Plant J , IF:6.141 , 2019 Apr , V98 (2) : P260-276 doi: 10.1111/tpj.14209
Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica.
Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China.; Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA.; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350003, China.; Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China.
Alternative polyadenylation (APA) is a widespread post-transcriptional mechanism that regulates gene expression through mRNA metabolism, playing a pivotal role in modulating phenotypic traits in rice (Oryza sativa L.). However, little is known about the APA-mediated regulation underlying the distinct characteristics between two major rice subspecies, indica and japonica. Using a poly(A)-tag sequencing approach, polyadenylation (poly(A)) site profiles were investigated and compared pairwise from germination to the mature stage between indica and japonica, and extensive differentiation in APA profiles was detected genome-wide. Genes with subspecies-specific poly(A) sites were found to contribute to subspecies characteristics, particularly in disease resistance of indica and cold-stress tolerance of japonica. In most tissues, differential usage of APA sites exhibited an apparent impact on the gene expression profiles between subspecies, and genes with those APA sites were significantly enriched in quantitative trait loci (QTL) related to yield traits, such as spikelet number and 1000-seed weight. In leaves of the booting stage, APA site-switching genes displayed global shortening of 3' untranslated regions with increased expression in indica compared with japonica, and they were overrepresented in the porphyrin and chlorophyll metabolism pathways. This phenomenon may lead to a higher chlorophyll content and photosynthesis in indica than in japonica, being associated with their differential growth rates and yield potentials. We further constructed an online resource for querying and visualizing the poly(A) atlas in these two rice subspecies. Our results suggest that APA may be largely involved in developmental differentiations between two rice subspecies, especially in leaf characteristics and the stress response, broadening our knowledge of the post-transcriptional genetic basis underlying the divergence of rice traits.
PMID: 30570805
Int J Mol Sci , IF:4.556 , 2019 Apr , V20 (9) doi: 10.3390/ijms20092107
UMP Kinase Regulates Chloroplast Development and Cold Response in Rice.
State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China. dongqing66job@sina.com.; State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China. zhangyingxin@caas.cn.; State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China. stresszhou@163.com.; State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China. liuqunen202@163.com.; State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China. cdb840925@163.com.; State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China. wjiyinh@126.com.; State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China. chengshihua@caas.cn.; State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China. caoliyong@caas.cn.; State Key Laboratory of Rice Biology and Key Laboratory for Zhejiang Super Rice Research, China National Rice Research Institute, Hangzhou 310006, China. shenxihong@caas.cn.
Pyrimidine nucleotides are important metabolites that are building blocks of nucleic acids, which participate in various aspects of plant development. Only a few genes involved in pyrimidine metabolism have been identified in rice and the majority of their functions remain unclear. In this study, we used a map-based cloning strategy to isolate a UMPK gene in rice, encoding the UMP kinase that phosphorylates UMP to form UDP, from a recessive mutant with pale-green leaves. In the mutant, UDP content always decreased, while UTP content fluctuated with the development of leaves. Mutation of UMPK reduced chlorophyll contents and decreased photosynthetic capacity. In the mutant, transcription of plastid-encoded RNA polymerase-dependent genes, including psaA, psbB, psbC and petB, was significantly reduced, whereas transcription of nuclear-encoded RNA polymerase-dependent genes, including rpoA, rpoB, rpoC1, and rpl23, was elevated. The expression of UMPK was significantly induced by various stresses, including cold, heat, and drought. Increased sensitivity to cold stress was observed in the mutant, based on the survival rate and malondialdehyde content. High accumulation of hydrogen peroxide was found in the mutant, which was enhanced by cold treatment. Our results indicate that the UMP kinase gene plays important roles in regulating chloroplast development and stress response in rice.
PMID: 31035645
Sci Rep , IF:3.998 , 2019 Apr , V9 (1) : P6638 doi: 10.1038/s41598-019-43269-5
Identification and functional prediction of cold-related long non-coding RNA (lncRNA) in grapevine.
