1
|
Aina O, Bakare OO, Fadaka AO, Keyster M, Klein A. Plant biomarkers as early detection tools in stress management in food crops: a review. PLANTA 2024; 259:60. [PMID: 38311674 PMCID: PMC10838863 DOI: 10.1007/s00425-024-04333-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 01/07/2024] [Indexed: 02/06/2024]
Abstract
MAIN CONCLUSION Plant Biomarkers are objective indicators of a plant's cellular state in response to abiotic and biotic stress factors. They can be explored in crop breeding and engineering to produce stress-tolerant crop species. Global food production safely and sustainably remains a top priority to feed the ever-growing human population, expected to reach 10 billion by 2050. However, abiotic and biotic stress factors negatively impact food production systems, causing between 70 and 100% reduction in crop yield. Understanding the plant stress responses is critical for developing novel crops that can adapt better to various adverse environmental conditions. Using plant biomarkers as measurable indicators of a plant's cellular response to external stimuli could serve as early warning signals to detect stresses before severe damage occurs. Plant biomarkers have received considerable attention in the last decade as pre-stress indicators for various economically important food crops. This review discusses some biomarkers associated with abiotic and biotic stress conditions and highlights their importance in developing stress-resilient crops. In addition, we highlighted some factors influencing the expression of biomarkers in crop plants under stress. The information presented in this review would educate plant researchers, breeders, and agronomists on the significance of plant biomarkers in stress biology research, which is essential for improving plant growth and yield toward sustainable food production.
Collapse
Affiliation(s)
- Omolola Aina
- Plant Omics Laboratory, Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, 7530, South Africa
| | - Olalekan O Bakare
- Department of Biochemistry, Faculty of Basic Medical Sciences, Olabisi Onabanjo University, Sagamu, 121001, Nigeria
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, 7530, South Africa
| | - Adewale O Fadaka
- Plant Omics Laboratory, Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, 7530, South Africa
| | - Marshall Keyster
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, 7530, South Africa
| | - Ashwil Klein
- Plant Omics Laboratory, Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, 7530, South Africa.
| |
Collapse
|
2
|
Janni M, Maestri E, Gullì M, Marmiroli M, Marmiroli N. Plant responses to climate change, how global warming may impact on food security: a critical review. FRONTIERS IN PLANT SCIENCE 2024; 14:1297569. [PMID: 38250438 PMCID: PMC10796516 DOI: 10.3389/fpls.2023.1297569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024]
Abstract
Global agricultural production must double by 2050 to meet the demands of an increasing world human population but this challenge is further exacerbated by climate change. Environmental stress, heat, and drought are key drivers in food security and strongly impacts on crop productivity. Moreover, global warming is threatening the survival of many species including those which we rely on for food production, forcing migration of cultivation areas with further impoverishing of the environment and of the genetic variability of crop species with fall out effects on food security. This review considers the relationship of climatic changes and their bearing on sustainability of natural and agricultural ecosystems, as well as the role of omics-technologies, genomics, proteomics, metabolomics, phenomics and ionomics. The use of resource saving technologies such as precision agriculture and new fertilization technologies are discussed with a focus on their use in breeding plants with higher tolerance and adaptability and as mitigation tools for global warming and climate changes. Nevertheless, plants are exposed to multiple stresses. This study lays the basis for the proposition of a novel research paradigm which is referred to a holistic approach and that went beyond the exclusive concept of crop yield, but that included sustainability, socio-economic impacts of production, commercialization, and agroecosystem management.
