RNA transcriptome analysis of floral buds of male-fertile and male-sterile tomato
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ABSTRACT:
ORGANISM(S): Solanum lycopersicum
PROVIDER: GSE102374 | GEO | 2017/08/10
SECONDARY ACCESSION(S): PRJNA397585
REPOSITORIES: GEO
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Project description:Radish cytoplasmic male sterility (CMS) has been widely used for breeding in Raphanus and Brassica genera. However, the detailed regulation network of the male sterility remains to be determined. Our previous work has shown that the abnormalities in a CMS radish appeared shortly after the tetrad stage when microspores were malformed and the tapetal cells grew abnormally large. In this work, histological analysis shows that anthers are at the tetrad stage when the radish buds are about 1.5 mm in length. Furthermore, a high throughput RNA sequencing technology was employed to characterize the transcriptome of radish buds with length about 1.5 mm from two CMS lines possessing the CMS-inducing orf138 gene and corresponding near-isogenic maintainer lines. A total of 67,140 unigenes were functionally annotated. Functional terms for these genes are significantly enriched in 55 Gene Ontology (GO) groups and 323 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The transcriptome detected transcripts for 72 out of a total of 79 protein genes encoded in the chloroplast genome from radish. In contrast, the radish mitochondrial genome contains 34 protein genes, but only 16 protein transcripts were detected from the transcriptome. The transcriptome comparison between CMS and near-isogenic maintainer lines revealed 539 differentially expressed genes (DEGs), indicating that the false positive rate for comparative transcriptome profiling was clearly decreased using two groups of CMS/maintainer lines with different nuclear background. The level of 127 transcripts was increased and 412 transcripts were decreased in the CMS lines. No change in levels of transcripts except CMS-inducing orf138 was identified from the mitochondrial and chloroplast genomes. Some DEGs which would be associated with the CMS, encoding MYB and bHLH transcription factors, pentatricopeptide repeat (PPR) proteins, heat shock transcription factors (HSFs) and heat shock proteins (HSPs), are discussed. The transcriptome dataset and comparative analysis will provide an important resource for further understanding anther development, the CMS mechanism and to improve molecular breeding in radish.
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Project description:Male sterility is an important mechanism for the production of hybrid seeds in watermelon. Although fruit development has been studied extensively in watermelon, there are no reports on gene expression in floral organs. In this study, RNA-sequencing (RNA-seq) was performed in two near-isogenic watermelon lines (genic male sterile [GMS] line, DAH3615-MS and male fertile line, DAH3615) to identify the differentially expressed genes (DEGs) related to male sterility.DEG analysis showed that 1259 genes were significantly associated with male sterility at a FDR P-value of?<?0.01. Most of these genes were only expressed in the male fertile line. In addition, 11 functional clusters were identified using DAVID functional classification analysis. Of detected genes in RNA-seq analysis, 19 were successfully validated by qRT-PCR.In this study, we carried out a comprehensive floral transcriptome sequence comparison of a male fertile line and its near-isogenic male sterile line in watermelon. This analysis revealed essential genes responsible for stamen development, including pollen development and pollen tube elongation, and allowed their functional classification. These results provided new information on global mechanisms related to male sterility in watermelon.
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Project description:Male sterility is important mechanism in watermelon for production of hybrid seed. While some fruit development related studies were widely performed in watermelon, there are no reports of profiling gene expression in floral organs of watermelon. RNA-seq analysis was performed in order to identify male sterility related genes from two different groups of watermelon (genetic male-sterile (GMS) DAH3615-MS line and male-fertile DAH3615 line, respectively) to identify the differentially expressed genes (DEGs).
2016-01-04 | GSE69073 | GEO
Project description:Male sterility is important mechanism in watermelon for production of hybrid seed. While some fruit development related studies were widely performed in watermelon, there are no reports of profiling gene expression in floral organs of watermelon. RNA-seq analysis was performed in order to identify male sterility related genes from two different groups of watermelon (genetic male-sterile (GMS) DAH3615-MS line and male-fertile DAH3615 line, respectively) to identify the differentially expressed genes (DEGs). This study employed tophat and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 2 tissues obtained from 2 different breeds of watermelon
2016-01-04 | E-GEOD-69073 | biostudies-arrayexpress
Project description:The common potato, Solanum tuberosum L., is the fourth most important agricultural crop worldwide. Until recently, vegetative propagation by tubers has been the main method of potato cultivation. A shift of interest to sexual potato reproduction by true botanical seeds is due to the appearance of a new hybrid seed breeding strategy whose successful application for many crop species has been supported by male sterility. This investigation was focused on the study of differences in the metabolite profiles of anthers at the mature pollen stage from male-fertile and male-sterile genotypes of S. tuberosum. Application of gas chromatography coupled with a mass spectrometry method allowed detection of metabolic profiles for 192 compounds. Further data analysis with several libraries fully identified 75 metabolites; a similar amount was defined up to the classes. Metabolic profiles in the anthers of fertile genotypes were significantly distinguished from male-sterile ones by the accumulation of carbohydrates, while the anthers of sterile genotypes contained a higher amount of amino acids. In comparison with male-fertile plants, male-sterile genotypes had undeveloped pollen grain characters; i.e., smaller grain size, a thicker exine, "permanent tetrads" that failed to disintegrate into microspores, and the absence of pollen apertures that might be due to a disorder in the metabolism of carbohydrates and fatty acids.