Shandong Academy of Grape, Shandong engineering research center for Grape cultivation and deep-processing, Jinan, 250100, P.R. China. fengqiaoyouzi@126.com.; Key Laboratory of Urban Agriculture (East China), Ministry of Agriculture, Jinan, P.R. China. fengqiaoyouzi@126.com.; School of Pharmacy, Binzhou Medical University, Yantai, 264003, P.R. China.; Institute of special animal and plant sciences of CAAS, Changchun, P.R. China.; National Field Gene Bank for Amur Grapvine, Zuojia, P.R. China.; Shandong Academy of Grape, Shandong engineering research center for Grape cultivation and deep-processing, Jinan, 250100, P.R. China. wangym228@126.com.; Key Laboratory of Urban Agriculture (East China), Ministry of Agriculture, Jinan, P.R. China. wangym228@126.com.; Shandong Academy of Grape, Shandong engineering research center for Grape cultivation and deep-processing, Jinan, 250100, P.R. China. rensd65@163.com.; Key Laboratory of Urban Agriculture (East China), Ministry of Agriculture, Jinan, P.R. China. rensd65@163.com.
Plant long non-coding RNA (lncRNA) undergoes dynamic regulation and acts in developmental and stress regulation. In this study, we surveyed the expression dynamics of lncRNAs in grapevine (Vitis vinifera L.) under cold stress using high-throughput sequencing. Two-hundred and three known lncRNAs were significantly up-regulated and 144 known lncRNAs were significantly down-regulated in cold-treated grapevine. In addition, 2 088 novel lncRNA transcripts were identified in this study, with 284 novel lncRNAs significantly up-regulated and 182 novel lncRNAs significantly down-regulated in cold-treated grapevine. Two-hundred and forty-two differentially expressed grapevine lncRNAs were predicted to target 326 protein-coding genes in a cis-regulatory relationship. Many differentially expressed grapevine lncRNAs targeted stress response-related genes, such as CBF4 transcription factor genes, late embryogenesis abundant protein genes, peroxisome biogenesis protein genes, and WRKY transcription factor genes. Sixty-two differentially expressed grapevine lncRNAs were predicted to target 100 protein-coding genes in a trans-regulatory relationship. The expression of overall target genes in both cis and trans-regulatory relationships were positively related to the expression of lncRNAs in grapevines under cold stress. We identified 31 known lncRNAs as 34 grapevine micro RNA (miRNA) precursors and some miRNAs may be derived from multiple lncRNAs. We found 212 lncRNAs acting as targets of miRNAs in grapevines, involving 150 miRNAs; additionally, 120 grapevine genes were predicted as targets of grapevine miRNAs and lncRNAs. We found one gene cluster that was up-regulated and showed the same expression trend. In this cluster, many genes may be involved in abiotic stress response such as WRKY, Hsf, and NAC transcription factor genes.
PMID: 31036931
J Proteomics , IF:3.509 , 2019 Apr , V197 : P71-81 doi: 10.1016/j.jprot.2018.11.008
Temporal proteomics of Arabidopsis plasma membrane during cold- and de-acclimation.
Department of Plant-bioscience, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan.; United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan; Max-Planck-Institut fur Molekulare Pflanzenphysiologie, Am Muhlenberg 1, Potsdam D-14476, Germany.; Department of Plant-bioscience, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan; United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan.; Department of Plant-bioscience, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan; United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan. Electronic address: uemura@iwate-u.ac.jp.