Collapse
Affiliation(s)
- Michela Janni
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Bari, Italy
- Institute of Materials for Electronics and Magnetism (IMEM), National Research Council (CNR), Parma, Italy
| | - Elena Maestri
- Department of Chemistry, Life Sciences and Environmental Sustainability, Interdepartmental Centers SITEIA.PARMA and CIDEA, University of Parma, Parma, Italy
| | - Mariolina Gullì
- Department of Chemistry, Life Sciences and Environmental Sustainability, Interdepartmental Centers SITEIA.PARMA and CIDEA, University of Parma, Parma, Italy
| | - Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, Interdepartmental Centers SITEIA.PARMA and CIDEA, University of Parma, Parma, Italy
| | - Nelson Marmiroli
- Consorzio Interuniversitario Nazionale per le Scienze Ambientali (CINSA) Interuniversity Consortium for Environmental Sciences, Parma/Venice, Italy
| |
Collapse
|
3
|
Yu J, Li P, Tu S, Feng N, Chang L, Niu Q. Integrated Analysis of the Transcriptome and Metabolome of Brassica rapa Revealed Regulatory Mechanism under Heat Stress. Int J Mol Sci 2023; 24:13993. [PMID: 37762295 PMCID: PMC10531312 DOI: 10.3390/ijms241813993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Affected by global warming; heat stress is the main limiting factor for crop growth and development. Brassica rapa prefers cool weather, and heat stress has a significant negative impact on its growth, development, and metabolism. Understanding the regulatory patterns of heat-resistant and heat-sensitive varieties under heat stress can help deepen understanding of plant heat tolerance mechanisms. In this study, an integrative analysis of transcriptome and metabolome was performed on the heat-tolerant ('WYM') and heat-sensitive ('AJH') lines of Brassica rapa to reveal the regulatory networks correlated to heat tolerance and to identify key regulatory genes. Heat stress was applied to two Brassica rapa cultivars, and the leaves were analyzed at the transcriptional and metabolic levels. The results suggest that the heat shock protein (HSP) family, plant hormone transduction, chlorophyll degradation, photosynthetic pathway, and reactive oxygen species (ROS) metabolism play an outstanding role in the adaptation mechanism of plant heat tolerance. Our discovery lays the foundation for future breeding of horticultural crops for heat resistance.
Collapse
Affiliation(s)
| | | | | | | | | | - Qingliang Niu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (J.Y.); (P.L.); (S.T.); (N.F.) (L.C.)
| |
Collapse
|
4
|
Roychowdhury R, Das SP, Gupta A, Parihar P, Chandrasekhar K, Sarker U, Kumar A, Ramrao DP, Sudhakar C. Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant's Abiotic Stress Tolerance Responses. Genes (Basel) 2023; 14:1281. [PMID: 37372461 DOI: 10.3390/genes14061281] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/03/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The present day's ongoing global warming and climate change adversely affect plants through imposing environmental (abiotic) stresses and disease pressure. The major abiotic factors such as drought, heat, cold, salinity, etc., hamper a plant's innate growth and development, resulting in reduced yield and quality, with the possibility of undesired traits. In the 21st century, the advent of high-throughput sequencing tools, state-of-the-art biotechnological techniques and bioinformatic analyzing pipelines led to the easy characterization of plant traits for abiotic stress response and tolerance mechanisms by applying the 'omics' toolbox. Panomics pipeline including genomics, transcriptomics, proteomics, metabolomics, epigenomics, proteogenomics, interactomics, ionomics, phenomics, etc., have become very handy nowadays. This is important to produce climate-smart future crops with a proper understanding of the molecular mechanisms of abiotic stress responses by the plant's genes, transcripts, proteins, epigenome, cellular metabolic circuits and resultant phenotype. Instead of mono-omics, two or more (hence 'multi-omics') integrated-omics approaches can decipher the plant's abiotic stress tolerance response very well. Multi-omics-characterized plants can be used as potent genetic resources to incorporate into the future breeding program. For the practical utility of crop improvement, multi-omics approaches for particular abiotic stress tolerance can be combined with genome-assisted breeding (GAB) by being pyramided with improved crop yield, food quality and associated agronomic traits and can open a new era of omics-assisted breeding. Thus, multi-omics pipelines together are able to decipher molecular processes, biomarkers, targets for genetic engineering, regulatory networks and precision agriculture solutions for a crop's variable abiotic stress tolerance to ensure food security under changing environmental circumstances.
