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Genome-wide analysis of spatiotemporal gene expression patterns during floral organ development in Brassica rapa. Mol Genet Genomics 2019; 294:1403-1420. [PMID: 31222475 DOI: 10.1007/s00438-019-01585-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/10/2019] [Indexed: 12/12/2022]
Abstract
Flowering is a key agronomic trait that directly influences crop yield and quality and serves as a model system for elucidating the molecular basis that controls successful reproduction, adaptation, and diversification of flowering plants. Adequate knowledge of continuous series of expression data from the floral transition to maturation is lacking in Brassica rapa. To unravel the genome expression associated with the development of early small floral buds (< 2 mm; FB2), early large floral buds (2-4 mm; FB4), stamens (STs) and carpels (CPs), transcriptome profiling was carried out with a Br300K oligo microarray. The results showed that at least 6848 known nonredundant genes (30% of the genes of the Br300K) were differentially expressed during the floral transition from vegetative tissues to maturation. Functional annotation of the differentially expressed genes (DEGs) (fold change ≥ 5) by comparison with a close relative, Arabidopsis thaliana, revealed 6552 unigenes (4579 upregulated; 1973 downregulated), including 131 Brassica-specific and 116 functionally known floral Arabidopsis homologs. Additionally, 1723, 236 and 232 DEGs were preferentially expressed in the tissues of STs, FB2, and CPs. These DEGs also included 43 transcription factors, mainly AP2/ERF-ERF, NAC, MADS-MIKC, C2H2, bHLH, and WRKY members. The differential gene expression during flower development induced dramatic changes in activities related to metabolic processes (23.7%), cellular (22.7%) processes, responses to the stimuli (7.5%) and reproduction (1%). A relatively large number of DEGs were observed in STs and were overrepresented by photosynthesis-related activities. Subsequent analysis via semiquantitative RT-PCR, histological analysis performed with in situ hybridization of BrLTP1 and transgenic reporter lines (BrLTP promoter::GUS) of B. rapa ssp. pekinensis supported the spatiotemporal expression patterns. Together, these results suggest that a temporally and spatially regulated process of the selective expression of distinct fractions of the same genome leads to the development of floral organs. Interestingly, most of the differentially expressed floral transcripts were located on chromosomes 3 and 9. This study generated a genome expression atlas of the early floral transition to maturation that represented the flowering regulatory elements of Brassica rapa.
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Transcriptomic analysis of contrasting inbred lines and F 2 segregant of Chinese cabbage provides valuable information on leaf morphology. Genes Genomics 2019; 41:811-829. [PMID: 30900192 DOI: 10.1007/s13258-019-00809-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/07/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Leaf morphology influences plant growth and productivity and is controlled by genetic and environmental cues. The various morphotypes of Brassica rapa provide an excellent resource for genetic and molecular studies of morphological traits. OBJECTIVE This study aimed to identify genes regulating leaf morphology using segregating B. rapa p F2 population. METHODS Phenotyping and transcriptomic analyses were performed on an F2 population derived from a cross between Rapid cycling B. rapa (RCBr) and B. rapa ssp. penkinensis, inbred line Kenshin. Analyses focused on four target traits: lamina (leaf) length (LL), lamina width (LW), petiole length (PL), and leaf margin (LM). RESULTS All four traits were controlled by multiple QTLs, and expression of 466 and 602 genes showed positive and negative correlation with leaf phenotypes, respectively. From this microarray analysis, large numbers of genes were putatively identified as leaf morphology-related genes. The Gene Ontology (GO) category containing the highest number of differentially expressed genes (DEGs) was "phytohormones". The sets of genes enriched in the four leaf phenotypes did not overlap, indicating that each phenotype was regulated by a different set of genes. The expression of BrAS2, BrAN3, BrCYCB1;2, BrCYCB2;1,4, BrCYCB3;1, CrCYCBD3;2, BrULT1, and BrANT seemed to be related to leaf size traits (LL and LW), whereas BrCUC1, BrCUC2, and BrCUC3 expression for LM trait. CONCLUSION An analysis integrating the results of the current study with previously published data revealed that Kenshin alleles largely determined LL and LW but LM resulted from RCBr alleles. Genes identified in this study could be used to develop molecular markers for use in Brassica breeding projects and for the dissection of gene function.
