1
|
Fu C, Zhou Y, Liu A, Chen R, Yin L, Li C, Mao H. Genome-wide association study for seedling heat tolerance under two temperature conditions in bread wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2024; 24:430. [PMID: 38773371 PMCID: PMC11107014 DOI: 10.1186/s12870-024-05116-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND As the greenhouse effect intensifies, global temperatures are steadily increasing, posing a challenge to bread wheat (Triticum aestivum L.) production. It is imperative to comprehend the mechanism of high temperature tolerance in wheat and implement breeding programs to identify and develop heat-tolerant wheat germplasm and cultivars. RESULTS To identify quantitative trait loci (QTL) related to heat stress tolerance (HST) at seedling stage in wheat, a panel of 253 wheat accessions which were re-sequenced used to conduct genome-wide association studies (GWAS) using the factored spectrally transformed linear mixed models (FaST-LMM). For most accessions, the growth of seedlings was found to be inhibited under heat stress. Analysis of the phenotypic data revealed that under heat stress conditions, the main root length, total root length, and shoot length of seedlings decreased by 47.46%, 49.29%, and 15.19%, respectively, compared to those in normal conditions. However, 17 varieties were identified as heat stress tolerant germplasm. Through GWAS analysis, a total of 115 QTLs were detected under both heat stress and normal conditions. Furthermore, 15 stable QTL-clusters associated with heat response were identified. By combining gene expression, haplotype analysis, and gene annotation information within the physical intervals of the 15 QTL-clusters, two novel candidate genes, TraesCS4B03G0152700/TaWRKY74-B and TraesCS4B03G0501400/TaSnRK3.15-B, were responsive to temperature and identified as potential regulators of HST in wheat at the seedling stage. CONCLUSIONS This study conducted a detailed genetic analysis and successfully identified two genes potentially associated with HST in wheat at the seedling stage, laying a foundation to further dissect the regulatory mechanism underlying HST in wheat under high temperature conditions. Our finding could serve as genomic landmarks for wheat breeding aimed at improving adaptation to heat stress in the face of climate change.
Collapse
Affiliation(s)
- Chao Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ying Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ankui Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rui Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Yin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cong Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
2
|
Azameti MK, Ranjan A, Singh PK, Gaikwad K, Singh AK, Dalal M, Arora A, Rai V, Padaria JC. Transcriptome profiling reveals the genes and pathways involved in thermo-tolerance in wheat (Triticum aestivum L.) genotype Raj 3765. Sci Rep 2022; 12:14831. [PMID: 36050336 PMCID: PMC9437100 DOI: 10.1038/s41598-022-18625-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
Wheat, one of the most widely consumed staple food crops globally, is relatively vulnerable to high temperature-induced heat stress. It is therefore essential to gain more insight into the comprehensive mechanism of thermotolerance of wheat in order to safeguard its production. In view of this, we analysed heat stress responsive transcriptome data of wheat to determine its gene expression level under heat stress. A total of 7990 DEGs, including 4483 up-regulated and 3507 down regulated genes were identified. Gene Ontology (GO) analysis categorized 3910 DEGs into different ontology families. 146 pathways involving 814 DEGs were enriched during KEGG analysis. Metabolic pathways and biosynthesis of secondary metabolites were the major pathways enriched. MYB (myeloblastosis) transcription factors (TFs) and many other TFs as bHLH, WRKY, NAC, ERF, were determined to be quite abundant in the DEGs. Since various reports indicate that these TFs play important role in plants abiotic stress, it is an indication that our DEGs are functional in heat stress tolerance. Verification of few selected DEGs using RT-qPCR produced expression levels similar to the transcriptome data. This indicates that the transcriptome data is reliable. These results could be helpful in enhancing our understanding of the mechanism underlying thermotolerance in wheat.