Collapse
Affiliation(s)
- Rajib Roychowdhury
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO)-The Volcani Institute, Rishon Lezion 7505101, Israel
| | - Soumya Prakash Das
- School of Bioscience, Seacom Skills University, Bolpur 731236, West Bengal, India
| | - Amber Gupta
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, Faculty of Science, Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
| | - Parul Parihar
- Department of Biotechnology and Bioscience, Banasthali Vidyapith, Banasthali 304022, Rajasthan, India
| | - Kottakota Chandrasekhar
- Department of Plant Biochemistry and Biotechnology, Sri Krishnadevaraya College of Agricultural Sciences (SKCAS), Affiliated to Acharya N.G. Ranga Agricultural University (ANGRAU), Guntur 522034, Andhra Pradesh, India
| | - Umakanta Sarker
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Ajay Kumar
- Department of Botany, Maharshi Vishwamitra (M.V.) College, Buxar 802102, Bihar, India
| | - Devade Pandurang Ramrao
- Department of Biotechnology, Mizoram University, Pachhunga University College Campus, Aizawl 796001, Mizoram, India
| | - Chinta Sudhakar
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapur 515003, Andhra Pradesh, India
| |
Collapse
|
5
|
Mahmood U, Li X, Fan Y, Chang W, Niu Y, Li J, Qu C, Lu K. Multi-omics revolution to promote plant breeding efficiency. FRONTIERS IN PLANT SCIENCE 2022; 13:1062952. [PMID: 36570904 PMCID: PMC9773847 DOI: 10.3389/fpls.2022.1062952] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Crop production is the primary goal of agricultural activities, which is always taken into consideration. However, global agricultural systems are coming under increasing pressure from the rising food demand of the rapidly growing world population and changing climate. To address these issues, improving high-yield and climate-resilient related-traits in crop breeding is an effective strategy. In recent years, advances in omics techniques, including genomics, transcriptomics, proteomics, and metabolomics, paved the way for accelerating plant/crop breeding to cope with the changing climate and enhance food production. Optimized omics and phenotypic plasticity platform integration, exploited by evolving machine learning algorithms will aid in the development of biological interpretations for complex crop traits. The precise and progressive assembly of desire alleles using precise genome editing approaches and enhanced breeding strategies would enable future crops to excel in combating the changing climates. Furthermore, plant breeding and genetic engineering ensures an exclusive approach to developing nutrient sufficient and climate-resilient crops, the productivity of which can sustainably and adequately meet the world's food, nutrition, and energy needs. This review provides an overview of how the integration of omics approaches could be exploited to select crop varieties with desired traits.
Collapse
Affiliation(s)
- Umer Mahmood
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Xiaodong Li
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yonghai Fan
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Wei Chang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yue Niu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jiana Li
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Cunmin Qu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Kun Lu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| |
Collapse
|
6
|
Hudzenko VM, Buniak NM, Tsentylo LV, Demydov OA, Fedorenko IV, Fedorenko MV, Ishchenko VA, Kozelets HM, Khudolii LV, Lashuk SO, Syplyva NO. Evaluation of grain yield performance and its stability in various spring barley accessions under condition of different agroclimatic zones of Ukraine. BIOSYSTEMS DIVERSITY 2022. [DOI: 10.15421/012240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
Two extremely urgent problems of biological and agronomic research nowadays are ensuring an optimal balance between usage of natural resources to meet rapidly growing needs for food production and preservation of biodiversity. It is also important to extend the genetic diversity of the main crop varieties in agroecosystems. At the same time, modern varieties should be characterized by a combination of high yield and preserving yield stability under variable conditions. Solving the outlined tasks requires comprehensive research and involvement in breeding process of the genetical diversity concentrated in genebanks of the world. Barley (Hordeum vulgare L.) is one of the most important crops that satisfy the various needs of humanity. In respect to this, in 2020–2022, a multi-environment trial was conducted in three agroclimatic zones of Ukraine (Forest-Steppe, Polissia, and Northern Steppe). We studied 44 spring barley collection accessions of different ecological and geographical origin, different subspecies and groups of botanical varieties which were obtained from the National Center for Plant Genetic Resources of Ukraine. Statistical indices (Hom, Sc) and graphical models (GGE biplot, AMMI) were used to interpret the yield performance and its stability. Both individual ecological sites in different years and combinations of different sites and years of trials were characterized for productivity, discriminating power and representativeness. The environments differed quite strongly among themselves in terms of these indicators. It was established that most of the genotypes were characterized by higher adaptability to individual environmental conditions (stability in different years), compared to adaptability for all agroclimatic zones (wide adaptation). A strong cross-over genotype by environment interaction was found for most studied accessions. Nevertheless, both genotypes with very high stability in only one agroclimatic zone (Amil (UKR), Gateway (CAN)) and genotypes with a combination of high adaptability to one or two ecological niches and relatively higher wide adaptability (Stymul (UKR), Ly-1064 (UKR), Rannij (KAZ), Shedevr (UKR), and Arthur (CZE)) were identified. There were also the accessions which did not show maximum performance in the individual sites, but had relatively higher wide adaptability (Ly-1059 (UKR), Ly-1120 (UKR), Diantus (UKR), and Danielle (CZE)). In general, the naked barley genotypes were inferior to the covered ones in terms of yield potential and wide adaptability, but at the same time, some of them (CDC ExPlus (CAN), CDC Gainer (CAN), and Roseland (CAN)), accordingly to the statistical indicators, had increased stability in certain ecological sites. Among naked barley accessions relatively better wide adaptability according to the graphical analysis was found in the accession CDC McGwire (CAN), and by the statistical parameters CDC ExPlus (CAN) was better than standard. The peculiarities of yield manifestation and its variability in different spring barley genotypes in the multi-environment trial revealed in this study will contribute to the complementation and deepening of existing data in terms of the genotype by environment interaction. Our results can be used in further studies for developing spring barley variety models both with specific and wide adaptation under conditions of different agroclimatic zones of Ukraine. The disitnguished accessions of different origin and botanical affiliation are recommended for creating a new breeding material with the aim of simultaneously increasing yield potential and stability, as well as widening the genetic basis of spring barley varieties.