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Genome-Wide Identification and Characterization of Warming-Related Genes in Brassica rapa ssp. pekinensis. Int J Mol Sci 2018; 19:ijms19061727. [PMID: 29891774 PMCID: PMC6032310 DOI: 10.3390/ijms19061727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 05/29/2018] [Accepted: 06/06/2018] [Indexed: 12/14/2022] Open
Abstract
For sustainable crop cultivation in the face of global warming, it is important to unravel the genetic mechanisms underlying plant adaptation to a warming climate and apply this information to breeding. Thermomorphogenesis and ambient temperature signaling pathways have been well studied in model plants, but little information is available for vegetable crops. Here, we investigated genes responsive to warming conditions from two Brassica rapa inbred lines with different geographic origins: subtropical (Kenshin) and temperate (Chiifu). Genes in Gene Ontology categories “response to heat”, “heat acclimation”, “response to light intensity”, “response to oxidative stress”, and “response to temperature stimulus” were upregulated under warming treatment in both lines, but genes involved in “response to auxin stimulus” were upregulated only in Kenshin under both warming and minor-warming conditions. We identified 16 putative high temperature (HT) adaptation-related genes, including 10 heat-shock response genes, 2 transcription factor genes, 1 splicing factor gene, and 3 others. BrPIF4, BrROF2, and BrMPSR1 are candidate genes that might function in HT adaptation. Auxin response, alternative splicing of BrHSFA2, and heat shock memory appear to be indispensable for HT adaptation in B. rapa. These results lay the foundation for molecular breeding and marker development to improve warming tolerance in B. rapa.
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Zuther E, Lee YP, Erban A, Kopka J, Hincha DK. Natural Variation in Freezing Tolerance and Cold Acclimation Response in Arabidopsis thaliana and Related Species. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1081:81-98. [DOI: 10.1007/978-981-13-1244-1_5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Kayum MA, Park JI, Nath UK, Saha G, Biswas MK, Kim HT, Nou IS. Genome-wide characterization and expression profiling of PDI family gene reveals function as abiotic and biotic stress tolerance in Chinese cabbage (Brassica rapa ssp. pekinensis). BMC Genomics 2017; 18:885. [PMID: 29145809 PMCID: PMC5691835 DOI: 10.1186/s12864-017-4277-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 11/03/2017] [Indexed: 11/10/2022] Open
Abstract
Background Protein disulfide isomerase (PDI) and PDI-like proteins contain thioredoxin domains that catalyze protein disulfide bond, inhibit aggregation of misfolded proteins, and function in isomerization during protein folding in endoplasmic reticulum and responses during abiotic stresses.Chinese cabbage is widely recognized as an economically important, nutritious vegetable, but its yield is severely hampered by various biotic and abiotic stresses. Because of, it is prime need to identify those genes whose are responsible for biotic and abiotic stress tolerance. PDI family genes are among of them. Results We have identified 32 PDI genes from the Br135K microarray dataset, NCBI and BRAD database, and in silico characterized their sequences. Expression profiling of those genes was performed using cDNA of plant samples imposed to abiotic stresses; cold, salt, drought and ABA (Abscisic Acid) and biotic stress; Fusarium oxysporum f. sp. conglutinans infection. The Chinese cabbage PDI genes were clustered in eleven groups in phylogeny. Among them, 15 PDI genes were ubiquitously expressed in various organs, while 24 PDI genes were up-regulated under salt and drought stress. By contrast, cold and ABA stress responsive gene number were ten and nine, respectively. In case of F. oxysporum f. sp. conglutinans infection 14 BrPDI genes were highly up-regulated. Interestingly, BrPDI1–1 gene was identified as putative candidate against abiotic (salt and drought) and biotic stresses, BrPDI5–2 gene for ABA stress, and BrPDI1–4, 6–1 and 9–2 were putative candidate genes for both cold and chilling injury stresses. Conclusions Our findings help to elucidate the involvement of PDI genes in stress responses, and they lay the foundation for functional genomics in future studies and molecular breeding of Brassica rapa crops. The stress-responsive PDI genes could be potential resources for molecular breeding of Brassica crops resistant to biotic and abiotic stresses. Electronic supplementary material The online version of this article (10.1186/s12864-017-4277-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Md Abdul Kayum
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea
| | - Gopal Saha
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea
| | - Manosh Kumar Biswas
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea
| | - Hoy-Taek Kim
- University-Industry Cooperation Foundation, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.