Freezing stress is one of the most important limiting factors of plant survival. Plants have developed a freezing adaptation mechanism upon sensing low temperatures (cold acclimation). Compositional changes in the plasma membrane, one of the initial sites of freezing injury, is prerequisite of achieving cold acclimation and have been investigated in several plant species. Conversely, the cold dehardening process at elevated temperatures (de-acclimation) has not yet been fully characterized and few studies have addressed the importance of the plasma membrane in the de-acclimation process. In the present study, we conducted shotgun proteomics with label-free semiquantification on plasma membrane fractions of Arabidopsis leaves during cold acclimation and de-acclimation. We consequently obtained a list of 873 proteins with significantly changed proteins in response to the two processes. Although the cold-acclimation-responsive proteins were globally returned to non-acclimated levels by de-acclimation, several representative cold-acclimation-responsive proteins tended to remain at higher abundance during de-acclimation process. Taken together, our results suggest plants deharden right after cold acclimation to restart growth and development but some cold-acclimation-induced changes of the plasma membrane may be maintained under de-acclimation to cope with the threat of sudden freezing during de-acclimation process. SIGNIFICANCE: Plant freezing tolerance can be enhanced by low temperature treatment (cold acclimation), while elevated temperatures right after cold acclimation can result in the dehardening of freezing tolerance (de-acclimation). However, the de-acclimation process, particularly its relevance to the plasma membrane as the primary site of freezing injury, has not been elucidated. In the present study, a comprehensive proteomic analysis of the plasma membrane during cold acclimation and de-acclimation was carried out as a first step to elucidating how plants respond to rising temperatures. Cold acclimation induced a number of proteomic changes as reported in previous studies, but most proteins, in general, immediately returned to NA levels during de-acclimation treatment for two days. However, the abundances of stress-related proteins (e.g. LTI29, COR78 and TIL) decreased slower than other functional proteins during de-acclimation. Therefore, plants harden during cold acclimation by aborting growth and development and accumulating stress-responsive proteins but seem to deharden quickly under subsequent elevated temperature to resume these processes while guarding against the threat of sudden temperature drops.
PMID: 30447334
BMC Plant Biol , IF:3.497 , 2019 Apr , V19 (1) : P161 doi: 10.1186/s12870-019-1760-8
Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri).
College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.; College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China. taost@njau.edu.cn.; College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China. huangxs@njau.edu.cn.
BACKGROUND: Although the genome of Chinese white pear ('Dangshansuli') has been released, little is known about the functions, evolutionary history and expression patterns of NAC families in this species to date. RESULTS: In this study, we identified a total of 183 NAC transcription factors (TFs) in the pear genome, among which 146 pear NAC (PbNAC) members were mapped onto 16 chromosomes, and 37 PbNAC genes were located on scaffold contigs. No PbNAC genes were mapped to chromosome 2. Based on gene structure, protein motif analysis, and topology of the phylogenetic tree, the pear PbNAC family was classified into 33 groups. By comparing and analyzing the unique NAC subgroups in Rosaceae, we identified 19 NAC subgroups specific to pear. We also found that whole-genome duplication (WGD)/segmental duplication played critical roles in the expansion of the NAC family in pear, such as the 83 PbNAC duplicated gene pairs dated back to the two WGD events. Further, we found that purifying selection was the primary force driving the evolution of PbNAC family genes. Next, we used transcriptomic data to study responses to drought and cold stresses in pear, and we found that genes in groups C2f, C72b, and C100a were related to drought and cold stress response. CONCLUSIONS: Through the phylogenetic, evolutionary, and expression analyses of the NAC gene family in Chinese white pear, we indentified 11 PbNAC TFs associated with abiotic stress in pear.
PMID: 31023218
Mol Genet Genomics , IF:2.797 , 2019 Apr , V294 (2) : P379-393 doi: 10.1007/s00438-018-1516-4
MicroRNA156 amplifies transcription factor-associated cold stress tolerance in plant cells.
College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, 434025, People's Republic of China.; College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, 434025, People's Republic of China. wt10yu604@gmail.com.
MicroRNAs may increase cold stress tolerance by regulating stress-related signal transduction pathways and by modulating the expression of transcription factors. However, the molecular mechanism by which microRNAs enhance cold stress tolerance is not fully understood. Here, we report that overexpression of rice microRNA156 (OsmiR156) results in increased cell viability and growth rate under cold stress in Arabidopsis, pine, and rice. OsmiR156 increases cold stress tolerance by targeting OsSPL3. OsSPL3 positively regulates the expression of OsWRKY71, a negative regulator of the transcription factors OsMYB2 and OsMYB3R-2. OsMYB2 counteracts cold stress by activating the expression of the stress-response genes OsLEA3, OsRab16A, and OsDREB2A. OsMYB3R-2 counteracts cold stress by activating the expression of OsKNOLLE2, OsCTP1, OsCycB1.1, OsCycB2.1, and OsCDC20.1. In OsmiR156 transgenic rice cell lines, the transcript levels of OsLEA3, OsRab16A, OsDREB2A, OsKNOLLE2, OsCTP1, OsCycB1.1, OsCycB2.1, and OsCDC20.1 were increased by OsWRKY71 knockdown and inversely regulated by OsWRKY71 overexpression, indicating that OsmiR156 enhances cold stress tolerance by regulating the expression of transcription factor genes in plant cells. These results will increase our understanding of microRNA-related cold stress tolerance in different plant species, including monocotyledonous, dicotyledonous, and gymnosperm plant species, and will be valuable in plant molecular biotechnology.
