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Sadikiel Mmbando G, Ngongolo K. The recent genetic modification techniques for improve soil conservation, nutrient uptake and utilization. GM CROPS & FOOD 2024; 15:233-247. [PMID: 39008437 PMCID: PMC11253881 DOI: 10.1080/21645698.2024.2377408] [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: 04/25/2024] [Accepted: 07/03/2024] [Indexed: 07/17/2024]
Abstract
Advances in genetic modification (GM) techniques have generated huge interest in improving nutrient utilization, maximizing nutrient uptake, and conserving soil in the pursuit of sustainable agriculture. Unfortunately, little is still known about the recent advancements in the application of GM tactics to enhance each of these areas. This review explores the latest GM strategies intended to support soil conservation, maximize nutrient uptake, and improve nutrient utilization in farming, highlighting the critical roles that soil health and nutrient management play in sustainable farming. GM strategies such as improving the efficiency of nutrient uptake through enhanced root systems and increased nutrient transport mechanisms are well discussed. This study suggests that addressing potential obstacles, such as ethical and regulatory concerns, is a necessity for long-term sustainability applications of GM technologies to raise agricultural yields.
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Affiliation(s)
- Gideon Sadikiel Mmbando
- Department of Biology, College of Natural and Mathematical Sciences, The University of Dodoma, Dodoma, United Republic of Tanzania
| | - Kelvin Ngongolo
- Department of Biology, College of Natural and Mathematical Sciences, The University of Dodoma, Dodoma, United Republic of Tanzania
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2
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Zhao P, Liu Z, Shi X, Hou W, Cheng M, Liu Y, Simmonds J, Ji W, Uauy C, Xu S, Wang X. Modern wheat breeding selection synergistically improves above- and belowground traits. PLANT PHYSIOLOGY 2024; 196:47-50. [PMID: 38739540 DOI: 10.1093/plphys/kiae270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 05/16/2024]
Affiliation(s)
- Peng Zhao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zihui Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xue Shi
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenyang Hou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingzhu Cheng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuxiu Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Wanquan Ji
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Shengbao Xu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoming Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
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3
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Ju Y, Liu AE, Oestreich K, Wang T, Topp CN, Ju T. TopoRoot+: computing whorl and soil line traits of field-excavated maize roots from CT imaging. PLANT METHODS 2024; 20:132. [PMID: 39187896 PMCID: PMC11348750 DOI: 10.1186/s13007-024-01240-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 07/17/2024] [Indexed: 08/28/2024]
Abstract
BACKGROUND The use of 3D imaging techniques, such as X-ray CT, in root phenotyping has become more widespread in recent years. However, due to the complexity of the root structure, analyzing the resulting 3D volumes to obtain detailed architectural root traits remains a challenging computational problem. When it comes to image-based phenotyping of excavated maize root crowns, two types of root features that are notably missing from existing methods are the whorls and soil line. Whorls refer to the distinct areas located at the base of each stem node from which roots sprout in a circular pattern (Liu S, Barrow CS, Hanlon M, Lynch JP, Bucksch A. Dirt/3D: 3D root phenotyping for field-grown maize (zea mays). Plant Physiol. 2021;187(2):739-57. https://doi.org/10.1093/plphys/kiab311 .). The soil line is where the root stem meets the ground. Knowledge of these features would give biologists deeper insights into the root system architecture (RSA) and the below- and above-ground root properties. RESULTS We developed TopoRoot+, a computational pipeline that produces architectural traits from 3D X-ray CT volumes of excavated maize root crowns. Building upon the TopoRoot software (Zeng D, Li M, Jiang N, Ju Y, Schreiber H, Chambers E, et al. Toporoot: A method for computing hierarchy and fine-grained traits of maize roots from 3D imaging. Plant Methods. 2021;17(1). https://doi.org/10.1186/s13007-021-00829-z .) for computing fine-grained root traits, TopoRoot + adds the capability to detect whorls, identify nodal roots at each whorl, and compute the soil line location. The new algorithms in TopoRoot + offer an additional set of fine-grained traits beyond those provided by TopoRoot. The addition includes internode distances, root traits at every hierarchy level associated with a whorl, and root traits specific to above or below the ground. TopoRoot + is validated on a diverse collection of field-grown maize root crowns consisting of nine genotypes and spanning across three years. TopoRoot + runs in minutes for a typical volume size of [Formula: see text] on a desktop workstation. Our software and test dataset are freely distributed on Github. CONCLUSIONS TopoRoot + advances the state-of-the-art in image-based phenotyping of excavated maize root crowns by offering more detailed architectural traits related to whorls and soil lines. The efficiency of TopoRoot + makes it well-suited for high-throughput image-based root phenotyping.
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Grants
- NSF DBI-1759836, DBI-1759796, EF-1921728 National Science Foundation
- NSF DBI-1759836, DBI-1759796, EF-1921728 National Science Foundation
- NSF DBI-1759836, DBI-1759796, EF-1921728 National Science Foundation
- NSF DBI-1759836, DBI-1759796, EF-1921728 National Science Foundation
- NSF DBI-1759836, DBI-1759796, EF-1921728 National Science Foundation
- Subterranean Influences on Nitrogen and Carbon Cycling Center (SINC) of Excellence at the Donald Danforth Plant Science Center
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Affiliation(s)
- Yiwen Ju
- Washington University in Saint Louis, St. Louis, USA
| | - Alexander E Liu
- Washington University in Saint Louis, St. Louis, USA
- Donald Danforth Plant Science Center, Creve Coeur, USA
| | | | - Tina Wang
- Marquette High School, Chesterfield, MO, USA
| | | | - Tao Ju
- Washington University in Saint Louis, St. Louis, USA.
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4
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Gupta S, Groen SC, Zaidem ML, Sajise AGC, Calic I, Natividad MA, McNally KL, Vergara GV, Satija R, Franks SJ, Singh RK, Joly-Lopez Z, Purugganan MD. Systems genomics of salinity stress response in rice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596807. [PMID: 38895411 PMCID: PMC11185513 DOI: 10.1101/2024.05.31.596807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Populations can adapt to stressful environments through changes in gene expression. However, the role of gene regulation in mediating stress response and adaptation remains largely unexplored. Here, we use an integrative field dataset obtained from 780 plants of Oryza sativa ssp. indica (rice) grown in a field experiment under normal or moderate salt stress conditions to examine selection and evolution of gene expression variation under salinity stress conditions. We find that salinity stress induces increased selective pressure on gene expression. Further, we show that trans-eQTLs rather than cis-eQTLs are primarily associated with rice's gene expression under salinity stress, potentially via a few master-regulators. Importantly, and contrary to the expectations, we find that cis-trans reinforcement is more common than cis-trans compensation which may be reflective of rice diversification subsequent to domestication. We further identify genetic fixation as the likely mechanism underlying this compensation/reinforcement. Additionally, we show that cis- and trans-eQTLs are under different selection regimes, giving us insights into the evolutionary dynamics of gene expression variation. By examining genomic, transcriptomic, and phenotypic variation across a rice population, we gain insights into the molecular and genetic landscape underlying adaptive salinity stress responses, which is relevant for other crops and other stresses.
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Affiliation(s)
- Sonal Gupta
- Center for Genomics and Systems Biology, New York University, New York, NY USA
| | - Simon C Groen
- Center for Genomics and Systems Biology, New York University, New York, NY USA
- Department of Nematology and Department of Botany & Plant Sciences, University of California, Riverside, CA USA
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA USA
| | - Maricris L. Zaidem
- Center for Genomics and Systems Biology, New York University, New York, NY USA
- Department of Biology, University of Oxford, Oxford, England
| | | | - Irina Calic
- Department of Biological Sciences, Fordham University, Bronx, NY USA
- Inari Agriculture Nv, Gent, Belgium
| | | | | | - Georgina V. Vergara
- International Rice Research Institute, Los Baños, Philippines
- Institute of Crop Science, University of the Philippines, Los Baños, Philippines
| | - Rahul Satija
- Center for Genomics and Systems Biology, New York University, New York, NY USA
- New York Genome Center, New York, NY USA
| | - Steven J. Franks
- Department of Biological Sciences, Fordham University, Bronx, NY USA
| | - Rakesh K. Singh
- International Rice Research Institute, Los Baños, Philippines
- International Center for Biosaline Agriculture, Dubai, UAE (current affiliation)
| | - Zoé Joly-Lopez
- Center for Genomics and Systems Biology, New York University, New York, NY USA
- Département de Chimie, Université du Quebéc à Montréal, Montreal, Quebec, Canada
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5
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Xiang Y, Li G, Li Q, Niu Y, Pan Y, Cheng Y, Bian X, Zhao C, Wang Y, Zhang A. Autophagy receptor ZmNBR1 promotes the autophagic degradation of ZmBRI1a and enhances drought tolerance in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1068-1086. [PMID: 38607264 DOI: 10.1111/jipb.13662] [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: 12/16/2023] [Accepted: 03/26/2024] [Indexed: 04/13/2024]
Abstract
Drought stress is a crucial environmental factor that limits plant growth, development, and productivity. Autophagy of misfolded proteins can help alleviate the damage caused in plants experiencing drought. However, the mechanism of autophagy-mediated drought tolerance in plants remains largely unknown. Here, we cloned the gene for a maize (Zea mays) selective autophagy receptor, NEXT TO BRCA1 GENE 1 (ZmNBR1), and identified its role in the response to drought stress. We observed that drought stress increased the accumulation of autophagosomes. RNA sequencing and reverse transcription-quantitative polymerase chain reaction showed that ZmNBR1 is markedly induced by drought stress. ZmNBR1 overexpression enhanced drought tolerance, while its knockdown reduced drought tolerance in maize. Our results established that ZmNBR1 mediates the increase in autophagosomes and autophagic activity under drought stress. ZmNBR1 also affects the expression of genes related to autophagy under drought stress. Moreover, we determined that BRASSINOSTEROID INSENSITIVE 1A (ZmBRI1a), a brassinosteroid receptor of the BRI1-like family, interacts with ZmNBR1. Phenotype analysis showed that ZmBRI1a negatively regulates drought tolerance in maize, and genetic analysis indicated that ZmNBR1 acts upstream of ZmBRI1a in regulating drought tolerance. Furthermore, ZmNBR1 facilitates the autophagic degradation of ZmBRI1a under drought stress. Taken together, our results reveal that ZmNBR1 regulates the expression of autophagy-related genes, thereby increasing autophagic activity and promoting the autophagic degradation of ZmBRI1a under drought stress, thus enhancing drought tolerance in maize. These findings provide new insights into the autophagy degradation of brassinosteroid signaling components by the autophagy receptor NBR1 under drought stress.
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Affiliation(s)
- Yang Xiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangdong Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qian Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yingxue Niu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yitian Pan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuan Cheng
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiangli Bian
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chongyang Zhao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuanhong Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Aying Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Sanya, 572025, China
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Gholizadeh S, Nemati I, Vestergård M, Barnes CJ, Kudjordjie EN, Nicolaisen M. Harnessing root-soil-microbiota interactions for drought-resilient cereals. Microbiol Res 2024; 283:127698. [PMID: 38537330 DOI: 10.1016/j.micres.2024.127698] [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: 01/16/2024] [Revised: 03/14/2024] [Accepted: 03/17/2024] [Indexed: 04/17/2024]
Abstract
Cereal plants form complex networks with their associated microbiome in the soil environment. A complex system including variations of numerous parameters of soil properties and host traits shapes the dynamics of cereal microbiota under drought. These multifaceted interactions can greatly affect carbon and nutrient cycling in soil and offer the potential to increase plant growth and fitness under drought conditions. Despite growing recognition of the importance of plant microbiota to agroecosystem functioning, harnessing the cereal root microbiota remains a significant challenge due to interacting and synergistic effects between root traits, soil properties, agricultural practices, and drought-related features. A better mechanistic understanding of root-soil-microbiota associations could lead to the development of novel strategies to improve cereal production under drought. In this review, we discuss the root-soil-microbiota interactions for improving the soil environment and host fitness under drought and suggest a roadmap for harnessing the benefits of these interactions for drought-resilient cereals. These methods include conservative trait-based approaches for the selection and breeding of plant genetic resources and manipulation of the soil environments.