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Jung HJ, Kayum MA, Thamilarasan SK, Nath UK, Park JI, Chung MY, Hur Y, Nou IS. Molecular characterisation and expression profiling of calcineurin B-like (CBL) genes in Chinese cabbage under abiotic stresses. FUNCTIONAL PLANT BIOLOGY : FPB 2017; 44:739-750. [PMID: 32480603 DOI: 10.1071/fp16437] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/28/2017] [Indexed: 06/11/2023]
Abstract
Calcium signals act as a second messenger in plant responses to various abiotic stresses, which regulate a range of physiological processes. Calcium-binding proteins, like calcineurin B-like (CBL) proteins, belong to a unique group of calcium sensors that play a role in calcium signalling. However, their identities and functions are unknown in Chinese cabbage. In this study, 17 CBL genes were identified from the Brassica rapa L. (Chinese cabbage) database and Br135K microarray datasets. They were used to construct a phylogenetic tree with known CBL proteins of other species. Analysis of genomic distribution and evolution revealed different gene duplication in Chinese cabbage compared to Arabidopsis. The microarray expression analysis showed differential expression of BrCBL genes at various temperatures. Organ-specific expression was observed by RT-PCR, and qRT-PCR analyses revealed responsiveness of BrCBL genes to cold, drought and salt stresses. Our findings confirm that CBL genes are involved in calcium signalling and regulate responses to environmental stimuli, suggesting this family gene have crucial role to play in plant responses to abiotic stresses. The results facilitate selection of candidate genes for further functional characterisation. In addition, abiotic stress-responsive genes reported in this study might be exploited for marker-aided backcrossing of Chinese cabbage.
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Affiliation(s)
- Hee-Jeong Jung
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, South Korea
| | - Md Abdul Kayum
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, South Korea
| | - Senthil Kumar Thamilarasan
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, South Korea
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, South Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, South Korea
| | - Mi-Young Chung
- Department of Agricultural Education, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, South Korea
| | - Yoonkang Hur
- Department of Biology, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922, South Korea
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Kayum MA, Park JI, Nath UK, Biswas MK, Kim HT, Nou IS. Genome-wide expression profiling of aquaporin genes confer responses to abiotic and biotic stresses in Brassica rapa. BMC PLANT BIOLOGY 2017; 17:23. [PMID: 28122509 PMCID: PMC5264328 DOI: 10.1186/s12870-017-0979-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/17/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Plants contain a range of aquaporin (AQP) proteins, which act as transporter of water and nutrient molecules through living membranes. AQPs also participate in water uptake through the roots and contribute to water homeostasis in leaves. RESULTS In this study, we identified 59 AQP genes in the B. rapa database and Br135K microarray dataset. Phylogenetic analysis revealed four distinct subfamilies of AQP genes: plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), NOD26-like intrinsic proteins (NIPs) and small basic intrinsic proteins (SIPs). Microarray analysis showed that the majority of PIP subfamily genes had differential transcript abundance between two B. rapa inbred lines Chiifu and Kenshin that differ in their susceptibility to cold. In addition, all BrPIP genes showed organ-specific expression. Out of 22 genes, 12, 7 and 17 were up-regulated in response to cold, drought and salt stresses, respectively. In addition, 18 BrPIP genes were up-regulated under ABA treatment and 4 BrPIP genes were up-regulated upon F. oxysporum f. sp. conglutinans infection. Moreover, all BrPIP genes showed down-regulation under waterlogging stress, reflecting likely the inactivation of AQPs controlling symplastic water movement. CONCLUSIONS This study provides a comprehensive analysis of AQPs in B. rapa and details the expression of 22 members of the BrPIP subfamily. These results provide insight into stress-related biological functions of each PIP gene of the AQP family, which will promote B. rapa breeding programs.