PMID: 30478522
Funct Plant Biol , IF:2.617 , 2019 Apr , V46 (5) : P482-491 doi: 10.1071/FP18241
Heterologous expression of rice RNA-binding glycine-rich (RBG) gene OsRBGD3 in transgenic Arabidopsis thaliana confers cold stress tolerance.
ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, 110003, India.; ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India.; ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, 695017, India.; ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and Department of Immunology, School of Medicine, University of Pittsburgh, PA 15261, USA.; ICAR-Indian Agricultural Research Institute, Division of Plant Physiology, New Delhi, 110012, India.; ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, 110003, India; and Corresponding author. Email: kailashbansal@hotmail.com.
Imparting cold stress tolerance to crops is a major challenge in subtropical agriculture. New genes conferring cold tolerance needs to be identified and characterised for sustainable crop production in low-temperature stress affected areas. Here we report functional characterisation of OsRBGD3, classified previously as a class D glycine-rich RNA recognition motif (RRM) containing proteins from a drought-tolerant Indica rice cultivar N22. The gene was isolated by screening yeast one-hybrid library using the minimal promoter region of the OsMYB38 that is necessary for cold stress-responsive expression. OsRBGD3 exhibited cold, drought and salt stress inductive expression in a drought tolerant N22 rice cultivar as compared with susceptible variety IR64. OsRBGD3 was found to be localised to both nuclear and cytoplasmic subcellular destinations. Constitutive overexpression of the OsRBGD3 in transgenic Arabidopsis conferred tolerance to cold stress. ABA sensitivity was also observed in transgenic lines suggesting the regulatory role of this gene in the ABA signalling pathway. OsRBGD3 overexpression also attributed to significant root development and early flowering in transgenics. Hence, OsRBGD3 could be an important target for developing cold tolerant early flowering rice and other crops' genotypes for increasing production in low temperature affected areas.
PMID: 30940336
Mol Biol Rep , IF:1.402 , 2019 Apr , V46 (2) : P2427-2445 doi: 10.1007/s11033-019-04704-y
Transcriptomic response of durum wheat to cold stress at reproductive stage.
Departamento de Biologia, Bioquimica y Farmacia, Universidad Nacional del Sur (UNS), Comision de Investigaciones Cientificas (CIC), Bahia Blanca, Buenos Aires, Argentina. mldiaz@criba.edu.ar.; Centro de Recursos Naturales Renovables de la Zona Semiarida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahia Blanca, Argentina.; Departamento de Agronomia, Universidad Nacional del Sur (UNS), Bahia Blanca, Argentina.
Understanding the genetic basis of cold tolerance is a key step towards obtaining new and improved crop varieties. Current geographical distribution of durum wheat in Argentina exposes the plants to frost damage when spikes have already emerged. Biochemical pathways involved in cold tolerance are known to be early activated at above freezing temperatures. In this study we reported the transcriptome of CBW0101 spring durum wheat by merging data from untreated control and cold (5 degrees C) treated plant samples at reproductive stage. A total of 128,804 unigenes were predicted. Near 62% of the unigenes were annotated in at least one database. In total 876 unigenes were differentially expressed (DEGs), 562 were up-regulated and 314 down-regulated in treated samples. DEGs are involved in many critical processes including, photosynthetic activity, lipid and carbohydrate synthesis and accumulation of amino acids and seed proteins. Twenty-eight transcription factors (TFs) belonging to 14 families resulted differentially expressed from which eight families comprised of only TFs induced by cold. We also found 31 differentially expressed Long non-coding RNAs (lncRNAs), most of them up-regulated in treated plants. Two of these lncRNAs could operate via microRNAs (miRNAs) target mimic. Our results suggest a reprogramming of expression patterns in CBW0101 that affects a number of genes that is closer to the number reported in winter genotypes. These observations could partially explain its moderate tolerance (low proportion of frost-damaged spikes) when exposed to freezing days in the field.