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Affiliation(s)
- Somayeh Gholizadeh
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Iman Nemati
- Department of Plant Production and Genetics Engineering, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Mette Vestergård
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Christopher James Barnes
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Enoch Narh Kudjordjie
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Mogens Nicolaisen
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark.
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Siddiqui MN, Jahiu M, Kamruzzaman M, Sanchez-Garcia M, Mason AS, Léon J, Ballvora A. Genetic control of root architectural traits under drought stress in spring barley (Hordeum vulgare L.). THE PLANT GENOME 2024; 17:e20463. [PMID: 38764204 DOI: 10.1002/tpg2.20463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/22/2024] [Accepted: 04/12/2024] [Indexed: 05/21/2024]
Abstract
Root architectural traits play pivotal roles in plant adaptation to drought stress, and hence they are considered promising targets in breeding programs. Here, we phenotyped eight root architecture traits in response to well-watered and drought stress conditions in 200 spring barley (Hordeum vulgare L.) inbred lines over two consecutive field seasons. Root architecture traits were less developed under drought in both seasons when compared with control treatments. Genetic variation in root architectural traits was dissected employing a genome-wide association study (GWAS) coupled with linkage disequilibrium mapping. GWAS uncovered a total of 186 significant single nucleotide polymorphism-trait associations for eight root traits under control, drought, and drought-related indices. Of these, a few loci for root traits were detected on chromosomes 3 and 5, which co-located with QTL identified in previous studies. Interestingly, 13 loci showed simultaneou associations with multiple root traits under drought and drought-related indices. These loci harbored candidate genes, which included a wide range of drought-responsive components such as transcription factors, binding proteins, protein kinases, nutrient and ion transporters, and stress signaling factors. For instance, two candidate genes, HORVU7Hr3G0713160 and HORVU6H r3G0626550, are orthologous to AtACX3 and AtVAMPs, which have reported functions in root length-mediated drought tolerance and as a key protein in abiotic stress tolerance, respectively. Interestingly, one of these loci underlying a high-confidence candidate gene NEW ENHANCER OF ROOT DWARFISM1 (NERD1) showed involvement with root development. An allelic variation of this locus in non-coding region was significantly associated with increased root length under drought. Collectively, these results offer promising multi-trait affecting loci and candidate genes underlying root phenotypic responses to drought stress, which may provide valuable resources for genetic improvement of drought tolerance in barley.
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Affiliation(s)
- Md Nurealam Siddiqui
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Melisa Jahiu
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Mohammad Kamruzzaman
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Miguel Sanchez-Garcia
- Department of Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Annaliese S Mason
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Jens Léon
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
- Field Lab Campus Klein-Altendorf, University of Bonn, Rheinbach, Germany
| | - Agim Ballvora
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
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8
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Zhang Y, Wu X, Wang X, Dai M, Peng Y. Crop root system architecture in drought response. J Genet Genomics 2024:S1673-8527(24)00100-0. [PMID: 38723744 DOI: 10.1016/j.jgg.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 07/27/2024]
Abstract
Drought is a natural disaster that profoundly impacts on global agricultural production, significantly reduces crop yields, and thereby poses a severe threat to worldwide food security. Addressing the challenge of effectively improving crop drought resistance (DR) to mitigate yield loss under drought conditions is a global issue. An optimal root system architecture (RSA) plays a pivotal role in enhancing crops' capacity to efficiently uptake water and nutrients, which consequently strengthens their resilience against environmental stresses. In this review, we discuss the compositions and roles of crop RSA and summarize the most recent developments in augmenting drought tolerance in crops by manipulating RSA-related genes. Based on the current research, we propose the potential optimal RSA configuration that could be helpful in enhancing crop DR. Lastly, we discussed the existing challenges and future directions for breeding crops with enhanced DR capabilities through genetic improvements targeting RSA.
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Affiliation(s)
- Yanjun Zhang
- College of Agronomy, Gansu Agricultural University, Lanzhou, Gansu 730070, China; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu 730070, China; Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China; Key Laboratory of Crop Gene Resources and Germplasm Innovation in Northwest Cold and Arid Regions, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu 730070, China
| | - Xi Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, HuBei 430070, China
| | - Xingrong Wang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China; Key Laboratory of Crop Gene Resources and Germplasm Innovation in Northwest Cold and Arid Regions, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu 730070, China
| | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, HuBei 430070, China.
| | - Yunling Peng
- College of Agronomy, Gansu Agricultural University, Lanzhou, Gansu 730070, China; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
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9
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Junaid MD, Chaudhry UK, Şanlı BA, Gökçe AF, Öztürk ZN. A review of the potential involvement of small RNAs in transgenerational abiotic stress memory in plants. Funct Integr Genomics 2024; 24:74. [PMID: 38600306 DOI: 10.1007/s10142-024-01354-7] [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: 01/12/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Crop production is increasingly threatened by the escalating weather events and rising temperatures associated with global climate change. Plants have evolved adaptive mechanisms, including stress memory, to cope with abiotic stresses such as heat, drought, and salinity. Stress memory involves priming, where plants remember prior stress exposures, providing enhanced responses to subsequent stress events. Stress memory can manifest as somatic, intergenerational, or transgenerational memory, persisting for different durations. The chromatin, a central regulator of gene expression, undergoes modifications like DNA acetylation, methylation, and histone variations in response to abiotic stress. Histone modifications, such as H3K4me3 and acetylation, play crucial roles in regulating gene expression. Abiotic stresses like drought and salinity are significant challenges to crop production, leading to yield reductions. Plant responses to stress involve strategies like escape, avoidance, and tolerance, each influencing growth stages differently. Soil salinity affects plant growth by disrupting water potential, causing ion toxicity, and inhibiting nutrient uptake. Understanding plant responses to these stresses requires insights into histone-mediated modifications, chromatin remodeling, and the role of small RNAs in stress memory. Histone-mediated modifications, including acetylation and methylation, contribute to epigenetic stress memory, influencing plant adaptation to environmental stressors. Chromatin remodeling play a crucial role in abiotic stress responses, affecting the expression of stress-related genes. Small RNAs; miRNAs and siRNAs, participate in stress memory pathways by guiding DNA methylation and histone modifications. The interplay of these epigenetic mechanisms helps plants adapt to recurring stress events and enhance their resilience. In conclusion, unraveling the epigenetic mechanisms in plant responses to abiotic stresses provides valuable insights for developing resilient agricultural techniques. Understanding how plants utilize stress memory, histone modifications, chromatin remodeling, and small RNAs is crucial for designing strategies to mitigate the impact of climate change on crop production and global food security.
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Affiliation(s)
- Muhammad Daniyal Junaid
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey.
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan.
| | - Usman Khalid Chaudhry
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey
- Pakistan Environmental Protection Agency, Ministry of Climate Change & Environmental Coordination, Islamabad, Pakistan
| | - Beyazıt Abdurrahman Şanlı
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey
| | - Ali Fuat Gökçe
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey
| | - Zahide Neslihan Öztürk
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey
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10
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Koua AP, Siddiqui MN, Heß K, Klag N, Kambona CM, Duarte-Delgado D, Oyiga BC, Léon J, Ballvora A. Genome-wide dissection and haplotype analysis identified candidate loci for nitrogen use efficiency under drought conditions in winter wheat. THE PLANT GENOME 2024; 17:e20394. [PMID: 37880495 DOI: 10.1002/tpg2.20394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 10/27/2023]
Abstract
Climate change causes extreme conditions like prolonged drought, which results in yield reductions due to its effects on nutrient balances such as nitrogen uptake and utilization by plants. Nitrogen (N) is a crucial nutrient element for plant growth and productivity. Understanding the mechanistic basis of nitrogen use efficiency (NUE) under drought conditions is essential to improve wheat (Triticum aestivum L.) yield. Here, we evaluated the genetic variation of NUE-related traits and photosynthesis response in a diversity panel of 200 wheat genotypes under drought and nitrogen stress conditions to uncover the inherent genetic variation and identify quantitative trait loci (QTLs) underlying these traits. The results revealed significant genetic variations among the genotypes in response to drought stress and nitrogen deprivation. Drought impacted plant performance more than N deprivation due to its effect on water and nutrient uptake. GWAS identified a total of 27 QTLs with a significant main effect on the drought-related traits, while 10 QTLs were strongly associated with the NUE traits. Haplotype analysis revealed two different haplotype blocks within the associated region on chromosomes 1B and 5A. The two haplotypes showed contrasting effects on N uptake and use efficiency traits. The in silico and transcript analyses implicated candidate gene coding for cold shock protein. This gene was the most highly expressed gene under several stress conditions, including drought stress. Upon validation, these QTLs on 1B and 5A could be used as a diagnostic marker for NUE and drought tolerance screening in wheat.
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Affiliation(s)
- Ahossi Patrice Koua
- INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Md Nurealam Siddiqui
- INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Katrin Heß
- INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Nikko Klag
- INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | | | | | | | - Jens Léon
- INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
- Field Lab Campus Klein-Altendorf, University of Bonn, Rheinbach, Germany
| | - Agim Ballvora
- INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
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11
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Wang X, Zhao W, Wei X, Sun Y, Dong S. Molecular mechanism of drought resistance in soybean roots revealed using physiological and multi-omics analyses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108451. [PMID: 38402799 DOI: 10.1016/j.plaphy.2024.108451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
Soybeans are one of the most cultivated crops worldwide and drought can seriously affect their growth and development. Many studies have elucidated the mechanisms through which soybean leaves respond to drought; however, little is known about these mechanisms in roots. We used two soybean varieties with different drought tolerances to study the morphological, physiological, and molecular response mechanisms of the root system to drought stress in seedlings. We found that drought stress led to a significant decrease in the root traits and an increase in antioxidant enzyme activity in the two varieties. Drought-resistant varieties accumulate large amounts of flavonoids and phenolic acids at the metabolic level, which causes variations in drought resistance. Additionally, differences in gene expression and drought-resistance pathways between the two varieties were clarified using transcriptome analysis. Through a multi-omics joint analysis, phenylpropanoid and isoflavonoid biosynthesis were identified as the core drought resistance pathways in soybean roots. Candidate genes and marker metabolites affecting drought resistance were identified. The phenylpropanoid pathway confers drought tolerance to roots by maintaining a high level of POD activity and mediates the biosynthesis of various secondary drought-resistant metabolites to resist drought stress. This study provides useful data for investigating plant root drought responses and offers theoretical support for plant breeding for drought resistance.
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Affiliation(s)
- Xiyue Wang
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Wei Zhao
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Xinhe Wei
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Yanbin Sun
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Shoukun Dong
- College of Agriculture, Northeast Agricultural University, Harbin, China.
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12
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Kalra A, Goel S, Elias AA. Understanding role of roots in plant response to drought: Way forward to climate-resilient crops. THE PLANT GENOME 2024; 17:e20395. [PMID: 37853948 DOI: 10.1002/tpg2.20395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 07/26/2023] [Accepted: 09/18/2023] [Indexed: 10/20/2023]
Abstract
Drought stress leads to a significant amount of agricultural crop loss. Thus, with changing climatic conditions, it is important to develop resilience measures in agricultural systems against drought stress. Roots play a crucial role in regulating plant development under drought stress. In this review, we have summarized the studies on the role of roots and root-mediated plant responses. We have also discussed the importance of root system architecture (RSA) and the various structural and anatomical changes that it undergoes to increase survival and productivity under drought. Various genes, transcription factors, and quantitative trait loci involved in regulating root growth and development are also discussed. A summarization of various instruments and software that can be used for high-throughput phenotyping in the field is also provided in this review. More comprehensive studies are required to help build a detailed understanding of RSA and associated traits for breeding drought-resilient cultivars.
