scholarly journals MicroRNAs Involved in Regulatory Cytoplasmic Male Sterility by Analysis RNA-seq and Small RNA-seq in Soybean

2021 ◽  
Vol 12 ◽  
Author(s):  
Chunbao Zhang ◽  
Fuyou Fu ◽  
Chunjing Lin ◽  
Xiaoyang Ding ◽  
Jingyong Zhang ◽  
...  
Keyword(s):  
Cytoplasmic Male Sterility ◽  
Male Sterility ◽  
Regulatory Network ◽  
Target Genes ◽  
Reproductive Development ◽  
Differentially Expressed ◽  
Hybrid Breeding ◽  
Rna Seq ◽  
Maintainer Line ◽  
Cms Line

Cytoplasmic male sterility (CMS) is an important plant characteristic for exploiting heterosis to enhance crop traits during breeding. However, the CMS regulatory network remains unclear in plants, even though researchers have attempted to isolate genes associated with CMS. In this study, we performed high-throughput sequencing and degradome analyses to identify microRNAs (miRNAs) and their targets in a soybean CMS line (JLCMS9A) and its maintainer line (JLCMS9B). Additionally, the differentially expressed genes during reproductive development were identified using RNA-seq data. A total of 280 miRNAs matched soybean miRNA sequences in miRBase, including mature miRNAs and pre-miRNAs. Of the 280 miRNAs, 30, 23, and 21 belonged to the miR166, miR156, and miR171 families, respectively. Moreover, 410 novel low-abundant miRNAs were identified in the JLCMS9A and JLCMS9B flower buds. Furthermore, 303 and 462 target genes unique to JLCMS9A and JLCMS9B, respectively, as well as 782 common targets were predicted based on the degradome analysis. Target genes differentially expressed between the CMS line and the maintainer line were revealed by an RNA-seq analysis. Moreover, all target genes were annotated with diverse functions related to biological processes, cellular components, and molecular functions, including transcriptional regulation, the nucleus, meristem maintenance, meristem initiation, cell differentiation, auxin-activated signaling, plant ovule development, and anther development. Finally, a network was built based on the interactions. Analyses of the miRNA, degradome, and transcriptome datasets generated in this study provided a comprehensive overview of the reproductive development of a CMS soybean line. The data presented herein represent useful information for soybean hybrid breeding. Furthermore, the study results indicate that miRNAs might contribute to the soybean CMS regulatory network by modulating the expression of CMS-related genes. These findings lay the foundation for future studies on the molecular mechanisms underlying soybean CMS.

scholarly journals Comparative profile analysis reveals differentially expressed microRNAs regulate anther and pollen development in kenaf cytoplasmic male sterility line

Genome ◽  
2019 ◽  
Vol 62 (7) ◽  
pp. 455-466
Author(s):  
Peng Chen ◽  
Qiqi Shi ◽  
Zhichen Liang ◽  
Hai Lu ◽  
Ru Li
Keyword(s):  
Cytoplasmic Male Sterility ◽  
Male Sterility ◽  
Regulatory Network ◽  
Pollen Development ◽  
Protein Modification ◽  
Target Genes ◽  
Profile Analysis ◽  
Differentially Expressed ◽  
Auxin Signaling ◽  
Mirna Regulation

Cytoplasmic male sterility (CMS) is advantageous in extensive crop breeding and represents a perfect model for understanding anther and pollen development research. MicroRNAs (miRNAs) play key roles in regulating various biological processes. However, the miRNA-mediated regulatory network in kenaf CMS occurrence remains largely unknown. In the present study, a comparative deep sequencing approach was used to investigate the miRNAs and their roles in regulating anther and pollen development during CMS occurrence. We identified 283 known and 46 new candidate miRNAs in kenaf anther. A total of 67 differentially expressed miRNAs (DEMs) were discovered between CMS and its maintainer line. Among them, 40 and 27 miRNAs were up- and downregulated, respectively. These 67 DEMs were predicted to target 189 genes. Validation of DEMs and putative target genes were confirmed by using real-time quantitative PCR. In addition, a potential miRNA-mediated regulatory network, which mainly involves the auxin signaling pathway, signal transduction, glycolysis and energy metabolism, gene expression, transmembrane transport, protein modification and metabolism, and floral development, that mediates anther development during CMS occurrence was proposed. Taken together, our findings provide a better understanding of the molecular mechanism of miRNA regulation in pollen development and CMS occurrence in kenaf.

