Ontology highlight
ABSTRACT:
PROVIDER: PRJNA885599 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21763641_1.fastq.gz | Fastqsanger.gz | |||
| SRR21763641_2.fastq.gz | Fastqsanger.gz | |||
| SRR21763642_1.fastq.gz | Fastqsanger.gz | |||
| SRR21763642_2.fastq.gz | Fastqsanger.gz | |||
| SRR21763643_1.fastq.gz | Fastqsanger.gz |
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Project description:Parthenocarpy—the production of seedless fruits without fertilization—is very useful for fruit cultivation. Among pear cultivars (Japanese, Chinese, and European pears and their interspecific hybrids) subjected to flower emasculation and left unpollinated, only some of the European pears had a stable and high degree of fruit set and fruit enlargement. Almost all the enlarged fruits formed no seeds. Comparison of fruits produced by using emasculation without pollination or with self-pollination ruled out the possibility of stenospermocarpy in these parthenocarpic pears. The results suggested that the abovementioned characteristics were inherited maternally by the next generation and that it should be possible to introduce parthenocarpy into Japanese pears. Neither Chinese nor Japanese pears treated with emasculation and no pollination showed consistently stable fruit set or fruit enlargement. In Chinese pears, these characteristics varied greatly from year to year, and in Japanese pears they were stable but weak. Although in each cultivar highly parthenocarpic fruits weighed slightly less than cross-pollinated ones, the cortexes of the emasculated fruits were enlarged and the fruits were not greatly inferior to those of cross-pollinated ones. By using a customized pear cDNA microarray, we compared the gene expression profiles of highly and weakly parthenocarpic cultivars before flowering. Expression of several phenylpropanoid-related genes and photosystem-related genes differed significantly between the two groups. Some of these genes were contained in the chloroplast genome. These results showed the unique mechanism of genetic parthenocarpy in pome fruits as opposed to non-pome fruits. The gene expression profiles between high and low parthenocarpy group before flowering were compared.
2012-01-10 | E-GEOD-27090 | biostudies-arrayexpress
Project description:Parthenocarpy—the production of seedless fruits without fertilization—is very useful for fruit cultivation. Among pear cultivars (Japanese, Chinese, and European pears and their interspecific hybrids) subjected to flower emasculation and left unpollinated, only some of the European pears had a stable and high degree of fruit set and fruit enlargement. Almost all the enlarged fruits formed no seeds. Comparison of fruits produced by using emasculation without pollination or with self-pollination ruled out the possibility of stenospermocarpy in these parthenocarpic pears. The results suggested that the abovementioned characteristics were inherited maternally by the next generation and that it should be possible to introduce parthenocarpy into Japanese pears. Neither Chinese nor Japanese pears treated with emasculation and no pollination showed consistently stable fruit set or fruit enlargement. In Chinese pears, these characteristics varied greatly from year to year, and in Japanese pears they were stable but weak. Although in each cultivar highly parthenocarpic fruits weighed slightly less than cross-pollinated ones, the cortexes of the emasculated fruits were enlarged and the fruits were not greatly inferior to those of cross-pollinated ones. By using a customized pear cDNA microarray, we compared the gene expression profiles of highly and weakly parthenocarpic cultivars before flowering. Expression of several phenylpropanoid-related genes and photosystem-related genes differed significantly between the two groups. Some of these genes were contained in the chloroplast genome. These results showed the unique mechanism of genetic parthenocarpy in pome fruits as opposed to non-pome fruits.
2012-01-10 | GSE27090 | GEO
Project description:To evaluate the role of seeds in fruit quality, we induced parthenocarpy in tomato by regulating ovule-specific auxin synthesis or responsiveness using the INO promoter from A. thaliana, which is expressed in the outer layer of the integuments during early stages of ovule development. We compared these to fruit where the same coding regions were expressed from the DeFH9 promoter which is expressed in carpel tissues during early stages of ovule development. Expression of auxin synthesis or responsiveness genes by both of these promoters produced seedless parthenocarpic tomato fruit. We compared fruit samples using the Affymetrix tomato GeneChip (GPL4741) to determine how gene regulation and expression differed between wild-type and transgenic fruit. Keywords: genetic modification
2009-08-31 | GSE14358 | GEO
Project description:To evaluate the role of seeds in fruit quality, we induced parthenocarpy in tomato by regulating ovule-specific auxin synthesis or responsiveness using the INO promoter from A. thaliana, which is expressed in the outer layer of the integuments during early stages of ovule development. We compared these to fruit where the same coding regions were expressed from the DeFH9 promoter which is expressed in carpel tissues during early stages of ovule development. Expression of auxin synthesis or responsiveness genes by both of these promoters produced seedless parthenocarpic tomato fruit. We compared fruit samples using the Affymetrix tomato GeneChip (GPL4741) to determine how gene regulation and expression differed between wild-type and transgenic fruit. Experiment Overall Design: Wild-type fruit with seeds was compared with transgenic lines INO-IaaM, DefH9-IaaM, INO-RolB, and DefH9-RolB. To find genes with seed-specific expression, we also compared the control with wild-type fruit from which seeds had been manually removed. We had three biological replicates for each treatment and control except DefH9-RolB, for which only two replicates were available. Each CEL file from the microarray represents one plant from each line.
