Dataset Information

Transcriptome Sequencing Analyses between the Cytoplasmic Male Sterile Line and Its Maintainer Line in Welsh Onion (Allium fistulosum L.).

ABSTRACT: Cytoplasmic male sterility (CMS) is important for exploiting heterosis in crop plants and also serves as a model for investigating nuclear-cytoplasmic interaction. The molecular mechanism of cytoplasmic male sterility and fertility restoration was investigated in several important economic crops but remains poorly understood in the Welsh onion. Therefore, we compared the differences between the CMS line 64-2 and its maintainer line 64-1 using transcriptome sequencing with the aim of determining critical genes and pathways associated with male sterility. This study combined two years of RNA-seq data; there were 1504 unigenes (in May 2013) and 2928 unigenes (in May 2014) that were differentially expressed between the CMS and cytoplasmic male maintainer Welsh onion varieties. Known CMS-related genes were found in the set of differentially expressed genes and checked by qPCR. These genes included F-type ATPase, NADH dehydrogenase, cytochrome c oxidase, etc. Overall, this study demonstrated that the CMS regulatory genes and pathways may be associated with the mitochondria and nucleus in the Welsh onion. We believe that this transcriptome dataset will accelerate the research on CMS gene clones and other functional genomics research on A. fistulosum L.

SUBMITTER: Liu Q

PROVIDER: S-EPMC4964434 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

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Transcriptome Sequencing Analyses between the Cytoplasmic Male Sterile Line and Its Maintainer Line in Welsh Onion (Allium fistulosum L.).

Liu Qianchun Q Lan Yanping Y Wen Changlong C Zhao Hong H Wang Jian J Wang Yongqin Y

International journal of molecular sciences 20160701 7

Cytoplasmic male sterility (CMS) is important for exploiting heterosis in crop plants and also serves as a model for investigating nuclear-cytoplasmic interaction. The molecular mechanism of cytoplasmic male sterility and fertility restoration was investigated in several important economic crops but remains poorly understood in the Welsh onion. Therefore, we compared the differences between the CMS line 64-2 and its maintainer line 64-1 using transcriptome sequencing with the aim of determining ...[more]

PMID: 27376286

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Project description:BACKGROUND:The optimized illumination of plants using light-emitting diodes (LEDs) is beneficial to their photosynthetic performance, and in recent years, LEDs have been widely used in horticultural facilities. However, there are significant differences in the responses of different crops to different wavelengths of light. Thus, the influence of artificial light on photosynthesis requires further investigation to provide theoretical guidelines for the light environments used in industrial crop production. In this study, we tested the effects of different LEDs (white, W; blue, B; green, G; yellow, Y; and red, R) with the same photon flux density (300??mol/m2·s) on the growth, development, photosynthesis, chlorophyll fluorescence characteristics, leaf structure, and chloroplast ultrastructure of Welsh onion (Allium fistulosum L.) plants. RESULTS:Plants in the W and B treatments had significantly higher height, leaf area, and fresh weight than those in the other treatments. The photosynthetic pigment content and net photosynthetic rate (Pn) in the W treatment were significantly higher than those in the monochromatic light treatments, the transpiration rate (E) and stomatal conductance (Gs) were the highest in the B treatment, and the intercellular CO2 concentration (Ci) was the highest in the Y treatment. The non-photochemical quenching coefficient (NPQ) was the highest in the Y treatment, but the other chlorophyll fluorescence characteristics differed among treatments in the following order: W?>?B?>?R?>?G?>?Y. This includes the maximum photochemical efficiency of photosystem II (PSII) under dark adaptation (Fv/Fm), maximum photochemical efficiency of PSII under light adaptation (Fv'/Fm'), photochemical quenching coefficient (qP), actual photochemical efficiency (?PSII), and apparent electron transport rate (ETR). Finally, the leaf structure and chloroplast ultrastructure showed the most complete development in the B treatment. CONCLUSIONS:White and blue light significantly improved the photosynthetic efficiency of Welsh onions, whereas yellow light reduced the photosynthetic efficiency.

