Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Variation in CRABS CLAW (CsCRC) contributes to fruit length modulation in cucumber

ABSTRACT: 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.

ORGANISM(S): Cucumis sativus

PROVIDER: GSE169075 | GEO | 2022/03/18

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

A Functional Allele of CsFUL1 Regulates Fruit Length through Repressing CsSUP and Inhibiting Auxin Transport in Cucumber

Project description:Cucumber (Cucumis sativus L.) is an important vegetable crop bearing fleshy pepo fruits that harvested immature. The fruit length is one of the most important agricultural traits that directly determine the fruit yield and affects fruit quality, but the regulatory mechanism of fruit length variation remains elusive. Here we found a FRUITFULL-like MADS-box gene CsFUL1 functions as a key repressor for fruit length regulation in cucumber. The expression of CsFUL1 is highly enriched in male flowers and fruits, and negatively correlated with fruit length in different cucumber lines. Notably, a key SNP in CsFUL1 was selected during cucumber domestication for long fruit. Ectopic expression of CsFUL1 was unable to rescue the indehiscent fruit phenotype of ful-1 in Arabidopsis. Overexpression of CsFUL1 resulted in increased floral organs and reduced fruit length, whereas knockdown of CsFUL1 led to elongated fruit in cucumber. Transcriptome and biochemical analyses showed that CsFUL1 regulates fruit length through two pathways: one by inhibiting the PIN-FORWED (PIN1/7)-mediated auxin transport and thus downregulates auxin related genes in the fruit, and the other by forming a tetramer with other MADS-box genes to repress the CsSUP-mediated cell division and cell expansion. In addition, we found that CsFUL1 promotes locule number variation through the classical CsWUS-CsCLV pathway. Our findings uncover the regulatory commonality and specificity during development of different fruit types, and provide an important candidate gene to customize fruit length during cucumber breeding.

2020-03-28 | GSE103592 | GEO

Variation in CRABS CLAW (CsCRC) contributes to fruit length modulation in cucumber

Project description:Variation in CRABS CLAW (CsCRC) contributes to fruit length modulation in cucumber

| PRJNA715168 | ENA

Transcriptome Profiling of bending fruit and Functional Analysis of an ERF/AP2 Family Gene CsERF025 Involved in bending fruit development in cucumber (Cucumis sativus L.)

Project description:To identify the differentially expressed genes(DEGs) in the ventral and dorsal of cucumber bending fruits，cucumber bending fruit mRNA profiles of 2-day-old ventral and dorsal were generated by deep sequencing. After removing the low quality reads, the total number of clean reads in two library were 27.07 million and16.52 million, accounted for 85.21% and 80.71% of total reads .We identified a total of 4313 sequences differentially expressed in ventral and dorsal of bending fruit with a 2-fold or greater change and P < 0.01 , the Dorsal (D2) served as a control, in which 2351 up-regulated genes and 1962 down-regulated genes.For up-regulated genes, protein kinase activity, ethylene mediated signaling pathway, regulation of cell shape, auxin polar transport were significantly enriched, whereas down-regulated genes, the functional classes photosynthesis, oxidation reduction, response to auxin stimulus were significantly enriched. Moreover, among DEGs related to ethylene, we identified an ERF/AP2 gene CsERF025 that was significant difference in the dorsal and ventral of cucumber. up-regulation of CsERF025 in cucumber promoted fruit bendng and Increased the fruit bending angle, suggesting that CsERF025 plays an important role in cucumber bending fruit.

2019-12-07 | GSE91085 | GEO

Comparative transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus)

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

Comparative transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus)

2015-08-11 | E-GEOD-60346 | biostudies-arrayexpress

Identification of candidate genes related to astringency in cucumber via RNA-seq based transcriptome profiling

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

CsFUL1 and auxin participate in the CsCLV3-CsWUS mediated carpel number variation in cucumber (Cucumis sativus L.)

Project description:The carpel number (CN) is an important fruit trait affecting fruit shape, size, and internal quality in cucumber. CsCLAVATA3 (CsCLV3) was previously showed to be the simply inherited gene responsible for carpel number variation in cucumber, but the molecular mechanism of CsCLV3 regulating carpel number remains elusive. Here, we found that the expression of CsCLV3 was negatively correlated with carpel number variation in different cucumber lines. Knock down of CsCLV3 by RNAi led to increased number of petals and carpels, suggesting that CsCLV3 functions as a negative regulator for floral organ number in cucumber. WUSCHEL (WUS) has been well characterized to promote CLV3-expressing stem cell activity in a non-cell autonomous manner to regulate meristem maintenance and floral organ number. However, here we found the expression region of CsCLV3 overlaps with CsWUS in the basal domain of meristem, and CsCLV3 interact with CsWUS at the protein level through binding to the WUS-box motif. Overexpression of CsFUL1, a FRUITFULL-like MADS-box gene involved in fruit length regulation, resulted in increased number of floral organs in cucumber. Biochemical analyses indicated that CsFUL1 can directly bind to CsWUS promoter to stimulate its expression. Further, we found that auxin participates in carpel number variation in cucumber through physical interaction of AUXIN RESPONSE FACTOR 14 (CsARF14) and CsWUS. Therefore, CsFUL1 and CsARF14 are two new players in the WUS-CLV pathway in determining carpel number variation in cucumber.

2020-03-26 | GSE125899 | GEO

Gene expression analysis of the inflorescence of knu-1 and crc-1 knu-1

Project description:Analyis gene expression in crc-1 knu-1 compared with knu-1 Initiation of the carpel primordia is marked by the termination of floral stem cells. Although genetic evidences have suggested that the YABBY gene CRABS CLAW (CRC) regulates the development of carpel, as well as the floral meristem determinacy as a target of the homeotic protein AGAMOUS, the underlying mechanism remains unclear. Here we show that the tetraspanin-encoding gene TONADO2 (TRN2) and the auxin biosynthesis gene YUCCA4 (YUC4) act as downstream targets of CRC.

2017-09-30 | GSE88969 | GEO

Transcriptome profiling reveals roles of meristem regulators and polarity genes during multicellular fruit trichome development in cucumber (Cucumis sativus L.).

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

Transcription profiling of Capsicum fruit ripening process

Project description:Pepper fruits at four different developmental stages were collected: early fruit [EF; 1 cm long; 7 days after pollination (dap)], mature green fruit (MG; 6-7 cm length; 20 dap), breaking or turning red fruit (BR; fruit are partially red; 35 dap), and red ripe fruit (RR; fully red; 40 dap). Tomato fruits at corresponding developmental stages were also collected: EF (less than 1cm; 7 dap), MG (40 dap), BR (50 dap), and RR (55 dap). For the monitoring of fruit-specific and fruit ripening-related genes, we did array hybridization by using the leaves as a common reference and each corresponding fruit developmental stage sample.

2005-03-01 | E-MEXP-260 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data