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Affiliation(s)
- Md. Abdul Kayum
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Manosh Kumar Biswas
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Hoy-Taek Kim
- University-Industry Cooperation Foundation, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 57922 South Korea
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Glutathione Transferases Superfamily: Cold-Inducible Expression of Distinct GST Genes in Brassica oleracea. Int J Mol Sci 2016; 17:ijms17081211. [PMID: 27472324 PMCID: PMC5000609 DOI: 10.3390/ijms17081211] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/15/2016] [Accepted: 07/15/2016] [Indexed: 02/08/2023] Open
Abstract
Plants, as sessile organisms, can suffer serious growth and developmental consequences under cold stress conditions. Glutathione transferases (GSTs, EC 2.5.1.18) are ubiquitous and multifunctional conjugating proteins, which play a major role in stress responses by preventing oxidative damage by reactive oxygen species (ROS). Currently, understanding of their function(s) during different biochemical and signaling pathways under cold stress condition remain unclear. In this study, using combined computational strategy, we identified 65 Brassica oleracea glutathione transferases (BoGST) and characterized them based on evolutionary analysis into 11 classes. Inter-species and intra-species duplication was evident between BoGSTs and Arabidopsis GSTs. Based on localization analyses, we propose possible pathways in which GST genes are involved during cold stress. Further, expression analysis of the predicted putative functions for GST genes were investigated in two cold contrasting genotypes (cold tolerance and susceptible) under cold condition, most of these genes were highly expressed at 6 h and 1 h in the cold tolerant (CT) and cold susceptible (CS) lines, respectively. Overall, BoGSTU19, BoGSTU24, BoGSTF10 are candidate genes highly expressed in B. oleracea. Further investigation of GST superfamily in B. oleracea will aid in understanding complex mechanism underlying cold tolerance in plants.
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Saha G, Park JI, Ahmed NU, Kayum MA, Kang KK, Nou IS. Characterization and expression profiling of MYB transcription factors against stresses and during male organ development in Chinese cabbage (Brassica rapa ssp. pekinensis). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 104:200-15. [PMID: 27038155 DOI: 10.1016/j.plaphy.2016.03.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 03/13/2016] [Accepted: 03/13/2016] [Indexed: 05/27/2023]
Abstract
MYB proteins comprise a large family of plant transcription factors that play regulatory roles in different biological processes such as plant development, metabolism, and defense responses. To gain insight into this gene superfamily and to elucidate its roles in stress resistance, we performed a comprehensive genome-wide identification, characterization, and expression analysis of MYB genes in Chinese cabbage (Brassica rapa ssp. pekinensis). We identified 475 Chinese cabbage MYB genes, among which most were from R2R3-MYB (256 genes) and MYB-related (202) subfamilies. Analysis of sequence characteristics, phylogenetic classification, and protein motif structures confirmed the existence of several categories (1R, 2R, 3R, 4R, and 5R) of Chinese cabbage MYB genes, which is comparable with MYB genes of other crops. An extensive in silico functional analysis, based on established functional properties of MYB genes from different crop species, revealed 11 and four functional clades within the Chinese cabbage R2R3-MYB and MYB-related subfamilies, respectively. In this study, we reported a MYB-like group within the MYB-related subfamily contains 77 MYB genes. Expression analysis using low temperature-treated whole-genome microarray data revealed variable transcript abundance of 1R/2R/3R/4R/5R-MYB genes in 11 clusters between two inbred lines of Chinese cabbage, Chiifu and Kenshin, which differ in cold tolerance. In further validation tests, we used qRT-PCR to examine the cold-responsive expression patterns of 27 BrMYB genes; surprisingly, the MYB-related genes were induced more highly than the R2R3-MYB genes. In addition, we identified 10 genes with corresponsive expression patterns from a set of salt-, drought-, ABA-, JA-, and SA-induced R2R3-MYB genes. We identified 11 R2R3-MYBs functioning in resistance against biotic stress, including 10 against Fusarium oxysporum f.sp. conglutinans and one against Pectobacterium carotovoram subsp. caratovorum. Furthermore, based on organ-specific expression data, we identified nine R2R3-MYBs that were constitutively expressed in male reproductive tissue, which may provide an important key for studying male sterility in Chinese cabbage. The extensive annotation and transcriptome profiling reported in this study will be useful for understanding the involvement of MYB genes in stress resistance in addition to their growth regulatory functions, ultimately providing the basis for functional characterization and exploitation of the candidate MYB genes for genetic engineering of Chinese cabbage.
