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Jamil S, Ahmad S, Shahzad R, Umer N, Kanwal S, Rehman HM, Rana IA, Atif RM. Leveraging Multiomics Insights and Exploiting Wild Relatives' Potential for Drought and Heat Tolerance in Maize. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38980762 DOI: 10.1021/acs.jafc.4c01375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Climate change, particularly drought and heat stress, may slash agricultural productivity by 25.7% by 2080, with maize being the hardest hit. Therefore, unraveling the molecular nature of plant responses to these stressors is vital for the development of climate-smart maize. This manuscript's primary objective was to examine how maize plants respond to these stresses, both individually and in combination. Additionally, the paper delved into harnessing the potential of maize wild relatives as a valuable genetic resource and leveraging AI-based technologies to boost maize resilience. The role of multiomics approaches particularly genomics and transcriptomics in dissecting the genetic basis of stress tolerance was also highlighted. The way forward was proposed to utilize a bunch of information obtained through omics technologies by an interdisciplinary state-of-the-art forward-looking big-data, cyberagriculture system, and AI-based approach to orchestrate the development of climate resilient maize genotypes.
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Affiliation(s)
- Shakra Jamil
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Shakeel Ahmad
- Seed Centre and Plant Genetic Resources Bank Ministry of Environment, Water and Agriculture, Riyadh 14712, Saudi Arabia
| | - Rahil Shahzad
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Noroza Umer
- Dr. Ikram ul Haq - Institute of Industrial Biotechnology, Government College University, Lahore 54590, Pakistan
| | - Shamsa Kanwal
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Hafiz Mamoon Rehman
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38000, Pakistan
| | - Iqrar Ahmad Rana
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad 38000, Pakistan
| | - Rana Muhammad Atif
- Department of Plant Sciences, University of California Davis, California 95616, United States
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan
- Precision Agriculture and Analytics Lab, Centre for Advanced Studies in Agriculture and Food Security, National Centre in Big Data and Cloud Computing, University of Agriculture, Faisalabad 38000, Pakistan
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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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Yu Q, Xiong Y, Su X, Xiong Y, Dong Z, Zhao J, Shu X, Bai S, Lei X, Yan L, Ma X. Integrating Full-Length Transcriptome and RNA Sequencing of Siberian Wildrye ( Elymus sibiricus) to Reveal Molecular Mechanisms in Response to Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:2719. [PMID: 37514333 PMCID: PMC10385362 DOI: 10.3390/plants12142719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
Drought is one of the most significant limiting factors affecting plant growth and development on the Qinghai-Tibet Plateau (QTP). Mining the drought-tolerant genes of the endemic perennial grass of the QTP, Siberian wildrye (Elymus sibiricus), is of great significance to creating new drought-resistant varieties which can be used in the development of grassland livestock and restoring natural grassland projects in the QTP. To investigate the transcriptomic responsiveness of E. sibiricus to drought stress, PEG-induced short- and long-term drought stress was applied to two Siberian wildrye genotypes (drought-tolerant and drought-sensitive accessions), followed by third- and second-generation transcriptome sequencing analysis. A total of 40,708 isoforms were detected, of which 10,659 differentially expressed genes (DEGs) were common to both genotypes. There were 2107 and 2498 unique DEGs in the drought-tolerant and drought-sensitive genotypes, respectively. Additionally, 2798 and 1850 DEGs were identified in the drought-tolerant genotype only under short- and long-term conditions, respectively. DEGs numbering 1641 and 1330 were identified in the drought-sensitive genotype only under short- and long-term conditions, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that all the DEGs responding to drought stress in E. sibiricus were mainly associated with the mitogen-activated protein kinase (MAKP) signaling pathway, plant hormone signal transduction, the linoleic acid metabolism pathway, the ribosome pathway, and plant circadian rhythms. In addition, Nitrate transporter 1/Peptide transporter family protein 3.1 (NPF3.1) and Auxin/Indole-3-Acetic Acid (Aux/IAA) family protein 31(IAA31) also played an important role in helping E. sibiricus resist drought. This study used transcriptomics to investigate how E. sibiricus responds to drought stress, and may provide genetic resources and references for research into the molecular mechanisms of drought resistance in native perennial grasses and for breeding drought-tolerant varieties.
