Identification of A Key Major-Effect QTL Associated With Pre-Harvest Sprouting in Cucumber (Cucumis Sativus L.) Using the QTL-Seq Method

Abstract Background: Cucumber (Cucumis sativusL.) is cultivated worldwide, and it is essential to produce enough high-quality seeds to meet demand. Pre-harvest sprouting (PHS) in cucumber is a critical problem and causes serious damage to seed production and quality. Nevertheless, the genetic basis and molecular mechanisms underlying cucumber PHS remain unclear. QTL-seq is an efficient approach for rapid quantitative trait loci (QTL) identificationthat simultaneously takes advantage of bulked-segregant analysis (BSA) and whole-genome resequencing. In the present research, QTL-seq analysis was performed to identify QTLs associated with PHS in cucumber using an F2 segregating population.Results: Two QTLs that spanned 7.3 Mb on Chromosome 4 and 0.15 Mb on Chromosome 5 were identified by QTL-seq and named qPHS4.1and qPHS5.1, respectively. Subsequently, SNP and InDel markers selected fromthe candidate regions were used to refine the intervals using the extended F2populations grown in the 2016 and 2017 seasons. Finally, qPHS4.1 was narrowed to 0.53 Mb on chromosome 4 flanked by the markers SNP-16 and SNP-24 and was found to explain 19-22% of the phenotypic variation in cucumber PHS. These results reveal that qPHS4.1 is the key major-effect QTL associated with PHS in cucumber. Based on gene annotations and qRT-PCR expression analyses, Csa4G622760and Csa4G622800 were proposed as the candidate genes. Conclusions: These results provide novel insights into the genetic mechanism controlling PHS in cucumber and highlight the potential for marker-assisted selection of PHS resistance breeding.

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Identification of a major-effect QTL associated with pre-harvest sprouting in cucumber (Cucumis sativus L.) using the QTL-seq method

BMC Genomics ◽

10.1186/s12864-021-07548-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Mingming Cao ◽

Shuju Li ◽

Qiang Deng ◽

Huizhe Wang ◽

Ruihuan Yang

Keyword(s):

Cucumis Sativus ◽

Molecular Mechanisms ◽

Bulked Segregant Analysis ◽

Resistance Breeding ◽

Major Effect ◽

Chromosome 4 ◽

Cucumis Sativus L ◽

Whole Genome Resequencing ◽

Candidate Regions ◽

Segregating Population

Abstract Background Cucumber (Cucumis sativus L.) is cultivated worldwide, and it is essential to produce enough high-quality seeds to meet demand. Pre-harvest sprouting (PHS) in cucumber is a critical problem and causes serious damage to seed production and quality. Nevertheless, the genetic basis and molecular mechanisms underlying cucumber PHS remain unclear. QTL-seq is an efficient approach for rapid quantitative trait loci (QTL) identification that simultaneously takes advantage of bulked-segregant analysis (BSA) and whole-genome resequencing. In the present research, QTL-seq analysis was performed to identify QTLs associated with PHS in cucumber using an F2 segregating population. Results Two QTLs that spanned 7.3 Mb on Chromosome 4 and 0.15 Mb on Chromosome 5 were identified by QTL-seq and named qPHS4.1 and qPHS5.1, respectively. Subsequently, SNP and InDel markers selected from the candidate regions were used to refine the intervals using the extended F2 populations grown in the 2016 and 2017 seasons. Finally, qPHS4.1 was narrowed to 0.53 Mb on chromosome 4 flanked by the markers SNP-16 and SNP-24 and was found to explain 19–22% of the phenotypic variation in cucumber PHS. These results reveal that qPHS4.1 is a major-effect QTL associated with PHS in cucumber. Based on gene annotations and qRT-PCR expression analyses, Csa4G622760 and Csa4G622800 were proposed as the candidate genes. Conclusions These results provide novel insights into the genetic mechanism controlling PHS in cucumber and highlight the potential for marker-assisted selection of PHS resistance breeding.

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Genome-wide analysis of valine-glutamine motif-containing proteins related to abiotic stress response in cucumber (Cucumis sativus L.)

BMC Plant Biology ◽

10.1186/s12870-021-03242-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Nan Shan ◽

Zijin Xiang ◽

Jingyu Sun ◽

Qianglong Zhu ◽

Yao Xiao ◽

...

