anther development might be the result of down-regulated oxidation-reduction biological processes in MT. To reveal the mechanism behind the male sterility in MT at the post-transcriptional stage, proteome profiling and integrative analysis on previously obtained transcriptome and proteome data were performed in two strains.ResultsThe proteome profiling was performed by iTRAQ (isobaric Tags for relative and absolute quantitation) analysis and 6201 high-confidence proteins were identified, among which there were 487 differentially expressed proteins (DEPs) in one or more developmental stages of anthers between MT and WT. The main functional subcategories associated with the main category biological process into which the DEPs were classified were sporopollenin biosynthesis process and pollen exine formation. The enriched pathways were phenylpropanoid biosynthesis, flavonoid biosynthesis, and phenylalanine metabolism. Moreover, there were eight pathways linked in terms of being related to phenylpropanoid metabolism. Eighteen important genes related to phenylpropanoid metabolism were also analysized by qRT-PCR (quantitative real time PCR). An integrative analysis of the fold change at the transcript (log2 FPKM ratios) and protein (log1.2 iTRAQ ratios) levels was performed to reveal the consistency of gene expression at transcriptional and proteomic level. In general, the expression of genes and proteins tended to be positively correlated, in which the correlation coefficients were 0.3414 (all genes and all proteins) and 0.5686 (DEPs and according genes).ConclusionThis study is the first to offer a comprehensive understanding of the gene regulation in ‘Wuzi Ougan’ and its wild type, especially during the microsporocyte to meiosis stage. Specifically, the involved genes include those in phenylpropanoid biosynthesis, flavonoid biosynthesis, and phenylalanine metabolism, as determined by integrative transcriptome and proteome analysis.Electronic supplementary materialThe online version of this article (10.1186/s12863-018-0693-9) contains supplementary material, which is available to authorized users.

Integrated proteome and transcriptome analyses revealed key factors involved in tomato (Solanum lycopersicum) under high temperature stress

“…The transcript levels of DEGs in tomato leaves indicated poorly their according proteins in response to HT. This also confirmed some previous studies of transcriptome and genome based on similar conditions (Liu et al., 2018; Lou et al., 2018; Zhang et al., 2018). For example, 122,081 genes and 1,210 DEGs, but only 4,582 proteins and 300 DEPs, were identified in loquat under cold stress (Lou et al., 2018).…”

“…Moreover, the best method is integrating transcriptome and proteome approaches (e.g., RNA‐Seq, iTRAQ) to provide more information (Lou, Wang, Ni, Gao, & Iqbal, 2018). It has been reported that the combination of RNA‐Seq and iTRAQ is used to reveal the molecular and physiological changes in certain biological processes and developmental stages or responses to various abiotic and biological changes (Liu, Xing, Fang, Ai, & Cheng, 2018; Lou et al., 2018; Zhang et al., 2018). However, few studies have been reported in plants under HT stress.…”

Transcriptomic and Proteomic Analyses of a New Cytoplasmic Male Sterile Line with wild Gossypium bickii. Genetic Background

“…Proteome analyses in cotton indicated that the differentially expressed proteins (DEPs) mainly involved in pyruvate, carbohydrate and fatty acid metabolism had been identified between the male-sterile line 1355A and the male-fertile line 1355B (9) . Integrated analysis of the transcriptome and proteome can afford a complete picture in regard to the molecular mechanism of CMS, and have been reported in Chinese cabbage (12) , Brassica napus (13) , Pepper (14) , Citrus suavissima (15) involved CMS studies. The conjoint analysis of the transcriptome and proteome in Shaan2A CMS and its maintainer line revealed that the sterility gene from mitochondrion might suppress the expression of relevant transcription factor genes in the nucleus, affecting early anther development (13) .…”

Transcriptomic analysis reveals candidate genes for male sterility in Prunus sibirica

“…The middle layer cells are located between the tapetum and endothecium, and play an important role in the differentiation and function of tapetum cells (Ma et al, 2007;Roque et al, 2007). In recent years, with the rapid development of high-throughput sequencing technology, specifically transcriptomic sequencing, has been widely used in the study of male sterility in herbs or cereals such as Salvia miltiorrhiza Bunge (Yu et al, 2021), wheat (Liu et al, 2020aLiu et al, 2020b), Cucumis melo (Dai et al, 2019), onion (Yuan et al, 2018) and woody plant such as Vernicia fordii (Liu et al, 2019a;Liu et al, 2019b), and Citrus suavissima (Zhang et al, 2018a;Zhang et al, 2018b). However, to our knowledge, no study has used a transcriptomics approach to investigate male sterility in Prunus.…”