Collapse
Affiliation(s)
- Mawuli K Azameti
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.,ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.,CSIR-Food Research Institute, Accra, Ghana
| | - Alok Ranjan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - P K Singh
- Division of Genetics, Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Anil Kumar Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Monika Dalal
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Ajay Arora
- Division of Plant Physiology, Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Vandna Rai
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Jasdeep C Padaria
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India. .,ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
| |
Collapse
|
3
|
Zhang Y, Du P, Xiong F, Zhang X, Song H. WRKY Genes Improve Drought Tolerance in Arachis duranensis. FRONTIERS IN PLANT SCIENCE 2022; 13:910408. [PMID: 35720609 PMCID: PMC9199494 DOI: 10.3389/fpls.2022.910408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
WRKY transcription factor participates in plant growth and development and response to biotic and abiotic stresses. Arachis duranensis, a turfgrass, has high drought tolerance, yet little is known about AdWRKYs response to drought stress in A. duranensis. In this study, RNA-seq identified five AdWRKYs, including AdWRKY18, AdWRKY40, AdWRKY42, AdWRKY56, and AdWRKY64, which were upregulated under drought stress. Orthologous relationships between AdWRKYs and Arabidopsis WRKY were determined to predict the regulatory networks of the five AdWRKYs based on AtWRKYs. Additionally, protein-protein interactions were predicted using differentially expressed proteins from RNA-seq. The quantitative real-time PCR (qRT-PCR) results showed that AdWRKY40 was upregulated, while AdWRKY42, AdWRKY56, and AdWRKY64 were downregulated at different time-points under drought stress. The predicted regulatory networks showed that AdWRKY40 activates COR47, RD21, and RD29A expression under drought stress. Besides, AdWRKY56 regulated CesA8 under drought stress. Aradu.YIQ80 (NAC019) interacted with AdWRKY40, AdWRKY42, AdWRKY56, and AdWRKY64, while Aradu.Z5H58 (NAC055) interacted with AdWRKY42 and AdWRKY64 under drought stress. This study used Arabidopsis to assess AdWRKYs function and regulatory networks, providing a basis for understanding drought tolerance in A. duranensis.
Collapse
Affiliation(s)
- Yongli Zhang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Pei Du
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, China
| | - Faqian Xiong
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiaojun Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Hui Song
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| |
Collapse
|
4
|
Han S, Jiang S, Xiong R, Shafique K, Zahid KR, Wang Y. Response and tolerance mechanism of food crops under high temperature stress: a review. BRAZ J BIOL 2022; 82:e253898. [PMID: 35107484 DOI: 10.1590/1519-6984.253898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 11/23/2021] [Indexed: 01/15/2023] Open
Abstract
High temperature stress events are critical factors inhibiting crop yield. Meanwhile, world population is growing very rapidly and will be reached up to 9 billion by 2050. To feed increasing world population, it is challenging task to increase about 70% global food productions. Food crops have significant contribution toward global food demand and food security. However, consequences from increasing heat stress events are demolishing their abilities to survive and sustain yield when subjected to extreme high temperature stress. Therefore, there is dire need to better understand response and tolerance mechanism of food crops following exposure to heat stress. Here, we aimed to provide recent update on impact of high temperature stress on crop yield of food crops, pollination, pollinators, and novel strategies for improving tolerance of food crop under high temperature stress. Importantly, development of heat-resistant transgenic food crops can grant food security through transformation of superior genes into current germplasm, which are associated with various signaling pathways as well as epigenetic regulation in response to extreme high temperature stress.
Collapse
Affiliation(s)
- S Han
- Liupanshui Normal University, School of Biological Sciences and Technology, Liupanshui, China
| | - S Jiang
- Zhengzhou Normal University, Bioengineering Research Center, Zhengzhou, Henan, P.R. China
| | - R Xiong
- Liupanshui Normal University, School of Biological Sciences and Technology, Liupanshui, China
| | - K Shafique
- Government Sadiq College Women University, Department of Botany, Bahawalpur, Pakistan
| | - K R Zahid
- Shenzhen University, Carson International Cancer Center, College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen, Guangdong, China
| | - Y Wang
- Liupanshui Normal University, School of Biological Sciences and Technology, Liupanshui, China
| |
Collapse
|
5
|
Plant Transcription Factors Involved in Drought and Associated Stresses. Int J Mol Sci 2021; 22:ijms22115662. [PMID: 34073446 PMCID: PMC8199153 DOI: 10.3390/ijms22115662] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/14/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022] Open
Abstract
Transcription factors (TFs) play a significant role in signal transduction networks spanning the perception of a stress signal and the expression of corresponding stress-responsive genes. TFs are multi-functional proteins that may simultaneously control numerous pathways during stresses in plants-this makes them powerful tools for the manipulation of regulatory and stress-responsive pathways. In recent years, the structure-function relationships of numerous plant TFs involved in drought and associated stresses have been defined, which prompted devising practical strategies for engineering plants with enhanced stress tolerance. Vast data have emerged on purposely basic leucine zipper (bZIP), WRKY, homeodomain-leucine zipper (HD-Zip), myeloblastoma (MYB), drought-response elements binding proteins/C-repeat binding factor (DREB/CBF), shine (SHN), and wax production-like (WXPL) TFs that reflect the understanding of their 3D structure and how the structure relates to function. Consequently, this information is useful in the tailored design of variant TFs that enhances our understanding of their functional states, such as oligomerization, post-translational modification patterns, protein-protein interactions, and their abilities to recognize downstream target DNA sequences. Here, we report on the progress of TFs based on their interaction pathway participation in stress-responsive networks, and pinpoint strategies and applications for crops and the impact of these strategies for improving plant stress tolerance.
