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Mallikarjuna MG, Tomar R, Lohithaswa HC, Sahu S, Mishra DC, Rao AR, Chinnusamy V. Genome-wide identification of potassium channels in maize showed evolutionary patterns and variable functional responses to abiotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108235. [PMID: 38039585 DOI: 10.1016/j.plaphy.2023.108235] [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: 07/20/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023]
Abstract
Potassium (K) channels are essential components of plant biology, mediating not only K ion (K+) homeostasis but also regulating several physiological processes and stress tolerance. In the current investigation, we identified 27 K+ channels in maize and deciphered the evolution and divergence pattern with four monocots and five dicot species. Chromosomal localization and expansion of K+ channel genes showed uneven distribution and were independent of genome size. The dispersed duplication is the major force in expanding K+ channels in the target genomes. The mean Ka/Ks ratio of <0.5 in paralogs and orthologs indicates horizontal and vertical expansions of K+ channel genes under strong purifying selection. The one-to-one K+ channel orthologs were prominent among the closely related species, with higher synteny between maize and the rest of the monocots. Comprehensive K+ channels promoter analysis revealed various cis-regulatory elements mediating stress tolerance with the predominance of MYB and STRE binding sites. The regulatory network showed AP2-EREBP TFs, miR164 and miR399 are prominent regulatory elements of K+ channels. The qRT-PCR analysis of K+ channels and regulatory miRNAs showed significant expressions in response to drought and waterlogging stresses. The present study expanded the knowledge on K+ channels in maize and will serve as a basis for an in-depth functional analysis.
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Affiliation(s)
| | - Rakhi Tomar
- Division of Genetics, ICAR- Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Sarika Sahu
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Dwijesh Chandra Mishra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Atmakuri Ramakrishna Rao
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR- Indian Agricultural Research Institute, New Delhi, 110012, India
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2
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Singh A, Pandey H, Pandey S, Lal D, Chauhan D, Aparna, Antre SH, B S, Kumar A. Drought stress in maize: stress perception to molecular response and strategies for its improvement. Funct Integr Genomics 2023; 23:296. [PMID: 37697159 DOI: 10.1007/s10142-023-01226-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/13/2023]
Abstract
Given the future demand for food crops, increasing crop productivity in drought-prone rainfed areas has become essential. Drought-tolerant varieties are warranted to solve this problem in major crops, with drought tolerance as a high-priority trait for future research. Maize is one such crop affected by drought stress, which limits production, resulting in substantial economic losses. It became a more serious issue due to global climate change. The most drought sensitive among all stages of maize is the reproductive stages and the most important for overall maize production. The exact molecular basis of reproductive drought sensitivity remains unclear due to genes' complex regulation of drought stress. Understanding the molecular biology and signaling of the unexplored area of reproductive drought tolerance will provide an opportunity to develop climate-smart drought-tolerant next-generation maize cultivars. In recent decades, significant progress has been made in maize to understand the drought tolerance mechanism. However, improving maize drought tolerance through breeding is ineffective due to the complex nature and multigenic control of drought traits. With the help of advanced breeding techniques, molecular genetics, and a precision genome editing approach like CRISPR-Cas, candidate genes for drought-tolerant maize can be identified and targeted. This review summarizes the effects of drought stress on each growth stage of maize, potential genes, and transcription factors that determine drought tolerance. In addition, we discussed drought stress sensing, its molecular mechanisms, different approaches to developing drought-resistant maize varieties, and how molecular breeding and genome editing will help with the current unpredictable climate change.
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Affiliation(s)
- Ashutosh Singh
- Centre for Advanced Studies On Climate Change, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848125, India.
| | | | - Saurabh Pandey
- Department of Agriculture, Guru Nanak Dev University, Amritsar, Punjab, 143005, India.
| | - Dalpat Lal
- College of Agriculture, Jodhpur Agriculture University, Jodhpur, Rajasthan, 342304, India
| | - Divya Chauhan
- Banasthali University, Radha Kishanpura, Rajasthan, 304022, India
| | - Aparna
- Departments of Agriculture, Jagan Nath University, Jaipur, Rajasthan, 303901, India
| | - Suresh H Antre
- Advanced Centre of Plant Biotechnology, UAS, GKVK, Bangalore, Karnataka, 560065, India
| | - Santhosh B
- Centre for Advanced Studies On Climate Change, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848125, India
| | - Amarjeet Kumar
- Department of Genetics and Plant Breeding, MTTC & VTC, Selesih, CAU, Imphal, 795001, India
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Charfeddine M, Chiab N, Charfeddine S, Ferjani A, Gargouri-Bouzid R. Heat, drought, and combined stress effect on transgenic potato plants overexpressing the StERF94 transcription factor. JOURNAL OF PLANT RESEARCH 2023; 136:549-562. [PMID: 36988761 DOI: 10.1007/s10265-023-01454-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/17/2023] [Indexed: 06/09/2023]
Abstract
Despite their economic importance worldwide, potato plants are sensitive to various abiotic constraints, such as drought and high temperatures, which cause significant losses in yields and tuber quality. Moreover, because of the climate change phenomenon, plants are frequently subjected to combined stresses, mainly high temperatures and drought. In this context, breeding for tolerant varieties should consider not only plant response to drought or high temperature but also to combined stresses. In the current study, we studied transgenic potato plants overexpressing an ethylene response transcription factor (TF; StERF94) involved in abiotic stress response signaling pathways. Our previous results showed that these transgenic plants display tolerance to salt stress more than wildtype (WT). In this work, we aimed to investigate the effects of drought, heat, and combined stresses on transgenic potato plants overexpressing StERF94 TF under in vitro culture conditions. The obtained results revealed that StERF94 overexpression improved the tolerance of the transgenic plants to drought, heat, and combined stresses through better control of the leaf water and chlorophyll contents, activation of antioxidant enzymes, and an accumulation of proline, especially in the leaves. Indeed, the expression level of antioxidant enzyme-encoding genes (CuZnSOD, FeSOD, CAT1, and CAT2) was significantly induced by the different stress conditions in the transgenic potato plants compared with the WT plants. This study further confirms that StERF94 TF may be implicated in regulating the expression of target genes encoding antioxidant enzymes.
