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Singh D, Singh CK, Taunk J, Tomar RSS, Chaturvedi AK, Gaikwad K, Pal M. Transcriptome analysis of lentil (Lens culinaris Medikus) in response to seedling drought stress. BMC Genomics 2017; 18:206. [PMID: 28241862 PMCID: PMC5327544 DOI: 10.1186/s12864-017-3596-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 02/20/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Drought stress is one of the most harmful abiotic stresses in crop plants. As a moderately drought tolerant crop, lentil is a major crop in rainfed areas and a suitable candidate for drought stress tolerance research work. Screening for drought tolerance stress under hydroponic conditions at seedling stage with air exposure is an efficient technique to select genotypes with contrasting traits. Transcriptome analysis provides valuable resources, especially for lentil, as here the information on complete genome sequence is not available. Hence, the present studies were carried out. RESULTS This study was undertaken to understand the biochemical mechanisms and transcriptome changes involved in imparting adaptation to drought stress at seedling stage in drought-tolerant (PDL-2) and drought-sensitive (JL-3) cultivars. Among different physiological and biochemical parameters, a significant increase was recorded in proline, glycine betaine contents and activities of SOD, APX and GPX in PDL-2 compared to JL-3while chlorophyll, RWC and catalase activity decreased significantly in JL-3. Transcriptome changes between the PDL-2 and JL-3 under drought stress were evaluated using Illumina HiSeq 2500 platform. Total number of bases ranged from 5.1 to 6.7 Gb. Sequence analysis of control and drought treated cDNA libraries of PDL-2 and JL-3 produced 74032, 75500, 78328 and 81523 contigs, respectively with respective N50 value of 2011, 2008, 2000 and 1991. Differential gene expression of drought treated genotypes along with their controls revealed a total of 11,435 upregulated and 6,934 downregulated transcripts. For functional classification of DEGs, KEGG pathway annotation analysis extracted a total of 413 GO annotation terms where 176 were within molecular process, 128 in cellular and 109 in biological process groups. CONCLUSION The transcriptional profiles provide a foundation for deciphering the underlying mechanism for drought tolerance in lentil. Transcriptional regulation, signal transduction and secondary metabolism in two genotypes revealed significant differences at seedling stage under severe drought. Our finding suggests role of candidate genes for improving drought tolerance in lentil.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Chandan Kumar Singh
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Jyoti Taunk
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012 India
| | | | - Ashish Kumar Chaturvedi
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Kishor Gaikwad
- National Research Centre on Plant Biotechnology, ICAR, New Delhi, 110012 India
| | - Madan Pal
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012 India
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Chen Q, Li M, Zhang Z, Tie W, Chen X, Jin L, Zhai N, Zheng Q, Zhang J, Wang R, Xu G, Zhang H, Liu P, Zhou H. Integrated mRNA and microRNA analysis identifies genes and small miRNA molecules associated with transcriptional and post-transcriptional-level responses to both drought stress and re-watering treatment in tobacco. BMC Genomics 2017; 18:62. [PMID: 28068898 PMCID: PMC5223433 DOI: 10.1186/s12864-016-3372-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 12/02/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Drought stress is one of the most severe problem limited agricultural productivity worldwide. It has been reported that plants response to drought-stress by sophisticated mechanisms at both transcriptional and post-transcriptional levels. However, the precise molecular mechanisms governing the responses of tobacco leaves to drought stress and water status are not well understood. To identify genes and miRNAs involved in drought-stress responses in tobacco, we performed both mRNA and small RNA sequencing on tobacco leaf samples from the following three treatments: untreated-control (CL), drought stress (DL), and re-watering (WL). RESULTS In total, we identified 798 differentially expressed genes (DEGs) between the DL and CL (DL vs. CL) treatments and identified 571 DEGs between the WL and DL (WL vs. DL) treatments. Further analysis revealed 443 overlapping DEGs between the DL vs. CL and WL vs. DL comparisons, and, strikingly, all of these genes exhibited opposing expression trends between these two comparisons, strongly suggesting that these overlapping DEGs are somehow involved in the responses of tobacco leaves to drought stress. Functional annotation analysis showed significant up-regulation of genes annotated to be involved in responses to stimulus and stress, (e.g., late embryogenesis abundant proteins and heat-shock proteins) antioxidant defense (e.g., peroxidases and glutathione S-transferases), down regulation of genes related to the cell cycle pathway, and photosynthesis processes. We also found 69 and 56 transcription factors (TFs) among the DEGs in, respectively, the DL vs. CL and the WL vs. DL comparisons. In addition, small RNA sequencing revealed 63 known microRNAs (miRNA) from 32 families and 368 novel miRNA candidates in tobacco. We also found that five known miRNA families (miR398, miR390, miR162, miR166, and miR168) showed differential regulation under drought conditions. Analysis to identify negative correlations between the differentially expressed miRNAs (DEMs) and DEGs revealed 92 mRNA-miRNA interactions between CL and DL plants, and 32 mRNA-miRNA interactions between DL and WL plants. CONCLUSIONS This study provides a global view of the transcriptional and the post-transcriptional responses of tobacco under drought stress and re-watering conditions. Our results establish an empirical foundation that should prove valuable for further investigations into the molecular mechanisms through which tobacco, and plants more generally, respond to drought stress at multiple molecular genetic levels.