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Affiliation(s)
- Anmol Kalra
- Department of Botany, University of Delhi, North Campus, Delhi, India
| | - Shailendra Goel
- Department of Botany, University of Delhi, North Campus, Delhi, India
| | - Ani A Elias
- ICFRE - Institute of Forest Genetics and Tree Breeding (ICFRE - IFGTB), Coimbatore, India
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13
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Hostetler AN, Morais de Sousa Tinoco S, Sparks EE. Root responses to abiotic stress: a comparative look at root system architecture in maize and sorghum. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:553-562. [PMID: 37798135 DOI: 10.1093/jxb/erad390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023]
Abstract
Under all environments, roots are important for plant anchorage and acquiring water and nutrients. However, there is a knowledge gap regarding how root architecture contributes to stress tolerance in a changing climate. Two closely related plant species, maize and sorghum, have distinct root system architectures and different levels of stress tolerance, making comparative analysis between these two species an ideal approach to resolve this knowledge gap. However, current research has focused on shared aspects of the root system that are advantageous under abiotic stress conditions rather than on differences. Here we summarize the current state of knowledge comparing the root system architecture relative to plant performance under water deficit, salt stress, and low phosphorus in maize and sorghum. Under water deficit, steeper root angles and deeper root systems are proposed to be advantageous for both species. In saline soils, a reduction in root length and root number has been described as advantageous, but this work is limited. Under low phosphorus, root systems that are shallow and wider are beneficial for topsoil foraging. Future work investigating the differences between these species will be critical for understanding the role of root system architecture in optimizing plant production for a changing global climate.
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Affiliation(s)
- Ashley N Hostetler
- Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | | | - Erin E Sparks
- Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
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14
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Mahmoud A, Qi R, Chi X, Liao N, Malangisha GK, Ali A, Moustafa-Farag M, Yang J, Zhang M, Hu Z. Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild Watermelon. Int J Mol Sci 2023; 25:65. [PMID: 38203237 PMCID: PMC10779233 DOI: 10.3390/ijms25010065] [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: 10/07/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 01/12/2024] Open
Abstract
Drought stress has detrimental effects on crop productivity worldwide. A strong root system is crucial for maintaining water and nutrients uptake under drought stress. Wild watermelons possess resilient roots with excellent drought adaptability. However, the genetic factors controlling this trait remain uninvestigated. In this study, we conducted a bulk segregant analysis (BSA) on an F2 population consisting of two watermelon genotypes, wild and domesticated, which differ in their lateral root development under drought conditions. We identified two quantitative trait loci (qNLR_Dr. Chr01 and qNLR_Dr. Chr02) associated with the lateral root response to drought. Furthermore, we determined that a small region (0.93 Mb in qNLR_Dr. Chr01) is closely linked to drought adaptation through quantitative trait loci (QTL) validation and fine mapping. Transcriptome analysis of the parent roots under drought stress revealed unique effects on numerous genes in the sensitive genotype but not in the tolerant genotype. By integrating BSA, fine mapping, and the transcriptome, we identified six genes, namely L-Ascorbate Oxidase (AO), Cellulose Synthase-Interactive Protein 1 (CSI1), Late Embryogenesis Abundant Protein (LEA), Zinc-Finger Homeodomain Protein 2 (ZHD2), Pericycle Factor Type-A 5 (PFA5), and bZIP transcription factor 53-like (bZIP53-like), that might be involved in the drought adaptation. Our findings provide valuable QTLs and genes for marker-assisted selection in improving water-use efficiency and drought tolerance in watermelon. They also lay the groundwork for the genetic manipulation of drought-adapting genes in watermelon and other Cucurbitacea species.
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Affiliation(s)
- Ahmed Mahmoud
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
- Horticulture Research Institute, Agricultural Research Center, 9 Cairo University St, Giza 12619, Egypt;
| | - Rui Qi
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
| | - Xiaolu Chi
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
| | - Nanqiao Liao
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
| | - Guy Kateta Malangisha
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
| | - Abid Ali
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
| | - Mohamed Moustafa-Farag
- Horticulture Research Institute, Agricultural Research Center, 9 Cairo University St, Giza 12619, Egypt;
| | - Jinghua Yang
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Mingfang Zhang
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Zhongyuan Hu
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
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15
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Sharma A, Choudhary P, Chakdar H, Shukla P. Molecular insights and omics-based understanding of plant-microbe interactions under drought stress. World J Microbiol Biotechnol 2023; 40:42. [PMID: 38105277 DOI: 10.1007/s11274-023-03837-4] [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: 09/29/2023] [Accepted: 11/11/2023] [Indexed: 12/19/2023]
Abstract
The detrimental effects of adverse environmental conditions are always challenging and remain a major concern for plant development and production worldwide. Plants deal with such constraints by physiological, biochemical, and morphological adaptations as well as acquiring mutual support of beneficial microorganisms. As many stress-responsive traits of plants are influenced by microbial activities, plants have developed a sophisticated interaction with microbes to cope with adverse environmental conditions. The production of numerous bioactive metabolites by rhizospheric, endo-, or epiphytic microorganisms can directly or indirectly alter the root system architecture, foliage production, and defense responses. Although plant-microbe interactions have been shown to improve nutrient uptake and stress resilience in plants, the underlying mechanisms are not fully understood. "Multi-omics" application supported by genomics, transcriptomics, and metabolomics has been quite useful to investigate and understand the biochemical, physiological, and molecular aspects of plant-microbe interactions under drought stress conditions. The present review explores various microbe-mediated mechanisms for drought stress resilience in plants. In addition, plant adaptation to drought stress is discussed, and insights into the latest molecular techniques and approaches available to improve drought-stress resilience are provided.
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Affiliation(s)
- Aditya Sharma
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Prassan Choudhary
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, 275103, India
| | - Hillol Chakdar
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, 275103, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
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16
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Gao M, Abdallah MF, Song M, Xu Y, Sun D, Lu P, Wang J. Novel Endophytic Pseudescherichia sp. GSE25 Strain Significantly Controls Fusarium graminearum and Reduces Deoxynivalenol in Wheat. Toxins (Basel) 2023; 15:702. [PMID: 38133206 PMCID: PMC10747052 DOI: 10.3390/toxins15120702] [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: 11/01/2023] [Revised: 12/09/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Fusarium heading blight (FHB) is a devastating disease in wheat, primarily caused by field invasion of Fusarium graminearum. Due to the scarcity of resistant wheat varieties, the agricultural sector resorts to chemical fungicides to control FHB incidence. On the other hand, biocontrol represents a promising, eco-friendly approach aligned with sustainable and green agriculture concepts. In the present study, a bacterial endophyte, Pseudescherichia sp. (GSE25), was isolated from wheat seeds and identified through complete genome sequencing and phylogenetic analysis. In vitro testing of this endophytic strain demonstrated strong antifungal activity against F. graminearum PH-1 by inhibiting spore germination, suppressing germ tube growth, and causing cell membrane damage. Under field conditions, the strain GSE25 significantly reduced the FHB incidence and the associated deoxynivalenol mycotoxin accumulation by over 60% and 80%, respectively. These findings highlight the potential of the isolated bacterial endophyte Pseudescherichia sp. GSE25 strain as a biocontrol agent in protecting wheat from FHB-caused F. graminearum. This is the first report showing a biocontrol effect of Pseudescherichia sp. a strain against phytopathogens.
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Affiliation(s)
- Meiling Gao
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China;
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (M.S.)
| | - Mohamed F. Abdallah
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Gent, Belgium;
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Assiut University, Assiut 71515, Egypt
| | - Minggui Song
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (M.S.)
| | - Yiqian Xu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (M.S.)
| | - Daiyuan Sun
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (M.S.)
| | - Ping Lu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Jianhua Wang
- Institute for Agri-Food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
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17
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Hou J, Wan H, Liang K, Cui B, Ma Y, Chen Y, Liu J, Wang Y, Liu X, Zhang J, Wei Z, Liu F. Biochar amendment combined with partial root-zone drying irrigation alleviates salinity stress and improves root morphology and water use efficiency in cotton plant. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166978. [PMID: 37704141 DOI: 10.1016/j.scitotenv.2023.166978] [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: 06/23/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023]
Abstract
An adsorption experiment and a pot experiment were executed in order to explore the mechanisms by which biochar amendment in combination with reduced irrigation affects sodium and potassium uptake, root morphology, water use efficiency, and salinity tolerance of cotton plants. In the adsorption experiment, ten NaCl concentration gradients (0, 50, 100, 150, 200, 250, 300, 350, 400, and 500 mM) were set for testing isotherm adsorption of Na+ by biochar. It was found that the isotherms of Na+ adsorption by wheat straw biochar (WSP) and softwood biochar (SWP) were in accordance with the Langmuir isotherm model, and the Na+ adsorption ability of WSP (55.20 mg g-1) was superior to that of SWP (47.38 mg g-1). The pot experiment consisted three factors, viz., three biochar amendments (no biochar, WSP, and SWP), three irrigation strategies (deficit irrigation, partial root-zone drying irrigation - PRD, full irrigation), and two NaCl concentrations gradients (0 mM and 200 mM). The findings indicated that salinity stress lowered K+ concentration, root length, root surface area, and root volume (RV), but increased Na+ concentration, root average diameter, and root tissue density. However, biochar amendment decreased Na+ concentration, increased K+ concentration, and improved root morphology. In particular, the combination of WSP and PRD increased K+/Na+ ratio, RV, root weight density, root surface area density, water use efficiency, and partial factor productivity under salt stress, which can be a promising strategy to cope with drought and salinity stress in cotton production.
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Affiliation(s)
- Jingxiang Hou
- College of Water Resources and Architectural Engineering, Northwest A&F University, Weihui Road 23, 712100 Yangling, Shaanxi, China; Department of Plant and Environmental Science, Faculty of Science, University of Copenhagen, Højbakkegård Allé 13, DK-2630 Tåstrup, Denmark; Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Heng Wan
- College of Water Resources and Architectural Engineering, Northwest A&F University, Weihui Road 23, 712100 Yangling, Shaanxi, China; Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, Northwest A&F University, Yangling, Shaanxi 712100, China; Soil Physics and Land Management Group, Wageningen University, P.O. Box 47, Wageningen, 6700 AA, Netherlands
| | - Kehao Liang
- Department of Plant and Environmental Science, Faculty of Science, University of Copenhagen, Højbakkegård Allé 13, DK-2630 Tåstrup, Denmark
| | - Bingjing Cui
- College of Water Resources and Architectural Engineering, Northwest A&F University, Weihui Road 23, 712100 Yangling, Shaanxi, China; Department of Plant and Environmental Science, Faculty of Science, University of Copenhagen, Højbakkegård Allé 13, DK-2630 Tåstrup, Denmark; Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yingying Ma
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710129, China
| | - Yiting Chen
- Department of Plant and Environmental Science, Faculty of Science, University of Copenhagen, Højbakkegård Allé 13, DK-2630 Tåstrup, Denmark
| | - Jie Liu
- College of Water Resources and Architectural Engineering, Northwest A&F University, Weihui Road 23, 712100 Yangling, Shaanxi, China; Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yin Wang
- College of Resources and Environmental Sciences, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Xuezhi Liu
- School of Civil and Hydraulic Engineering, Ningxia University, Yinchuan 750021, China
| | - Jiarui Zhang
- College of Water Resources and Architectural Engineering, Northwest A&F University, Weihui Road 23, 712100 Yangling, Shaanxi, China; Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhenhua Wei
- College of Water Resources and Architectural Engineering, Northwest A&F University, Weihui Road 23, 712100 Yangling, Shaanxi, China; Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Fulai Liu
- Department of Plant and Environmental Science, Faculty of Science, University of Copenhagen, Højbakkegård Allé 13, DK-2630 Tåstrup, Denmark.