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Affiliation(s)
- Gopal Saha
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 540-950, South Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 540-950, South Korea
| | - Nasar Uddin Ahmed
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, 8602, Bangladesh
| | - Md Abdul Kayum
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 540-950, South Korea
| | - Kwon-Kyoo Kang
- Department of Horticulture, Hankyong National University, Ansung, Kyonggi-do, 456-749, South Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 540-950, South Korea.
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Moustafa K, Cross JM. Genetic Approaches to Study Plant Responses to Environmental Stresses: An Overview. BIOLOGY 2016; 5:biology5020020. [PMID: 27196939 PMCID: PMC4929534 DOI: 10.3390/biology5020020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/02/2016] [Accepted: 05/10/2016] [Indexed: 12/31/2022]
Abstract
The assessment of gene expression levels is an important step toward elucidating gene functions temporally and spatially. Decades ago, typical studies were focusing on a few genes individually, whereas now researchers are able to examine whole genomes at once. The upgrade of throughput levels aided the introduction of systems biology approaches whereby cell functional networks can be scrutinized in their entireties to unravel potential functional interacting components. The birth of systems biology goes hand-in-hand with huge technological advancements and enables a fairly rapid detection of all transcripts in studied biological samples. Even so, earlier technologies that were restricted to probing single genes or a subset of genes still have their place in research laboratories. The objective here is to highlight key approaches used in gene expression analysis in plant responses to environmental stresses, or, more generally, any other condition of interest. Northern blots, RNase protection assays, and qPCR are described for their targeted detection of one or a few transcripts at a once. Differential display and serial analysis of gene expression represent non-targeted methods to evaluate expression changes of a significant number of gene transcripts. Finally, microarrays and RNA-seq (next-generation sequencing) contribute to the ultimate goal of identifying and quantifying all transcripts in a cell under conditions or stages of study. Recent examples of applications as well as principles, advantages, and drawbacks of each method are contrasted. We also suggest replacing the term “Next-Generation Sequencing (NGS)” with another less confusing synonym such as “RNA-seq”, “high throughput sequencing”, or “massively parallel sequencing” to avoid confusion with any future sequencing technologies.
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Affiliation(s)
- Khaled Moustafa
- Conservatoire National des Arts et Métiers, Paris 75003, France.
| | - Joanna M Cross
- Faculty of Agriculture, Inonu University, Malatya 44000, Turkey.
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Eremina M, Rozhon W, Poppenberger B. Hormonal control of cold stress responses in plants. Cell Mol Life Sci 2016; 73:797-810. [PMID: 26598281 PMCID: PMC11108489 DOI: 10.1007/s00018-015-2089-6] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/20/2015] [Accepted: 11/05/2015] [Indexed: 10/22/2022]
Abstract
Cold stress responses in plants are highly sophisticated events that alter the biochemical composition of cells for protection from damage caused by low temperatures. In addition, cold stress has a profound impact on plant morphologies, causing growth repression and reduced yields. Complex signalling cascades are utilised to induce changes in cold-responsive gene expression that enable plants to withstand chilling or even freezing temperatures. These cascades are governed by the activity of plant hormones, and recent research has provided a better understanding of how cold stress responses are integrated with developmental pathways that modulate growth and initiate other events that increase cold tolerance. Information on the hormonal control of cold stress signalling is summarised to highlight the significant progress that has been made and indicate gaps that still exist in our understanding.
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Affiliation(s)
- Marina Eremina
- Biotechnology of Horticultural Crops, TUM School of Life Sciences Weihenstephan, Technische Universität München, 85354, Freising, Germany
| | - Wilfried Rozhon
- Biotechnology of Horticultural Crops, TUM School of Life Sciences Weihenstephan, Technische Universität München, 85354, Freising, Germany
| | - Brigitte Poppenberger
- Biotechnology of Horticultural Crops, TUM School of Life Sciences Weihenstephan, Technische Universität München, 85354, Freising, Germany.
