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ABSTRACT: RNA-seq of an Ogura CMS line and its maintainer line in radish

PROVIDER: PRJNA691680 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13423815_1.fastq.gz	Fastqsanger.gz
	SRR13423815_2.fastq.gz	Fastqsanger.gz
	SRR13423816_1.fastq.gz	Fastqsanger.gz
	SRR13423816_2.fastq.gz	Fastqsanger.gz
	SRR13423817_1.fastq.gz	Fastqsanger.gz

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Project description:RNA-seq of an Ogura CMS line and its maintainer line in radish

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Identification of differentially expressed genes related to cytoplasmic male sterility in radish (Raphanus sativus L.) by comparative transcriptome analysis

Project description:Cytoplasmic male sterility (CMS), a typically maternally inherited trait, causes a failure in producing functional pollen. Although the radish CMS has be widely used to produce hybrid varieties in breeding program, the molecular mechanism of CMS in radish is poorly understood. In this study, two radish CMS lines (HYBP-A and YH-A) and their corresponding maintainer lines (HYBP-B and YH-B) were used to identify genes potentially involving in CMS using Illumina pair-end sequencing. A total of 167.86 million clean sequence reads were generated from the eight libraries (two replicates for each line). These reads were eventually assembled into 130,240 unigenes. Of them, 67,173 (51.6%) unigenes were annotated for their function. Comparison of gene expression levels between CMS line and maintainer line revealed 5,893 differentially expressed genes (DEGs) in HYBP, and 3,739 DEGs inYH. There were 990 DEGs commonly identified in both HYBP and YH, with same direction of expression change in two CMS lines relative to their corresponding maintainer lines, which suggested these 990 DEGs is likely related to CMS of radish. The expression levels of 20 DEGs were further confirmed by real-time quantitative PCR (qRT-PCR). Two pathways and eight functional categories exhibited a significant enrichment with DEGs in HYBP, and one pathway and six functional categories were markedly enriched by DEGs in YH. Among these pathways/functional categories, four of them were enriched in both varieties. A series of candidate genes and pathways that may contribute to the CMS will be helpful for increasing our understanding for this trait in radish.

2016-01-21 | GSE65142 | GEO

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Project description:Ogura-CMS sterile line (Tyms) and its maintainer line (231-330) of Chinese cabbage transcriptome

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miRNA profiling in cytoplasmic male sterile (CMS) and its maintainer fertile (MF) lines of Brassica juncea by deep sequencing

Project description:Here, we employed high-throughput sequencing to identify microRNAs in CMS and its maintainer fertile (MF) lines of Brassica juncea. We identified 197 known and 78 new candidate microRNAs during reproductive development of B. juncea. A total of 47 differentially expressed microRNAs between CMS and its maintainer fertile lines were discovered, according to their sequencing read number.

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The radish Ogura fertility restorer impedes translation elongation along its cognate CMS-causing mRNA [RNA-seq]

Project description:The radish Ogura fertility restorer impedes translation elongation along its cognate CMS-causing mRNA [RNA-seq]

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pepper stamen LC-MSMS - Proteomic analysis reveals strong mitochondrial involvement in cytoplasmic male sterility of pepper (Capsicum annuum L

Project description:We used a high-throughput proteomics method called label-free to compare protein abundance across a pepper CMS line and its isogenic maintainer line.This study explained the mechanisms of cytoplasmic male sterility and contribute to the improvement of pepper hybrid breeding.

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comparative analysis of DNA methylation of soybean

Project description:In this study, comparative genome-wide DNA methylation profiles of the soybean CMS line NJCMS5A and its maintainer NJCMS5B were completed by whole-genome bisulfite sequencing. The results showed that 3,527 differentially methylated regions (DMRs) and 485 differentially methylated genes (DMGs), including 353 high-credible methylated genes, 56 methylated genes coding unknown protein and 76 novel methylated genes with no known function were identified. Finally, 14 key DMGs were identified as potentially related to CMS in soybean.

2017-07-20 | GSE101652 | GEO

The radish Ogura fertility restorer impedes translation elongation along its cognate CMS-causing mRNA

Project description:The radish Ogura fertility restorer impedes translation elongation along its cognate CMS-causing mRNA

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