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Affiliation(s)
- Qiansi Chen
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Meng Li
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410000, China
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410000, China
| | - Zhongchun Zhang
- School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Xia Chen
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Lifeng Jin
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Niu Zhai
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Qingxia Zheng
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Jianfeng Zhang
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Ran Wang
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Guoyun Xu
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Hui Zhang
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Pingping Liu
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
| | - Huina Zhou
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
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Das G, Patra JK, Baek KH. Insight into MAS: A Molecular Tool for Development of Stress Resistant and Quality of Rice through Gene Stacking. FRONTIERS IN PLANT SCIENCE 2017; 8:985. [PMID: 28659941 PMCID: PMC5469070 DOI: 10.3389/fpls.2017.00985] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 05/24/2017] [Indexed: 05/21/2023]
Abstract
Rice yield is subjected to severe losses due to adverse effect of a number of stress factors. The most effective method of controlling reduced crop production is utilization of host resistance. Recent technological advances have led to the improvement of DNA based molecular markers closely linked to genes or QTLs in rice chromosome that bestow tolerance to various types of abiotic stresses and resistance to biotic stress factors. Transfer of several genes with potential characteristics into a single genotype is possible through the process of marker assisted selection (MAS), which can quicken the advancement of tolerant/resistant cultivars in the lowest number of generations with the utmost precision through the process of gene pyramiding. Overall, this review presented various types of molecular tools including MAS that can be reasonable and environmental friendly approach for the improvement of abiotic and biotic stress resistant rice with enhanced quality.
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Affiliation(s)
- Gitishree Das
- Research Institute of Biotechnology and Medical Converged Science, Dongguk University SeoulGoyang-si, South Korea
| | - Jayanta Kumar Patra
- Research Institute of Biotechnology and Medical Converged Science, Dongguk University SeoulGoyang-si, South Korea
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam UniversityGyeongsan, South Korea
- *Correspondence: Kwang-Hyun Baek
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Merewitz E, Xu Y, Huang B. Differentially Expressed Genes Associated with Improved Drought Tolerance in Creeping Bentgrass Overexpressing a Gene for Cytokinin Biosynthesis. PLoS One 2016; 11:e0166676. [PMID: 27855226 PMCID: PMC5113972 DOI: 10.1371/journal.pone.0166676] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 11/02/2016] [Indexed: 12/03/2022] Open
Abstract
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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Affiliation(s)
- Emily Merewitz
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, 48824, United States of America
| | - Yi Xu
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, 08901, United States of America
| | - Bingru Huang
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ, 08901, United States of America
- * E-mail:
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Wang W, Qin Q, Sun F, Wang Y, Xu D, Li Z, Fu B. Genome-Wide Differences in DNA Methylation Changes in Two Contrasting Rice Genotypes in Response to Drought Conditions. FRONTIERS IN PLANT SCIENCE 2016; 7:1675. [PMID: 27877189 PMCID: PMC5099141 DOI: 10.3389/fpls.2016.01675] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/24/2016] [Indexed: 05/26/2023]
Abstract
Differences in drought stress tolerance within diverse rice genotypes have been attributed to genetic diversity and epigenetic alterations. DNA methylation is an important epigenetic modification that influences diverse biological processes, but its effects on rice drought stress tolerance are poorly understood. In this study, methylated DNA immunoprecipitation sequencing and an Affymetrix GeneChip rice genome array were used to profile the DNA methylation patterns and transcriptomes of the drought-tolerant introgression line DK151 and its drought-sensitive recurrent parent IR64 under drought and control conditions. The introgression of donor genomic DNA induced genome-wide DNA methylation changes in DK151 plants. A total of 1190 differentially methylated regions (DMRs) were detected between the two genotypes under normal growth conditions, and the DMR-associated genes in DK151 plants were mainly related to stress response, programmed cell death, and nutrient reservoir activity, which are implicated to constitutive drought stress tolerance. A comparison of the DNA methylation changes in the two genotypes under drought conditions indicated that DK151 plants have a more stable methylome, with only 92 drought-induced DMRs, than IR64 plants with 506 DMRs. Gene ontology analyses of the DMR-associated genes in drought-stressed plants revealed that changes to the DNA methylation status of genotype-specific genes are associated with the epigenetic regulation of drought stress responses. Transcriptome analysis further helped to identify a set of 12 and 23 DMR-associated genes that were differentially expressed in DK151 and IR64, respectively, under drought stress compared with respective controls. Correlation analysis indicated that DNA methylation has various effects on gene expression, implying that it affects gene expression directly or indirectly through diverse regulatory pathways. Our results indicate that drought-induced alterations to DNA methylation may influence an epigenetic mechanism that regulates the expression of unique genes responsible for drought stress tolerance.