PMID: 30798485
Mol Biol Rep , IF:1.402 , 2019 Apr , V46 (2) : P1649-1660 doi: 10.1007/s11033-019-04613-0
Genome-wide screening of hexokinase gene family and functional elucidation of HXK2 response to cold stress in Jatropha curcas.
Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, 655011, Yunnan, China.; Key Laboratory of Yunnan Province Universities of the Diversity and Ecological Adaptive Evolution for Animals and Plants on YunGui Plateau, Qujing Normal University, Qujing, 655011, Yunnan, China.; Academy of Forestry, Southwest Forestry University, Kunming, 650224, Yunnan, China.; College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, 655011, Yunnan, China.; Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, 655011, Yunnan, China. tanglizhou@mail.qjnu.edu.cn.; Key Laboratory of Yunnan Province Universities of the Diversity and Ecological Adaptive Evolution for Animals and Plants on YunGui Plateau, Qujing Normal University, Qujing, 655011, Yunnan, China. tanglizhou@mail.qjnu.edu.cn.
Hexokinase, the key rate-limiting enzyme of plant respiration and glycolysis metabolism, has been found to play a vital role in plant sugar sensing and sugar signal transduction. Using Jatropha curcas genome database and bioinformatics method, J. curcas HXK gene family (JcHXK) was identified and its phylogenetic evolution, functional domain, signal peptide at the N-terminal, and expression analysis were conducted. The results showed that a total of 4 HXK genes (JcHXK1, JcHXK2, JcHXK3, and JcHKL1) with 9 exons were systematically identified from J. curcas. JcHXK1, JcHXK3, and JcHKL1 with putative transmembrane domain at the N-terminal belonged to the type of secretory pathway protein, and JcHXK2 contained putative chloroplast targeting peptide. Quantitative real-time PCR (qRT-PCR) analysis revealed that all the four JcHXKs were expressed in different tissues of the leaves, roots, and seeds; however, JcHXK1 and JcHKL1 expression were higher in the roots, whereas JcHXK2 and JcHXK3 showed over-expression in the leaves and seeds, respectively. Furthermore, all the four JcHXKs were up-regulated in the leaves after cold stress at 12 degrees C; however, only JcHXK3 remarkably demonstrated cold-induced expression in the roots, which reached the highest expression level at 12 h (2.28-fold). According to the cis-acting element analysis results, JcHXK2 contained the most low temperature responsive elements, which was closely related to the cold resistance in J. curcas. A pET-28a-JcHXK2 prokaryotic recombinant expression vector was successfully constructed and a 57.0 kDa protein was obtained, JcHXK2 revealed catalytic activity towards glucose and fructose, with a higher affinity for glucose than fructose. The subcellular localization assays revealed that JcHXK2 was localized in the chloroplast. The results of this study might provide theoretical foundation for further studies on gene cloning and functional verification of HXK family in J. curcas.
PMID: 30756333
Mol Biol Rep , IF:1.402 , 2019 Apr , V46 (2) : P1809-1817 doi: 10.1007/s11033-019-04631-y
Selection of suitable reference genes for quantitative real-time PCR gene expression analysis in Mulberry (Morus alba L.) under different abiotic stresses.
Central Sericultural Research and Training Institute, Central Silk Board, NH-1A, Gallandar, Pampore -192 121, Jammu and Kashmir, Srinagar, India. shklpwn@gmail.com.; Seri-biotech Research Laboratory (SBRL), Carmelram Post, Kodathi, Bangalore, 560035, India.; Central Sericultural Research and Training Institute, Central Silk Board, NH-1A, Gallandar, Pampore -192 121, Jammu and Kashmir, Srinagar, India.