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Affiliation(s)
- Mariam Charfeddine
- Plant Amelioration and Valorization of Agri-resource Laboratory, National School of Engineers of Sfax (ENIS), Sfax, Tunisia
| | - Nour Chiab
- Plant Amelioration and Valorization of Agri-resource Laboratory, National School of Engineers of Sfax (ENIS), Sfax, Tunisia.
| | - Safa Charfeddine
- Plant Amelioration and Valorization of Agri-resource Laboratory, National School of Engineers of Sfax (ENIS), Sfax, Tunisia
| | - Aziza Ferjani
- Plant Amelioration and Valorization of Agri-resource Laboratory, National School of Engineers of Sfax (ENIS), Sfax, Tunisia
| | - Radhia Gargouri-Bouzid
- Plant Amelioration and Valorization of Agri-resource Laboratory, National School of Engineers of Sfax (ENIS), Sfax, Tunisia
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Semalaiyappan J, Selvanayagam S, Rathore A, Gupta SK, Chakraborty A, Gujjula KR, Haktan S, Viswanath A, Malipatil R, Shah P, Govindaraj M, Ignacio JC, Reddy S, Singh AK, Thirunavukkarasu N. Development of a new AgriSeq 4K mid-density SNP genotyping panel and its utility in pearl millet breeding. FRONTIERS IN PLANT SCIENCE 2023; 13:1068883. [PMID: 36704175 PMCID: PMC9871632 DOI: 10.3389/fpls.2022.1068883] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/15/2022] [Indexed: 06/18/2023]
Abstract
Pearl millet is a crucial nutrient-rich staple food in Asia and Africa and adapted to the climate of semi-arid topics. Since the genomic resources in pearl millet are very limited, we have developed a brand-new mid-density 4K SNP panel and demonstrated its utility in genetic studies. A set of 4K SNPs were mined from 925 whole-genome sequences through a comprehensive in-silico pipeline. Three hundred and seventy-three genetically diverse pearl millet inbreds were genotyped using the newly-developed 4K SNPs through the AgriSeq Targeted Genotyping by Sequencing technology. The 4K SNPs were uniformly distributed across the pearl millet genome and showed considerable polymorphism information content (0.23), genetic diversity (0.29), expected heterozygosity (0.29), and observed heterozygosity (0.03). The SNP panel successfully differentiated the accessions into two major groups, namely B and R lines, through genetic diversity, PCA, and structure models as per their pedigree. The linkage disequilibrium (LD) analysis showed Chr3 had higher LD regions while Chr1 and Chr2 had more low LD regions. The genetic divergence between the B- and R-line populations was 13%, and within the sub-population variability was 87%. In this experiment, we have mined 4K SNPs and optimized the genotyping protocol through AgriSeq technology for routine use, which is cost-effective, fast, and highly reproducible. The newly developed 4K mid-density SNP panel will be useful in genomics and molecular breeding experiments such as assessing the genetic diversity, trait mapping, backcross breeding, and genomic selection in pearl millet.
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Affiliation(s)
- Janani Semalaiyappan
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | - Sivasubramani Selvanayagam
- Accelerated Crop Improvement, International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Abhishek Rathore
- Excellence in Breeding (EiB) Platform, The International Maize and Wheat Improvement Center (CIMMYT), El Batán, Mexico
| | - SK. Gupta
- Accelerated Crop Improvement, International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Animikha Chakraborty
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | | | - Suren Haktan
- Bioinformatics, Thermo Fisher Scientific, Austin, TX, United States
| | - Aswini Viswanath
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | - Renuka Malipatil
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | - Priya Shah
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | | | - John Carlos Ignacio
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH, United States
| | - Sanjana Reddy
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
| | | | - Nepolean Thirunavukkarasu
- Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Rajendranagar, India
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Gillani SFA, Zhuang Z, Rasheed A, Haq IU, Abbasi A, Ahmed S, Wang Y, Khan MT, Sardar R, Peng Y. Brassinosteroids induced drought resistance of contrasting drought-responsive genotypes of maize at physiological and transcriptomic levels. FRONTIERS IN PLANT SCIENCE 2022; 13:961680. [PMID: 36388543 PMCID: PMC9641234 DOI: 10.3389/fpls.2022.961680] [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: 06/05/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
The present study investigated the brassinosteroid-induced drought resistance of contrasting drought-responsive maize genotypes at physiological and transcriptomic levels. The brassinosteroid (BR) contents along with different morphology characteristics, viz., plant height (PH), shoot dry weight (SDW), root dry weight (RDW), number of leaves (NL), the specific mass of the fourth leaf, and antioxidant activities, were investigated in two maize lines that differed in their degree of drought tolerance. In response to either control, drought, or brassinosteroid treatments, the KEGG enrichment analysis showed that plant hormonal signal transduction and starch and sucrose metabolism were augmented in both lines. In contrast, the phenylpropanoid biosynthesis was augmented in lines H21L0R1 and 478. Our results demonstrate drought-responsive molecular mechanisms and provide valuable information regarding candidate gene resources for drought improvement in maize crop. The differences observed for BR content among the maize lines were correlated with their degree of drought tolerance, as the highly tolerant genotype showed higher BR content under drought stress.
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Affiliation(s)
| | - Zelong Zhuang
- Gansu Provincial Key Lab of Arid Land Crop Science, College of Agronomy, Lanzhou, China
| | - Adnan Rasheed
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Crop Breeding Department, Jilin Changfa Modern Agricultural Science and Technology Group, co., Ltd., Changchun, China
| | - Inzamam Ul Haq
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Asim Abbasi
- Department of Environmental Sciences, Kohsar University, Murree, Pakistan
| | - Shakil Ahmed
- Institute of Botany, University of the Punjab, Lahore, Pakistan
| | - Yinxia Wang
- Gansu Provincial Key Lab of Arid Land Crop Science, College of Agronomy, Lanzhou, China
| | - Muhammad Tajammal Khan
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Rehana Sardar
- Institute of Botany, University of the Punjab, Lahore, Pakistan
| | - Yunling Peng
- Gansu Provincial Key Lab of Arid Land Crop Science, College of Agronomy, Lanzhou, China
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Chakraborty A, Viswanath A, Malipatil R, Semalaiyappan J, Shah P, Ronanki S, Rathore A, Singh SP, Govindaraj M, Tonapi VA, Thirunavukkarasu N. Identification of Candidate Genes Regulating Drought Tolerance in Pearl Millet. Int J Mol Sci 2022; 23:ijms23136907. [PMID: 35805919 PMCID: PMC9266394 DOI: 10.3390/ijms23136907] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 12/12/2022] Open
Abstract
Pearl millet is an important crop of the arid and semi-arid ecologies to sustain food and fodder production. The greater tolerance to drought stress attracts us to examine its cellular and molecular mechanisms via functional genomics approaches to augment the grain yield. Here, we studied the drought response of 48 inbreds representing four different maturity groups at the flowering stage. A set of 74 drought-responsive genes were separated into five major phylogenic groups belonging to eight functional groups, namely ABA signaling, hormone signaling, ion and osmotic homeostasis, TF-mediated regulation, molecular adaptation, signal transduction, physiological adaptation, detoxification, which were comprehensively studied. Among the conserved motifs of the drought-responsive genes, the protein kinases and MYB domain proteins were the most conserved ones. Comparative in-silico analysis of the drought genes across millet crops showed foxtail millet had most orthologs with pearl millet. Of 698 haplotypes identified across millet crops, MyC2 and Myb4 had maximum haplotypes. The protein–protein interaction network identified ABI2, P5CS, CDPK, DREB, MYB, and CYP707A3 as major hub genes. The expression assay showed the presence of common as well as unique drought-responsive genes across maturity groups. Drought tolerant genotypes in respective maturity groups were identified from the expression pattern of genes. Among several gene families, ABA signaling, TFs, and signaling proteins were the prospective contributors to drought tolerance across maturity groups. The functionally validated genes could be used as promising candidates in backcross breeding, genomic selection, and gene-editing schemes in pearl millet and other millet crops to increase the yield in drought-prone arid and semi-arid ecologies.