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Affiliation(s)
- Wensheng Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
| | - Qiao Qin
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
| | - Fan Sun
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yinxiao Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
| | - Dandan Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
- College of Agronomy, Anhui Agricultural UniversityHefei, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
- Shenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural SciencesShenzhen, China
| | - Binying Fu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
- Shenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural SciencesShenzhen, China
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Muthusamy M, Uma S, Backiyarani S, Saraswathi MS, Chandrasekar A. Transcriptomic Changes of Drought-Tolerant and Sensitive Banana Cultivars Exposed to Drought Stress. FRONTIERS IN PLANT SCIENCE 2016; 7:1609. [PMID: 27867388 PMCID: PMC5095140 DOI: 10.3389/fpls.2016.01609] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 10/12/2016] [Indexed: 05/23/2023]
Abstract
In banana, drought responsive gene expression profiles of drought-tolerant and sensitive genotypes remain largely unexplored. In this research, the transcriptome of drought-tolerant banana cultivar (Saba, ABB genome) and sensitive cultivar (Grand Naine, AAA genome) was monitored using mRNA-Seq under control and drought stress condition. A total of 162.36 million reads from tolerant and 126.58 million reads from sensitive libraries were produced and mapped onto the Musa acuminata genome sequence and assembled into 23,096 and 23,079 unigenes. Differential gene expression between two conditions (control and drought) showed that at least 2268 and 2963 statistically significant, functionally known, non-redundant differentially expressed genes (DEGs) from tolerant and sensitive libraries. Drought has up-regulated 991 and 1378 DEGs and down-regulated 1104 and 1585 DEGs respectively in tolerant and sensitive libraries. Among DEGs, 15.9% are coding for transcription factors (TFs) comprising 46 families and 9.5% of DEGs are constituted by protein kinases from 82 families. Most enriched DEGs are mainly involved in protein modifications, lipid metabolism, alkaloid biosynthesis, carbohydrate degradation, glycan metabolism, and biosynthesis of amino acid, cofactor, nucleotide-sugar, hormone, terpenoids and other secondary metabolites. Several, specific genotype-dependent gene expression pattern was observed for drought stress in both cultivars. A subset of 9 DEGs was confirmed using quantitative reverse transcription-PCR. These results will provide necessary information for developing drought-resilient banana plants.
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Affiliation(s)
| | - Subbaraya Uma
- *Correspondence: Subbaraya Uma, Muthusamy Muthusamy,
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57
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Ku L, Tian L, Su H, Wang C, Wang X, Wu L, Shi Y, Li G, Wang Z, Wang H, Song X, Dou D, Ren Z, Chen Y. Dual functions of the ZmCCT-associated quantitative trait locus in flowering and stress responses under long-day conditions. BMC PLANT BIOLOGY 2016; 16:239. [PMID: 27809780 PMCID: PMC5094027 DOI: 10.1186/s12870-016-0930-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/24/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND Photoperiodism refers to the ability of plants to measure day length to determine the season. This ability enables plants to coordinate internal biological activities with external changes to ensure normal growth. However, the influence of the photoperiod on maize flowering and stress responses under long-day (LD) conditions has not been analyzed by comparative transcriptome sequencing. The ZmCCT gene was previously identified as a homolog of the rice photoperiod response regulator Ghd7, and associated with the major quantitative trait locus (QTL) responsible for Gibberella stalk rot resistance in maize. However, its regulatory mechanism has not been characterized. RESULTS We mapped the ZmCCT-associated QTL (ZmCCT-AQ), which is approximately 130 kb long and regulates photoperiod responses and resistance to Gibberella stalk rot and drought in maize. To investigate the effects of ZmCCT-AQ under LD conditions, the transcriptomes of the photoperiod-insensitive inbred line Huangzao4 (HZ4) and its near-isogenic line (HZ4-NIL) containing ZmCCT-AQ were sequenced. A set of genes identified by RNA-seq exhibited higher basal expression levels in HZ4-NIL than in HZ4. These genes were associated with responses to circadian rhythm changes and biotic and abiotic stresses. The differentially expressed genes in the introgressed regions of HZ4-NIL conferred higher drought and heat tolerance, and stronger disease resistance relative to HZ4. Co-expression analysis and the diurnal expression rhythms of genes related to stress responses suggested that ZmCCT and one of the circadian clock core genes, ZmCCA1, are important nodes linking the photoperiod to stress tolerance responses under LD conditions. CONCLUSION Our study revealed that the photoperiod influences flowering and stress responses under LD conditions. Additionally, ZmCCT and ZmCCA1 are important functional links between the circadian clock and stress tolerance. The establishment of this particular molecular link has uncovered a new relationship between plant photoperiodism and stress responses.