scholarly journals Organelle genome composition and candidate gene identification for Nsa cytoplasmic male sterility in Brassica napus

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Shi-Fei Sang ◽  
De-Sheng Mei ◽  
Jia Liu ◽  
Qamar U. Zaman ◽  
Hai-Yan Zhang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Mitochondrial Genome ◽  
Cytoplasmic Male Sterility ◽  
Male Sterility ◽  
Parental Species ◽  
Sequencing Technology ◽  
Genome Composition ◽  
Maintainer Line ◽  
Organelle Genomes ◽  
Cms Line

Abstract Background Nsa cytoplasmic male sterility (CMS) is a novel alloplasmic male sterility system derived from somatic hybridization between Brassica napus and Sinapis arvensis. Identification of the CMS-associated gene is a prerequisite for a better understanding of the origin and molecular mechanism of this CMS. With the development of genome sequencing technology, organelle genomes of Nsa CMS line and its maintainer line were sequenced by pyro-sequencing technology, and comparative analysis of the organelle genomes was carried out to characterize the organelle genome composition of Nsa CMS as well as to identify the candidate Nsa CMS-associated genes. Results Nsa CMS mitochondrial genome showed a higher collinearity with that of S. arvensis than B. napus, indicating that Nsa CMS mitochondrial genome was mainly derived from S. arvensis. However, mitochondrial genome recombination of parental lines was clearly detected. In contrast, the chloroplast genome of Nsa CMS was highly collinear with its B. napus parent, without any evidence of recombination of the two parental chloroplast genomes or integration from S. arvensis. There were 16 open reading frames (ORFs) specifically existed in Nsa CMS mitochondrial genome, which could not be identified in the maintainer line. Among them, three ORFs (orf224, orf309, orf346) possessing chimeric and transmembrane structure are most likely to be the candidate CMS genes. Sequences of all three candidate CMS genes in Nsa CMS line were found to be 100% identical with those from S. arvensis mitochondrial genome. Phylogenetic and homologous analysis showed that all the mitochondrial genes were highly conserved during evolution. Conclusions Nsa CMS contains a recombined mitochondrial genome of its two parental species with the majority form S. arvensis. Three candidate Nsa CMS genes were identified and proven to be derived from S. arvensis other than recombination of its two parental species. Further functional study of the candidate genes will help to identify the gene responsible for the CMS and the underlying molecular mechanism.

scholarly journals Mitochondrial Proteomics and Transcriptional Analysis of Cytoplasmic Male Sterility in Sugar Beet using iTRAQ and qRT–PCR

2022 ◽  
Author(s):  
Tianjiao Liu ◽  
Dayou Cheng ◽  
Xue Han ◽  
Jie Cui ◽  
Cuihong Dai ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Cytoplasmic Male Sterility ◽  
Male Sterility ◽  
Raw Material ◽  
Differentially Expressed ◽  
Transcriptional Analysis ◽  
Hybrid Breeding ◽  
Male Sterile ◽  
Pollen Abortion ◽  
Absolute Quantitation

Abstract Sugar beet (Beta vulgaris L.) is an important raw material for the sugar industry, and its output is second only to sugar cane. Cytoplasmic male sterility (CMS) is a phenomenon of pollen abortion that has important implications in sugar beet hybrid breeding. Male plant sterility is usually considered to be associated with mitochondrial dysfunction. Although mitochondrial genes associated with male sterility have been well explored, the different mitochondrial proteomics of CMS in sugar beet are still poorly understood. In this study, differentially expressed mitochondrial proteomic analysis was performed on the flower buds of the male sterile line (DY5-CMS), its maintainer line (DY5-O) and a fertility restorer line (CL6), using an isobaric tag for relative and absolute quantitation (iTRAQ) technology. A total of 2260 proteins were identified by mass spectrometry, of which 538 were differentially expressed proteins. Most of them were involved in protein metabolism, carbohydrate and energy metabolism, and binding. More specifically, some cysteine and methionine metabolism proteins (A0A0J8BGE0, A0A0J8CZM6, A0A0J8D7W0 and A0A0J8BCR7) may play important roles during the formation of CMS. This study provided an in–depth understanding of the CMS molecular mechanism at the protein level in sugar beet.