Collapse
|
6
|
Crop reproductive meristems in the genomic era: a brief overview. Biochem Soc Trans 2020; 48:853-865. [PMID: 32573650 DOI: 10.1042/bst20190441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/15/2020] [Accepted: 05/27/2020] [Indexed: 11/17/2022]
Abstract
Modulation of traits beneficial for cultivation and yield is one of the main goals of crop improvement. One of the targets for enhancing productivity is changing the architecture of inflorescences since in many species it determines fruit and seed yield. Inflorescence shape and organization is genetically established during the early stages of reproductive development and depends on the number, arrangement, activities, and duration of meristems during the reproductive phase of the plant life cycle. Despite the variety of inflorescence architectures observable in nature, many key aspects of inflorescence development are conserved among different species. For instance, the genetic network in charge of specifying the identity of the different reproductive meristems, which can be indeterminate or determinate, seems to be similar among distantly related species. The availability of a large number of published transcriptomic datasets for plants with different inflorescence architectures, allowed us to identify transcription factor gene families that are differentially expressed in determinate and indeterminate reproductive meristems. The data that we review here for Arabidopsis, rice, barley, wheat, and maize, particularly deepens our knowledge of their involvement in meristem identity specification.
Collapse
|
7
|
Melatonin Suppressed the Heat Stress-Induced Damage in Wheat Seedlings by Modulating the Antioxidant Machinery. PLANTS 2020; 9:plants9070809. [PMID: 32605176 PMCID: PMC7412093 DOI: 10.3390/plants9070809] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/20/2020] [Accepted: 06/23/2020] [Indexed: 01/27/2023]
Abstract
Melatonin (N-acetyl-5-methoxytryptamine) is a pleiotropic signaling molecule that plays a crucial role in the regulation of various environmental stresses, including heat stress (HS). In this study, a 100 μM melatonin (MT) pretreatment followed by exposure to heat stress for different time periods was found to efficiently reduce oxidative stress by preventing the over-accumulation of hydrogen peroxide (H2O2), lowering the lipid peroxidation content (malondialdehyde (MDA) content), and increasing proline (Pro) biosynthesis. Moreover, the activities of antioxidant enzymes, such as superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD), were increased substantially in MT-pretreated wheat seedlings. The presence of MT significantly improved the heat tolerance of wheat seedlings by modulating their antioxidant defense system, activating the ascorbate–glutathione (AsA–GSH) cycle comprising ascorbate peroxidase (APX), and increasing glutathione reductase (GR) activities. It also held the photosynthetic machinery stable by increasing the chlorophyll content. Enhancement in the endogenous MT contents was also observed in the MT+HS-treated plants. Furthermore, the expression of reactive oxygen species (ROS)-related genes TaSOD, TaPOD, and TaCAT, and anti-stress responsive genes, such as TaMYB80, TaWRKY26, and TaWRKY39, was also induced in MT-treated seedlings. Due to these notable changes, an improvement in stress resistance was observed in MT-treated seedlings compared with control. Taken together, our findings suggest that MT can play a key role in boosting the stress tolerance of plants by modulating the antioxidant defense system and regulating the transcription of stress-responsive genes.