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Affiliation(s)
- Lixia Ku
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Lei Tian
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Huihui Su
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Cuiling Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471003 China
| | - Xiaobo Wang
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Liuji Wu
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Yong Shi
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Guohui Li
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Zhiyong Wang
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Huitao Wang
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Xiaoheng Song
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Dandan Dou
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Zhaobin Ren
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Yanhui Chen
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
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Zhang C, Liu J, Zhao T, Gomez A, Li C, Yu C, Li H, Lin J, Yang Y, Liu B, Lin C. A Drought-Inducible Transcription Factor Delays Reproductive Timing in Rice. PLANT PHYSIOLOGY 2016; 171:334-43. [PMID: 26945049 PMCID: PMC4854678 DOI: 10.1104/pp.16.01691] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/02/2016] [Indexed: 05/04/2023]
Abstract
The molecular mechanisms underlying photoperiod or temperature control of flowering time have been recently elucidated, but how plants regulate flowering time in response to other external factors, such as water availability, remains poorly understood. Using a large-scale Hybrid Transcription Factor approach, we identified a bZIP transcriptional factor, O. sativa ABA responsive element binding factor 1 (OsABF1), which acts as a suppressor of floral transition in a photoperiod-independent manner. Simultaneous knockdown of both OsABF1 and its closest homologous gene, OsbZIP40, in rice (Oryza sativa) by RNA interference results in a significantly earlier flowering phenotype. Molecular and genetic analyses demonstrate that a drought regime enhances expression of the OsABF1 gene, which indirectly suppresses expression of the Early heading date 1 (Ehd1) gene that encodes a key activator of rice flowering. Furthermore, we identified a drought-inducible gene named OsWRKY104 that is under the direct regulation of OsABF1 Overexpression of OsWRKY104 can suppress Ehd1 expression and confers a later flowering phenotype in rice. Together, these findings reveal a novel pathway by which rice modulates heading date in response to the change of ambient water availability.
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Affiliation(s)
- Chunyu Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Jun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Tao Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Adam Gomez
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Cong Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Chunsheng Yu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Hongyu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Jianzhong Lin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Yuanzhu Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Bin Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
| | - Chentao Lin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China (C.Z., J.L., T.Z., C.L., C.Y., H.L., B.L.); College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China (J.L.); State Key Laboratory of Hybrid Rice, Yahua Seeds Science Academy of Hunan, Changsha, 410119, China (Y.Y.); and Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 (A.G., C.L.)
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Hosseini SA, Hajirezaei MR, Seiler C, Sreenivasulu N, von Wirén N. A Potential Role of Flag Leaf Potassium in Conferring Tolerance to Drought-Induced Leaf Senescence in Barley. FRONTIERS IN PLANT SCIENCE 2016; 7:206. [PMID: 26955376 PMCID: PMC4768371 DOI: 10.3389/fpls.2016.00206] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 02/06/2016] [Indexed: 05/03/2023]
Abstract
Terminal drought stress decreases crop yields by inducing abscisic acid (ABA) and premature leaf senescence. As potassium (K) is known to interfere with ABA homeostasis we addressed the question whether there is genetic variability regarding the role of K nutrition in ABA homeostasis and drought tolerance. To compare their response to drought stress, two barley lines contrasting in drought-induced leaf senescence were grown in a pot experiment under high and low K supply for the analysis of flag leaves from the same developmental stage. Relative to the drought-sensitive line LPR, the line HPR retained more K in its flag leaves under low K supply and showed delayed flag leaf senescence under terminal drought stress. High K retention was further associated with a higher leaf water status, a higher concentration of starch and other primary carbon metabolites. With regard to ABA homeostasis, HPR accumulated less ABA but higher levels of the ABA degradation products phaseic acid (PA) and dehydro-PA. Under K deficiency this went along with higher transcript levels of ABA8'-HYDROXYLASE, encoding a key enzyme in ABA degradation. The present study provides evidence for a positive impact of the K nutritional status on ABA homeostasis and carbohydrate metabolism under drought stress. We conclude that genotypes with a high K nutritional status in the flag leaf show superior drought tolerance by promoting ABA degradation but attenuating starch degradation which delays flag leaf senescence. Flag leaf K levels may thus represent a useful trait for the selection of drought-tolerant barley cultivars.