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18
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Yang Y, Shi Y, Wei X, Han J, Wang J, Mu C, Zhang J. Changes in mass allocation play a more prominent role than morphology in resource acquisition of the rhizomatous Leymus chinensis under drought stress. ANNALS OF BOTANY 2023; 132:121-132. [PMID: 37279964 PMCID: PMC10550271 DOI: 10.1093/aob/mcad073] [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: 12/08/2022] [Accepted: 06/05/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND AND AIMS Plants can respond to drought by changing their relative investments in the biomass and morphology of each organ. The aims of this study were to quantify the relative contribution of changes in morphology vs. allocation and determine how they affect each other. These results should help us understand the mechanisms that plants use to respond to drought events. METHODS In a glasshouse experiment, we applied a drought treatment (well-watered vs. drought) at early and late stages of plant growth, leading to four treatment combinations (well-watered in both early and late periods, WW; drought in the early period and well-watered in the late period, DW; well-watered in the early period and drought in the late period, WD; drought in both early and late periods, DD). We used the variance partitioning method to compare the contribution of organ (leaf and root) biomass allocation and morphology to the leaf area ratio, root length ratio and root area ratio, for the rhizomatous grass Leymus chinensis (Trin.) Tzvelev. KEY RESULTS Compared with the continuously well-watered treatment, the leaf area ratio, root length ratio and root area ratio showed increasing trends under various drought treatments. The contribution of leaf mass allocation to leaf area ratio differed among the drought treatments and was 2.1- to 5.3-fold greater than leaf morphology, and the contribution of root mass allocation to root length ratio was ~2-fold greater than that of root morphology. In contrast, root morphology contributed more to the root area ratio than biomass allocation under drought in both the early and late periods. There was a negative correlation between the ratio of leaf mass fraction to root mass fraction and the ratio of specific leaf area to specific root length (or specific root area). CONCLUSIONS This study suggested that organ biomass allocation drove a larger proportion of variation than morphological traits for the absorption of resources in this rhizomatous grass. These findings should help us understand the adaptive mechanisms of plants when they are confronted with drought stress.
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Affiliation(s)
- Yuheng Yang
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun 130024, China
| | - Yujie Shi
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun 130024, China
| | - Xiaowei Wei
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun 130024, China
| | - Jiayu Han
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun 130024, China
| | - Junfeng Wang
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun 130024, China
| | - Chunsheng Mu
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun 130024, China
| | - Jinwei Zhang
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun 130024, China
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19
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Pixley KV, Cairns JE, Lopez-Ridaura S, Ojiewo CO, Dawud MA, Drabo I, Mindaye T, Nebie B, Asea G, Das B, Daudi H, Desmae H, Batieno BJ, Boukar O, Mukankusi CTM, Nkalubo ST, Hearne SJ, Dhugga KS, Gandhi H, Snapp S, Zepeda-Villarreal EA. Redesigning crop varieties to win the race between climate change and food security. MOLECULAR PLANT 2023; 16:1590-1611. [PMID: 37674314 DOI: 10.1016/j.molp.2023.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 08/17/2023] [Accepted: 09/03/2023] [Indexed: 09/08/2023]
Abstract
Climate change poses daunting challenges to agricultural production and food security. Rising temperatures, shifting weather patterns, and more frequent extreme events have already demonstrated their effects on local, regional, and global agricultural systems. Crop varieties that withstand climate-related stresses and are suitable for cultivation in innovative cropping systems will be crucial to maximize risk avoidance, productivity, and profitability under climate-changed environments. We surveyed 588 expert stakeholders to predict current and novel traits that may be essential for future pearl millet, sorghum, maize, groundnut, cowpea, and common bean varieties, particularly in sub-Saharan Africa. We then review the current progress and prospects for breeding three prioritized future-essential traits for each of these crops. Experts predict that most current breeding priorities will remain important, but that rates of genetic gain must increase to keep pace with climate challenges and consumer demands. Importantly, the predicted future-essential traits include innovative breeding targets that must also be prioritized; for example, (1) optimized rhizosphere microbiome, with benefits for P, N, and water use efficiency, (2) optimized performance across or in specific cropping systems, (3) lower nighttime respiration, (4) improved stover quality, and (5) increased early vigor. We further discuss cutting-edge tools and approaches to discover, validate, and incorporate novel genetic diversity from exotic germplasm into breeding populations with unprecedented precision, accuracy, and speed. We conclude that the greatest challenge to developing crop varieties to win the race between climate change and food security might be our innovativeness in defining and boldness to breed for the traits of tomorrow.
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Affiliation(s)
- Kevin V Pixley
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
| | - Jill E Cairns
- International Maize and Wheat Improvement Center (CIMMYT), Harare, Zimbabwe
| | | | - Chris O Ojiewo
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | | | - Inoussa Drabo
- International Maize and Wheat Improvement Center (CIMMYT), Dakar, Senegal
| | - Taye Mindaye
- Ethiopian Institute of Agricultural Research (EIAR), Addis Ababa, Ethiopia
| | - Baloua Nebie
- International Maize and Wheat Improvement Center (CIMMYT), Dakar, Senegal
| | - Godfrey Asea
- National Agricultural Research Organization (NARO), Kampala, Uganda
| | - Biswanath Das
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Happy Daudi
- Tanzania Agricultural Research Institute (TARI), Naliendele, Tanzania
| | - Haile Desmae
- International Maize and Wheat Improvement Center (CIMMYT), Dakar, Senegal
| | - Benoit Joseph Batieno
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Ousmane Boukar
- International Institute of Tropicl Agriculture (IITA), Kano, Nigeria
| | | | | | - Sarah J Hearne
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Kanwarpal S Dhugga
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Harish Gandhi
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Sieglinde Snapp
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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20
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Siddiqui N, Gabi MT, Kamruzzaman M, Ambaw AM, Teferi TJ, Dadshani S, Léon J, Ballvora A. Genetic dissection of root architectural plasticity and identification of candidate loci in response to drought stress in bread wheat. BMC Genom Data 2023; 24:38. [PMID: 37495985 PMCID: PMC10373353 DOI: 10.1186/s12863-023-01140-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/14/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND The frequency of droughts has dramatically increased over the last 50 years, causing yield declines in cereals, including wheat. Crop varieties with efficient root systems show great potential for plant adaptation to drought stress, however; genetic control of root systems in wheat under field conditions is not yet well understood. RESULTS Natural variation in root architecture plasticity (phenotypic alteration due to changing environments) was dissected under field-based control (well-irrigated) and drought (rain-out shelter) conditions by a genome-wide association study using 200 diverse wheat cultivars. Our results revealed root architecture and plasticity traits were differentially responded to drought stress. A total of 25 marker-trait associations (MTAs) underlying natural variations in root architectural plasticity were identified in response to drought stress. They were abundantly distributed on chromosomes 1 A, 1B, 2 A, 2B, 3 A, 3B, 4B, 5 A, 5D, 7 A and 7B of the wheat genome. Gene ontology annotation showed that many candidate genes associated with plasticity were involved in water-transport and water channel activity, cellular response to water deprivation, scavenging reactive oxygen species, root growth and development and hormone-activated signaling pathway-transmembrane transport, indicating their response to drought stress. Further, in silico transcript abundance analysis demonstrated that root plasticity-associated candidate genes were highly expressed in roots across different root growth stages and under drought treatments. CONCLUSION Our results suggest that root phenotypic plasticity is highly quantitative, and the corresponding loci are associated with drought stress that may provide novel ways to enable root trait breeding.
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Affiliation(s)
- Nurealam Siddiqui
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, 53115, Bonn, Germany
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Melesech T Gabi
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, 53115, Bonn, Germany
| | - Mohammad Kamruzzaman
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, 53115, Bonn, Germany
- Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh-2202, Bangladesh
| | - Abebaw M Ambaw
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, 53115, Bonn, Germany
| | - Tesfaye J Teferi
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, 53115, Bonn, Germany
| | - Said Dadshani
- INRES-Plant Nutrition, University of Bonn, 53115, Bonn, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, 53115, Bonn, Germany
- Field Lab Campus Klein-Altendorf, University of Bonn, Klein-Altendorf 2, 53359, Rheinbach, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, 53115, Bonn, Germany.
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21
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Shamuyarira KW, Shimelis H, Figlan S, Chaplot V. Combining ability analysis of yield and biomass allocation related traits in newly developed wheat populations. Sci Rep 2023; 13:11832. [PMID: 37481645 PMCID: PMC10363107 DOI: 10.1038/s41598-023-38961-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/18/2023] [Indexed: 07/24/2023] Open
Abstract
Increasing biomass allocation to the root system may increase soil-organic carbon stocks and confer drought adaptation in water-limited environments. Understanding the genetic bases and inheritance of biomass allocation is fundamental for drought tolerance breeding and soil health. The objective of this study was to determine the general and specific combining ability, maternal effects and the mode of gene action controlling the major yield and biomass allocation related traits in wheat to identify good combiners for breeding and enhanced carbon sequestration. Ten selected wheat genotypes were crossed in a full diallel mating design, and 90 F2 families were generated and evaluated in the field and greenhouse under drought-stressed and non-stressed conditions. Significant differences were recorded among the tested families revealing substantial variation for plant height (PH), kernels per spike (KPS), root biomass (RB), shoot biomass (SB), total plant biomass (PB) and grain yield (GY). Additive gene effects conditioned PH, SB, PB and GY under drought, suggesting the polygenic inheritance for drought tolerance. Strong maternal and reciprocal genetic effects were recorded for RB across the testing sites under drought-stressed conditions. Line BW162 had high yield and biomass production and can be used to transfer favourable genes to its progeny. The parental line LM75 maintained the general combining ability (GCA) effects in a positive and desirable direction for SB, PB and GY. Early generation selection using PH, SB, PB and GY will improve drought tolerance by exploiting additive gene action under drought conditions. Higher RB production may be maintained by a positive selection of male and female parents to capture the significant maternal and reciprocal effects found in this study.
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Affiliation(s)
- Kwame W Shamuyarira
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa.
| | - Hussein Shimelis
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Sandiswa Figlan
- Department of Agriculture and Animal Health, University of South Africa, Florida, South Africa
| | - Vincent Chaplot
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
- Laboratoire d'Océanographie et du Climat: Expérimentations et Approches Numériques (LOCEAN), UMR 7159, IRD/C NRS/UPMC/ MNHN, IPSL, Paris, France
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22
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Siddiqui MN, Pandey K, Bhadhury SK, Sadeqi B, Schneider M, Sanchez-Garcia M, Stich B, Schaaf G, Léon J, Ballvora A. Convergently selected NPF2.12 coordinates root growth and nitrogen use efficiency in wheat and barley. THE NEW PHYTOLOGIST 2023; 238:2175-2193. [PMID: 36808608 DOI: 10.1111/nph.18820] [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: 10/31/2022] [Accepted: 02/13/2023] [Indexed: 05/04/2023]
Abstract
Understanding the genetic and molecular function of nitrate sensing and acquisition across crop species will accelerate breeding of cultivars with improved nitrogen use efficiency (NUE). Here, we performed a genome-wide scan using wheat and barley accessions characterized under low and high N inputs that uncovered the NPF2.12 gene, encoding a homolog of the Arabidopsis nitrate transceptor NRT1.6 and other low-affinity nitrate transporters that belong to the MAJOR FACILITATOR SUPERFAMILY. Next, it is shown that variations in the NPF2.12 promoter correlated with altered NPF2.12 transcript levels where decreased gene expression was measured under low nitrate availability. Multiple field trials revealed a significantly enhanced N content in leaves and grains and NUE in the presence of the elite allele TaNPF2.12TT grown under low N conditions. Furthermore, the nitrate reductase encoding gene NIA1 was up-regulated in npf2.12 mutant upon low nitrate concentrations, thereby resulting in elevated levels of nitric oxide (NO) production. This increase in NO correlated with the higher root growth, nitrate uptake, and N translocation observed in the mutant when compared to wild-type. The presented data indicate that the elite haplotype alleles of NPF2.12 are convergently selected in wheat and barley that by inactivation indirectly contribute to root growth and NUE by activating NO signaling under low nitrate conditions.