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Affiliation(s)
- Animikha Chakraborty
- ICAR-Indian Institute of Millets Research, Hyderabad 500030, India; (A.C.); (A.V.); (R.M.); (J.S.); (P.S.); (S.R.); (V.A.T.)
| | - Aswini Viswanath
- ICAR-Indian Institute of Millets Research, Hyderabad 500030, India; (A.C.); (A.V.); (R.M.); (J.S.); (P.S.); (S.R.); (V.A.T.)
| | - Renuka Malipatil
- ICAR-Indian Institute of Millets Research, Hyderabad 500030, India; (A.C.); (A.V.); (R.M.); (J.S.); (P.S.); (S.R.); (V.A.T.)
| | - Janani Semalaiyappan
- ICAR-Indian Institute of Millets Research, Hyderabad 500030, India; (A.C.); (A.V.); (R.M.); (J.S.); (P.S.); (S.R.); (V.A.T.)
| | - Priya Shah
- ICAR-Indian Institute of Millets Research, Hyderabad 500030, India; (A.C.); (A.V.); (R.M.); (J.S.); (P.S.); (S.R.); (V.A.T.)
| | - Swarna Ronanki
- ICAR-Indian Institute of Millets Research, Hyderabad 500030, India; (A.C.); (A.V.); (R.M.); (J.S.); (P.S.); (S.R.); (V.A.T.)
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India;
| | - Sumer Pal Singh
- ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Mahalingam Govindaraj
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India;
- Correspondence: (M.G.); (N.T.)
| | - Vilas A. Tonapi
- ICAR-Indian Institute of Millets Research, Hyderabad 500030, India; (A.C.); (A.V.); (R.M.); (J.S.); (P.S.); (S.R.); (V.A.T.)
| | - Nepolean Thirunavukkarasu
- ICAR-Indian Institute of Millets Research, Hyderabad 500030, India; (A.C.); (A.V.); (R.M.); (J.S.); (P.S.); (S.R.); (V.A.T.)
- Correspondence: (M.G.); (N.T.)
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Shen X, He J, Ping Y, Guo J, Hou N, Cao F, Li X, Geng D, Wang S, Chen P, Qin G, Ma F, Guan Q. The positive feedback regulatory loop of miR160-Auxin Response Factor 17-HYPONASTIC LEAVES 1 mediates drought tolerance in apple trees. PLANT PHYSIOLOGY 2022; 188:1686-1708. [PMID: 34893896 PMCID: PMC8896624 DOI: 10.1093/plphys/kiab565] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/10/2021] [Indexed: 05/25/2023]
Abstract
Drought stress tolerance is a complex trait regulated by multiple factors. Here, we demonstrate that the miRNA160-Auxin Response Factor 17 (ARF17)-HYPONASTIC LEAVES 1 module is crucial for apple (Malus domestica) drought tolerance. Using stable transgenic plants, we found that drought tolerance was improved by higher levels of Mdm-miR160 or MdHYL1 and by decreased levels of MdARF17, whereas reductions in MdHYL1 or increases in MdARF17 led to greater drought sensitivity. Further study revealed that modulation of drought tolerance was achieved through regulation of drought-responsive miRNA levels by MdARF17 and MdHYL1; MdARF17 interacted with MdHYL1 and bound to the promoter of MdHYL1. Genetic analysis further suggested that MdHYL1 is a direct downstream target of MdARF17. Importantly, MdARF17 and MdHYL1 regulated the abundance of Mdm-miR160. In addition, the Mdm-miR160-MdARF17-MdHYL1 module regulated adventitious root development. We also found that Mdm-miR160 can move from the scion to the rootstock in apple and tomato (Solanum lycopersicum), thereby improving root development and drought tolerance of the rootstock. Our study revealed the mechanisms by which the positive feedback loop of Mdm-miR160-MdARF17-MdHYL1 influences apple drought tolerance.
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Affiliation(s)
- Xiaoxia Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yikun Ping
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junxing Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nan Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fuguo Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dali Geng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shicong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gege Qin
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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8
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Peng J, Wang P, Fang H, Zheng J, Zhong C, Yang Y, Yu W. Weighted Gene Co-Expression Analysis Network-Based Analysis on the Candidate Pathways and Hub Genes in Eggplant Bacterial Wilt-Resistance: A Plant Research Study. Int J Mol Sci 2021; 22:ijms222413279. [PMID: 34948076 PMCID: PMC8706084 DOI: 10.3390/ijms222413279] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 12/23/2022] Open
Abstract
Solanum melongena L. (eggplant) bacterial wilt is a severe soil borne disease. Here, this study aimed to explore the regulation mechanism of eggplant bacterial wilt-resistance by transcriptomics with weighted gene co-expression analysis network (WGCNA). The different expression genes (DEGs) of roots and stems were divided into 21 modules. The module of interest (root: indianred4, stem: coral3) with the highest correlation with the target traits was selected to elucidate resistance genes and pathways. The selected module of roots and stems co-enriched the pathways of MAPK signalling pathway, plant pathogen interaction, and glutathione metabolism. Each top 30 hub genes of the roots and stems co-enriched a large number of receptor kinase genes. A total of 14 interesting resistance-related genes were selected and verified with quantitative polymerase chain reaction (qPCR). The qPCR results were consistent with those of WGCNA. The hub gene of EGP00814 (namely SmRPP13L4) was further functionally verified; SmRPP13L4 positively regulated the resistance of eggplant to bacterial wilt by qPCR and virus-induced gene silencing (VIGS). Our study provides a reference for the interaction between eggplants and bacterial wilt and the breeding of broad-spectrum and specific eggplant varieties that are bacterial wilt-resistant.
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Waititu JK, Zhang X, Chen T, Zhang C, Zhao Y, Wang H. Transcriptome Analysis of Tolerant and Susceptible Maize Genotypes Reveals Novel Insights about the Molecular Mechanisms Underlying Drought Responses in Leaves. Int J Mol Sci 2021; 22:6980. [PMID: 34209553 PMCID: PMC8268334 DOI: 10.3390/ijms22136980] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 11/17/2022] Open
Abstract
Maize (Zea mays L.) is the most essential food crop in the world. However, maize is highly susceptible to drought stress, especially at the seedling stage, and the molecular mechanisms underlying drought tolerance remain elusive. In this study, we conducted comparative transcriptome and physiological analyses of drought-tolerant (CML69) and susceptible (LX9801) inbred lines subjected to drought treatment at the seedling stage for three and five days. The tolerant line had significantly higher relative water content in the leaves, as well as lower electrolyte leakage and malondialdehyde levels, than the susceptible line. Using an RNA-seq-based approach, we identified 10,084 differentially expressed genes (DEGs) with 6906 and 3178 DEGs been annotated and unannotated, respectively. Two critical sets of drought-responsive DEGs, including 4687 genotype-specific and 2219 common drought-responsive genes, were mined out of the annotated DEGs. The tolerant-line DEGs were predominantly associated with the cytoskeleton, cell wall modification, glycolysis/gluconeogenesis, transport, osmotic regulation, drought avoidance, ROS scavengers, defense, and transcriptional factors. For the susceptible line, the DEGs were highly enriched in the photosynthesis, histone, and carbon fixation pathways. The unannotated DEGs were implicated in lncRNAs, including 428 previously reported and 22% putative TE-lncRNAs. There was consensus on both the physiological response and RNA-seq outcomes. Collectively, our findings will provide a comprehensive basis of the molecular networks mediating drought stress tolerance of maize at the seedling stage.