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Affiliation(s)
- Seyed A. Hosseini
- Molecular Plant Nutrition Group, Physiology and Cell Biology, Leibniz-Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Mohammad R. Hajirezaei
- Molecular Plant Nutrition Group, Physiology and Cell Biology, Leibniz-Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Christiane Seiler
- Abiotic Stress Genomics Group, Molecular Genetics, Leibniz-Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Nese Sreenivasulu
- Abiotic Stress Genomics Group, Molecular Genetics, Leibniz-Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Nicolaus von Wirén
- Molecular Plant Nutrition Group, Physiology and Cell Biology, Leibniz-Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
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60
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Comparative transcriptome analysis highlights the crucial roles of photosynthetic system in drought stress adaptation in upland rice. Sci Rep 2016; 6:19349. [PMID: 26777777 PMCID: PMC4726002 DOI: 10.1038/srep19349] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 12/01/2015] [Indexed: 11/19/2022] Open
Abstract
Drought stress is one of the major adverse environmental factors reducing plant growth. With the aim to elucidate the underlying molecular basis of rice response to drought stress, comparative transcriptome analysis was conducted between drought susceptible rice cultivar Zhenshan97 and tolerant cultivar IRAT109 at the seedling stage. 436 genes showed differential expression and mainly enriched in the Gene Ontology (GO) terms of stress defence. A large number of variations exist between these two genotypes including 2564 high-quality insertion and deletions (INDELs) and 70,264 single nucleotide polymorphism (SNPs). 1041 orthologous gene pairs show the ratio of nonsynonymous nucleotide substitution rate to synonymous nucleotide substitutions rate (Ka/Ks) larger than 1.5, indicating the rapid adaptation to different environments during domestication. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of positive selection genes suggested that photosynthesis represents the most significant category. The collocation of positively selected genes with the QTLs of photosynthesis and the different photosynthesis performance of these two cultivars further illuminate the crucial function of photosynthesis in rice adaptation to drought stress. Our results also provide fruitful functional markers and candidate genes for future genetic research and improvement of drought tolerance in rice.
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61
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Liu CH, Fan C. De novo Transcriptome Assembly of Floral Buds of Pineapple and Identification of Differentially Expressed Genes in Response to Ethephon Induction. FRONTIERS IN PLANT SCIENCE 2016; 7:203. [PMID: 26955375 PMCID: PMC4767906 DOI: 10.3389/fpls.2016.00203] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 02/05/2016] [Indexed: 05/11/2023]
Abstract
A remarkable characteristic of pineapple is its ability to undergo floral induction in response to external ethylene stimulation. However, little information is available regarding the molecular mechanism underlying this process. In this study, the differentially expressed genes (DEGs) in plants exposed to 1.80 mL·L(-1) (T1) or 2.40 mL·L(-1) ethephon (T2) compared with Ct plants (control, cleaning water) were identified using RNA-seq and gene expression profiling. Illumina sequencing generated 65,825,224 high-quality reads that were assembled into 129,594 unigenes with an average sequence length of 1173 bp. Of these unigenes, 24,775 were assigned to specific KEGG pathways, of which metabolic pathways and biosynthesis of secondary metabolites were the most highly represented. Gene Ontology (GO) analysis of the annotated unigenes revealed that the majority were involved in metabolic and cellular processes, cell and cell part, catalytic activity and binding. Gene expression profiling analysis revealed 3788, 3062, and 758 DEGs in the comparisons of T1 with Ct, T2 with Ct, and T2 with T1, respectively. GO analysis indicated that these DEGs were predominantly annotated to metabolic and cellular processes, cell and cell part, catalytic activity, and binding. KEGG pathway analysis revealed the enrichment of several important pathways among the DEGs, including metabolic pathways, biosynthesis of secondary metabolites and plant hormone signal transduction. Thirteen DEGs were identified as candidate genes associated with the process of floral induction by ethephon, including three ERF-like genes, one ETR-like gene, one LTI-like gene, one FT-like gene, one VRN1-like gene, three FRI-like genes, one AP1-like gene, one CAL-like gene, and one AG-like gene. qPCR analysis indicated that the changes in the expression of these 13 candidate genes were consistent with the alterations in the corresponding RPKM values, confirming the accuracy and credibility of the RNA-seq and gene expression profiling results. Ethephon-mediated induction likely mimics the process of vernalization in the floral transition in pineapple by increasing LTI, FT, and VRN1 expression and promoting the up-regulation of floral meristem identity genes involved in flower development. The candidate genes screened can be used in investigations of the molecular mechanisms of the flowering pathway and of various other biological mechanisms in pineapple.
