Comparative transcript profiling of gene expression between self-incompatible and self-compatible mandarins by suppression subtractive hybridization and cDNA microarray

Miao, Hongxia; Ye, Zixing; Qin, Yonghua

doi:10.1007/s11032-015-0204-x

Cited by 12 publications

(14 citation statements)

References 45 publications

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“…Subtractive suppressive hybridization (SSH) remains to be an effective way to identify specific differentially-expressed genes or transcript accumulation for comparisons between different genotypes or environmental conditions, despite recent advances and availability of next-generation gene sequencing technologies [11–13]. SSH evaluation followed by sequence analysis has identified genes that play a role in conferring drought tolerance in a number of crop species such as cotton ( Gossypium arboretum ) [14], soybean ( Glycine max ) [15], and corn ( Zea mays ) [16].…”

Section: Introductionmentioning

confidence: 99%

Differentially Expressed Genes Associated with Improved Drought Tolerance in Creeping Bentgrass Overexpressing a Gene for Cytokinin Biosynthesis

Merewitz

Huang

2016

PLoS ONE

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Transformation with an isopentenyl transferase (ipt) gene controlling cytokinin (CK) synthesis has been shown to enhance plant drought tolerance. The objective of this study was to identify differentially-expressed genes (DEGs) in creeping bentgrass (Agrostis stolonifera) overexpressing ipt compared to non-transgenic plants. The ipt transgene was controlled by a senescence-activated promoter (SAG12). Both a null transformed line (NT) and SAG12-ipt plants were exposed to drought stress in an environmentally-controlled growth chamber until the soil water content declined to approximately 5% and leaf relative water content declined to 47%, which were both significantly below the well-watered controls. RNA was extracted from leaf samples of both well-watered and drought-stressed plants. Eight sets of subtractive hybridizations were performed for detection of up-regulated and down-regulated genes due to the presence of the transgene and due to drought stress in both NT and transgenic plants. Sequencing analysis revealed the identity of 252 DEGs due to either the transgene and drought stress. Sequencing analysis of 170 DEGs identified genes encoding for proteins that were related to energy production, metabolism, stress defense, signaling, protein synthesis and transport, and membrane transport could play major roles in the improved drought tolerance by overexpressing ipt in creeping bentgrass.

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Section: Introductionmentioning

confidence: 99%

Differentially Expressed Genes Associated with Improved Drought Tolerance in Creeping Bentgrass Overexpressing a Gene for Cytokinin Biosynthesis

Merewitz

Huang

2016

PLoS ONE

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“…Controls were also printed on glass slides using a SmartArray microarrayer (CapitalBio Corp.). The resulting images were analyzed with LuxScanTM3.0 software (CapitalBio Corp.) and identified using the methods of Miao et al [ 30 ]. DEGs were identified using a P value <0.05, false discovery rate (FDR) <0.05, and a fold change ≥2.0.…”

Section: Methodsmentioning

confidence: 99%

A Novel Role for Banana MaASR in the Regulation of Flowering Time in Transgenic Arabidopsis

Sun

Miao

et al. 2016

PLoS ONE

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The abscisic acid (ABA)-, stress-, and ripening-induced (ASR) protein is a plant-specific hydrophilic transcriptional factor involved in fruit ripening and the abiotic stress response. To date, there have been no studies on the role of ASR genes in delayed flowering time. Here, we found that the ASR from banana, designated as MaASR, was preferentially expressed in the banana female flowers from the eighth, fourth, and first cluster of the inflorescence. MaASR transgenic lines (L14 and L38) had a clear delayed-flowering phenotype. The number of rosette leaves, sepals, and pedicel trichomes in L14 and L38 was greater than in the wild type (WT) under long day (LD) conditions. The period of buds, mid-flowers, and full bloom of L14 and L38 appeared later than the WT. cDNA microarray and quantitative real-time PCR (qRT-PCR) analyses revealed that overexpression of MaASR delays flowering through reduced expression of several genes, including photoperiod pathway genes, vernalization pathway genes, gibberellic acid pathway genes, and floral integrator genes, under short days (SD) for 28 d (from vegetative to reproductive transition stage); however, the expression of the autonomous pathway genes was not affected. This study provides the first evidence of a role for ASR genes in delayed flowering time in plants.