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Affiliation(s)
- Md Nurealam Siddiqui
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Kailash Pandey
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
| | - Suzan Kumer Bhadhury
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
| | - Bahman Sadeqi
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
| | - Michael Schneider
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, Germany
| | - Miguel Sanchez-Garcia
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, 10101, Morocco
| | - Benjamin Stich
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Gabriel Schaaf
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Karlrobert-Kreiten-Str. 13, Bonn, D-53115, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
- Field Lab Campus Klein-Altendorf, University of Bonn, Klein-Altendorf 2, Rheinbach, 53359, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding, University of Bonn, Katzenburgweg 5, Bonn, D-53115, Germany
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23
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Li C, Guo J, Wang D, Chen X, Guan H, Li Y, Zhang D, Liu X, He G, Wang T, Li Y. Genomic insight into changes of root architecture under drought stress in maize. PLANT, CELL & ENVIRONMENT 2023; 46:1860-1872. [PMID: 36785485 DOI: 10.1111/pce.14567] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/03/2023] [Accepted: 02/11/2023] [Indexed: 05/04/2023]
Abstract
Drought stress is a central environmental factor that severely limits maize production worldwide. Root architecture plays an important role in drought tolerance and can be targeted in breeding programmes. Here, we conducted phenotyping of root architecture under different water treatments for 373 maize inbred lines, representative germplasm from both China and the United States in different breeding eras. We found that seminal root length in response to drought stress experienced convergent increase during breeding in both countries. Using a genome-wide association study, we identified a total of 221 associated loci underlying 13 root traits under well-watered and water-stressed conditions. These loci harboured many reported root- and abiotic stress-related genes. Furthermore, a total of 75 strong candidate genes were prioritised by integrating candidate genes associated with seminal root length and differentially expressed genes in seminal root. One of high-confidence candidate genes, ZmCIPK3 was functionally characterised and probably plays a role in enhancing drought tolerance through regulating seminal root growth. This study provides valuable information for genetic improvement of root architecture and drought tolerance in maize.
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Affiliation(s)
- Chunhui Li
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College, Yangzhou University, Yangzhou, China
| | - Dongmei Wang
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaojing Chen
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honghui Guan
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongxiang Li
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengfeng Zhang
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuyang Liu
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guanhua He
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianyu Wang
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Li
- State Key Lab of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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24
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Kopecká R, Kameniarová M, Černý M, Brzobohatý B, Novák J. Abiotic Stress in Crop Production. Int J Mol Sci 2023; 24:ijms24076603. [PMID: 37047573 PMCID: PMC10095105 DOI: 10.3390/ijms24076603] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
The vast majority of agricultural land undergoes abiotic stress that can significantly reduce agricultural yields. Understanding the mechanisms of plant defenses against stresses and putting this knowledge into practice is, therefore, an integral part of sustainable agriculture. In this review, we focus on current findings in plant resistance to four cardinal abiotic stressors—drought, heat, salinity, and low temperatures. Apart from the description of the newly discovered mechanisms of signaling and resistance to abiotic stress, this review also focuses on the importance of primary and secondary metabolites, including carbohydrates, amino acids, phenolics, and phytohormones. A meta-analysis of transcriptomic studies concerning the model plant Arabidopsis demonstrates the long-observed phenomenon that abiotic stressors induce different signals and effects at the level of gene expression, but genes whose regulation is similar under most stressors can still be traced. The analysis further reveals the transcriptional modulation of Golgi-targeted proteins in response to heat stress. Our analysis also highlights several genes that are similarly regulated under all stress conditions. These genes support the central role of phytohormones in the abiotic stress response, and the importance of some of these in plant resistance has not yet been studied. Finally, this review provides information about the response to abiotic stress in major European crop plants—wheat, sugar beet, maize, potatoes, barley, sunflowers, grapes, rapeseed, tomatoes, and apples.
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Affiliation(s)
- Romana Kopecká
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Michaela Kameniarová
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
| | - Jan Novák
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech Republic
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25
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Jiang Y, Su S, Chen H, Li S, Shan X, Li H, Liu H, Dong H, Yuan Y. Transcriptome analysis of drought-responsive and drought-tolerant mechanisms in maize leaves under drought stress. PHYSIOLOGIA PLANTARUM 2023; 175:e13875. [PMID: 36775906 DOI: 10.1111/ppl.13875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 01/18/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Maize is a major crop essential for food and feed, but its production is threatened by various biotic and abiotic stresses. Drought is one of the most common abiotic stresses, causing severe crop yield reduction. Although several studies have been devoted to selecting drought-tolerant maize lines and detecting the drought-responsive mechanism of maize, the transcriptomic differences between drought-tolerant and drought-susceptible maize lines are still largely unknown. In our study, RNA-seq was performed on leaves of the drought-tolerant line W9706 and the drought-susceptible line B73 after drought treatment. We identified 3147 differentially expressed genes (DEGs) between these two lines. The upregulated DEGs in W9706 were enriched in specific processes, including ABA signaling, wax biosynthesis, CHO metabolism, signal transduction and brassinosteroid biosynthesis-related processes, while the downregulated DEGs were enriched in specific processes, such as stomatal movement. Altogether, transcriptomic analysis suggests that the different drought resistances were correlated with the differential expression of genes, while the drought tolerance of W9706 is due to the more rapid response to stimulus, higher water retention capacity and stable cellular environment under water deficit conditions.
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Affiliation(s)
- Yuan Jiang
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Shengzhong Su
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Hao Chen
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Shipeng Li
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Xiaohui Shan
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - He Li
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Hongkui Liu
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Haixiao Dong
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
| | - Yaping Yuan
- Jilin Engineering Research Center for Crop Biotechnology Breeding, College of Plant Science, Jilin University, Changchun, China
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26
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Mani M, Mathiyazhagan C, Dey A, Faisal M, Alatar AA, Alok A, Shekhawat MS. Micro-morpho-anatomical transitions at various stages of in vitro development of Crinum malabaricum Lekhak and Yadav: A critically endangered medicinal plant. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:142-151. [PMID: 36040406 DOI: 10.1111/plb.13464] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Crinum malabaricum Lekhak & Yadav is a recently discovered and critically endangered aquatic bulbous plant of the family Amaryllidaceae. It gained attention as a wild source of the acetylcholinesterase inhibiting alkaloid 'galanthamine' used to treat Alzheimer and Parkinson diseases. The bulbs of this plant contain the highest amount of galanthamine among Crinum species. In vitro regeneration systems were developed to produce quality uniform plantlets of C. malabaricum. Bright field light microscopy was used to analyse micro-morpho-anatomical developments taking place in the leaves and roots during in vitro, ex vitro and in vivo transitions of plantlets. Leaves and roots of plants raised in vitro possessed a higher degree of microscopic structural anomalies, such as underdeveloped epicuticular wax deposition, immature and non-functional stomata, more aquiferous parenchyma with a reduced lumen. Roots developed in vitro were characterized by extremely large, uneven cortical cells and reduced intercellular spaces. The vascular tissues were under-developed and only primary vascular tissues were observed. As a result of ex vitro acclimation, there was a significant acceleration in the improvement of tissue systems in leaves and roots. Such plantlets can tolerate elevated temperatures and light under in vivo conditions. Thus, the microscopic evaluation of the structural trajectory in different stages of plantlet development provides an understanding of the acclimation process and structural adaptations, which could help enhance survival of in vitro raised plantlets under ex vitro and in vivo conditions.
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Affiliation(s)
- M Mani
- Biotechnology Unit, Kanchi Mamunivar Government Institute for Postgraduate Studies and Research, Puducherry, India
- Department of Botany, Siddha Clinical Research Unit, Central Council for Research in Siddha, Palayamkottai, Tamil Nadu, India
| | - C Mathiyazhagan
- Biotechnology Unit, Kanchi Mamunivar Government Institute for Postgraduate Studies and Research, Puducherry, India
| | - A Dey
- Department of Life Sciences, Presidency University, Kolkata, India
| | - M Faisal
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - A A Alatar
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - A Alok
- Department of Plant Pathology, University of Minnesota, Twin cities, Saint Paul, USA
| | - M S Shekhawat
- Biotechnology Unit, Kanchi Mamunivar Government Institute for Postgraduate Studies and Research, Puducherry, India
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27
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Raj SRG, Nadarajah K. QTL and Candidate Genes: Techniques and Advancement in Abiotic Stress Resistance Breeding of Major Cereals. Int J Mol Sci 2022; 24:6. [PMID: 36613450 PMCID: PMC9820233 DOI: 10.3390/ijms24010006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
At least 75% of the world's grain production comes from the three most important cereal crops: rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays). However, abiotic stressors such as heavy metal toxicity, salinity, low temperatures, and drought are all significant hazards to the growth and development of these grains. Quantitative trait locus (QTL) discovery and mapping have enhanced agricultural production and output by enabling plant breeders to better comprehend abiotic stress tolerance processes in cereals. Molecular markers and stable QTL are important for molecular breeding and candidate gene discovery, which may be utilized in transgenic or molecular introgression. Researchers can now study synteny between rice, maize, and wheat to gain a better understanding of the relationships between the QTL or genes that are important for a particular stress adaptation and phenotypic improvement in these cereals from analyzing reports on QTL and candidate genes. An overview of constitutive QTL, adaptive QTL, and significant stable multi-environment and multi-trait QTL is provided in this article as a solid framework for use and knowledge in genetic enhancement. Several QTL, such as DRO1 and Saltol, and other significant success cases are discussed in this review. We have highlighted techniques and advancements for abiotic stress tolerance breeding programs in cereals, the challenges encountered in introgressing beneficial QTL using traditional breeding techniques such as mutation breeding and marker-assisted selection (MAS), and the in roads made by new breeding methods such as genome-wide association studies (GWASs), the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, and meta-QTL (MQTL) analysis. A combination of these conventional and modern breeding approaches can be used to apply the QTL and candidate gene information in genetic improvement of cereals against abiotic stresses.
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Affiliation(s)
| | - Kalaivani Nadarajah
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
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28
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Schmidt L, Nagel KA, Galinski A, Sannemann W, Pillen K, Maurer A. Unraveling Genomic Regions Controlling Root Traits as a Function of Nitrogen Availability in the MAGIC Wheat Population WM-800. PLANTS (BASEL, SWITZERLAND) 2022; 11:3520. [PMID: 36559632 PMCID: PMC9785272 DOI: 10.3390/plants11243520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/29/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
An ever-growing world population demands to be fed in the future and environmental protection and climate change need to be taken into account. An important factor here is nitrogen uptake efficiency (NUpE), which is influenced by the root system (the interface between plant and soil). To understand the natural variation of root system architecture (RSA) as a function of nitrogen (N) availability, a subset of the multiparent advanced generation intercross (MAGIC) winter wheat population WM-800 was phenotyped under two contrasting N treatments in a high-throughput phenotyping system at the seedling stage. Fourteen root and shoot traits were measured. Subsequently, these traits were genetically analyzed using 13,060 polymorphic haplotypes and SNPs in a genome-wide association study (GWAS). In total, 64 quantitative trait loci (QTL) were detected; 60 of them were N treatment specific. Candidate genes for the detected QTL included NRT1.1 and genes involved in stress signaling under N-, whereas candidate genes under N+ were more associated with general growth, such as mei2 and TaWOX11b. This finding may indicate (i) a disparity of the genetic control of root development under low and high N supply and, furthermore, (ii) the need for an N specific selection of genes and genotypes in breeding new wheat cultivars with improved NUpE.
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Affiliation(s)
- Laura Schmidt
- Chair of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Kerstin A. Nagel
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Research Institute Jülich GmbH, 52425 Jülich, Germany
| | - Anna Galinski
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Research Institute Jülich GmbH, 52425 Jülich, Germany
| | - Wiebke Sannemann
- Chair of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Klaus Pillen
- Chair of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Andreas Maurer
- Chair of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle, Germany
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29
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Kou X, Han W, Kang J. Responses of root system architecture to water stress at multiple levels: A meta-analysis of trials under controlled conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:1085409. [PMID: 36570905 PMCID: PMC9780461 DOI: 10.3389/fpls.2022.1085409] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/28/2022] [Indexed: 05/31/2023]
Abstract
Plants are exposed to increasingly severe drought events and roots play vital roles in maintaining plant survival, growth, and reproduction. A large body of literature has investigated the adaptive responses of root traits in various plants to water stress and these studies have been reviewed in certain groups of plant species at a certain scale. Nevertheless, these responses have not been synthesized at multiple levels. This paper screened over 2000 literatures for studies of typical root traits including root growth angle, root depth, root length, root diameter, root dry weight, root-to-shoot ratio, root hair length and density and integrates their drought responses at genetic and morphological scales. The genes, quantitative trait loci (QTLs) and hormones that are involved in the regulation of drought response of the root traits were summarized. We then statistically analyzed the drought responses of root traits and discussed the underlying mechanisms. Moreover, we highlighted the drought response of 1-D and 2-D root length density (RLD) distribution in the soil profile. This paper will provide a framework for an integrated understanding of root adaptive responses to water deficit at multiple scales and such insights may provide a basis for selection and breeding of drought tolerant crop lines.