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Affiliation(s)
- Chuan-He Liu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural SciencesGuangzhou, China
- Key Laboratory of South Subtropical Fruit Biology, Genetic Resource Utilization Ministry of AgricultureGuangzhou, China
- *Correspondence: Chuan-He Liu
| | - Chao Fan
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural SciencesGuangzhou, China
- Key Laboratory of South Subtropical Fruit Biology, Genetic Resource Utilization Ministry of AgricultureGuangzhou, China
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Buffon G, Blasi ÉAR, Adamski JM, Ferla NJ, Berger M, Santi L, Lavallée-Adam M, Yates JR, Beys-da-Silva WO, Sperotto RA. Physiological and Molecular Alterations Promoted by Schizotetranychus oryzae Mite Infestation in Rice Leaves. J Proteome Res 2015; 15:431-46. [PMID: 26667653 DOI: 10.1021/acs.jproteome.5b00729] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Infestation of phytophagous mite Schizotetranychus oryzae in rice causes critical yield losses. To better understand this interaction, we employed Multidimensional Protein Identification Technology (MudPIT) approach to identify differentially expressed proteins. We detected 18 and 872 unique proteins in control and infested leaves, respectively, along with 32 proteins more abundant in control leaves. S. oryzae infestation caused decreased abundance of proteins related to photosynthesis (mostly photosystem II-related), carbon assimilation and energy production, chloroplast detoxification, defense, and fatty acid and gibberellin synthesis. On the contrary, infestation caused increased abundance of proteins involved in protein modification and degradation, gene expression at the translation level, protein partitioning to different organelles, lipid metabolism, actin cytoskeleton remodeling, and synthesis of jasmonate, amino acid, and molecular chaperones. Our results also suggest that S. oryzae infestation promotes cell-wall remodeling and interferes with ethylene biosynthesis in rice leaves. Proteomic data were positively correlated with enzymatic assays and RT-qPCR analysis. Our findings describe the protein expression patterns of infested rice leaves and suggest that the acceptor side of PSII is probably the major damaged target in the photosynthetic apparatus. These data will be useful in future biotechnological approaches aiming to induce phytophagous mite resistance in rice.
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Affiliation(s)
| | | | | | | | | | | | - Mathieu Lavallée-Adam
- Department of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92037, United States
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Moumeni A, Satoh K, Venuprasad R, Serraj R, Kumar A, Leung H, Kikuchi S. Transcriptional profiling of the leaves of near-isogenic rice lines with contrasting drought tolerance at the reproductive stage in response to water deficit. BMC Genomics 2015; 16:1110. [PMID: 26715311 PMCID: PMC4696290 DOI: 10.1186/s12864-015-2335-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 12/19/2015] [Indexed: 02/05/2023] Open
Abstract
Background Drought tolerance is a complex quantitative trait that involves the coordination of a vast array of genes belonging to different pathways. To identify genes related to the drought-tolerance pathway in rice, we carried out gene-expression profiling of the leaves of near-isogenic lines (NILs) with similar genetic backgrounds and different set of QTLs but contrasting drought tolerance levels in response to long-term drought-stress treatments. This work will help differentiate mechanisms of tolerance in contrasting NILs and accelerate molecular breeding programs to improve drought tolerance in this crop. Results The two pairs of rice NILs, developed at the International Rice Research Institute, along with the drought-susceptible parent, IR64, showed distinct gene-expression profiles in leaves under different water-deficit (WD) treatments. Drought tolerance in the highly drought-tolerant NIL (DTN), IR77298-14-1-2-B-10, could be attributed to the up-regulation of genes with calcium ion binding, transferase, hydrolase and transcription factor activities, whereas in the moderate DTN, IR77298-5-6-B-18, genes with transporter, catalytic and structural molecule activities were up-regulated under WD. In IR77298-14-1-2-B-10, the induced genes were characterized by the presence of regulatory motifs in their promoters, including TGGTTAGTACC and ([CT]AAC[GT]G){2}, which are specific to the TFIIIA and Myb transcription factors, respectively. In IR77298-5-6-B-18, promoters containing a GCAC[AG][ACGT][AT]TCCC[AG]A[ACGT]G[CT] motif, common to MADS(AP1), HD-ZIP, AP2 and YABBY, were induced, suggesting that these factors may play key roles in the regulation of drought tolerance in these two DTNs under severe WD. Conclusions We report here that the two pairs of NILs with different levels of drought tolerance may elucidate potential mechanisms and pathways through transcriptome data from leaf tissue. The present study serves as a resource for marker discovery and provides detailed insight into the gene-expression profiles of rice leaves, including the main functional categories of drought-responsive genes and the genes that are involved in drought-tolerance mechanisms, to help breeders identify candidate genes (both up- and down-regulated) associated with drought tolerance and suitable targets for manipulating the drought-tolerance trait in rice. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2335-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ali Moumeni
- Rice Research Institute of Iran, Mazandaran Branch, Agricultural Research, Education and Extension Organization (AREEO), PO Box 145, Postal Code 46191-91951, Km8 Babol Rd., Amol, Mazandaran, Iran.