2009-09-15 | E-GEOD-14358 | biostudies-arrayexpress
Project description:Fruit length is a key domestication trait that affects crop yield and appearance quality. Cucumber fruits vary from 5~60 cm in length. Despite multiple fruit length QTLs have been identified, the underlying genes and regulatory mechanisms are poorly understood. Map-based cloning identified a nonsynonymous SNP (G to A) in CRABS CLAW (CsCRC) confers the major effect fruit length QTL FS5.2. CsCRCA is a rare allele only exist in Xishuangbanna cucumber with round fruits. Construction of near-isogenic line (NIL) of CsCRCA led to 34~39% reduction in fruit length. Introduction of CsCRCG into the NIL rescued the short-fruit phenotype, and knockdown of CsCRCG resulted in reduced fruit length and decreased cell size. RNA-seq results showed that an auxin responsive protein CsARP1 expressed decreased in CsCRC-RNAi lines. Further, an auxin responsive protein Further, CsARP1 is the downstream target gene of CsCRCG, instead of CsCRCA. Knockout of CsARP1 produced decreased fruit length with smaller cells. Hence, our work suggested that CsCRCG positively regulates fruit elongation through transcriptional activation of CsARP1 and thus enhanced cell expansion. Utilization of CsCRC alleles provides a new strategy to manipulate fruit length in cucumber breeding.
2022-03-18 | GSE169075 | GEO
Project description:Cucumber (Cucumis sativus L.) is one of the most important fruit vegetable crops and is widely grown worldwide (FAO STAT 2016, http://faostat3.fao.org). Astringency greatly affects the flavor quality of cucumber fruits and can be irritating due to the unpleasant oral sensation it causes. However, there are no available report addressing the molecular mechanisms driving the development of cucumber fruit astringency at the transcriptome level. A few relatively basic research efforts have been carried out in our previous studies. In this study, genome-wide analysis of gene expression in the highly astringent cucumber inbred line ‘YB’ was performed using RNA-seq. The aims of this research were to identify the genes responsible for fruit astringency development and to provide new insights into the mechanism underlying the synthesis of astringent compounds in cucumber fruits.
2018-12-01 | GSE112666 | GEO
Project description:Cucumber (Cucumis sativus L.) fruit is a type of fleshy fruit that is harvested immaturely. Early fruit development directly determines the final fruit length and diameter, and consequently the fruit yield and quality. Different cucumber varieties display huge variations of fruit length, but how fruit length is determined at the molecular level remains poorly understood. To understand the genes and gene networks that regulate fruit length in cucumber, high throughout RNA-seq data were used to compare the transcriptomes of early fruit from two near isogenic lines with different fruit lengths. 3955 genes were found to be differentially expressed, among which 2368 genes were significantly up-regulated and 1587 down-regulated in the line with long fruit. Microtubule and cell cycle related genes were dramatically activated in the long fruit, and transcription factors were implicated in the fruit length regulation in cucumber. Thus, our results built a foundation to dissect the molecular mechanism of fruit length control in cucumber, a key agricultural trait of significant economic importance. Comparative analysis of fruit from two near-isogenic lines, 408 (long fruit) and 409 (short fruit), was employed to discover genes and networks that regulate the fruit length. Two biological replicates were used from each line.
2015-08-11 | E-GEOD-60346 | biostudies-arrayexpress
Project description:Cucumber (Cucumis sativus L.) fruit is a type of fleshy fruit that is harvested immaturely. Early fruit development directly determines the final fruit length and diameter, and consequently the fruit yield and quality. Different cucumber varieties display huge variations of fruit length, but how fruit length is determined at the molecular level remains poorly understood. To understand the genes and gene networks that regulate fruit length in cucumber, high throughout RNA-seq data were used to compare the transcriptomes of early fruit from two near isogenic lines with different fruit lengths. 3955 genes were found to be differentially expressed, among which 2368 genes were significantly up-regulated and 1587 down-regulated in the line with long fruit. Microtubule and cell cycle related genes were dramatically activated in the long fruit, and transcription factors were implicated in the fruit length regulation in cucumber. Thus, our results built a foundation to dissect the molecular mechanism of fruit length control in cucumber, a key agricultural trait of significant economic importance.
2015-08-11 | GSE60346 | GEO
Project description:Trichomes are the hair-like structures that are widely present on the surface of aerial organs and function in plant defense against biotic and abiotic stresses. Previous studies focus on the single cell trichomes in Arabidopsis and cotton, or multicellular glandular trichomes in tomato, but the developmental process and molecular mechanisms controlling multicellular non-glandular trichome development are largely neglected. Here, we extensively characterized the fruit trichome (spine) development in wild type cucumber and in a tiny branched hair (tbh) mutant that contains a spontaneous mutation and has hairless foliage and smooth fruit surface. Our data indicated that cucumber trichome was multicellular and non-glandular, with no branches or endoreduplication. Further, the major feature of cucumber trichome development was spine base expansion. Transcriptome profiling through Digital Gene Expression indicated that meristem-related genes and transcription factors were implicated in the fruit spine development, and polarity regulators were upregulated during spine base expansion. qRT-PCR verified the reliability of our RNA-SEQ data, and in situ hybridization confirmed the enriched expression of meristem regulators CUP-SHAPED COTYLEDON3 (CUC3) and STM (SHOOT MERISTEMLESS) , as well as the abaxial identity gene KANADI (KAN) in cucumber fruit spine. Together, our results suggest a distinct regulatory pathway involving meristem genes and polarity regulators in multicellular trichome development in cucumber. Using Digital Gene Expression technology to compare the genome-wide gene expression profiles in the fruit spines of wild type cucumber and the tbh mutant, as well as the fruit spines on fruits of 0.5cm and 1.6cm long, repectively. Two biological repelicates were generated for each tissue.
2014-07-01 | E-GEOD-49607 | biostudies-arrayexpress