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Affiliation(s)
- Joram Kiriga Waititu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xingen Zhang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Tianci Chen
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yang Zhao
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Agricultural Science and Technology Center, Chinese Academy of Agricultural Sciences, Chengdu 610213, China
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Liu S, Zenda T, Dong A, Yang Y, Wang N, Duan H. Global Transcriptome and Weighted Gene Co-expression Network Analyses of Growth-Stage-Specific Drought Stress Responses in Maize. Front Genet 2021; 12:645443. [PMID: 33574835 PMCID: PMC7870802 DOI: 10.3389/fgene.2021.645443] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/04/2021] [Indexed: 12/25/2022] Open
Abstract
Drought is the major abiotic stress threatening maize (Zea mays L.) production globally. Despite recent scientific headway in deciphering maize drought stress responses, the overall picture of key genes, pathways, and co-expression networks regulating maize drought tolerance is still fragmented. Therefore, deciphering the molecular basis of maize drought tolerance remains pertinent. Here, through a comprehensive comparative leaf transcriptome analysis of drought-tolerant hybrid ND476 plants subjected to water-sufficient and water-deficit treatment conditions at flared (V12), tasseling (VT), the prophase of grain filling (R2), and the anaphase of grain filling (R4) crop growth stages, we report growth-stage-specific molecular mechanisms regulating maize drought stress responses. Based on the transcriptome analysis, a total of 3,451 differentially expressed genes (DEGs) were identified from the four experimental comparisons, with 2,403, 650, 397, and 313 DEGs observed at the V12, VT, R1, and R4 stages, respectively. Subsequently, 3,451 DEGs were divided into 12 modules by weighted gene co-expression network analysis (WGCNA), comprising 277 hub genes. Interestingly, the co-expressed genes that clustered into similar modules exhibited diverse expression tendencies and got annotated to different GO terms at different stages. MapMan analysis revealed that DEGs related to stress signal transduction, detoxification, transcription factor regulation, hormone signaling, and secondary metabolites biosynthesis were universal across the four growth stages. However, DEGs associated with photosynthesis and amino acid metabolism; protein degradation; transport; and RNA transcriptional regulation were uniquely enriched at the V12, VT, R2, and R4 stages, respectively. Our results affirmed that maize drought stress adaptation is a growth-stage-specific response process, and aid in clarifying the fundamental growth-stage-specific mechanisms regulating drought stress responses in maize. Moreover, genes and metabolic pathways identified here can serve as valuable genetic resources or selection targets for further functional validation experiments.
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Affiliation(s)
- Songtao Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, China.,Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, China.,Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Anyi Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, China.,Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Yatong Yang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, China.,Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Nan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, China.,Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, China.,Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
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11
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Comparative transcriptomic analysis of contrasting hybrid cultivars reveal key drought-responsive genes and metabolic pathways regulating drought stress tolerance in maize at various stages. PLoS One 2020; 15:e0240468. [PMID: 33057352 PMCID: PMC7561095 DOI: 10.1371/journal.pone.0240468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 09/25/2020] [Indexed: 02/01/2023] Open
Abstract
Drought stress is the primary environmental factor that negatively influences plant growth and yield in cereal grain crops such as maize (Zea mays L.). Crop breeding efforts for enhanced drought resistance require improved knowledge of plant drought stress responses. In this study, we applied a 12-day water-deficit stress treatment to maize plants of two contrasting (drought tolerant ND476 and drought sensitive ZX978) hybrid cultivars at four (V12, VT, R1, and R4) crop growth stages and we report key cultivar-specific and growth-stage-specific molecular mechanisms regulating drought stress responses in maize. Based on the transcriptome analysis, a total of 3451 and 4088 differentially expressed genes (DEGs) were identified in ND476 and ZX978 from the four experimental comparisons, respectively. These gene expression changes effected corresponding metabolic pathway responses related to drought tolerance in maize. In ND476, the DEGs associated with the ribosome, starch and sucrose metabolism, phenylpropanoid biosynthesis and phenylpropanoid metabolism pathways were predominant at the V12, VT, R2, and R4 stages, respectively, whereas those in ZX978 were related to ribosome, pentose and glucuronate interconversions (PGI), MAPK signaling and sulfur metabolism pathways, respectively. MapMan analysis revealed that DEGs related to secondary metabolism, lipid metabolism, and amino acid metabolism were universal across the four growth stages in ND476. Meanwhile, the DEGs involved in cell wall, photosynthesis and amino acid metabolism were universal across the four growth stages in ZX978. However, K-means analysis clustered those DEGs into clear and distinct expression profiles in ND476 and ZX978 at each stage. Several functional and regulatory genes were identified in the special clusters related to drought defense response. Our results affirmed that maize drought stress adaptation is a cultivar-specific response as well as a stage-specific response process. Additionally, our findings enrich the maize genetic resources and enhance our further understanding of the molecular mechanisms regulating drought stress tolerance in maize. Further, the DEGs screened in this study may provide a foundational basis for our future targeted cloning studies.
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12
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Liu G, Zenda T, Liu S, Wang X, Jin H, Dong A, Yang Y, Duan H. Comparative transcriptomic and physiological analyses of contrasting hybrid cultivars ND476 and ZX978 identify important differentially expressed genes and pathways regulating drought stress tolerance in maize. Genes Genomics 2020; 42:937-955. [PMID: 32623576 DOI: 10.1007/s13258-020-00962-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/21/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Drought is the major abiotic stress factor that negatively influences growth and yield in cereal grain crops such as maize (Zea mays L.). A multitude of genes and pathways tightly modulate plant growth, development and responses to environmental stresses including drought. Therefore, crop breeding efforts for enhanced drought resistance require improved knowledge of plant drought responses. OBJECTIVE Here, we sought to elucidate the molecular and physiological mechanisms underpinning maize drought stress tolerance. METHODS We therefore applied a 12-day water-deficit stress treatment to maize plants of two contrasting (drought tolerant ND476 and drought sensitive ZX978) hybrid cultivars at the late vegetative (V12) growth stage and performed a large-scale RNA sequencing (RNA-seq) transcriptome analysis of the leaf tissues. RESULTS A comparative analysis of the two genotypes leaf transcriptomes and physiological parameters revealed the key differentially expressed genes (DEGs) and metabolic pathways that respond to drought in a genotype-specific manner. A total of 3114 DEGs were identified, with 21 DEGs being specifically expressed in tolerant genotype ND476 in response to drought stress. Of these, genes involved in secondary metabolites biosynthesis, transcription factor regulation, detoxification and stress defense were highly expressed in ND476. Physiological analysis results substantiated our RNA-seq data, with ND476 exhibiting better cell water retention, higher soluble protein content and guaiacol peroxidase activity, along with low lipid peroxidation extent than the sensitive cultivar ZX978 under drought conditions. CONCLUSION Our findings enrich the maize genetic resources and enhance our further understanding of the molecular mechanisms regulating drought stress tolerance in maize. Additionally, the DEGs screened in this study may provide a foundational basis for our future targeted cloning studies.