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Project description:Background:The tea plant is a crucial economic crop. The floral organ development consumes a large amount of nutrients, which affects the leaf yield. To understand the mechanism by which the tea plant produces sterile floral buds, we obtained a sterile tea plant by artificial hybridization. RNA-sequencing based transcriptome analysis was implemented in three samples to determine the differentially expressed genes (DEGs) related to flower development. Results:In this study, a total of 1991 DEGs were identified; 1057 genes were up-regulated and 934 genes were down-regulated in sterile hybrid floral buds. These were mainly distributed in the regulation of biological and metabolic processes. Significantly, auxin biosynthesis genes YUCCA, AUX1 and PIN were dramatically down-regulated, and ARF gene was up-regulated in the sterile hybrid floral buds, and flower development-related genes AP1, AP2 and SPL were changed. A total of 12 energy transfer-related genes were significantly decreased. Furthermore, the expression of 11 transcription factor genes was significantly different. Conclusion:The transcriptome analysis suggested that the production of sterile floral buds is a complex bioprocess, and that low auxin-related gene levels result in the formation of sterile floral buds in the tea plant.
| S-EPMC6474060 | biostudies-literature
Project description:we performed transcript profiling of male sterile and fertile buds from a multiple-allele inherited male sterile AB line using the Illumina high-throughput sequencing platform and analyzed differential gene expression at the transcriptional level.
2016-02-10 | GSE77427 | GEO
Project description:Male sterility is an important factor in improving crop quality and yield through heterosis breeding. In this study, we analyzed the transcriptomes of male fertile (MF) and male sterile (MS) alfalfa flower buds using the Illumina HiSeq™ 4000 platform. A total of 54.05 million clean reads were generated and assembled into 65,777 unigenes with an average length of 874 bp. The differentially expressed genes (DEGs) between the MF and MS flowers at three stages of pollen development were identified, and there were 3832, 5678 and 5925 DEGs respectively in stages 1, 2 and 3. GO and KEGG functional enrichment analysis revealed 12, 12, 6 and 12 key branch-point genes involved in circadian rhythm, transcription factors, pollen development and flavonoid biosynthesis. Our findings provide novel insights into the mechanism of male sterility in alfalfa.Supplementary informationThe online version contains supplementary material available at 10.1007/s12298-021-01026-x.
| S-EPMC8295440 | biostudies-literature
Project description:BackgroundThe Polima (pol) system of cytoplasmic male sterility (CMS) and its fertility restoration gene Rfp have been used in hybrid breeding in Brassica napus, which has greatly improved the yield of rapeseed. However, the mechanism of the male sterility transition in pol CMS remains to be determined.ResultsTo investigate the transcriptome during the male sterility transition in pol CMS, a near-isogenic line (NIL) of pol CMS was constructed. The phenotypic features and sterility stage were confirmed by anatomical analysis. Subsequently, we compared the genomic expression profiles of fertile and sterile young flower buds by RNA-Seq. A total of 105,481,136 sequences were successfully obtained. These reads were assembled into 112,770 unigenes, which composed the transcriptome of the bud. Among these unigenes, 72,408 (64.21%) were annotated using public protein databases and classified into functional clusters. In addition, we investigated the changes in expression of the fertile and sterile buds; the RNA-seq data showed 1,148 unigenes had significantly different expression and they were mainly distributed in metabolic and protein synthesis pathways. Additionally, some unigenes controlling anther development were dramatically down-regulated in sterile buds.ConclusionsThese results suggested that an energy deficiency caused by orf224/atp6 may inhibit a series of genes that regulate pollen development through nuclear-mitochondrial interaction. This results in the sterility of pol CMS by leading to the failure of sporogenous cell differentiation. This study may provide assistance for detailed molecular analysis and a better understanding of pol CMS in B. napus.
| S-EPMC4051170 | biostudies-literature
Project description:we performed transcript profiling of male sterile and fertile buds from a multiple-allele inherited male sterile AB line using the Illumina high-throughput sequencing platform and analyzed differential gene expression at the transcriptional level. Examination of mRNA levels in sterile and fertile buds of chinese cabbage Please note that the 'Table_S*.xls' files contain the further-processed supplementary data. The data processing details are provided in the readme.xlsx.
2016-02-10 | E-GEOD-77427 | biostudies-arrayexpress