Collapse
|
8
|
Li H, Guan H, Zhuo Q, Wang Z, Li S, Si J, Zhang B, Feng B, Kong LA, Wang F, Wang Z, Zhang L. Genome-wide characterization of the abscisic acid-, stress- and ripening-induced (ASR) gene family in wheat (Triticum aestivum L.). Biol Res 2020; 53:23. [PMID: 32448297 PMCID: PMC7247183 DOI: 10.1186/s40659-020-00291-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 05/16/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Abscisic acid-, stress-, and ripening-induced (ASR) genes are a class of plant specific transcription factors (TFs), which play important roles in plant development, growth and abiotic stress responses. The wheat ASRs have not been described in genome-wide yet. METHODS We predicted the transmembrane regions and subcellular localization using the TMHMM server, and Plant-mPLoc server and CELLO v2.5, respectively. Then the phylogeny tree was built by MEGA7. The exon-intron structures, conserved motifs and TFs binding sites were analyzed by GSDS, MEME program and PlantRegMap, respectively. RESULTS In wheat, 33ASR genes were identified through a genome-wide survey and classified into six groups. Phylogenetic analyses revealed that the TaASR proteins in the same group tightly clustered together, compared with those from other species. Duplication analysis indicated that the TaASR gene family has expanded mainly through tandem and segmental duplication events. Similar gene structures and conserved protein motifs of TaASRs in wheat were identified in the same groups. ASR genes contained various TF binding cites associated with the stress responses in the promoter region. Gene expression was generally associated with the expected group-specific expression pattern in five tissues, including grain, leaf, root, spike and stem, indicating the broad conservation of ASR genes function during wheat evolution. The qRT-PCR analysis revealed that several ASRs were up-regulated in response to NaCl and PEG stress. CONCLUSION We identified ASR genes in wheat and found that gene duplication events are the main driving force for ASR gene evolution in wheat. The expression of wheat ASR genes was modulated in responses to multiple abiotic stresses, including drought/osmotic and salt stress. The results provided important information for further identifications of the functions of wheat ASR genes and candidate genes for high abiotic stress tolerant wheat breeding.
Collapse
Affiliation(s)
- Huawei Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongyebei Road, Jinan, 250100 China
| | - Haiying Guan
- Maize Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory of Wheat and Maize/Key Laboratory of Biology and Genetic Improvement of Maize in Northern Yellow-Huai Rivers Plain, Ministry of Agriculture, Jinan, 250100 Shandong China
| | - Qicui Zhuo
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongyebei Road, Jinan, 250100 China
| | - Zongshuai Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongyebei Road, Jinan, 250100 China
| | - Shengdong Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongyebei Road, Jinan, 250100 China
| | - Jisheng Si
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongyebei Road, Jinan, 250100 China
| | - Bin Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongyebei Road, Jinan, 250100 China
| | - Bo Feng
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongyebei Road, Jinan, 250100 China
| | - Ling-an Kong
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongyebei Road, Jinan, 250100 China
| | - Fahong Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongyebei Road, Jinan, 250100 China
| | - Zheng Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongyebei Road, Jinan, 250100 China
| | - Lishun Zhang
- Jinan Yongfeng Seed Industry Co., Ltd, 3620 Pingannan Road, Jinan, 250100 China
| |
Collapse
|
9
|
Villano C, Esposito S, D'Amelia V, Garramone R, Alioto D, Zoina A, Aversano R, Carputo D. WRKY genes family study reveals tissue-specific and stress-responsive TFs in wild potato species. Sci Rep 2020; 10:7196. [PMID: 32346026 PMCID: PMC7188836 DOI: 10.1038/s41598-020-63823-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/06/2020] [Indexed: 01/30/2023] Open
Abstract
Wild potatoes, as dynamic resource adapted to various environmental conditions, represent a powerful and informative reservoir of genes useful for breeding efforts. WRKY transcription factors (TFs) are encoded by one of the largest families in plants and are involved in several biological processes such as growth and development, signal transduction, and plant defence against stress. In this study, 79 and 84 genes encoding putative WRKY TFs have been identified in two wild potato relatives, Solanum commersonii and S. chacoense. Phylogenetic analysis of WRKY proteins divided ScWRKYs and SchWRKYs into three Groups and seven subGroups. Structural and phylogenetic comparative analyses suggested an interspecific variability of WRKYs. Analysis of gene expression profiles in different tissues and under various stresses allowed to select ScWRKY045 as a good candidate in wounding-response, ScWRKY055 as a bacterial infection triggered WRKY and ScWRKY023 as a multiple stress-responsive WRKY gene. Those WRKYs were further studied through interactome analysis allowing the identification of potential co-expression relationships between ScWRKYs/SchWRKYs and genes of various pathways. Overall, this study enabled the discrimination of WRKY genes that could be considered as potential candidates in both breeding programs and functional studies.