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Affiliation(s)
- Qingqing Yu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoli Su
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhixiao Dong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xin Shu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Lijun Yan
- Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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Tang Y, Zhang J, Wang L, Wang H, Long H, Yang L, Li G, Guo J, Wang Y, Li Y, Yang Q, Shi W, Shao R. Water deficit aggravated the inhibition of photosynthetic performance of maize under mercury stress but is alleviated by brassinosteroids. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130365. [PMID: 36444077 DOI: 10.1016/j.jhazmat.2022.130365] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/24/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Mercury (Hg) significantly inhibits maize (Zea mays L.) production, which could be aggravated by water deficit (WD) due to climate change. However, there is no report on the maize in response to combined their stresses. This work was conducted for assessing the response and adaptive mechanism of maize to combined Hg and WD stress using two maize cultivars, Xianyu (XY) 335 and Yudan (YD) 132. The analysis was based on plant growth, physiological function, and transcriptomic data. Compared with the single Hg stress, Hg accumulation in whole plant and translocation factor (TF) under Hg+WD were increased by 64.51 % (1.44 mg kg-1) and 260.00 %, respectively, for XY 335; and 50.32 % (0.62 mg kg-1) and 220.02 %, respectively, for YD 132. Combined Hg and WD stress further increased the reactive oxygen species accumulation, aggravated the damage of the thylakoid membrane, and decreased chlorophyll content compared with single stress. For example, Chl a and Chl b contents of XY 335 were significantly decreased by 48.67 % and 28.08 %, respectively at 48 h after Hg+WD treatment compared with Hg stress. Furthermore, transcriptome analysis revealed that most of down-regulated genes were enriched in photosynthetic-antenna proteins, photosynthesis, chlorophyll and porphyrin metabolism pathways (PsbS1, PSBQ1 and FDX1 etc.) under combined stress, reducing light energy capture and electron transport. However, most genes related to the brassinosteroids (BRs) signaling pathway were up-regulated under Hg+WD stress. Correspondingly, exogenous BRs significantly enhanced the maize tolerance to stress by decreasing Hg accumulation and TF, and raising activities of antioxidant enzyme, the content of chlorophyll and photosynthetic performance. The PI, Fv/Fm and Fv/Fo of Hg+WD+BR treatment were increased by 29.88 %, 32.06 %, and 14.56 %, respectively, for XY 335 compared to Hg+WD. Overall, combined Hg and WD stress decreased photosynthetic efficiency by adversely affecting light absorption and electron transport, especially in stress-sensitive variety, but BRs could alleviate the inhibition of photosynthesis, providing a novel strategy for enhancing crop Hg and WD tolerance and food safety.
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Affiliation(s)
- Yulou Tang
- National Key Laboratory of Wheat and Maize Crop Science, Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Junjie Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Lijuan Wang
- National Key Laboratory of Wheat and Maize Crop Science, Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Hao Wang
- National Key Laboratory of Wheat and Maize Crop Science, Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Haochi Long
- National Key Laboratory of Wheat and Maize Crop Science, Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Liuyang Yang
- National Key Laboratory of Wheat and Maize Crop Science, Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Gengwei Li
- Xinxiang Grain, Oil and Feed Product Quality Supervision and Inspection Institute, Xinxiang 453000, China
| | - Jiameng Guo
- National Key Laboratory of Wheat and Maize Crop Science, Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Yongchao Wang
- National Key Laboratory of Wheat and Maize Crop Science, Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Yuling Li
- National Key Laboratory of Wheat and Maize Crop Science, Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Qinghua Yang
- National Key Laboratory of Wheat and Maize Crop Science, Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Weiyu Shi
- Chongqing Jinfo Mountain Karst Ecosystem National Observation and Research Station, School of Geographical Sciences, Southwest University, Chongqing 400715, China
| | - Ruixin Shao
- National Key Laboratory of Wheat and Maize Crop Science, Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan 450046, China.
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Subramani M, Urrea CA, Habib R, Bhide K, Thimmapuram J, Kalavacharla V. Comparative Transcriptome Analysis of Tolerant and Sensitive Genotypes of Common Bean ( Phaseolus vulgaris L.) in Response to Terminal Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12010210. [PMID: 36616341 PMCID: PMC9824821 DOI: 10.3390/plants12010210] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/06/2022] [Accepted: 12/14/2022] [Indexed: 06/10/2023]
Abstract
We conducted a genome-wide transcriptomic analysis of three drought tolerant and sensitive genotypes of common bean to examine their transcriptional responses to terminal drought stress. We then conducted pairwise comparisons between the root and leaf transcriptomes from the resulting tissue based on combined transcriptomic data from the tolerant and sensitive genotypes. Our transcriptomic data revealed that 491 (6.4%) DEGs (differentially expressed genes) were upregulated in tolerant genotypes, whereas they were downregulated in sensitive genotypes; likewise, 396 (5.1%) DEGs upregulated in sensitive genotypes were downregulated in tolerant genotypes. Several transcription factors, heat shock proteins, and chaperones were identified in the study. Several DEGs in drought DB (data Base) overlapped between genotypes. The GO (gene ontology) terms for biological processes showed upregulation of DEGs in tolerant genotypes for sulfate and drug transmembrane transport when compared to sensitive genotypes. A GO term for cellular components enriched with upregulated DEGs for the apoplast in tolerant genotypes. These results substantiated the temporal pattern of root growth (elongation and initiation of root growth), and ABA-mediated drought response in tolerant genotypes. KEGG (kyoto encyclopedia of genes and genomes) analysis revealed an upregulation of MAPK (mitogen activated protein kinase) signaling pathways and plant hormone signaling pathways in tolerant genotypes. As a result of this study, it will be possible to uncover the molecular mechanisms of drought tolerance in response to terminal drought stress in the field. Further, genome-wide transcriptomic analysis of both tolerant and sensitive genotypes will assist us in identifying potential genes that may contribute to improving drought tolerance in the common bean.
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Affiliation(s)
- Mayavan Subramani
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA
| | - Carlos A. Urrea
- Panhandle Research and Extension Center, University of Nebraska, 4502 Avenue I, Scottsbluff, NE 69361, USA
| | - Rasheed Habib
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA
| | - Ketaki Bhide
- Bioinformatics Core, Purdue University, West Lafayette, IN 47907, USA
| | | | - Venu Kalavacharla
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA
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