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Saha G, Park JI, Kayum MA, Nou IS. A Genome-Wide Analysis Reveals Stress and Hormone Responsive Patterns of TIFY Family Genes in Brassica rapa. FRONTIERS IN PLANT SCIENCE 2016; 7:936. [PMID: 27446164 PMCID: PMC4923152 DOI: 10.3389/fpls.2016.00936] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 06/13/2016] [Indexed: 05/13/2023]
Abstract
The TIFY family is a plant-specific group of proteins with a diversity of functions and includes four subfamilies, viz. ZML, TIFY, PPD, and JASMONATE ZIM-domain (JAZ) proteins. TIFY family members, particularly JAZ subfamily proteins, play roles in biological processes such as development and stress and hormone responses in Arabidopsis, rice, chickpea, and grape. However, there is no information about this family in any Brassica crop. This study identifies 36 TIFY genes in Brassica rapa, an economically important crop species in the Brassicaceae. An extensive in silico analysis of phylogenetic grouping, protein motif organization and intron-exon distribution confirmed that there are four subfamilies of BrTIFY proteins. Out of 36 BrTIFY genes, we identified 21 in the JAZ subfamily, seven in the TIFY subfamily, six in ZML and two in PPD. Extensive expression profiling of 21 BrTIFY JAZs in various tissues, especially in floral organs and at different flower growth stages revealed constitutive expression patterns, which suggest that BrTIFY JAZ genes are important during growth and development of B. rapa flowers. A protein interaction network analysis also pointed to association of these proteins with fertility and defense processes of B. rapa. Using a low temperature-treated whole-genome microarray data set, most of the JAZ genes were found to have variable transcript abundance between the contrasting inbred lines Chiifu and Kenshin of B. rapa. Subsequently, the expression of all 21 BrTIFY JAZs in response to cold stress was characterized in the same two lines via qPCR, demonstrating that nine genes were up-regulated. Importantly, the BrTIFY JAZs showed strong and differential expression upon JA treatment, pointing to their probable involvement in JA-mediated growth regulatory functions, especially during flower development and stress responses. Additionally, BrTIFY JAZs were induced in response to salt, drought, Fusarium, ABA, and SA treatments, and six genes (BrTIFY3a, 3b, 6a, 9a, 9b, and 9c) were identified to have co-responsive expression patterns. The extensive annotation and transcriptome profiling reported in this study will be useful for understanding the involvement of TIFY genes in stress resistance and different developmental functions, which ultimately provides the basis for functional characterization and exploitation of the candidate TIFY genes for genetic engineering of B. rapa.
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Huang W, Huang Y, Li MY, Wang F, Xu ZS, Xiong AS. Dof transcription factors in carrot: genome-wide analysis and their response to abiotic stress. Biotechnol Lett 2015; 38:145-55. [PMID: 26466595 DOI: 10.1007/s10529-015-1966-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/22/2015] [Indexed: 10/22/2022]
Abstract
OBJECTIVES The DNA-binding one zinc finger (Dof) family transcription factors (TF) are involved in stress response. Dof TFs in carrot were identified and the responses of DcDof genes to abiotic stresses were analyzed. RESULTS 46 DcDofs in carrot were identified from carrot genome database. Based on the conserved domain in Dof TF family of Arabidopsis thaliana, the DcDof TFs were divided into four classes, named class A, B, C and D. Carrot and Arabidopsis shared most motifs in the same subgroup. Real-time quantification PCR analysis showed tissue-specific expression patterns in DcDofs. DcDofs from eight subgroups responded to four abiotic stress treatments. CONCLUSIONS The expression profiles were different with the abiotic stresses changed, indicating complicated regulatory mechanisms in Dof TF family in higher plant, and the response mechanisms of Dof genes may be influenced by different plant species.