| | - Kouji Satoh
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Kan'non dai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Ramiah Venuprasad
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, Philippines. .,Africa Rice Centre (AfricaRice), Ibadan station, c/o IITA, PMB 5320 Oyo road, Ibadan, Nigeria.
| | - Rachid Serraj
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, Philippines. .,Agricultural Research (CGIAR ISPC), FAO, Rome, Italy.
| | - Arvind Kumar
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, Philippines.
| | - Hei Leung
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, Philippines.
| | - Shoshi Kikuchi
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Kan'non dai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan.
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64
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Shi B, Huang Z, Xiang X, Huang M, Wang WX, Ke C. Transcriptome analysis of the key role of GAT2 gene in the hyper-accumulation of copper in the oyster Crassostrea angulata. Sci Rep 2015; 5:17751. [PMID: 26648252 PMCID: PMC4673431 DOI: 10.1038/srep17751] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 11/03/2015] [Indexed: 11/26/2022] Open
Abstract
One paradigm of oysters as the hyper-accumulators of many toxic metals is the inter-individual variation of metals, but the molecular mechanisms remain very elusive. A comprehensive analysis of the transcriptome of Crassostrea angulata was conducted to reveal the relationship between gene expression and differential Cu body burden in oysters. Gene ontology analysis for the differentially expressed genes showed that the neurotransmitter transporter might affect the oyster behavior, which in turn led to difference in Cu accumulation. The ATP-binding cassette transporters superfamily played an important role in the maintenance of cell Cu homeostasis, vitellogenin and apolipophorin transport, and elimination of excess Cu. Gill and mantle Cu concentrations were significantly reduced after silencing the GABA transporter 2 (GAT2) gene, but increased after the injection of GABA receptor antagonists, suggesting that the function of GABA transporter 2 gene was strongly related to Cu accumulation. These findings demonstrated that GABA transporter can control the action of transmitter GABA in the nervous system, thereby affecting the Cu accumulation in the gills and mantles.
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Affiliation(s)
- Bo Shi
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, PR China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, PR China
| | - Zekun Huang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, PR China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, PR China
| | - Xu Xiang
- School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Miaoqin Huang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, PR China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, PR China
| | - Wen-Xiong Wang
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, PR China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, PR China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, PR China
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Prince SJ, Joshi T, Mutava RN, Syed N, Joao Vitor MDS, Patil G, Song L, Wang J, Lin L, Chen W, Shannon JG, Valliyodan B, Xu D, Nguyen HT. Comparative analysis of the drought-responsive transcriptome in soybean lines contrasting for canopy wilting. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 240:65-78. [PMID: 26475188 DOI: 10.1016/j.plantsci.2015.08.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 08/17/2015] [Accepted: 08/22/2015] [Indexed: 05/20/2023]
Abstract
Drought stress causes significant yield losses in major oil seed crops, such as soybean [Glycine max (L.) Merr]. Few soybean lines have been identified as canopy-wilting tolerant; however, the molecular mechanism conferring tolerance is not fully understood. To understand the biological process, a whole genome transcriptome analysis was performed for leaf tissues of two contrasting soybean lines: drought-susceptible (DS) Pana and drought-tolerant (DT) PI 567690. A pairwise comparison of the DS and DT lines under drought and control conditions detected 1914 and 670 genes with a greater than two-fold change in expression under drought conditions. Pairwise treatment comparison and gene enrichment analysis on the DT line showed the down-regulation of genes associated with protein binding, hydrolase activity, carbohydrate/lipid metabolism, xyloglucan endo-transglycosylases associated with cell-wall, apoplast, and chlorophyll a/b binding proteins. On the other hand, genes that were associated with the biotic stress response, ion binding and transport, the oxido-reductive process and electron carrier activity were up-regulated. Gene enrichment analysis detected UDP glucuronosyl transferase activity-encoding genes to be differentially expressed in PI 567690 under drought stress conditions. We found valuable SNPs variation in aquaporin genes of the DT line that are conserved in known slower canopy-wilting lines, this should facilitate marker-assisted selection in soybeans with improved drought tolerance.