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Affiliation(s)
- Guo Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Tinashe Zenda
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Songtao Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Xuan Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Hongyu Jin
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Anyi Dong
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Yatong Yang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China
| | - Huijun Duan
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China. .,North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding, 071001, China.
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13
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Liu S, Zenda T, Dong A, Yang Y, Liu X, Wang Y, Li J, Tao Y, Duan H. Comparative Proteomic and Morpho-Physiological Analyses of Maize Wild-Type Vp16 and Mutant vp16 Germinating Seed Responses to PEG-Induced Drought Stress. Int J Mol Sci 2019; 20:E5586. [PMID: 31717328 PMCID: PMC6888951 DOI: 10.3390/ijms20225586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/31/2019] [Accepted: 11/07/2019] [Indexed: 01/21/2023] Open
Abstract
Drought stress is a major abiotic factor compromising plant cell physiological and molecular events, consequently limiting crop growth and productivity. Maize (Zea mays L.) is among the most drought-susceptible food crops. Therefore, understanding the mechanisms underlying drought-stress responses remains critical for crop improvement. To decipher the molecular mechanisms underpinning maize drought tolerance, here, we used a comparative morpho-physiological and proteomics analysis approach to monitor the changes in germinating seeds of two incongruent (drought-sensitive wild-type Vp16 and drought-tolerant mutant vp16) lines exposed to polyethylene-glycol-induced drought stress for seven days. Our physiological analysis showed that the tolerant line mutant vp16 exhibited better osmotic stress endurance owing to its improved reactive oxygen species scavenging competency and robust osmotic adjustment as a result of greater cell water retention and enhanced cell membrane stability. Proteomics analysis identified a total of 1200 proteins to be differentially accumulated under drought stress. These identified proteins were mainly involved in carbohydrate and energy metabolism, histone H2A-mediated epigenetic regulation, protein synthesis, signal transduction, redox homeostasis and stress-response processes; with carbon metabolism, pentose phosphate and glutathione metabolism pathways being prominent under stress conditions. Interestingly, significant congruence (R2 = 81.5%) between protein and transcript levels was observed by qRT-PCR validation experiments. Finally, we propose a hypothetical model for maize germinating-seed drought tolerance based on our key findings identified herein. Overall, our study offers insights into the overall mechanisms underpinning drought-stress tolerance and provides essential leads into further functional validation of the identified drought-responsive proteins in maize.
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Affiliation(s)
- Songtao Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Tinashe Zenda
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Anyi Dong
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Yatong Yang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Xinyue Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Yafei Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Jiao Li
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Yongsheng Tao
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Huijun Duan
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China; (S.L.); (T.Z.); (A.D.); (Y.Y.); (X.L.); (Y.W.); (J.L.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
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14
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Wang B, Liu C, Zhang D, He C, Zhang J, Li Z. Effects of maize organ-specific drought stress response on yields from transcriptome analysis. BMC PLANT BIOLOGY 2019; 19:335. [PMID: 31370805 PMCID: PMC6676540 DOI: 10.1186/s12870-019-1941-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/17/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Drought is a serious causal factor of reduced crop yields than any other abiotic stresses. As one of the most widely distributed crops, maize plants frequently suffer from drought stress, which causes great losses in the final kernel yield. Drought stress response in plants showed tissue- and developmental stage-specific characteristics. RESULTS In this study, the ears at the V9 stage, kernels and ear leaf at the 5DAP (days after pollination) stage of maize were used for morphological, physiological and comparative transcriptomics analysis to understand the different features of "sink" or "source" organs and the effects on kernel yield under drought stress conditions. The ABA-, NAC-mediate signaling pathway, osmotic protective substance synthesis and protein folding response were identified as common drought stress response in the three organs. Tissue-specific drought stress responses and the regulators were identified, they were highly correlated with growth, physiological adaptation and yield loss under drought stress. For ears, drought stress inhibited ear elongation, led to the abnormal differentiation of the paired spikelet, and auxin signaling involved in the regulation of cell division and growth and primordium development changes. In the kernels, reduced kernel size caused by drought stress was observed, and the obvious differences of auxin, BR and cytokine signaling transduction appeared, which indicated the modification in carbohydrate metabolism, cell differentiation and growth retardation. For the ear leaf, dramatically and synergistically reduced the expression of photosynthesis genes were observed when suffered from drought stress, the ABA- and NAC- mediate signaling pathway played important roles in the regulation of photosynthesis. CONCLUSIONS Transcriptomic changes caused by drought were highly correlated with developmental and physiological adaptation, which was closely related to the final yield of maize, and a sketch of tissue- and developmental stage-specific responses to drought stress in maize was drafted.
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Affiliation(s)
- Baomei Wang
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Qingdao, 266237 Shandong China
| | - Can Liu
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Qingdao, 266237 Shandong China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Chunmei He
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Juren Zhang
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Qingdao, 266237 Shandong China
| | - Zhaoxia Li
- Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Qingdao, 266237 Shandong China
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15
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Wang X, Zenda T, Liu S, Liu G, Jin H, Dai L, Dong A, Yang Y, Duan H. Comparative Proteomics and Physiological Analyses Reveal Important Maize Filling-Kernel Drought-Responsive Genes and Metabolic Pathways. Int J Mol Sci 2019; 20:ijms20153743. [PMID: 31370198 PMCID: PMC6696053 DOI: 10.3390/ijms20153743] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/15/2019] [Accepted: 07/29/2019] [Indexed: 12/17/2022] Open
Abstract
Despite recent scientific headway in deciphering maize (Zea mays L.) drought stress responses, the overall picture of key proteins and genes, pathways, and protein-protein interactions regulating maize filling-kernel drought tolerance is still fragmented. Yet, maize filling-kernel drought stress remains devastating and its study is critical for tolerance breeding. Here, through a comprehensive comparative proteomics analysis of filling-kernel proteomes of two contrasting (drought-tolerant YE8112 and drought-sensitive MO17) inbred lines, we report diverse but key molecular actors mediating drought tolerance in maize. Using isobaric tags for relative quantification approach, a total of 5175 differentially abundant proteins (DAPs) were identified from four experimental comparisons. By way of Venn diagram analysis, four critical sets of drought-responsive proteins were mined out and further analyzed by bioinformatics techniques. The YE8112-exclusive DAPs chiefly participated in pathways related to "protein processing in the endoplasmic reticulum" and "tryptophan metabolism", whereas MO17-exclusive DAPs were involved in "starch and sucrose metabolism" and "oxidative phosphorylation" pathways. Most notably, we report that YE8112 kernels were comparatively drought tolerant to MO17 kernels attributable to their redox post translational modifications and epigenetic regulation mechanisms, elevated expression of heat shock proteins, enriched energy metabolism and secondary metabolites biosynthesis, and up-regulated expression of seed storage proteins. Further, comparative physiological analysis and quantitative real time polymerase chain reaction results substantiated the proteomics findings. Our study presents an elaborate understanding of drought-responsive proteins and metabolic pathways mediating maize filling-kernel drought tolerance, and provides important candidate genes for subsequent functional validation.