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Affiliation(s)
- Wei Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Meng-yao Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi-sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ai-sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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14
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Saha G, Park JI, Jung HJ, Ahmed NU, Kayum MA, Kang JG, Nou IS. Molecular characterization of BZR transcription factor family and abiotic stress induced expression profiling in Brassica rapa. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 92:92-104. [PMID: 25931321 DOI: 10.1016/j.plaphy.2015.04.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/20/2015] [Accepted: 04/20/2015] [Indexed: 05/07/2023]
Abstract
BRASSINAZOLE-RESISTANT (BZR) transcription factors (TFs) are primarily well known as positive regulators of Brassinosteroid (BR) signal transduction in different plants. BR is a plant specific steroid hormone, which has multiple stress resistance functions besides various growth regulatory roles. Being an important regulator of the BR synthesis, BZR TFs might have stress resistance related activities. However, no stress resistance related functional study of BZR TFs has been reported in any crop plants so far. Therefore, this study identified 15 BZR TFs of Brassica rapa (BrBZR) from a genome-wide survey and characterized them through sequence analysis and expression profiling against several abiotic stresses. Various systematic in silico analysis of these TFs validated the fundamental properties of BZRs, where a high degree of similarity also observed with recognized BZRs of other plant species from the comparison studies. In the organ specific expression analyses, 6 BrBZR TFs constitutively expressed in flower developmental stages indicating their flower specific functions. Subsequently, from the stress resistance related expression profiles differential transcript abundance levels were observed by 6 and 11 BrBZRs against salt and drought stresses, respectively. All BrBZRs showed several folds up-regulation against exogenous ABA treatment. All BrBZRs also showed differential expression against low temperature stress treatments and these TFs were proposed as transcriptional activators of CBF cold response pathway of B. rapa. Notably, three BrBZRs gave co-responsive expression against all the stresses tested here, suggesting their multiple stress resistance related functions. Thus, the findings would be helpful in resolving the complex regulatory mechanism of BZRs in stress resistance and further functional genomics study of these potential TFs in different Brassica crops.
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Affiliation(s)
- Gopal Saha
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 540-950, South Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 540-950, South Korea
| | - Hee-Jeong Jung
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 540-950, South Korea
| | - Nasar Uddin Ahmed
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 540-950, South Korea
| | - Md Abdul Kayum
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 540-950, South Korea
| | - Jong-Goo Kang
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 540-950, South Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam 540-950, South Korea.
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15
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Dong X, Yi H, Lee J, Nou IS, Han CT, Hur Y. Global Gene-Expression Analysis to Identify Differentially Expressed Genes Critical for the Heat Stress Response in Brassica rapa. PLoS One 2015; 10:e0130451. [PMID: 26102990 PMCID: PMC4477974 DOI: 10.1371/journal.pone.0130451] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 05/20/2015] [Indexed: 01/08/2023] Open
Abstract
Genome-wide dissection of the heat stress response (HSR) is necessary to overcome problems in crop production caused by global warming. To identify HSR genes, we profiled gene expression in two Chinese cabbage inbred lines with different thermotolerances, Chiifu and Kenshin. Many genes exhibited >2-fold changes in expression upon exposure to 0.5– 4 h at 45°C (high temperature, HT): 5.2% (2,142 genes) in Chiifu and 3.7% (1,535 genes) in Kenshin. The most enriched GO (Gene Ontology) items included ‘response to heat’, ‘response to reactive oxygen species (ROS)’, ‘response to temperature stimulus’, ‘response to abiotic stimulus’, and ‘MAPKKK cascade’. In both lines, the genes most highly induced by HT encoded small heat shock proteins (Hsps) and heat shock factor (Hsf)-like proteins such as HsfB2A (Bra029292), whereas high-molecular weight Hsps were constitutively expressed. Other upstream HSR components were also up-regulated: ROS-scavenging genes like glutathione peroxidase 2 (BrGPX2, Bra022853), protein kinases, and phosphatases. Among heat stress (HS) marker genes in Arabidopsis, only exportin 1A (XPO1A) (Bra008580, Bra006382) can be applied to B. rapa for basal thermotolerance (BT) and short-term acquired thermotolerance (SAT) gene. CYP707A3 (Bra025083, Bra021965), which is involved in the dehydration response in Arabidopsis, was associated with membrane leakage in both lines following HS. Although many transcription factors (TF) genes, including DREB2A (Bra005852), were involved in HS tolerance in both lines, Bra024224 (MYB41) and Bra021735 (a bZIP/AIR1 [Anthocyanin-Impaired-Response-1]) were specific to Kenshin. Several candidate TFs involved in thermotolerance were confirmed as HSR genes by real-time PCR, and these assignments were further supported by promoter analysis. Although some of our findings are similar to those obtained using other plant species, clear differences in Brassica rapa reveal a distinct HSR in this species. Our data could also provide a springboard for developing molecular markers of HS and for engineering HS tolerant B. rapa.