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Affiliation(s)
- Xinyue Kou
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Weihua Han
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Jian Kang
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
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Natural selection under conventional and organic cropping systems affect root architecture in spring barley. Sci Rep 2022; 12:20095. [PMID: 36418861 PMCID: PMC9684413 DOI: 10.1038/s41598-022-23298-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/29/2022] [Indexed: 11/24/2022] Open
Abstract
A beneficial root system is crucial for efficient nutrient uptake and stress tolerance. Therefore, evaluating the root system variation for breeding crop plants towards stress adaptation is critically important. Here, we phenotyped root architectural traits of naturally adapted populations from organic and conventional cropping systems under hydroponic and field trails. Long-term natural selection under these two cropping systems resulted in a microevolution of root morphological and anatomical traits. Barley lines developed under an organic system possessed longer roots with narrow root angle, larger surface area, increased root mass density, and a thinner root diameter with an increased number of metaxylem vessels. In contrast, lines adapted to the conventional system tend to have a shorter and wider root system with a larger root volume with a thicker diameter but fewer metaxylem vessels. Allometry analysis established a relationship between root traits and plant size among barley genotypes, which specifies that root angle could be a good candidate among studied root traits to determine root-borne shoot architecture. Further, multivariate analyses showed a strong tendency towards increased variability of the organically adapted population's root morphological and anatomical traits. The genotyping of ancestor populations validated the observations made in these experiments. Collectively, this results indicate significant differences in root phenotypes between conventional and organic populations, which could be useful in comparative genomics and breeding.
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Abbas M, Abid MA, Meng Z, Abbas M, Wang P, Lu C, Askari M, Akram U, Ye Y, Wei Y, Wang Y, Guo S, Liang C, Zhang R. Integrating advancements in root phenotyping and genome-wide association studies to open the root genetics gateway. PHYSIOLOGIA PLANTARUM 2022; 174:e13787. [PMID: 36169590 DOI: 10.1111/ppl.13787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/12/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Plant adaptation to challenging environmental conditions around the world has made root growth and development an important research area for plant breeders and scientists. Targeted manipulation of root system architecture (RSA) to increase water and nutrient use efficiency can minimize the adverse effects of climate change on crop production. However, phenotyping of RSA is a major bottleneck since the roots are hidden in the soil. Recently the development of 2- and 3D root imaging techniques combined with the genome-wide association studies (GWASs) have opened up new research tools to identify the genetic basis of RSA. These approaches provide a comprehensive understanding of the RSA, by accelerating the identification and characterization of genes involved in root growth and development. This review summarizes the latest developments in phenotyping techniques and GWAS for RSA, which are used to map important genes regulating various aspects of RSA under varying environmental conditions. Furthermore, we discussed about the state-of-the-art image analysis tools integrated with various phenotyping platforms for investigating and quantifying root traits with the highest phenotypic plasticity in both artificial and natural environments which were used for large scale association mapping studies, leading to the identification of RSA phenotypes and their underlying genetics with the greatest potential for RSA improvement. In addition, challenges in root phenotyping and GWAS are also highlighted, along with future research directions employing machine learning and pan-genomics approaches.
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Affiliation(s)
- Mubashir Abbas
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Ali Abid
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Manzar Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Peilin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chao Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Askari
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Umar Akram
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yulu Ye
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunxiao Wei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chengzhen Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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Mahmoud A, Qi R, Zhao H, Yang H, Liao N, Ali A, Malangisha GK, Ma Y, Zhang K, Zhou Y, Xia Y, Lyu X, Yang J, Zhang M, Hu Z. An allelic variant in the ACS7 gene promotes primary root growth in watermelon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3357-3373. [PMID: 35980402 DOI: 10.1007/s00122-022-04173-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Gene mining in a C. lanatus × C. amarus population revealed one gene, ACS7, linked to primary root elongation in watermelon. Watermelon is a xerophytic crop characterized by a long primary root and robust lateral roots. Therefore, watermelon serves as an excellent model for studying root elongation and development. However, the genetic mechanism underlying the primary root elongation in watermelon remains unknown. Herein, through bulk segregant analysis we identified a genetic locus, qPRL.Chr03, controlling primary root length (PRL) using two different watermelon species (Citrullus lanatus and Citrullus amarus) that differ in their root architecture. Fine mapping revealed that xaa-Pro dipeptidase and 1-aminocyclopropane-1-carboxylate synthase 7 (ACS7) are candidate regulators of the primary root growth. Allelic variation in the delimited region among 193 watermelon accessions indicated that the long-root alleles might only exist in C. amarus. Interestingly, the discrepancy in PRL among the C. amarus accessions was clearly associated with a nonsynonymous single nucleotide polymorphism variant within the ACS7 gene. The ACS7 expression and ethylene levels in the primary root tips suggested that ethylene is a negative regulator of root elongation in watermelon, as supported by the application of 1-aminocyclopropane-1-carboxylate (ACC, the ethylene precursor) or 2-aminoethoxyvinyl glycine (AVG, an ACS inhibitor). To the best of our knowledge, these findings provide the first description of the genetic basis of root elongation in watermelon. The detected markers of the ACS7 gene will facilitate marker-assisted selection for the PRL trait to improve water and nutrient use efficacy in watermelon and beyond.
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Affiliation(s)
- Ahmed Mahmoud
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Agriculture Research Center, Horticulture Research Institute, 9 Gmaa St, Giza, 12619, Egypt
| | - Rui Qi
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
| | - Haoshun Zhao
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Haiyang Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Nanqiao Liao
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Abid Ali
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Guy Kateta Malangisha
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yuyuan Ma
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Kejia Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yimei Zhou
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yuelin Xia
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China.
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China.
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China.
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China.
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Quantitative Assessment of Climate Change Impact and Anthropogenic Influence on Crop Production and Food Security in Shandong, Eastern China. ATMOSPHERE 2022. [DOI: 10.3390/atmos13081160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Food security plays an important role in maintaining national stability and sustainable development of human society, and its research has become a hot issue at present. Shandong is the main grain producing area in China, and its grain production plays an important role in national food security. Accordingly, this paper is based on the county climate change, grain yield, sown area, fertilizer use, total power of rural machinery, and total population data in Shandong Province from 1995 to 2020. The evolution process of the food security pattern was studied by the methods of spatial analysis and comprehensive evaluation, the influencing factors of food security were quantitatively analyzed, and the adaptive countermeasures to alleviate the food security risks in this region were discussed. The results show that: Grain production increased by 30.62% from 1995 to 2020. The total population and per capita food availability also increased. Since 2000, more than a quarter of counties have experienced a high risk of food insecurity. The spatial agglomeration of grain production was enhanced, and the local agglomeration characteristics were significantly different. The average temperature in the growing season, the sown area, and the total power of agricultural machinery had a significant positive impact on grain production, while the annual average temperature had a significant negative impact on grain production. Improving the food supply system, strengthening the protection of cultivated land, improving the efficiency of fertilizer utilization, and increasing investment in agricultural science and technology can effectively alleviate food security risks.
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Ahmad N, Su B, Ibrahim S, Kuang L, Tian Z, Wang X, Wang H, Dun X. Deciphering the Genetic Basis of Root and Biomass Traits in Rapeseed (Brassica napus L.) through the Integration of GWAS and RNA-Seq under Nitrogen Stress. Int J Mol Sci 2022; 23:ijms23147958. [PMID: 35887301 PMCID: PMC9323118 DOI: 10.3390/ijms23147958] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/16/2022] [Accepted: 07/16/2022] [Indexed: 02/06/2023] Open
Abstract
An excellent root system is responsible for crops with high nitrogen-use efficiency (NUE). The current study evaluated the natural variations in 13 root- and biomass-related traits under a low nitrogen (LN) treatment in a rapeseed association panel. The studied traits exhibited significant phenotypic differences with heritabilities ranging from 0.53 to 0.66, and most of the traits showed significant correlations with each other. The genome-wide association study (GWAS) found 51 significant and 30 suggestive trait–SNP associations that integrated into 14 valid quantitative trait loci (QTL) clusters and explained 5.7–21.2% phenotypic variance. In addition, RNA sequencing was performed at two time points to examine the differential expression of genes (DEGs) between high and low NUE lines. In total, 245, 540, and 399 DEGs were identified as LN stress-specific, high nitrogen (HN) condition-specific, and HNLN common DEGs, respectively. An integrated analysis of GWAS, weighted gene co-expression network, and DEGs revealed 16 genes involved in rapeseed root development under LN stress. Previous studies have reported that the homologs of seven out of sixteen potential genes control root growth and NUE. These findings revealed the genetic basis underlying nitrogen stress and provided worthwhile SNPs/genes information for the genetic improvement of NUE in rapeseed.
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Affiliation(s)
- Nazir Ahmad
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (N.A.); (B.S.); (S.I.); (L.K.); (Z.T.); (X.W.)
| | - Bin Su
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (N.A.); (B.S.); (S.I.); (L.K.); (Z.T.); (X.W.)
| | - Sani Ibrahim
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (N.A.); (B.S.); (S.I.); (L.K.); (Z.T.); (X.W.)
- Department of Plant Biology, Faculty of Life Sciences, College of Physical and Pharmaceutical Sciences, Bayero University, P.M.B. 3011, Kano 700006, Nigeria
| | - Lieqiong Kuang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (N.A.); (B.S.); (S.I.); (L.K.); (Z.T.); (X.W.)
| | - Ze Tian
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (N.A.); (B.S.); (S.I.); (L.K.); (Z.T.); (X.W.)
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (N.A.); (B.S.); (S.I.); (L.K.); (Z.T.); (X.W.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (N.A.); (B.S.); (S.I.); (L.K.); (Z.T.); (X.W.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Correspondence: (H.W.); (X.D.)
| | - Xiaoling Dun
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (N.A.); (B.S.); (S.I.); (L.K.); (Z.T.); (X.W.)
- Correspondence: (H.W.); (X.D.)
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RNA-Seq Analysis Demonstrates Different Strategies Employed by Tiger Nuts ( Cyperus esculentus L.) in Response to Drought Stress. LIFE (BASEL, SWITZERLAND) 2022; 12:life12071051. [PMID: 35888139 PMCID: PMC9322875 DOI: 10.3390/life12071051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/04/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022]
Abstract
Drought stress, an important abiotic stress, has affected global agricultural production by limiting the yield and the quality of crops. Tiger nuts (Cyperus esculentus L.) are C4 crops in the Cyperaceae family, which have high-quality wholesome ingredients. However, data on mechanisms underlying the response of tiger nuts to drought stress are few. Here, the variety of Jisha 1 and 15% polyethylene glycol (PEG; a drought stress simulator) were used to study the mechanisms of stress response in tiger nuts. Our evaluation of the changes in physiological indicators such as electrolyte leakage (El), malondialdehyde (MDA), hydrogen peroxide (H2O2), superoxide anion (O2−) and activities of reactive oxygen species (ROS) showed that 12 h was the most suitable time point to harvest and analyze the response to drought stress. Thereafter, we performed transcriptome (RNA-Seq) analysis in the control (CK) and stress treatment groups and showed that there was a total of 1760 differentially expressed genes (DEGs). Gene Ontology (GO) analysis showed that the DEGs were enriched in abscisic acid (ABA) terms, and pathways such as starch and sucrose metabolism (ko00500), phenylpropanoid biosynthesis (ko00940) and plant hormone signal transduction (ko04075) were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. In addition, quantitative real-time PCR (qRT-PCR) analysis of the DEGs demonstrated an upregulation of ABA and lignin content, as well as enzyme activities in enriched pathways, which validated the RNA-Seq data. These results revealed the pathways and mechanisms adopted by the tiger nuts in response to drought stress.