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Affiliation(s)
- Xuan Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Tinashe Zenda
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Songtao Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Guo Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Hongyu Jin
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Liang Dai
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Anyi Dong
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Yatong Yang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Huijun Duan
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
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16
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Lin F, Zhou L, He B, Zhang X, Dai H, Qian Y, Ruan L, Zhao H. QTL mapping for maize starch content and candidate gene prediction combined with co-expression network analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1931-1941. [PMID: 30887095 DOI: 10.1007/s00122-019-03326-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 03/11/2019] [Indexed: 05/28/2023]
Abstract
A major QTL Qsta9.1 was identified on chromosome 9, combined with GWAS, and co-expression network analysis showed that GRMZM2G110929 and GRMZM5G852704 are the potential candidates for association with maize kernel starch content. Increasing maize kernel starch content may not only lead to higher maize kernel yields and qualities, but also help meet industry demands. By using the intermated B73 × Mo17 population, QTLs were mapped for starch content in this study. A major QTL Qsta9.1 was detected in a 1.7 Mb interval on chromosome 9 and validated by allele frequency analysis in extreme tails of a newly constructed segregating population. According to genome-wide association study (GWAS) based on genotyping of a natural population, we identified a significant SNP for starch content within the ORF region of GRMZM5G852704_T01 colocalized with QTL Qsta9.1. Co-expression network analysis was also conducted, and 28 modules were constructed during six seed developmental stages. Functional enrichment was performed for each module, and one module showed the most possibility for the association with carbohydrate-related processes. In this module, one transcripts GRMZM2G110929_T01 located in the Qsta9.1 assigned 1.7 Mb interval encoding GLABRA2 expression modulator. Its expression level in B73 was lower than that in Mo17 across all seed developmental stages, implying the possibility for the candidate gene of Qsta9.1. Our studies combined GWAS, mRNA profiling, and traditional QTL analyses to identify a major locus for controlling seed starch content in maize.
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Affiliation(s)
- Feng Lin
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ling Zhou
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Bing He
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiaolin Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Huixue Dai
- Nanjing Institute of Vegetable Sciences, Nanjing, China
| | - Yiliang Qian
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Long Ruan
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Han Zhao
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
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17
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Zenda T, Liu S, Wang X, Liu G, Jin H, Dong A, Yang Y, Duan H. Key Maize Drought-Responsive Genes and Pathways Revealed by Comparative Transcriptome and Physiological Analyses of Contrasting Inbred Lines. Int J Mol Sci 2019; 20:ijms20061268. [PMID: 30871211 PMCID: PMC6470692 DOI: 10.3390/ijms20061268] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/08/2019] [Accepted: 03/08/2019] [Indexed: 02/06/2023] Open
Abstract
To unravel the molecular mechanisms underpinning maize (Zea mays L.) drought stress tolerance, we conducted comprehensive comparative transcriptome and physiological analyses of drought-tolerant YE8112 and drought-sensitive MO17 inbred line seedlings that had been exposed to drought treatment for seven days. Resultantly, YE8112 seedlings maintained comparatively higher leaf relative water and proline contents, greatly increased peroxidase activity, but decreased malondialdehyde content, than MO17 seedlings. Using an RNA sequencing (RNA-seq)-based approach, we identified a total of 10,612 differentially expressed genes (DEGs). From these, we mined out four critical sets of drought responsive DEGs, including 80 specific to YE8112, 5140 shared between the two lines after drought treatment (SD_TD), five DEGs of YE8112 also regulated in SD_TD, and four overlapping DEGs between the two lines. Drought-stressed YE8112 DEGs were primarily associated with nitrogen metabolism and amino-acid biosynthesis pathways, whereas MO17 DEGs were enriched in the ribosome pathway. Additionally, our physiological analyses results were consistent with the predicted RNA-seq-based findings. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) analysis and the RNA-seq results of twenty representative DEGs were highly correlated (R2 = 98.86%). Crucially, tolerant line YE8112 drought-responsive genes were predominantly implicated in stress signal transduction; cellular redox homeostasis maintenance; MYB, NAC, WRKY, and PLATZ transcriptional factor modulated; carbohydrate synthesis and cell-wall remodeling; amino acid biosynthesis; and protein ubiquitination processes. Our findings offer insights into the molecular networks mediating maize drought stress tolerance.
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Affiliation(s)
- Tinashe Zenda
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Songtao Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Xuan Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Guo Liu
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Hongyu Jin
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Anyi Dong
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Yatong Yang
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
| | - Huijun Duan
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China.
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China.
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18
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Bangar P, Chaudhury A, Tiwari B, Kumar S, Kumari R, Bhat KV. Morphophysiological and biochemical response of mungbean [Vigna radiata (L.) Wilczek] varieties at different developmental stages under drought stress. ACTA ACUST UNITED AC 2019; 43:58-69. [PMID: 30930636 PMCID: PMC6426646 DOI: 10.3906/biy-1801-64] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The present study was conducted to assess the morphophysiological and biochemical responses during different developmental stages in mungbean varieties subjected to drought stress, and to screen the varieties for drought tolerance. A field experiment was performed according to a completely randomized design on 25 mungbean varieties with 3 replicates per variety. Stress treatment was applied at 3 levels: control (no stress), vegetative stage (25 days after sowing), and reproductive stage (35 days after sowing). According to combined analysis of variance, there were significant effects from drought stress on relative water content (RWC), membrane stability index (MSI), protein and proline content of leaves, leaf area, plant height, and yield traits. MSI, RWC, protein content, leaf area, plant height, and yield traits were decreased during drought stress, while proline content was increased under drought stress conditions. The results showed that the vegetative stage was more sensitive to drought stress, which was further supported by correlation analysis. Taken together, Vigna sublobata, MCV-1, PLM-32, LGG-407, LGG-450, TM-96-2, and Sattya varieties were identified as drought tolerant as they maintained the higher values of RWC, MSI, protein, proline content, leaf area, plant height, and yield traits. These varieties could be used in breeding programs for better physiological drought tolerance traits.