Collapse
|
7
|
Singh AK, Mishra P, Kashyap SP, Karkute SG, Singh PM, Rai N, Bahadur A, Behera TK. Molecular insights into mechanisms underlying thermo-tolerance in tomato. FRONTIERS IN PLANT SCIENCE 2022; 13:1040532. [PMID: 36388532 PMCID: PMC9645296 DOI: 10.3389/fpls.2022.1040532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Plant productivity is being seriously compromised by climate-change-induced temperature extremities. Agriculture and food safety are threatened due to global warming, and in many cases the negative impacts have already begun. Heat stress leads to significant losses in yield due to changes in growth pattern, plant phonologies, sensitivity to pests, flowering, grain filling, maturity period shrinkage, and senescence. Tomato is the second most important vegetable crop. It is very sensitive to heat stress and thus, yield losses in tomato due to heat stress could affect food and nutritional security. Tomato plants respond to heat stress with a variety of cellular, physiological, and molecular responses, beginning with the early heat sensing, followed by signal transduction, antioxidant defense, osmolyte synthesis and regulated gene expression. Recent findings suggest that specific plant organs are extremely sensitive to heat compared to the entire plant, redirecting the research more towards generative tissues. This is because, during sexual reproduction, developing pollens are the most sensitive to heat. Often, just a few degrees of temperature elevation during pollen development can have a negative effect on crop production. Furthermore, recent research has discovered certain genetic and epigenetic mechanisms playing key role in thermo-tolerance and have defined new directions for tomato heat stress response (HSR). Present challenges are to increase the understanding of molecular mechanisms underlying HS, and to identify superior genotypes with more tolerance to extreme temperatures. Several metabolites, genes, heat shock factors (HSFs) and microRNAs work together to regulate the plant HSR. The present review provides an insight into molecular mechanisms of heat tolerance and current knowledge of genetic and epigenetic control of heat-tolerance in tomato for sustainable agriculture in the future. The information will significantly contribute to improve breeding programs for development of heat tolerant cultivars.
Collapse
Affiliation(s)
- Achuit K. Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Pallavi Mishra
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Sarvesh Pratap Kashyap
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Suhas G. Karkute
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Prabhakar Mohan Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Nagendra Rai
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Anant Bahadur
- Division of Crop Production, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Tusar K. Behera
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| |
Collapse
|
8
|
Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops. Int J Mol Sci 2022; 23:ijms231912053. [PMID: 36233352 PMCID: PMC9570234 DOI: 10.3390/ijms231912053] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/02/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
The major challenges that agriculture is facing in the twenty-first century are increasing droughts, water scarcity, flooding, poorer soils, and extreme temperatures due to climate change. However, most crops are not tolerant to extreme climatic environments. The aim in the near future, in a world with hunger and an increasing population, is to breed and/or engineer crops to tolerate abiotic stress with a higher yield. Some crop varieties display a certain degree of tolerance, which has been exploited by plant breeders to develop varieties that thrive under stress conditions. Moreover, a long list of genes involved in abiotic stress tolerance have been identified and characterized by molecular techniques and overexpressed individually in plant transformation experiments. Nevertheless, stress tolerance phenotypes are polygenetic traits, which current genomic tools are dissecting to exploit their use by accelerating genetic introgression using molecular markers or site-directed mutagenesis such as CRISPR-Cas9. In this review, we describe plant mechanisms to sense and tolerate adverse climate conditions and examine and discuss classic and new molecular tools to select and improve abiotic stress tolerance in major crops.
Collapse
|