Integrated analysis of transcriptome and proteome changes related to the Ogura cytoplasmic male sterility in cabbage

Abstract

Cabbage (Brassica oleracea L. var. capitata), an important vegetable crop in the Brassicaceae family, is economically important worldwide. In the process of hybrid seed production, Ogura cytoplasmic male sterility (OguCMS), controlled by the mitochondrial gene orf138, has been extensively used for cabbage hybrid production with complete and stable male sterility. To identify the critical genes and pathways involved in the sterility and to better understand the underlying molecular mechanisms, the anther of OguCMS line R2P2CMS and the fertile line R2P2 were used for RNA-seq and iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) proteome analysis. RNA-seq analysis generated 13,037,109 to 13,066,594 SE50-clean reads, from the sterile and fertile lines, which were assembled into 36,890 unigenes. Among them, 1,323 differentially expressed genes (DEGs) were identified, consisting of 307 up- and 1016 down-regulated genes. For ITRAQ analysis, a total of 7,147 unique proteins were identified, and 833 were differentially expressed including 538 up- and 295 down-regulated proteins. These were mainly annotated to the ribosome, spliceosome and mRNA surveillance pathways. Combined transcriptomic and proteomic analyses identified 22 and 70 genes with the same and opposite expression profiles, respectively. Using KEGG analysis of DEGs, gibberellin mediated signaling pathways regulating tapetum programmed cell death and four different pathways involved in sporopollenin synthesis were identified. Secretion and translocation of the sporopollenin precursors were identified, and the key genes participating in these pathways were all significantly down-regulated in R2P2CMS. Light and transmission electron (TE) microscopy revealed fat abnormal tapetum rather than vacuolization and degradation at the tetrad and microspore stages of the OguCMS line. This resulted in the failed deposition of sporopollenin on the pollen resulting in sterility. This study provides a comprehensive understanding of the mechanism underlying OguCMS in cabbage.

Transcriptomic and Proteomic Analyses of a New Cytoplasmic Male Sterile Line with wildGossypium 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) .…”

iTRAQ-Based Proteomic Analysis of Ogura-CMS Cabbage and Its Maintainer Line

“…High-throughput next-generation sequencing (NGS) has facilitated transcriptome analyses of Ogura-CMS materials (including Chinese cabbage, cabbage, broccoli) and may help provide a comprehensive understanding of the mechanisms underlying Ogura-CMS [ 22 , 23 , 24 , 25 ]. Xing et al performed transcriptome and proteome analyses (focused on the transcriptome) and identified gibberellin, and sporopollenin synthesis as important pathways in Ogura-CMS cabbage [ 25 ].…”

“…High-throughput next-generation sequencing (NGS) has facilitated transcriptome analyses of Ogura-CMS materials (including Chinese cabbage, cabbage, broccoli) and may help provide a comprehensive understanding of the mechanisms underlying Ogura-CMS [ 22 , 23 , 24 , 25 ]. Xing et al performed transcriptome and proteome analyses (focused on the transcriptome) and identified gibberellin, and sporopollenin synthesis as important pathways in Ogura-CMS cabbage [ 25 ]. Other studies performing proteomic analyses using two-dimensional gel electrophoresis (2-DE) have identified distinct differences in the proteomes of Ogura-CMS and fertile plants [ 26 , 27 ], including the down-accumulated protein species associated with processes that include carbohydrate and energy metabolism, cell wall remodelling, flavonoid synthesis and up-accumulated protein species like protease inhibitors.…”

Differentially expressed genes and phenotypic variation in florets among the isogenic Ogura-CMS, DGMS and inbred lines of broccoli

“…The Ogura-CMS line contributes signi cantly to hybrid seed production in Brassica crops; therefore, some studies focus on Ogura-CMS, although the mechanism of hybrid seed production has not been elucidated. Previous transcriptome and proteome analyses of the Ogura-CMS line have provided basic information about the DEGs and differential abundant proteins (DAPs) between Ogura-CMS lines and their maintainer lines [12,13,17,18,28]. In this study, some signi cant differences in agronomic traits associated with growth and reproductive growth and development were noted among the Ogura-CMS and DGMS lines and their maintainer line in a two-year investigation with statistical analysis.…”

“…Transcriptome analyses based on RNA sequencing (RNA-Seq) technology are important methods with which to understand the differentially expressed genes (DEGs) involved in various biological processes, and these analyses have been widely performed on Brassica plants [12,13,17,18]. For example, small RNA-Seq has revealed DEGs in the early development of broccoli pollen [19], and transcriptome analyses have been used to examine four transcription factors in normal and abortive buds of an Ogura-CMS line and its maintainer line [12].…”