Keyword(s):

Cucumis Sativus ◽

Genetic Basis ◽

Resistance Breeding ◽

Abiotic Stress Response ◽

Phylogenetic Tree Analysis ◽

Cucumis Sativus L ◽

Genome Wide Analysis ◽

Genome Wide ◽

Specific Proteins ◽

Spatio Temporal

Abstract Background Cucumber (Cucumis sativus L.) is one of the most important economic crops and is susceptible to various abiotic stresses. The valine-glutamine (VQ) motif-containing proteins are plant-specific proteins with a conserved “FxxhVQxhTG” amino acid sequence that regulates plant growth and development. However, little is known about the function of VQ proteins in cucumber. Results In this study, a total of 32 CsVQ proteins from cucumber were confirmed and characterized using comprehensive genome-wide analysis, and they all contain a conserved motif with 10 variations. Phylogenetic tree analysis revealed that these CsVQ proteins were classified into nine groups by comparing the CsVQ proteins with those of Arabidopsis thaliana, melon and rice. CsVQ genes were distributed on seven chromosomes. Most of these genes were predicted to be localized in the nucleus. In addition, cis-elements in response to different stresses and hormones were observed in the promoters of the CsVQ genes. A network of CsVQ proteins interacting with WRKY transcription factors (CsWRKYs) was proposed. Moreover, the transcripts of CsVQ gene were spatio-temporal specific and were induced by abiotic adversities. CsVQ4, CsVQ6, CsVQ16–2, CsVQ19, CsVQ24, CsVQ30, CsVQ32, CsVQ33, and CsVQ34 were expressed in the range of organs and tissues at higher levels and could respond to multiple hormones and different stresses, indicating that these genes were involved in the response to stimuli. Conclusions Together, our results reveal novel VQ resistance gene resources, and provide critical information on CsVQ genes and their encoded proteins, which supplies important genetic basis for VQ resistance breeding of cucumber plants.

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Physiological and Molecular Investigation of Urea Uptake Dynamics in Cucumis sativus L. Plants Fertilized With Urea-Doped Amorphous Calcium Phosphate Nanoparticles

Frontiers in Plant Science ◽

10.3389/fpls.2021.745581 ◽

2021 ◽

Vol 12 ◽

Author(s):

Sebastian B. Feil ◽

Giacomo Rodegher ◽

Federica Gaiotti ◽

Monica Yorlady Alzate Zuluaga ◽

Francisco J. Carmona ◽

...

Keyword(s):

Calcium Phosphate ◽

Cucumis Sativus ◽

Amorphous Calcium Phosphate ◽

Molecular Mechanisms ◽

Growth Parameters ◽

Growth And Yield ◽

Uptake System ◽

Cucumis Sativus L ◽

Urea Uptake ◽

Calcium Phosphate Nanoparticles

At present, the quest for innovative and sustainable fertilization approaches aiming to improve agricultural productivity represents one of the major challenges for research. In this context, nanoparticle-based fertilizers can indeed offer an interesting alternative with respect to traditional bulk fertilizers. Several pieces of evidence have already addressed the effectiveness of amorphous calcium phosphate-based nanoparticles as carriers for macronutrients, such as nitrogen (N), demonstrating increase in crop productivity and improvement in quality. Nevertheless, despite N being a fundamental nutrient for crop growth and productivity, very little research has been carried out to understand the physiological and molecular mechanisms underpinning N-based fertilizers supplied to plants via nanocarriers. For these reasons, this study aimed to investigate the responses of Cucumis sativus L. to amorphous calcium phosphate nanoparticles doped with urea (U-ACP). Urea uptake dynamics at root level have been investigated by monitoring both the urea acquisition rates and the modulation of urea transporter CsDUR3, whereas growth parameters, the accumulation of N in both root and shoots, and the general ionomic profile of both tissues have been determined to assess the potentiality of U-ACP as innovative fertilizers. The slow release of urea from nanoparticles and/or their chemical composition contributed to the upregulation of the urea uptake system for a longer period (up to 24 h after treatment) as compared to plants treated with bulk urea. This prolonged activation was mirrored by a higher accumulation of N in nanoparticle-treated plants (approximately threefold increase in the shoot of NP-treated plants compared to controls), even when the concentration of urea conveyed through nanoparticles was halved. In addition, besides impacting N nutrition, U-ACP also enhanced Ca and P concentration in cucumber tissues, thus having possible effects on plant growth and yield, and on the nutritional value of agricultural products.