Project description:BackgroundBolting reduces the quality and commercial yield of Welsh onion (Allium fistulosum L.) in production. However, seed production is directly dependent on flower induction and bolting. The Welsh onion belongs to the green plant vernalisation type, specific seedling characteristics and sufficient accumulated time at low temperature are indispensible for the completion of its vernalisation process. Only if these conditions for vernalisation are fulfilled, the plants will bolt in the following year. The present investigation evaluated the effects of cultivar, sowing date and transplant location in field on the bolting of Welsh onion at the Horticultural Farm of the College of Horticulture, Northwest A&F University, Yangling, Shannxi Province, China in two succeeding production years: 2010-2011 and 2011-2012. A strip split plot layout within a randomised complete block design with three replications was used.ResultsThe results revealed that all three factors (cultivar, sowing date and transplant location) and their interaction had significant effects on the initiation and final rate of bolting observed by 30 April. The earliest bolting date (14 February, 2011 and 15 February, 2012) and the highest bolting rate (100% in 2011 and 62% in 2012) occurred when the JinGuan cultivar was sown on 20 August and transplanted in a plastic tunnel, whereas the latest date and lowest rate (no bolting observed until 30 April) of bolting occurred when the XiaHei cultivar was sown on 29 September and transplanted in an open field.ConclusionsThese results suggest that we can control bolting in Welsh onion production by choosing an appropriate cultivar, sowing date and transplant location. Choosing a late bolting cultivar, such as cultivar XiaHei, sowing around October, and transplanting in the open field can significantly delay bolting, while a sowing date in late August should be selected for seed production, and the seedlings should be transplanted in a plastic tunnel to accelerate development of the flower buds.

Project description:BackgroundCytoplasmic male sterility (CMS) is a natural phenomenon of pollen abortion caused by the interaction between cytoplasmic genes and nuclear genes. CMS is a simple and effective pollination control system, and plays an important role in crop heterosis utilization. Circular RNAs (circRNAs) are a vital type of non-coding RNAs, which play crucial roles in microRNAs (miRNAs) function and post-transcription control. To explore the expression profile and possible functions of circRNAs in the soybean CMS line NJCMS1A and its maintainer NJCMS1B, high-throughput deep sequencing coupled with RNase R enrichment strategy was conducted.ResultsCircRNA libraries were constructed from flower buds of NJCMS1A and its maintainer NJCMS1B with three biological replicates. A total of 2867 circRNAs were identified, with 1009 circRNAs differentially expressed between NJCMS1A and NJCMS1B based on analysis of high-throughput sequencing. Of the 12 randomly selected circRNAs with different expression levels, 10 showed consistent expression patterns based on high-throughput sequencing and quantitative real-time PCR analyses. Tissue specific expression patterns were also verified with two circRNAs by quantitative real-time PCR. Most parental genes of differentially expressed circRNAs were mainly involved in biological processes such as metabolic process, biological regulation, and reproductive process. Moreover, 83 miRNAs were predicted from the differentially expressed circRNAs, some of which were strongly related to pollen development and male fertility; The functions of miRNA targets were analyzed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and the target mRNAs were significantly enriched in signal transduction and programmed cell death. Furthermore, a total of 165 soybean circRNAs were predicted to contain at least one internal ribosome entry site (IRES) element and an open reading frame, indicating their potential to encode polypeptides or proteins.ConclusionsOur study indicated that the circRNAs might participate in the regulation of flower and pollen development, which could provide a new insight into the molecular mechanisms of CMS in soybean.

Project description:BackgroundThe utilization of soybean heterosis is probably one of the potential approaches in future yield breakthrough as was the situation in rice breeding in China. Cytoplasmic male sterility (CMS) plays an important role in the production of hybrid seeds. However, the molecular mechanism of CMS in soybean remains unclear.ResultsThe comparative transcriptome analysis between cytoplasmic male sterile line NJCMS1A and its near-isogenic maintainer NJCMS1B in soybean was conducted using Illumina sequencing technology. A total of 88,643 transcripts were produced in Illumina sequencing. Then 56,044 genes were obtained matching soybean reference genome. Three hundred and sixty five differentially expressed genes (DEGs) between NJCMS1A and NJCMS1B were screened by threshold, among which, 339 down-regulated and 26 up-regulated in NJCMS1A compared to in NJCMS1B. Gene Ontology (GO) annotation showed that 242 DEGs were annotated to 19 functional categories. Clusters of Orthologous Groups of proteins (COG) annotation showed that 265 DEGs were classified into 19 categories. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that 46 DEGs were assigned to 33 metabolic pathways. According to functional and metabolic pathway analysis combined with reported literatures, the relations between some key DEGs and the male sterility of NJCMS1A were discussed. qRT-PCR analysis validated that the gene expression pattern in RNA-Seq was reliable. Finally, enzyme activity assay showed that energy supply was decreased in NJCMS1A compared to in NJCMS1B.ConclusionsWe concluded that the male sterility of NJCMS1A might be related to the disturbed functions and metabolism pathways of some key DEGs, such as DEGs involved in carbohydrate and energy metabolism, transcription factors, regulation of pollen development, elimination of reactive oxygen species (ROS), cellular signal transduction, and programmed cell death (PCD) etc. Future research will focus on cloning and transgenic function validation of possible candidate genes associated with soybean CMS.

Dataset Information

Transcriptome Sequencing Analyses between the Cytoplasmic Male Sterile Line and Its Maintainer Line in Welsh Onion (Allium fistulosum L.).

Publications

Transcriptome Sequencing Analyses between the Cytoplasmic Male Sterile Line and Its Maintainer Line in Welsh Onion (Allium fistulosum L.).

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