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“…S5B). However, CrSKP1-e was different from CrWSKP1 obtained from the suppression subtractive hybridization (SSH) library of 'Wuzishatangju' (Miao et al, 2015). The CrSKP1-e protein consisted of β1 and β2 sheets in the N-terminus, which connects the F-box domain and the seven helices (α1-α7) binding the CUL1 protein in the C-terminus (Fig.…”

Section: Cloning and Phylogenetic Analyses Of Crskp1-ementioning

confidence: 99%

“…In Citrus , an SKP1-like gene involved in flower development of pummelo ( C. grandis ), CgSKP1 , was identified from ‘Shatian’ cultivar and it was highly expressed in leaf and flower ( Chai et al, 2010 ). In our previous work, we isolated full-length cDNA and DNA sequences of CrWSKP1 from ‘Wuzishatangju’ ( Miao et al, 2015 ). However, we did not clarify whether these genes are involved in SI response of Citrus .…”

Section: Introductionmentioning

confidence: 99%

SKP1-like protein, CrSKP1-e, interacts with pollen-specific F-box proteins and assembles into SCF-type E3 complex in ‘Wuzishatangju’ (Citrus reticulata Blanco) pollen

Ren

Hua

Pan

et al. 2020

PeerJ

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S-ribonuclease (S-RNase)-based self-incompatibility (SI) mechanisms have been extensively studied in Solanaceae, Rosaceae and Plantaginaceae. S-RNase-based SI is controlled by two closely related genes, S-RNase and S-locus F-box (SLF), located at a polymorphic S-locus. In the SI system, the SCF-type (SKP1-CUL1-F-box-RBX1) complex functions as an E3 ubiquitin ligase complex for ubiquitination of non-self S-RNase. Pummelo (Citrus grandis) and several mandarin cultivars are suggested to utilize an S-RNase-based SI system. However, the molecular mechanism of the non-S-factors involved in the SI reaction is not straightforward in Citrus. To investigate the SCF-type E3 complex responsible for the SI reaction in mandarin, SLF, SKP1-like and CUL1 candidates potentially involved in the SI reaction of ‘Wuzishatangju’ (Citrus reticulata Blanco) were identified based on the genome-wide identification and expression analyses. Sixteen pollen-specific F-box genes (CrFBX1-CrFBX16), one pollen-specific SKP1-like gene (CrSKP1-e) and two CUL1 genes (CrCUL1A and CrCUL1B) were identified and cloned from ‘Wuzishatangju’. Yeast two-hybrid (Y2H) and in vitro binding assays showed that five CrFBX proteins could bind to CrSKP1-e, which is an ortholog of SSK1 (SLF-interacting-SKP1-like), a non-S-factor responsible for the SI reaction. Luciferase complementation imaging (LCI) and in vitro binding assays also showed that CrSKP1-e interacts with the N-terminal region of both CrCUL1A and CrCUL1B. These results indicate that CrSKP1-e may serve as a functional member of the SCF-type E3 ubiquitin ligase complex in ‘Wuzishatangju’.

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Comparative transcript profiling of gene expression between self-incompatible and self-compatible mandarins by suppression subtractive hybridization and cDNA microarray

Cited by 12 publications

References 45 publications

Differentially Expressed Genes Associated with Improved Drought Tolerance in Creeping Bentgrass Overexpressing a Gene for Cytokinin Biosynthesis

Differentially Expressed Genes Associated with Improved Drought Tolerance in Creeping Bentgrass Overexpressing a Gene for Cytokinin Biosynthesis

A Novel Role for Banana MaASR in the Regulation of Flowering Time in Transgenic Arabidopsis

SKP1-like protein, CrSKP1-e, interacts with pollen-specific F-box proteins and assembles into SCF-type E3 complex in ‘Wuzishatangju’ (Citrus reticulata Blanco) pollen

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