Collapse
Affiliation(s)
- Clizia Villano
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy
| | - Salvatore Esposito
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy.,CREA Via Cavalleggeri 25, 84098, Pontecagnano-Faiano, Italy
| | - Vincenzo D'Amelia
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy.,National Research Council of Italy, Institute of Biosciences and Bioresources (CNR-IBBR), Via Università 133, Portici, NA, Italy
| | - Raffaele Garramone
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy
| | - Daniela Alioto
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy
| | | | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy.
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055, Portici, Italy.
| |
Collapse
|
10
|
Javed T, Shabbir R, Ali A, Afzal I, Zaheer U, Gao SJ. Transcription Factors in Plant Stress Responses: Challenges and Potential for Sugarcane Improvement. PLANTS (BASEL, SWITZERLAND) 2020; 9:E491. [PMID: 32290272 PMCID: PMC7238037 DOI: 10.3390/plants9040491] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/08/2020] [Accepted: 04/08/2020] [Indexed: 02/06/2023]
Abstract
Increasing vulnerability of crops to a wide range of abiotic and biotic stresses can have a marked influence on the growth and yield of major crops, especially sugarcane (Saccharum spp.). In response to various stresses, plants have evolved a variety of complex defense systems of signal perception and transduction networks. Transcription factors (TFs) that are activated by different pathways of signal transduction and can directly or indirectly combine with cis-acting elements to modulate the transcription efficiency of target genes, which play key regulators for crop genetic improvement. Over the past decade, significant progresses have been made in deciphering the role of plant TFs as key regulators of environmental responses in particular important cereal crops; however, a limited amount of studies have focused on sugarcane. This review summarizes the potential functions of major TF families, such as WRKY, NAC, MYB and AP2/ERF, in regulating gene expression in the response of plants to abiotic and biotic stresses, which provides important clues for the engineering of stress-tolerant cultivars in sugarcane.
Collapse
Affiliation(s)
- Talha Javed
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.J.); (R.S.); (A.A.); (U.Z.)
- Seed Physiology Lab., Department of Agronomy, University of Agriculture, Faisalabad-38040, Pakistan;
| | - Rubab Shabbir
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.J.); (R.S.); (A.A.); (U.Z.)
- Seed Physiology Lab., Department of Agronomy, University of Agriculture, Faisalabad-38040, Pakistan;
| | - Ahmad Ali
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.J.); (R.S.); (A.A.); (U.Z.)
| | - Irfan Afzal
- Seed Physiology Lab., Department of Agronomy, University of Agriculture, Faisalabad-38040, Pakistan;
| | - Uroosa Zaheer
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.J.); (R.S.); (A.A.); (U.Z.)
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.J.); (R.S.); (A.A.); (U.Z.)
| |
Collapse
|
11
|
In silico based screening of WRKY genes for identifying functional genes regulated by WRKY under salt stress. Comput Biol Chem 2019; 83:107131. [DOI: 10.1016/j.compbiolchem.2019.107131] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/18/2019] [Accepted: 09/18/2019] [Indexed: 11/21/2022]
|
12
|
Baillo EH, Kimotho RN, Zhang Z, Xu P. Transcription Factors Associated with Abiotic and Biotic Stress Tolerance and Their Potential for Crops Improvement. Genes (Basel) 2019; 10:E771. [PMID: 31575043 PMCID: PMC6827364 DOI: 10.3390/genes10100771] [Citation(s) in RCA: 236] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/17/2019] [Accepted: 09/17/2019] [Indexed: 01/24/2023] Open
Abstract
In field conditions, crops are adversely affected by a wide range of abiotic stresses including drought, cold, salt, and heat, as well as biotic stresses including pests and pathogens. These stresses can have a marked effect on crop yield. The present and future effects of climate change necessitate the improvement of crop stress tolerance. Plants have evolved sophisticated stress response strategies, and genes that encode transcription factors (TFs) that are master regulators of stress-responsive genes are excellent candidates for crop improvement. Related examples in recent studies include TF gene modulation and overexpression approaches in crop species to enhance stress tolerance. However, much remains to be discovered about the diverse plant TFs. Of the >80 TF families, only a few, such as NAC, MYB, WRKY, bZIP, and ERF/DREB, with vital roles in abiotic and biotic stress responses have been intensively studied. Moreover, although significant progress has been made in deciphering the roles of TFs in important cereal crops, fewer TF genes have been elucidated in sorghum. As a model drought-tolerant crop, sorghum research warrants further focus. This review summarizes recent progress on major TF families associated with abiotic and biotic stress tolerance and their potential for crop improvement, particularly in sorghum. Other TF families and non-coding RNAs that regulate gene expression are discussed briefly. Despite the emphasis on sorghum, numerous examples from wheat, rice, maize, and barley are included. Collectively, the aim of this review is to illustrate the potential application of TF genes for stress tolerance improvement and the engineering of resistant crops, with an emphasis on sorghum.