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Affiliation(s)
- Pooja Bangar
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus , New Delhi , India.,Guru Jambheshwar University of Science and Technology , Hissar , India
| | - Ashok Chaudhury
- Guru Jambheshwar University of Science and Technology , Hissar , India
| | - Bhavana Tiwari
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus , New Delhi , India
| | - Sanjay Kumar
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus , New Delhi , India
| | - Ratna Kumari
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus , New Delhi , India
| | - Kangila Venkataramana Bhat
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus , New Delhi , India
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19
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Dash PK, Rai R, Rai V, Pasupalak S. Drought Induced Signaling in Rice: Delineating Canonical and Non-canonical Pathways. Front Chem 2018; 6:264. [PMID: 30258837 PMCID: PMC6143666 DOI: 10.3389/fchem.2018.00264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 06/12/2018] [Indexed: 11/13/2022] Open
Abstract
Drought induced stress is often a bottleneck of agricultural crop production. Invariably, field crops across all agro-ecological regions succumb to it with an yield penalty. Drought massively affects the growth and harvestable yield in crops and has become an imminent problem necessitating breeding of tolerant crops. It induces myriad changes of biochemical, molecular, and physiological nature that manifest into aberrant plant morphology. The response to drought in plants incites a signaling cascade that involves perception and translation of drought signal leading to concomitant modulation of gene expression and de novo osmolyte synthesis. The intricate patterns of expression of these genes vary from early induction to late responsive genes. While one class of genes codes for products imparting osmotolerance and protection to plants, the second class predominantly modulates target gene expression by an intricate signal transduction mechanism. This review summarizes both canonical and non-canonical cascades of drought stress response in plants, delineating the mechanism in rice (Oryza sativa) and emphasizes hydropenia induced lipid signaling.
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Affiliation(s)
- Prasanta K. Dash
- ICAR-NRC on Plant Biotechnology, Pusa Institute, New Delhi, India
| | - Rhitu Rai
- ICAR-NRC on Plant Biotechnology, Pusa Institute, New Delhi, India
| | - Vandna Rai
- ICAR-NRC on Plant Biotechnology, Pusa Institute, New Delhi, India
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20
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Mittal S, Banduni P, Mallikarjuna MG, Rao AR, Jain PA, Dash PK, Thirunavukkarasu N. Structural, Functional, and Evolutionary Characterization of Major Drought Transcription Factors Families in Maize. Front Chem 2018; 6:177. [PMID: 29876347 PMCID: PMC5974147 DOI: 10.3389/fchem.2018.00177] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 05/03/2018] [Indexed: 01/22/2023] Open
Abstract
Drought is one of the major threats to the maize yield especially in subtropical production systems. Understanding the genes and regulatory mechanisms of drought tolerance is important to sustain the yield. Transcription factors (TFs) play a major role in gene regulation under drought stress. In the present study, a set of 15 major TF families comprising 1,436 genes was structurally and functionally characterized. The functional annotation indicated that the genes were involved in ABA signaling, ROS scavenging, photosynthesis, stomatal regulation, and sucrose metabolism. Duplication was identified as the primary force in divergence and expansion of TF families. Phylogenetic relationship was developed for individual TF and combined TF families. Phylogenetic analysis clustered the genes into specific and mixed groups. Gene structure analysis revealed that more number of genes were intron-rich as compared to intron-less. Drought-responsive cis-regulatory elements such as ABREA, ABREB, DRE1, and DRECRTCOREAT have been identified. Expression and interaction analyses identified leaf-specific bZIP TF, GRMZM2G140355, as a potential contributor toward drought tolerance in maize. Protein-protein interaction network of 269 drought-responsive genes belonging to different TFs has been provided. The information generated on structural and functional characteristics, expression, and interaction of the drought-related TF families will be useful to decipher the drought tolerance mechanisms and to breed drought-tolerant genotypes in maize.
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Affiliation(s)
- Shikha Mittal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pooja Banduni
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Atmakuri R Rao
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Prashant A Jain
- Department of Computational Biology & Bioinformatics, J.I.B.B., Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, India
| | - Prasanta K Dash
- National Research Centre on Plant Biotechnology, New Delhi, India
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21
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Nepolean T, Kaul J, Mukri G, Mittal S. Genomics-Enabled Next-Generation Breeding Approaches for Developing System-Specific Drought Tolerant Hybrids in Maize. FRONTIERS IN PLANT SCIENCE 2018; 9:361. [PMID: 29696027 PMCID: PMC5905169 DOI: 10.3389/fpls.2018.00361] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/05/2018] [Indexed: 05/28/2023]
Abstract
Breeding science has immensely contributed to the global food security. Several varieties and hybrids in different food crops including maize have been released through conventional breeding. The ever growing population, decreasing agricultural land, lowering water table, changing climate, and other variables pose tremendous challenge to the researchers to improve the production and productivity of food crops. Drought is one of the major problems to sustain and improve the productivity of food crops including maize in tropical and subtropical production systems. With advent of novel genomics and breeding tools, the way of doing breeding has been tremendously changed in the last two decades. Drought tolerance is a combination of several component traits with a quantitative mode of inheritance. Rapid DNA and RNA sequencing tools and high-throughput SNP genotyping techniques, trait mapping, functional characterization, genomic selection, rapid generation advancement, and other tools are now available to understand the genetics of drought tolerance and to accelerate the breeding cycle. Informatics play complementary role by managing the big-data generated from the large-scale genomics and breeding experiments. Genome editing is the latest technique to alter specific genes to improve the trait expression. Integration of novel genomics, next-generation breeding, and informatics tools will accelerate the stress breeding process and increase the genetic gain under different production systems.
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Affiliation(s)
- Thirunavukkarsau Nepolean
- Maize Research Lab, Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Mittal S, Mallikarjuna MG, Rao AR, Jain PA, Dash PK, Thirunavukkarasu N. Comparative Analysis of CDPK Family in Maize, Arabidopsis, Rice, and Sorghum Revealed Potential Targets for Drought Tolerance Improvement. Front Chem 2017; 5:115. [PMID: 29312925 PMCID: PMC5742180 DOI: 10.3389/fchem.2017.00115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/28/2017] [Indexed: 12/19/2022] Open
Abstract
Calcium dependent protein kinases (CDPKs) play significant role in regulation of plant growth and development in response to various stresses including drought. A set of 32 CDPK genes identified in maize were further used for searching of orthologs in the model plant Arabidopsis (72) and major food crops such as rice (78) and sorghum (91). We comprehensively studied the phylogenetic relationship, annotations, gene duplications, gene structure, divergence time, 3-D protein structures and tissue-specific drought induced expression of CDPK genes in all four species. Variation in intron frequency in the studied species was one of the reasons for the functional diversity of CDPK genes to various stress responses. Protein kinase and protein kinase C phosphorylation site domains were the most conserved motifs identified in all species. Four groups were identified from the sequence-based phylogenetic analysis, in which maize CDPKs were clustered in group III. Expression data showed that the CDPK genes were highly expressed in leaf of maize, rice, and sorghum whereas in Arabidopsis the maximum expression was observed in root. The expression assay showed 5, 6, 11, and 9 were the commonly and differentially expressed drought-related orthologous genes in maize, Arabidopsis, rice, and sorghum, respectively. 3-D protein structure were predicted for the nine genes (Arabidopsis: 2, maize: 2, rice: 3, and sorghum: 2) showing differential expression in at least three species. The predicted 3-D structures were further evaluated and validated by Ramachandran plot, ANOLEA, ProSA, and Verify-3D. The superimposed 3-D structure of drought-related orthologous proteins retained similar folding pattern owing to their conserved nature. Functional annotation revealed the involvement of CDPK genes in various pathways such as osmotic homeostasis, cell protection, and root growth. The interactions of CDPK genes in various pathways play crucial role in imparting drought tolerance through different ABA and MAPK signaling cascades. These selected candidate genes could be targeted in development of drought tolerant genotypes in maize, rice, and sorghum through appropriate breeding approaches. Our comparative experiments of CDPK genes could also be extended in the drought stress breeding programmes of the related species.