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Wahab A, Abdi G, Saleem MH, Ali B, Ullah S, Shah W, Mumtaz S, Yasin G, Muresan CC, Marc RA. Plants' Physio-Biochemical and Phyto-Hormonal Responses to Alleviate the Adverse Effects of Drought Stress: A Comprehensive Review. PLANTS (BASEL, SWITZERLAND) 2022; 11:1620. [PMID: 35807572 PMCID: PMC9269229 DOI: 10.3390/plants11131620] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 05/19/2023]
Abstract
Water, a necessary component of cell protoplasm, plays an essential role in supporting life on Earth; nevertheless, extreme changes in climatic conditions limit water availability, causing numerous issues, such as the current water-scarce regimes in many regions of the biome. This review aims to collect data from various published studies in the literature to understand and critically analyze plants' morphological, growth, yield, and physio-biochemical responses to drought stress and their potential to modulate and nullify the damaging effects of drought stress via activating natural physiological and biochemical mechanisms. In addition, the review described current breakthroughs in understanding how plant hormones influence drought stress responses and phytohormonal interaction through signaling under water stress regimes. The information for this review was systematically gathered from different global search engines and the scientific literature databases Science Direct, including Google Scholar, Web of Science, related studies, published books, and articles. Drought stress is a significant obstacle to meeting food demand for the world's constantly growing population. Plants cope with stress regimes through changes to cellular osmotic potential, water potential, and activation of natural defense systems in the form of antioxidant enzymes and accumulation of osmolytes including proteins, proline, glycine betaine, phenolic compounds, and soluble sugars. Phytohormones modulate developmental processes and signaling networks, which aid in acclimating plants to biotic and abiotic challenges and, consequently, their survival. Significant progress has been made for jasmonates, salicylic acid, and ethylene in identifying important components and understanding their roles in plant responses to abiotic stress. Other plant hormones, such as abscisic acid, auxin, gibberellic acid, brassinosteroids, and peptide hormones, have been linked to plant defense signaling pathways in various ways.
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Affiliation(s)
- Abdul Wahab
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China;
| | - Gholamreza Abdi
- Department of Biotechnology, Persian Gulf Research Institute, Persian Gulf University, Bushehr 75169, Iran;
| | - Muhammad Hamzah Saleem
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Saqib Ullah
- Department of Botany, Islamia College, Peshawar 25120, Pakistan;
| | - Wadood Shah
- Department of Botany, University of Peshawar, Peshawar 25120, Pakistan;
| | - Sahar Mumtaz
- Department of Botany, Division of Science and Technology, University of Education, Lahore 54770, Pakistan;
| | - Ghulam Yasin
- Department of Botany, Bahauddin Zakariya University, Multan 60800, Pakistan;
| | - Crina Carmen Muresan
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Science and Veterinary Medicine Cluj-Napoca, 3-5 Calea Mănăştur Street, 400372 Cluj-Napoca, Romania;
| | - Romina Alina Marc
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Science and Veterinary Medicine Cluj-Napoca, 3-5 Calea Mănăştur Street, 400372 Cluj-Napoca, Romania;
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Overview of Identified Genomic Regions Associated with Various Agronomic and Physiological Traits in Barley under Abiotic Stresses. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12105189] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Climate change has caused breeders to focus on varieties that are able to grow under unfavorable conditions, such as drought, high and low temperatures, salinity, and other stressors. In recent decades, progress in biotechnology and its related tools has provided opportunities to dissect and decipher the genetic basis of tolerance to various stress conditions. One such approach is the identification of genomic regions that are linked with specific or multiple characteristics. Cereal crops have a key role in supplying the energy required for human and animal populations. However, crop products are dramatically affected by various environmental stresses. Barley (Hordeum vulgare L.) is one of the oldest domesticated crops that is cultivated globally. Research has shown that, compared with other cereals, barley is well adapted to various harsh environmental conditions. There is ample literature regarding these responses to abiotic stressors, as well as the genomic regions associated with the various morpho-physiological and biochemical traits of stress tolerance. This review focuses on (i) identifying the tolerance mechanisms that are important for stable growth and development, and (ii) the applicability of QTL mapping and association analysis in identifying genomic regions linked with stress-tolerance traits, in order to help breeders in marker-assisted selection (MAS) to quickly screen tolerant germplasms in their breeding cycles. Overall, the information presented here will inform and assist future barley breeding programs.
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Bapela T, Shimelis H, Tsilo TJ, Mathew I. Genetic Improvement of Wheat for Drought Tolerance: Progress, Challenges and Opportunities. PLANTS (BASEL, SWITZERLAND) 2022; 11:1331. [PMID: 35631756 PMCID: PMC9144332 DOI: 10.3390/plants11101331] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/27/2022] [Accepted: 05/04/2022] [Indexed: 06/01/2023]
Abstract
Wheat production and productivity are challenged by recurrent droughts associated with climate change globally. Drought and heat stress resilient cultivars can alleviate yield loss in marginal production agro-ecologies. The ability of some crop genotypes to thrive and yield in drought conditions is attributable to the inherent genetic variation and environmental adaptation, presenting opportunities to develop drought-tolerant varieties. Understanding the underlying genetic, physiological, biochemical, and environmental mechanisms and their interactions is key critical opportunity for drought tolerance improvement. Therefore, the objective of this review is to document the progress, challenges, and opportunities in breeding for drought tolerance in wheat. The paper outlines the following key aspects: (1) challenges associated with breeding for adaptation to drought-prone environments, (2) opportunities such as genetic variation in wheat for drought tolerance, selection methods, the interplay between above-ground phenotypic traits and root attributes in drought adaptation and drought-responsive attributes and (3) approaches, technologies and innovations in drought tolerance breeding. In the end, the paper summarises genetic gains and perspectives in drought tolerance breeding in wheat. The review will serve as baseline information for wheat breeders and agronomists to guide the development and deployment of drought-adapted and high-performing new-generation wheat varieties.
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Affiliation(s)
- Theresa Bapela
- African Centre for Crop Improvement, University of Kwa-Zulu Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa; (H.S.); (I.M.)
- Agricultural Research Council—Small Grain, Bethlehem 9700, South Africa;
| | - Hussein Shimelis
- African Centre for Crop Improvement, University of Kwa-Zulu Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa; (H.S.); (I.M.)
| | - Toi John Tsilo
- Agricultural Research Council—Small Grain, Bethlehem 9700, South Africa;
| | - Isack Mathew
- African Centre for Crop Improvement, University of Kwa-Zulu Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa; (H.S.); (I.M.)
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Gobu R, Dash GK, Lal JP, Swain P, Mahender A, Anandan A, Ali J. Unlocking the Nexus between Leaf-Level Water Use Efficiency and Root Traits Together with Gas Exchange Measurements in Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11091270. [PMID: 35567271 PMCID: PMC9101036 DOI: 10.3390/plants11091270] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 05/19/2023]
Abstract
Drought stress severely affects plant growth and development, causing significant yield loss in rice. This study demonstrates the relevance of water use efficiency with deeper rooting along with other root traits and gas exchange parameters. Forty-nine rice genotypes were evaluated in the basket method to examine leaf-level water use efficiency (WUEi) variation and its relation to root traits. Significant variation in WUEi was observed (from 2.29 to 7.39 µmol CO2 mmol−1 H2O) under drought stress. Regression analysis revealed that high WUEi was associated with higher biomass accumulation, low transpiration rate, and deep rooting ratio. The ratio of deep rooting was also associated with low internal CO2 concentration. The association of deep rooting with lower root number and root dry weight suggests that an ideal drought-tolerant genotype with higher water use efficiency should have deeper rooting (>30% RDR) with moderate root number and root dry weight to be sustained under drought for a longer period. The study also revealed that, under drought stress conditions, landraces are more water-use efficient with superior root traits than improved genotypes.
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Affiliation(s)
- Ramasamy Gobu
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, Odisha, India; (R.G.); (G.K.D.)
- Division of Crop Improvement and Biotechnology, Indian Council of Agricultural Research (ICAR)-Indian Institute of Spices Research (IISR), Kozhikode 673012, Kerala, India
| | - Goutam Kumar Dash
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, Odisha, India; (R.G.); (G.K.D.)
- Crop Physiology and Biochemistry Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, Odisha, India;
| | - Jai Prakash Lal
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India;
| | - Padmini Swain
- Crop Physiology and Biochemistry Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, Odisha, India;
| | - Anumalla Mahender
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños 4031, Philippines;
| | - Annamalai Anandan
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, Odisha, India; (R.G.); (G.K.D.)
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Seed Science (IISS), Bangalore 560065, India
- Correspondence: (A.A.); (J.A.); Tel.: +671-2367768-783 (ext. 2227) (A.A.); +63-2580-5600 (ext. 2541) (J.A.)
| | - Jauhar Ali
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños 4031, Philippines;
- Correspondence: (A.A.); (J.A.); Tel.: +671-2367768-783 (ext. 2227) (A.A.); +63-2580-5600 (ext. 2541) (J.A.)
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Nykiel M, Gietler M, Fidler J, Prabucka B, Rybarczyk-Płońska A, Graska J, Boguszewska-Mańkowska D, Muszyńska E, Morkunas I, Labudda M. Signal Transduction in Cereal Plants Struggling with Environmental Stresses: From Perception to Response. PLANTS (BASEL, SWITZERLAND) 2022; 11:1009. [PMID: 35448737 PMCID: PMC9026486 DOI: 10.3390/plants11081009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 05/13/2023]
Abstract
Cereal plants under abiotic or biotic stressors to survive unfavourable conditions and continue growth and development, rapidly and precisely identify external stimuli and activate complex molecular, biochemical, and physiological responses. To elicit a response to the stress factors, interactions between reactive oxygen and nitrogen species, calcium ions, mitogen-activated protein kinases, calcium-dependent protein kinases, calcineurin B-like interacting protein kinase, phytohormones and transcription factors occur. The integration of all these elements enables the change of gene expression, and the release of the antioxidant defence and protein repair systems. There are still numerous gaps in knowledge on these subjects in the literature caused by the multitude of signalling cascade components, simultaneous activation of multiple pathways and the intersection of their individual elements in response to both single and multiple stresses. Here, signal transduction pathways in cereal plants under drought, salinity, heavy metal stress, pathogen, and pest attack, as well as the crosstalk between the reactions during double stress responses are discussed. This article is a summary of the latest discoveries on signal transduction pathways and it integrates the available information to better outline the whole research problem for future research challenges as well as for the creative breeding of stress-tolerant cultivars of cereals.
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Affiliation(s)
- Małgorzata Nykiel
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland; (M.G.); (J.F.); (B.P.); (A.R.-P.); (J.G.); (M.L.)
| | - Marta Gietler
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland; (M.G.); (J.F.); (B.P.); (A.R.-P.); (J.G.); (M.L.)
| | - Justyna Fidler
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland; (M.G.); (J.F.); (B.P.); (A.R.-P.); (J.G.); (M.L.)
| | - Beata Prabucka
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland; (M.G.); (J.F.); (B.P.); (A.R.-P.); (J.G.); (M.L.)
| | - Anna Rybarczyk-Płońska
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland; (M.G.); (J.F.); (B.P.); (A.R.-P.); (J.G.); (M.L.)
| | - Jakub Graska
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland; (M.G.); (J.F.); (B.P.); (A.R.-P.); (J.G.); (M.L.)
| | | | - Ewa Muszyńska
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland;
| | - Iwona Morkunas
- Department of Plant Physiology, Poznań University of Life Sciences, Wołyńska 35, 60-637 Poznań, Poland;
| | - Mateusz Labudda
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland; (M.G.); (J.F.); (B.P.); (A.R.-P.); (J.G.); (M.L.)
