Comprehensive analysis of Ogura cytoplasmic male sterility-related genes in turnip (Brassica rapa ssp. rapifera) using RNA sequencing analysis and bioinformatics

Lin, Sue; Miao, Yingjing; Su, Shiwen; Xu, Jian; Jin, Libo; Sun, Da; Peng, Renyi; Huang, Li; Cao, Jiashu

doi:10.1371/journal.pone.0218029

Cited by 17 publications

(22 citation statements)

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“…Thus, we assayed 6 RNA-Seq datasets from B. rapa male-sterile mutants [26,28], GMS [29,30] and CMS [27,31] lines, and found that 9 BrPERK genes were downregulated in at least five MS lines (Fig. 6a).…”

Section: Discussionmentioning

confidence: 99%

“…Seven raw RNA-Seq datasets of B. rapa plant were obtained from the NCBI Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA) [26][27][28][29][30][31]60]. One of these datasets consisted of the genome-wide transcriptomes of tissues [60], and the other six datasets consisted of the transcriptomes of male-sterile lines, including two male-sterile mutants [26,28], two GMS lines [29,30] and two ogu-CMS lines [27,31]. These male-sterile lines are no pollen phenotype and their anther abortion occurs during the tetrad period.…”

Section: Rna-seq Data Analysismentioning

confidence: 99%

“…The biophysical properties of BrPERK genes were determined. Furthermore, RNA-Seq data from six malesterile plants (two male-sterile mutants [26,28], two GMS lines [29,30] and two ogu-CMS lines [27,31]) were analyzed, and tissue-specific expression patterns were examined to identify the specific PERK genes related to pollen development and male sterility in B. rapa. The present study will contribute to a detailed understanding of the molecular and biological functions of BrPERK genes in male-sterile plants of B. rapa.…”

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confidence: 99%

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Genome-wide analysis of proline-rich extension-like receptor protein kinase (PERK) in Brassica rapa and its association with the pollen development

Chen

Wang

et al. 2020

BMC Genomics

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Background: Proline-rich extension-like receptor protein kinases (PERKs) are an important class of receptor kinases located in the plasma membrane, most of which play a vital role in pollen development. Results: Our study identified 25 putative PERK genes from the whole Brassica rapa genome (AA). Phylogenetic analysis of PERK protein sequences from 16 Brassicaceae species divided them into four subfamilies. The biophysical properties of the BrPERKs were investigated. Gene duplication and synteny analyses and the calculation of Ka/Ks values suggested that all 80 orthologous/paralogous gene pairs between B. rapa and A. thaliana, B. nigra and B. oleracea have experienced strong purifying selection. RNA-Seq data and qRT-PCR analyses showed that several BrPERK genes were expressed in different tissues, while some BrPERKs exhibited high expression levels only in buds. Furthermore, comparative transcriptome analyses from six male-sterile lines of B. rapa indicated that 7 BrPERK genes were downregulated in all six male-sterile lines. Meanwhile, the interaction networks of the BrPERK genes were constructed and 13 PERK coexpressed genes were identified, most of which were downregulated in the male sterile buds. Conclusion: Combined with interaction networks, coexpression and qRT-PCR analyses, these results demonstrated that two BrPERK genes, Bra001723.1 and Bra037558.1 (the orthologs of AtPERK6 (AT3G18810)), were downregulated beginning in the meiosis II period of male sterile lines and involved in anther development. Overall, this comprehensive analysis of some BrPERK genes elucidated their roles in male sterility.

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Section: Discussionmentioning

confidence: 99%

Section: Rna-seq Data Analysismentioning

confidence: 99%

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confidence: 99%

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Genome-wide analysis of proline-rich extension-like receptor protein kinase (PERK) in Brassica rapa and its association with the pollen development

Chen

Wang

et al. 2020

BMC Genomics

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“…In recent years, advancement in molecular technology, has enabled breeders and molecular researchers to identify various plant transcription factors, genes and explore protein expression at the translational, transcriptome and proteome level, such as the CMS studies of the Chinese cabbage (5) , turnip (6) , Cucumis melo L. (7) , cotton (8, 9) , rice (10) , Brassica napus L. (11) . Transcriptomic analysis in cotton (CMS-D8) revealed that the reactive oxygen species (ROS) were released from mitochondria and served as important signal molecules in the nucleus, causing the formation of abnormal tapetum (8) .…”