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Affiliation(s)
- Xiangshu Dong
- Department of Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Hankuil Yi
- Department of Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Jeongyeo Lee
- Department of Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
| | - Ching-Tack Han
- Department of Life Science, Sogang University, Seoul, Republic of Korea
- * E-mail: (YH); (CTH)
| | - Yoonkang Hur
- Department of Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
- * E-mail: (YH); (CTH)
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16
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Ahmed NU, Park JI, Jung HJ, Hur Y, Nou IS. Anthocyanin biosynthesis for cold and freezing stress tolerance and desirable color in Brassica rapa. Funct Integr Genomics 2014; 15:383-94. [PMID: 25504198 DOI: 10.1007/s10142-014-0427-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 11/27/2014] [Accepted: 11/30/2014] [Indexed: 01/08/2023]
Abstract
Flavonoids are divided into several structural classes, including anthocyanins, which provide flower and leaf colors and other derivatives that play diverse roles in plant development and interactions with the environment. This study characterized four anthocyanidin synthase (ANS) genes of Brassica rapa, a structural gene of the anthocyanin biosynthetic pathway, and investigated their association with pigment formation, cold and freezing tolerance in B. rapa. Sequences of these genes were analyzed and compared with similar gene sequences from other species, and a high degree of homology with their respective functions was found. Organ-specific expression analysis revealed that these genes were only expressed in the colored portion of leaves of different lines of B. rapa. Conversely, B. rapa anthocyanidin synthase (BrANS) genes also showed responses to cold and freezing stress treatment in B. rapa. BrANSs were also shown to be regulated by two transcription factors, BrMYB2-2 and BrTT8, contrasting with anthocyanin accumulation and cold stress. Thus, the above results suggest the association of these genes with anthocyanin biosynthesis and cold and freezing stress tolerance and might be useful resources for development of cold-resistant Brassica crops with desirable colors as well.
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Affiliation(s)
- Nasar Uddin Ahmed
- Department of Horticulture, Sunchon National University, 413 Jungang-ro, Suncheon, Jeonnam, 540-950, Republic of Korea
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17
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Ahmed NU, Jung HJ, Park JI, Cho YG, Hur Y, Nou IS. Identification and expression analysis of cold and freezing stress responsive genes of Brassica oleracea. Gene 2014; 554:215-23. [PMID: 25445291 DOI: 10.1016/j.gene.2014.10.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/15/2014] [Accepted: 10/27/2014] [Indexed: 10/24/2022]
Abstract
Cold and freezing stress is a major environmental constraint to the production of Brassica crops. Enhancement of tolerance by exploiting cold and freezing tolerance related genes offers the most efficient approach to address this problem. Cold-induced transcriptional profiling is a promising approach to the identification of potential genes related to cold and freezing stress tolerance. In this study, 99 highly expressed genes were identified from a whole genome microarray dataset of Brassica rapa. Blast search analysis of the Brassica oleracea database revealed the corresponding homologous genes. To validate their expression, pre-selected cold tolerant and susceptible cabbage lines were analyzed. Out of 99 BoCRGs, 43 were differentially expressed in response to varying degrees of cold and freezing stress in the contrasting cabbage lines. Among the differentially expressed genes, 18 were highly up-regulated in the tolerant lines, which is consistent with their microarray expression. Additionally, 12 BoCRGs were expressed differentially after cold stress treatment in two contrasting cabbage lines, and BoCRG54, 56, 59, 62, 70, 72 and 99 were predicted to be involved in cold regulatory pathways. Taken together, the cold-responsive genes identified in this study provide additional direction for elucidating the regulatory network of low temperature stress tolerance and developing cold and freezing stress resistant Brassica crops.
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Affiliation(s)
- Nasar Uddin Ahmed
- Department of Horticulture, Sunchon National University, 413 Jungang-ro, Suncheon, Jeonnam 540-950, Republic of Korea
| | - Hee-Jeong Jung
- Department of Horticulture, Sunchon National University, 413 Jungang-ro, Suncheon, Jeonnam 540-950, Republic of Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 413 Jungang-ro, Suncheon, Jeonnam 540-950, Republic of Korea
| | - Yong-Gu Cho
- Department of Crop Science, Chungbuk National University, 410 Seongbongro, Heungdokgu, Cheongju 361-763, Republic of Korea
| | - Yoonkang Hur
- Department of Biology, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 413 Jungang-ro, Suncheon, Jeonnam 540-950, Republic of Korea.
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