Identification of Differentially Expressed miRNAs between a Wheat K-type Cytoplasmic Male Sterility Line and Its Near-Isogenic Restorer Line

2019 ◽  
Vol 60 (7) ◽  
pp. 1604-1618
Author(s):  
Hongxia Li ◽  
Jinglei Guo ◽  
Chengyang Zhang ◽  
Weijun Zheng ◽  
Yulong Song ◽  
...  
Keyword(s):  
Cytoplasmic Male Sterility ◽  
Male Sterility ◽  
Target Genes ◽  
Expression Profiles ◽  
Rna Degradation ◽  
Differentially Expressed ◽  
Striking Difference ◽  
Small Rna Sequencing ◽  
Restorer Line ◽  
Hybrid Wheat

Abstract K-type cytoplasmic male sterility (KCMS) lines were ideal material for three-line hybrid wheat system due to the major role in hybrid wheat production. In this study, the morphology of developing microspore and mature pollen was compared between a KCMS line and its near-isogenic restorer line (KCMS-NIL). The most striking difference is that the microspore was unable to develop into tricellular pollen in the KCMS line. MicroRNA plays vital roles in flowering and gametophyte development. Small RNA sequencing identified a total of 274 known and 401 novel miRNAs differentially expressed between two lines or two developmental stages. Most of miRNAs with high abundance were differentially expressed at the uninucleate stage, and their expression level recovered or remained at the binucleate stage. Further degradome sequencing identified target genes which were mainly enriched in transcription regulation, phytohormone signaling and RNA degradation pathways. Combining with the transcriptome data, a correlation was found between the abnormal anther development, such as postmeiotic mitosis cessation, deformative pollen wall and the chromosome condensation of the vegetative cell, and the alterations in the related miRNA and their targets expression profiles. According to the correlation and pathway analysis, we propose a hypothetic miRNA-mediated network for the control of KCMS restoration.

scholarly journals Discovery of Four Novel ORFs Responsible for Cytoplasmic Male Sterility (CMS) in Cotton (Gossypium hirsutum L.) through Comparative Analysis of the Mitochondrial Genomes of Four Isoplasmic Lines

Agronomy ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 765
Author(s):  
Min Li ◽  
Li Chen ◽  
Danfeng Tang ◽  
Xiaofang Liao ◽  
Xiangjun Kong ◽  
...  
Keyword(s):  
Cytoplasmic Male Sterility ◽  
Male Sterility ◽  
Ribosomal Proteins ◽  
High Throughput Sequencing ◽  
Open Reading Frames ◽  
Maintainer Line ◽  
Protein Coding ◽  
Synonymous Mutations ◽  
Protein Coding Genes ◽  
Cms Line

Cytoplasmic male sterility (CMS) is an important feature for achieving heterosis in the development of hybrid crops. Mitochondria contribute to CMS, especially via mitochondrial DNA (mtDNA) rearrangements and chimeric genes. However, the mechanisms of CMS have not been fully elucidated, and the isonuclear alloplasmic lines used in previous studies have limited utility in cotton CMS research. In this study, three CMS lines (J4A-1, J4A-2 and J4A-3) and their isoplasmic maintainer line (J4B) were analyzed for mtDNA structural differences via high-throughput sequencing. The results showed that mtDNA was conserved (with similarities higher than 99%) among the three CMS lines and their isoplasmic maintainer line. All lines harbored 36 known protein-coding genes, 3 rRNAs, and 15 tRNAs. The protein-coding genes with non-synonymous mutations mainly encoded two types of proteins: ATPase and ribosomal proteins. Four new open reading frames (ORFs) (orf116b, orf186a-1, orf186a-2 and orf305a) were identified as candidate ORFs responsible for CMS. Two of the ORFs (orf186a-1 and orf186a-2) were identified as orf4 and orf4-2 of the upland cotton CMS line 2074A (a line with Gossypium harknessii Brandegee CMS-D2-2 cytoplasm), respectively. These findings provide a reference for CMS research in cotton or other crops.

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