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Affiliation(s)
- Silvas J Prince
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA
| | - Trupti Joshi
- Department of Computer Science, Informatics Institute, University of Missouri, Columbia, MO 65211, USA
| | - Raymond N Mutava
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA
| | - Naeem Syed
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury CT1 1QU, United Kingdom
| | | | - Gunvant Patil
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA
| | - Li Song
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA
| | - JiaoJiao Wang
- Department of Computer Science, Informatics Institute, University of Missouri, Columbia, MO 65211, USA
| | - Li Lin
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA
| | - Wei Chen
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA
| | - J Grover Shannon
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA
| | - Babu Valliyodan
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA
| | - Dong Xu
- Department of Computer Science, Informatics Institute, University of Missouri, Columbia, MO 65211, USA; School of Human and Life Sciences, Canterbury Christ Church University, Canterbury CT1 1QU, United Kingdom
| | - Henry T Nguyen
- National Center for Soybean Biotechnology and Division of Plant Sciences University of Missouri, Columbia, MO 65211, USA.
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Mondal TK, Ganie SA, Debnath AB. Identification of Novel and Conserved miRNAs from Extreme Halophyte, Oryza coarctata, a Wild Relative of Rice. PLoS One 2015; 10:e0140675. [PMID: 26506249 PMCID: PMC4623511 DOI: 10.1371/journal.pone.0140675] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/29/2015] [Indexed: 01/25/2023] Open
Abstract
Oryza coarctata, a halophyte and wild relative of rice, is grown normally in saline water. MicroRNAs (miRNAs) are non-coding RNAs that play pivotal roles in every domain of life including stress response. There are very few reports on the discovery of salt-responsive miRNAs from halophytes. In this study, two small RNA libraries, one each from the control and salt-treated (450 mM NaCl for 24 h) leaves of O. coarctata were sequenced, which yielded 338 known and 95 novel miRNAs. Additionally, we used publicly available transcriptomics data of O. coarctata which led to the discovery of additional 48 conserved miRNAs along with their pre-miRNA sequences through in silico analysis. In total, 36 known and 7 novel miRNAs were up-regulated whereas, 12 known and 7 novel miRNAs were down-regulated under salinity stress. Further, 233 and 154 target genes were predicted for 48 known and 14 novel differentially regulated miRNAs respectively. These targets with the help of gene ontology analysis were found to be involved in several important biological processes that could be involved in salinity tolerance. Relative expression trends of majority of the miRNAs as detected by real time-PCR as well as predicted by Illumina sequencing were found to be coherent. Additionally, expression of most of the target genes was negatively correlated with their corresponding miRNAs. Thus, the present study provides an account of miRNA-target networking that is involved in salinity adaption of O. coarctata.
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Affiliation(s)
- Tapan Kumar Mondal
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi-4, 110012, India
| | - Showkat Ahmad Ganie
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi-4, 110012, India
| | - Ananda Bhusan Debnath
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi-4, 110012, India
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Comparative Analysis of the Brassica napus Root and Leaf Transcript Profiling in Response to Drought Stress. Int J Mol Sci 2015; 16:18752-77. [PMID: 26270661 PMCID: PMC4581270 DOI: 10.3390/ijms160818752] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 02/03/2023] Open
Abstract
Drought stress is one of the major abiotic factors affecting Brassica napus (B. napus) productivity. In order to identify genes of potential importance to drought stress and obtain a deeper understanding of the molecular mechanisms regarding the responses of B. napus to dehydration stress, we performed large-scale transcriptome sequencing of B. napus plants under dehydration stress using the Illumina sequencing technology. In this work, a relatively drought tolerant B. napus line, Q2, identified in our previous study, was used. Four cDNA libraries constructed from mRNAs of control and dehydration-treated root and leaf were sequenced by Illumina technology. A total of 6018 and 5377 differentially expressed genes (DEGs) were identified in root and leaf. In addition, 1745 genes exhibited a coordinated expression profile between the two tissues under drought stress, 1289 (approximately 74%) of which showed an inverse relationship, demonstrating different regulation patterns between the root and leaf. The gene ontology (GO) enrichment test indicated that up-regulated genes in root were mostly involved in “stimulus” “stress” biological process, and activated genes in leaf mainly functioned in “cell” “cell part” components. Furthermore, a comparative network related to plant hormone signal transduction and AREB/ABF, AP2/EREBP, NAC, WRKY and MYC/MYB transcription factors (TFs) provided a view of different stress tolerance mechanisms between root and leaf. Some of the DEGs identified may be candidates for future research aimed at detecting drought-responsive genes and will be useful for understanding the molecular mechanisms of drought tolerance in root and leaf of B. napus.
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