Section: Introductionmentioning

confidence: 99%

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

Zhao

Wang

et al. 2020

Preprint

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39Cotton is an important fiber crop but has serious effects of heterosis, in which cytoplasmic male 40 sterility (CMS) being the major cause of heterosis in plants. However, there are no studies done on 41 CMS Yamian A in cotton with the genetic background of the Australian wild Gossypium bickii. 42 Transcriptomic and proteomic results showed that UDP-glucosyltransferase -in the nucleus, 60S 43 ribosomal protein L13a-in the cytoplasm, ribulose-1,5-bisphosphate carboxylase/oxygenase -in the 44 chloroplast, glutathione S-transferase -in the cytoplasm, and ATP synthase F1 subunit 1 -in the 45 mitochondrion were upregulated; while low molecular weight heat shock protein -in the chloroplast 46 and ATP synthase D chain-in the mitochondrion were down-regulated expression at the microspore 47 58 Cotton is an important cash crop with high-quality fiber, edible oil, and protein which is mainly 59 used as animal feeds (1) . Heterosis in cotton is quite apparent and has been widely used in yield quality, 60 and resistance studies in cotton (2) . The adoption of the production of hybrid seeds is the most 61 important link among some links of cotton heterosis use. At present, the castration in the production 62 of hybrid seeds often relies on hand emasculation and male-sterile lines including chemically induced 63 male sterility (IMS), genic male sterility (GMS), and cytoplasmic male sterility (CMS) (3) . The 64 production practice showed that CMS is an effective way of heterosis utilization in crop and widely 65 used to produce hybrid seeds, because it eliminates the need for artificial emasculation, saves 66 manpower and material resources, enhance the purity of hybrid seeds and increases the output of 67 crops (3, 4) . All over the world, cotton studies started in the 1960s, since then a number of germplasms 68 have been developed, such as G. arboreum L, G. harknessii Brandegee, G. trilobum (DC.) Skov., G. 69 hirsutum, G. barbadense L., among others. However, there is no report on CMS in cotton with 70 genetic background of Australian wild Gossypium bickii, which has been reported despite the 71 enormous effects of heterosis in cotton germplasm development. 72 In recent years, advancement in molecular technology, has enabled breeders and molecular 73 researchers to identify various plant transcription factors, genes and explore protein expression at the 74 translational, transcriptome and proteome level, such as the CMS studies of the Chinese cabbage (5) , 75 turnip (6) , Cucumis melo L. (7) , cotton (8,9) , rice (10) , Brassica napus L. (11) . Transcriptomic analysis in 76 5 cotton (CMS-D8) revealed that the reactive oxygen species (ROS) were released from mitochondria 77 and served as important signal molecules in the nucleus, causing the formation of abnormal 78 tapetum (8) . Proteome analyses in cotton indicated that the differentially expressed proteins (DEPs) 79 mainly involved in pyruvate, carbohydrate and fatty acid metabolism had been identified between the 80 male-sterile line 1355A a...

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“…Previously, an Ogura-CMS line 'BY10-2A' and its maintainer fertile (MF) line 'BY10-2B' of turnip (B. rapa ssp. rapifera) were characterized [52]. Mutation of mitochondrial orf138 retroregulates the expression of nuclear genes, and interactions between them are responsible for male sterility in Ogura-CMS turnip.…”

Section: Introductionmentioning

confidence: 99%

Identification of microRNAs and their targets in inflorescences of an Ogura-type cytoplasmic male-sterile line and its maintainer fertile line of turnip (Brassica rapa ssp. rapifera) via high-throughput sequencing and degradome analysis

Lin

Jin

et al. 2020

PLoS ONE

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Cytoplasmic male sterility (CMS) is a widely used trait in angiosperms caused by perturbations in nucleus-mitochondrion interactions that suppress the production of functional pollen. MicroRNAs (miRNAs) are small non-coding RNAs that act as regulatory molecules of transcriptional or post-transcriptional gene silencing in plants. The discovery of miRNAs and their possible implications in CMS induction provides clues for the intricacies and complexity of this phenomenon. Previously, we characterized an Ogura-CMS line of turnip (Brassica rapa ssp. rapifera) that displays distinct impaired anther development with defective microspore production and premature tapetum degeneration. In the present study, high-throughput sequencing was employed for a genome-wide investigation of miRNAs. Six small RNA libraries of inflorescences collected from the Ogura-CMS line and its maintainer fertile (MF) line of turnip were constructed. A total of 120 pre-miRNAs corresponding to 89 mature miR-NAs were identified, including 87 conversed miRNAs and 33 novel miRNAs. Among these miRNAs, the expression of 10 differentially expressed mature miRNAs originating from 12 pre-miRNAs was shown to have changed by more than twofold between inflorescences of the Ogura-CMS line and inflorescences of the MF line, including 8 down-and 2 up-regulated miRNAs. The expression profiles of the differentially expressed miRNAs were confirmed by stem-loop quantitative real-time PCR. In addition, to identify the targets of the identified miR-NAs, a degradome analysis was performed. A total of 22 targets of 25 miRNAs and 17 targets of 28 miRNAs were identified as being involved in the reproductive development for Ogura-CMS and MF lines of turnip, respectively. Negative correlations of expression patterns between partial miRNAs and their targets were detected. Some of these identified targets, such as squamosa promoter-binding-like transcription factor family proteins, auxin response factors and pentatricopeptide repeat-containing proteins, were previously

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Comprehensive analysis of Ogura cytoplasmic male sterility-related genes in turnip (Brassica rapa ssp. rapifera) using RNA sequencing analysis and bioinformatics

Cited by 17 publications

References 115 publications

Genome-wide analysis of proline-rich extension-like receptor protein kinase (PERK) in Brassica rapa and its association with the pollen development

Genome-wide analysis of proline-rich extension-like receptor protein kinase (PERK) in Brassica rapa and its association with the pollen development

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

Identification of microRNAs and their targets in inflorescences of an Ogura-type cytoplasmic male-sterile line and its maintainer fertile line of turnip (Brassica rapa ssp. rapifera) via high-throughput sequencing and degradome analysis

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