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Affiliation(s)
- Shikha Mittal
- Division of Genetics, Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | - Atmakuri R. Rao
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR), New Delhi, India
| | - Prashant A. Jain
- Department of Computational Biology & Bioinformatics, Sam Higginbottom University of Agriculture, Technology, and Sciences, Allahabad, India
| | - Prasanta K. Dash
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
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Van Gioi H, Mallikarjuna MG, Shikha M, Pooja B, Jha SK, Dash PK, Basappa AM, Gadag RN, Rao AR, Nepolean T. Variable Level of Dominance of Candidate Genes Controlling Drought Functional Traits in Maize Hybrids. FRONTIERS IN PLANT SCIENCE 2017; 8:940. [PMID: 28649253 PMCID: PMC5465259 DOI: 10.3389/fpls.2017.00940] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/19/2017] [Indexed: 05/23/2023]
Abstract
Breeding maize for drought tolerance necessitates the knowledge on tolerant genotypes, molecular basis of drought tolerance mechanism, action, and expression pattern of genes. Studying the expression pattern and gene action of candidate genes during drought stress in the hybrids will help in choosing target genes for drought tolerance breeding. In the present investigation, a set of five hybrids and their seven parents with a variable level of tolerance to drought stress was selected to study the magnitude and the direction of 52 drought-responsive candidate genes distributed across various biological functions, viz., stomatal regulation, root development, detoxification, hormone signaling, photosynthesis, and sugar metabolism. The tolerant parents, HKI1105 and CML425, and their hybrid, ADWLH2, were physiologically active under drought stress, since vital parameters viz., chlorophyll, root length and relative water content, were on par with the respective well-watered control. All the genes were up-regulated in ADWLH2, many were down-regulated in HM8 and HM9, and most were down-regulated in PMH1 and PMH3 in the shoots and roots. The nature of the gene action was controlled by the parental combination rather than the parent per se. The differentially expressed genes in all five hybrids explained a mostly non-additive gene action over additivity, which was skewed toward any of the parental lines. Tissue-specific gene action was also noticed in many of the genes. The non-additive gene action is driven by genetic diversity, allele polymorphism, events during gene regulation, and small RNAs under the stress condition. Differential regulation and cross-talk of genes controlling various biological functions explained the basis of drought tolerance in subtropical maize hybrids. The nature of the gene action and the direction of the expression play crucial roles in designing introgression and hybrid breeding programmes to breed drought tolerant maize hybrids.
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Affiliation(s)
- Ha Van Gioi
- Division of Genetics, Indian Agricultural Research Institute (ICAR)New Delhi, India
- Forage Crops Department, Maize Research InstituteHa Noi, Vietnam
| | | | - Mittal Shikha
- Division of Genetics, Indian Agricultural Research Institute (ICAR)New Delhi, India
| | - Banduni Pooja
- Division of Genetics, Indian Agricultural Research Institute (ICAR)New Delhi, India
| | - Shailendra K. Jha
- Division of Genetics, Indian Agricultural Research Institute (ICAR)New Delhi, India
| | - Prasanta K. Dash
- National Research Centre on Plant Biotechnology (ICAR)New Delhi, India
| | - Arunkumar M. Basappa
- Division of Seed Science and Technology, Indian Agricultural Research Institute (ICAR)New Delhi, India
| | - Raveendra N. Gadag
- Division of Genetics, Indian Agricultural Research Institute (ICAR)New Delhi, India
| | - Atmakuri Ramakrishna Rao
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute (ICAR)New Delhi, India
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Aravind J, Rinku S, Pooja B, Shikha M, Kaliyugam S, Mallikarjuna MG, Kumar A, Rao AR, Nepolean T. Identification, Characterization, and Functional Validation of Drought-responsive MicroRNAs in Subtropical Maize Inbreds. FRONTIERS IN PLANT SCIENCE 2017; 8:941. [PMID: 28626466 PMCID: PMC5454542 DOI: 10.3389/fpls.2017.00941] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
MicroRNA-mediated gene regulation plays a crucial role in controlling drought tolerance. In the present investigation, 13 drought-associated miRNA families consisting of 65 members and regulating 42 unique target mRNAs were identified from drought-associated microarray expression data in maize and were subjected to structural and functional characterization. The largest number of members (14) was found in the zma-miR166 and zma-miR395 families, with several targets. However, zma-miR160, zma-miR390, zma-miR393, and zma-miR2275 each showed a single target. Twenty-three major drought-responsive cis-regulatory elements were found in the upstream regions of miRNAs. Many drought-related transcription factors, such as GAMYB, HD-Zip III, and NAC, were associated with the target mRNAs. Furthermore, two contrasting subtropical maize genotypes (tolerant: HKI-1532 and sensitive: V-372) were used to understand the miRNA-assisted regulation of target mRNA under drought stress. Approximately 35 and 31% of miRNAs were up-regulated in HKI-1532 and V-372, respectively. The up-regulation of target mRNAs was as high as 14.2% in HKI-1532 but was only 2.38% in V-372. The expression patterns of miRNA-target mRNA pairs were classified into four different types: Type I- up-regulation, Type II- down-regulation, Type III- neutral regulation, and Type IV- opposite regulation. HKI-1532 displayed 46 Type I, 13 Type II, and 23 Type III patterns, whereas V-372 had mostly Type IV interactions (151). A low level of negative regulations of miRNA associated with a higher level of mRNA activity in the tolerant genotype helped to maintain crucial biological functions such as ABA signaling, the auxin response pathway, the light-responsive pathway and endosperm expression under stress conditions, thereby leading to drought tolerance. Our study identified candidate miRNAs and mRNAs operating in important pathways under drought stress conditions, and these candidates will be useful in the development of drought-tolerant maize hybrids.
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Affiliation(s)
- Jayaraman Aravind
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
- Division of Germplasm Conservation, National Bureau of Plant Genetic ResourcesNew Delhi, India
| | - Sharma Rinku
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
- Department of Life Sciences, Shiv Nadar UniversityGautam Buddha Nagar, India
| | - Banduni Pooja
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
| | - Mittal Shikha
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
| | - Shiriga Kaliyugam
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
| | | | - Arun Kumar
- National Phytotron Facility, Indian Agricultural Research InstituteNew Delhi, India
| | - Atmakuri Ramakrishna Rao
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research InstituteNew Delhi, India
| | - Thirunavukkarasu Nepolean
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
- *Correspondence: Thirunavukkarasu Nepolean ;
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