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Genetic and Transcriptomic Analysis Reveal the Molecular Basis of Photoperiod-Regulated Flowering in Xishuangbanna Cucumber (Cucumis sativus L. var. xishuangbannesis Qi et Yuan)

Genes ◽

10.3390/genes12071064 ◽

2021 ◽

Vol 12 (7) ◽

pp. 1064

Author(s):

Zhen Tian ◽

Molly Jahn ◽

Xiaodong Qin ◽

Hesbon Ochieng Obel ◽

Fan Yang ◽

...

Keyword(s):

Cucumis Sativus ◽

Molecular Basis ◽

Agronomic Traits ◽

Major Effect ◽

Transcriptomic Analysis ◽

Sequencing Data ◽

Cucumis Sativus L ◽

Carbohydrate Storage ◽

Photoperiodic Flowering ◽

Photoperiod Sensitive

Xishuangbanna (XIS) cucumber (Cucumis sativus L. var. xishuangbannesis Qi et Yuan), is a botanical variety of cucumber cultivars native to southwest China that possesses excellent agronomic traits for cucumber improvement. However, breeding utilization of XIS cucumber is limited due to the current poor understanding of its photoperiod-sensitive flowering characteristics. In this study, genetic and transcriptomic analysis were conducted to reveal the molecular basis of photoperiod-regulated flowering in XIS cucumber. A major-effect QTL locus DFF1.1 was identified that controls the days to first flowering (DFF) of XIS cucumbers with a span of 1.38 Mb. Whole-genome re-sequencing data of 9 cucumber varieties with different flowering characteristics in response to photoperiod suggested that CsaNFYA1 was the candidate gene of DFF1.1, which harbored a single non-synonymous mutation in its fifth exon. Transcriptomic analysis revealed the positive roles of auxin and ethylene in accelerating flowering under short-day (SD) light-dark cycles when compared with equal-day/night treatment. Carbohydrate storage and high expression levels of related genes were important reasons explaining early flowering of XIS cucumber under SD conditions. By combining with the RNA-Seq data, the co-expression network suggested that CsaNFYA1 integrated multiple types of genes to regulate the flowering of XIS cucumber. Our findings explain the internal regulatory mechanisms of a photoperiodic flowering pathway. These findings may guide the use of photoperiod shifts to promote flowering of photoperiod-sensitive crops.

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Overexpression of an APETALA1-like gene from cucumber (Cucumis sativus L.) induces earlier flowering and abnormal leaf development in transgenic Arabidopsis

Canadian Journal of Plant Science ◽

10.1139/cjps-2018-0107 ◽

2019 ◽

Vol 99 (2) ◽

pp. 210-220 ◽

Cited By ~ 1

Author(s):

Yong Zhou ◽

Lifang Hu ◽

Shuifeng Ye ◽

Lunwei Jiang ◽

Shiqiang Liu

Keyword(s):

Cucumis Sativus ◽

Plant Development ◽

Flower Development ◽

Leaf Development ◽

Molecular Mechanisms ◽

Transgenic Arabidopsis ◽

Functional Characterization ◽

Ectopic Expression ◽

Mads Box ◽

Cucumis Sativus L

MADS-box proteins are important transcription factors that play essential roles in various aspects of plant development, particularly in flower development. In this study, we performed the identification and functional characterization of CsMADS09 isolated from cucumber (Cucumis sativus L.). CsMADS09 contains a 648-bp open reading frame encoding 215 amino acid residues, and shares high sequence identities with the members of the AP1/FUL family of MADS-box proteins, especially the euAPETALA1 (euAP1) subclade. Many cis-elements related to plant development, stress response, and hormones were identified in the promoter region of CsMADS09. Quantitative real-time polymerase chain reaction results showed that CsMADS09 was mainly expressed in reproductive tissues such as male flowers and unexpanded ovaries, while its expression was low in roots and only traceable in fertilized ovaries. Moreover, the results revealed that CsMADS09 expression tended to decline during male flower development and stayed nearly constant during female flower development. Ectopic expression of CsMADS09 resulted in earlier flowering and abnormal leaf development in transgenic Arabidopsis. This study is the first functional analysis of an AP1-like gene from cucumber and provides some clues for revealing the molecular mechanisms of flower development in cucumber.

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