Mulberry (Morus alba L.) is the sole food source for the mulberry silkworm, Bombyx mori and therefore important for sericulture industry. Different abiotic stress conditions like drought, salt, heat and cold stress adversely affect the productivity and quality of mulberry leaves. Quantitative real time PCR (qPCR) is a reliable and widely used method to identify abiotic stress responsive genes and molecular mechanism in different plant species. Selection of suitable reference genes is important requirement for normalizing the expression of genes through qRT-PCR study. In the present study, we have selected eight candidate reference genes in mulberry for analyzing their expression stability in different abiotic stress treatments including drought, salt, heat and cold stresses. The expression stability of these reference genes was determined using geNorm, NormFinder and RefFinder statistical algorithms. The results showed that Ubiquitin and protein phosphatase 2A regulatory subunit A (PP2A) were the most stable genes across all the treatment samples. However, analysis of individual stresses revealed different expression profiles and stability of reference genes. Actin3 and PP2A were most stable in drought and salt conditions respectively. RPL3 most preferred in heat stress and Ubiquitin was most stable in cold stress. We propose the ubiquitin and PP2A are the preferred reference genes for normalization of gene expression data from abiotic stresses. In addition, Actin3 are preferred for drought stress, PP2A for salt stress, RPL3 for heat stress and Ubiquitin for cold stress studies.
PMID: 30694457
Genes Genomics , IF:1.188 , 2019 Apr , V41 (4) : P467-481 doi: 10.1007/s13258-018-00780-9
Genome-wide identification and expression analyses of WRKY transcription factor family members from chickpea (Cicer arietinum L.) reveal their role in abiotic stress-responses.
Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.; Centre for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan.; Department of Bioinformatics and Biotechnology, GC University, Faisalabad, Pakistan.; Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan.; Education Scientific Center of Nanotechnology, Far Eastern Federal University, Vladivostok, Russian Federation.; Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea.; Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan. dratif@uaf.edu.pk.; Centre for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan. dratif@uaf.edu.pk.; Center for Advanced Studies in Agriculture & Food Security, University of Agriculture, Faisalabad, Pakistan. dratif@uaf.edu.pk.
BACKGROUND: WRKY proteins play a vital role in the regulation of several imperative plant metabolic processes and pathways, especially under biotic and abiotic stresses. Although WRKY genes have been characterized in various major crop plants, their identification and characterization in pulse legumes is still in its infancy. Chickpea (Cicer arietinum L.) is the most important pulse legume grown in arid and semi-arid tropics. OBJECTIVE: In silico identification and characterization of WRKY transcription factor-encoding genes in chickpea genome. METHODS: For this purpose, a systematic genome-wide analysis was carried out to identify the non-redundant WRKY transcription factors in the chickpea genome. RESULTS: We have computationally identified 70 WRKY-encoding non-redundant genes which were randomly distributed on all the chickpea chromosomes except chromosome 8. The evolutionary phylogenetic analysis classified the WRKY proteins into three major groups (I, II and III) and seven sub-groups (IN, IC, IIa, IIb, IIc, IId and IIe). The gene structure analysis revealed the presence of 2-7 introns among the family members. Along with the presence of absolutely conserved signatory WRKY domain, 19 different domains were also found to be conserved in a group-specific manner. Insights of gene duplication analysis revealed the predominant role of segmental duplications for the expansion of WRKY genes in chickpea. Purifying selection seems to be operated during the evolution and expansion of paralogous WRKY genes. The transcriptome data-based in silico expression analysis revealed the differential expression of CarWRKY genes in root and shoot tissues under salt, drought, and cold stress conditions. Moreover, some of these genes showed identical expression pattern under these stresses, revealing the possibility of involvement of these genes in conserved abiotic stress-response pathways. CONCLUSION: This genome-wide computational analysis will serve as a base to accelerate the functional characterization of WRKY TFs especially under biotic and abiotic stresses.
PMID: 30637579