Collapse
Affiliation(s)
- Elamin Hafiz Baillo
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
- Agricultural Research Corporation (ARC), Ministry of Agriculture, Gezira 21111, Sudan.
| | - Roy Njoroge Kimotho
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhengbin Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ping Xu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
13
|
Lachagari VBR, Gupta R, Lekkala SP, Mahadevan L, Kuriakose B, Chakravartty N, Mohan Katta AVSK, Santhosh S, Reddy AR, Thomas G. Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace ( Oryza sativa ssp. indica cv. Purpleputtu). FRONTIERS IN PLANT SCIENCE 2019; 10:513. [PMID: 31134103 PMCID: PMC6516047 DOI: 10.3389/fpls.2019.00513] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/03/2019] [Indexed: 05/27/2023]
Abstract
Purpleputtu (Oryza sativa ssp. indica cv. Purpleputtu) is a unique rice landrace from southern India that exhibits predominantly purple color. This study reports the underlying genetic complexity of the trait, associated domestication and de-domestication processes during its coevolution with present day cultivars. Along-with genome level allelic variations in the entire gene repertoire associated with the purple, red coloration of grain and other plant parts. Comparative genomic analysis using 'a panel of 108 rice lines' revealed a total of 3,200,951 variants including 67,774 unique variations in Purpleputtu (PP) genome. Multiple sequence alignment uncovered a 14 bp deletion in Rc (Red colored, a transcription factor of bHLH class) locus of PP, a key regulatory gene of anthocyanin biosynthetic pathway. Interestingly, this deletion in Rc gene is a characteristic feature of the present-day white pericarped rice cultivars. Phylogenetic analysis of Rc locus revealed a distinct clade showing proximity to the progenitor species Oryza rufipogon and O. nivara. In addition, PP genome exhibits a well conserved 4.5 Mbp region on chromosome 5 that harbors several loci associated with domestication of rice. Further, PP showed 1,387 unique when SNPs compared to 3,023 lines of rice (SNP-Seek database). The results indicate that PP genome is rich in allelic diversity and can serve as an excellent resource for rice breeding for a variety of agronomically important traits such as disease resistance, enhanced nutritional values, stress tolerance, and protection from harmful UV-B rays.
Collapse
Affiliation(s)
- V. B. Reddy Lachagari
- AgriGenome Labs Pvt. Ltd., Biotechnology Incubation Center, MN iHub, Genome Valley, Hyderabad, India
| | - Ravi Gupta
- Medgenome Labs Ltd., Bengaluru, India
- SciGenom Labs Pvt. Ltd., Cochin, India
| | - Sivarama Prasad Lekkala
- AgriGenome Labs Pvt. Ltd., Biotechnology Incubation Center, MN iHub, Genome Valley, Hyderabad, India
| | - Lakshmi Mahadevan
- Medgenome Labs Ltd., Bengaluru, India
- SciGenom Labs Pvt. Ltd., Cochin, India
| | - Boney Kuriakose
- SciGenom Research Foundation, Cheruthuruthy, India
- AgriGenome Labs Pvt. Ltd., Kakkanad, India
| | - Navajeet Chakravartty
- AgriGenome Labs Pvt. Ltd., Biotechnology Incubation Center, MN iHub, Genome Valley, Hyderabad, India
| | - A. V. S. K. Mohan Katta
- AgriGenome Labs Pvt. Ltd., Biotechnology Incubation Center, MN iHub, Genome Valley, Hyderabad, India
| | - Sam Santhosh
- SciGenom Research Foundation, Cheruthuruthy, India
| | - Arjula R. Reddy
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - George Thomas
- SciGenom Research Foundation, Cheruthuruthy, India
- AgriGenome Labs Pvt. Ltd., Kakkanad, India
| |
Collapse
|