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Liu T, Liu Y, Fu G, Chen J, Lv T, Su D, Wang Y, Hu X, Su X, Harris AJ. Identification of genes involved in drought tolerance in seedlings of the desert grass, Psammochloa villosa (Poaceae), based on full-length isoform sequencing and de novo assembly from short reads. JOURNAL OF PLANT PHYSIOLOGY 2022; 271:153630. [PMID: 35193087 DOI: 10.1016/j.jplph.2022.153630] [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: 10/22/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Psammochloa villosa is a perennial herbaceous plant that is dominant within arid regions of the Inner Mongolian Plateau and the Qinghai-Tibet Plateau in China, where it is an endemic species and exhibits strong drought tolerance and wind resistance. To study drought tolerance in P. villosa and determine its molecular basis, we simulated high and moderate drought stress in a controlled environment and then analyzed transcriptome sequences by combining long-read sequences from a representative, wild-grown individual with short reads from the treatment groups. We obtained 184,076 high-quality isoforms as a reference and 168,650 genes (91.6%), which we were able to annotate according to public databases. Ultimately, we obtained 119,005 unigenes representing the transcriptome of P. villosa under drought stress and, among these, we identified 3089 differentially expressed genes and 1484 transcription factors. Physiologically, P. villosa that was exposed to high and moderate drought stress had reduced germination rates and shorter buds but generated more chlorophyll, which is atypical under drought stress and possibly reflects an adaptation of these plants to their arid environment. We inferred that significantly upregulated genes were annotated as 'Chlorophyll a-b binding protein' and 'Light-harvesting chlorophyll-protein' among drought and control groups. Broadly, our analyses revealed that drought stress triggered many genome-level responses, especially related to mitigation of radical oxygen species (ROS), which increase in concentration under drought stress. In particular, in the high drought stress group compared with the control, GO enrichment analysis revealed a significant enrichment of upregulated genes (n = 10) involved in mitigation of oxidative stress. Similarly, using KEGG we found significant enrichment of genes in the phenylpropanoid biosynthesis pathway (11 genes), which yields phenols that scavenge ROS. We also inferred that many genes involved in metabolism of arginine and proline, which may serve as both scavengers of ROS and osmoprotectants that interact with stress response genes based on our protein-protein interaction network analysis. We verified the relative expression levels of eight genes associated with mitigation of ROS, DNA repair, and transmembrane transporter activity using qRT-PCR, and the results were consistent with our inferences from transcriptomes. This study provides insights into the genomic and physiological basis of drought tolerance in P. villosa and represents a resource for development of the species as a forage crop via molecular breeding within arid lands.
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Affiliation(s)
- Tao Liu
- School of Geography, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Yuping Liu
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Gui Fu
- School of Geography, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Jinyuan Chen
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Ting Lv
- School of Geography, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Dandan Su
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Yanan Wang
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Xiayu Hu
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China
| | - Xu Su
- School of Life Sciences, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China; Academy of Plateau Science and Sustainability, Xueyuan Road, Xining, 810016, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, No. 38 Wusixi Road, Xining, 810008, China; Key Laboratory of Education Ministry of Earth Surface Processes and Ecological Conservation of the Qinghai-Tibet Plateau, Qinghai Normal University, No. 38 Wusixi Road, Xining, Xining, 810008, China.
| | - A J Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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Kevei Z, Ferreira SDS, Casenave CMP, Kurowski T, Mohareb F, Rickett D, Stain C, Thompson AJ. Missense mutation of a class B heat shock factor is responsible for the tomato bushy root-2 phenotype. MOLECULAR HORTICULTURE 2022; 2:4. [PMID: 37789386 PMCID: PMC10515254 DOI: 10.1186/s43897-022-00025-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/18/2022] [Indexed: 10/05/2023]
Abstract
The bushy root-2 (brt-2) tomato mutant has twisting roots, and slower plant development. Here we used whole genome resequencing and genetic mapping to show that brt-2 is caused by a serine to cysteine (S75C) substitution in the DNA binding domain (DBD) of a heat shock factor class B (HsfB) encoded by SolycHsfB4a. This gene is orthologous to the Arabidopsis SCHIZORIZA gene, also known as AtHsfB4. The brt-2 phenotype is very similar to Arabidopsis lines in which the function of AtHsfB4 is altered: a proliferation of lateral root cap and root meristematic tissues, and a tendency for lateral root cap cells to easily separate. The brt-2 S75C mutation is unusual because all other reported amino acid substitutions in the highly conserved DBD of eukaryotic heat shock factors are dominant negative mutations, but brt-2 is recessive. We further show through reciprocal grafting that brt-2 exerts its effects predominantly through the root genotype even through BRT-2 is expressed at similar levels in both root and shoot meristems. Since AtHsfB4 is induced by root knot nematodes (RKN), and loss-of-function mutants of this gene are resistant to RKNs, BRT-2 could be a target gene for RKN resistance, an important trait in tomato rootstock breeding.Gene & accession numbersSolycHsfB4a - Solyc04g078770.
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Affiliation(s)
- Zoltan Kevei
- Cranfield Soil and AgriFood Institute, College Road, Cranfield University, Bedfordshire, MK43 0AL, UK.
| | | | | | - Tomasz Kurowski
- Cranfield Soil and AgriFood Institute, College Road, Cranfield University, Bedfordshire, MK43 0AL, UK
| | - Fady Mohareb
- Cranfield Soil and AgriFood Institute, College Road, Cranfield University, Bedfordshire, MK43 0AL, UK
| | - Daniel Rickett
- Syngenta Crop Protection, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK
| | - Chris Stain
- Syngenta Crop Protection, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK
| | - Andrew J Thompson
- Cranfield Soil and AgriFood Institute, College Road, Cranfield University, Bedfordshire, MK43 0AL, UK
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Tayade R, Kim SH, Tripathi P, Choi YD, Yoon JB, Kim YH. High-Throughput Root Imaging Analysis Reveals Wide Variation in Root Morphology of Wild Adzuki bean (Vigna angularis) Accessions. PLANTS 2022; 11:plants11030405. [PMID: 35161386 PMCID: PMC8840753 DOI: 10.3390/plants11030405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 12/24/2022]
Abstract
Root system architecture and morphological diversification in wild accessions are important for crop improvement and productivity in adzuki beans. In this study, via analysis using 2-dimensional (2D) root imaging and WinRHIZO Pro software, we described the root traits of 61 adzuki bean accessions in their early vegetative growth stage. These accessions were chosen for study because they are used in Korea’s crop improvement programs; however, their root traits have not been sufficiently investigated. Analysis of variance revealed a significant difference between the accessions of all measured root traits. Distribution analysis demonstrated that most of the root traits followed normal distribution. The accessions showed up to a 17-fold increase in the values in contrasting accessions for the root traits. For total root length (TRL), the values ranged from 82.43 to 1435 cm, and for surface area (SA), they ranged from 12.30 to 208.39 cm2. The values for average diameter (AD) ranged from 0.23 to 0.56 mm. Significant differences were observed for other traits. Overall, the results showed that the accession IT 305544 had the highest TRL, SA, and number of tips (NT), whereas IT 262477 and IT 262492 showed the lowest values for TRL, SA, and AD. Principal component analysis showed an 89% variance for PC1 and PC2. K-mean clustering explained 77.4% of the variance in the data and grouped the accessions into three clusters. All six root traits had greater coefficients of variation (≥15%) among the tested accessions. Furthermore, to determine which root traits best distinguished different accessions, the correlation within our set of accessions provided trait-based ranking depending on their contribution. The identified accessions may be advantageous for the development of new crossing combinations to improve root features in adzuki beans during the early growth stage. The root traits assessed in this study could be attributes for future adzuki bean crop selection and improvement.
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Affiliation(s)
- Rupesh Tayade
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (R.T.); (P.T.); (Y.-D.C.)
| | - Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea;
| | - Pooja Tripathi
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (R.T.); (P.T.); (Y.-D.C.)
| | - Yi-Dam Choi
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (R.T.); (P.T.); (Y.-D.C.)
| | - Jung-Beom Yoon
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Jeonju 54874, Korea;
| | - Yoon-Ha Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (R.T.); (P.T.); (Y.-D.C.)
- Correspondence: ; Tel.: +82-53-950-5710
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Rane J, Singh AK, Tiwari M, Prasad PVV, Jagadish SVK. Effective Use of Water in Crop Plants in Dryland Agriculture: Implications of Reactive Oxygen Species and Antioxidative System. FRONTIERS IN PLANT SCIENCE 2022; 12:778270. [PMID: 35082809 PMCID: PMC8784697 DOI: 10.3389/fpls.2021.778270] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/02/2021] [Indexed: 05/03/2023]
Abstract
Under dryland conditions, annual and perennial food crops are exposed to dry spells, severely affecting crop productivity by limiting available soil moisture at critical and sensitive growth stages. Climate variability continues to be the primary cause of uncertainty, often making timing rather than quantity of precipitation the foremost concern. Therefore, mitigation and management of stress experienced by plants due to limited soil moisture are crucial for sustaining crop productivity under current and future harsher environments. Hence, the information generated so far through multiple investigations on mechanisms inducing drought tolerance in plants needs to be translated into tools and techniques for stress management. Scope to accomplish this exists in the inherent capacity of plants to manage stress at the cellular level through various mechanisms. One of the most extensively studied but not conclusive physiological phenomena is the balance between reactive oxygen species (ROS) production and scavenging them through an antioxidative system (AOS), which determines a wide range of damage to the cell, organ, and the plant. In this context, this review aims to examine the possible roles of the ROS-AOS balance in enhancing the effective use of water (EUW) by crops under water-limited dryland conditions. We refer to EUW as biomass produced by plants with available water under soil moisture stress rather than per unit of water (WUE). We hypothesize that EUW can be enhanced by an appropriate balance between water-saving and growth promotion at the whole-plant level during stress and post-stress recovery periods. The ROS-AOS interactions play a crucial role in water-saving mechanisms and biomass accumulation, resulting from growth processes that include cell division, cell expansion, photosynthesis, and translocation of assimilates. Hence, appropriate strategies for manipulating these processes through genetic improvement and/or application of exogenous compounds can provide practical solutions for improving EUW through the optimized ROS-AOS balance under water-limited dryland conditions. This review deals with the role of ROS-AOS in two major EUW determining processes, namely water use and plant growth. It describes implications of the ROS level or content, ROS-producing, and ROS-scavenging enzymes based on plant water status, which ultimately affects photosynthetic efficiency and growth of plants.
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Affiliation(s)
- Jagadish Rane
- ICAR-National Institute of Abiotic Stress Management, Baramati, India
| | - Ajay Kumar Singh
- ICAR-National Institute of Abiotic Stress Management, Baramati, India
| | - Manish Tiwari
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - P. V. Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
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Boursiac Y, Protto V, Rishmawi L, Maurel C. Experimental and conceptual approaches to root water transport. PLANT AND SOIL 2022; 478:349-370. [PMID: 36277078 PMCID: PMC9579117 DOI: 10.1007/s11104-022-05427-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/03/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Root water transport, which critically contributes to the plant water status and thereby plant productivity, has been the object of extensive experimental and theoretical studies. However, root systems represent an intricate assembly of cells in complex architectures, including many tissues at distinct developmental stages. Our comprehension of where and how molecular actors integrate their function in order to provide the root with its hydraulic properties is therefore still limited. SCOPE Based on current literature and prospective discussions, this review addresses how root water transport can be experimentally measured, what is known about the underlying molecular actors, and how elementary water transport processes are scaled up in numerical/mathematical models. CONCLUSIONS The theoretical framework and experimental procedures on root water transport that are in use today have been established a few decades ago. However, recent years have seen the appearance of new techniques and models with enhanced resolution, down to a portion of root or to the tissue level. These advances pave the way for a better comprehension of the dynamics of water uptake by roots in the soil.
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Affiliation(s)
- Yann Boursiac
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Virginia Protto
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Louai Rishmawi
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Christophe Maurel
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
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Zeng D, Li M, Jiang N, Ju Y, Schreiber H, Chambers E, Letscher D, Ju T, Topp CN. TopoRoot: a method for computing hierarchy and fine-grained traits of maize roots from 3D imaging. PLANT METHODS 2021; 17:127. [PMID: 34903248 PMCID: PMC8667396 DOI: 10.1186/s13007-021-00829-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND 3D imaging, such as X-ray CT and MRI, has been widely deployed to study plant root structures. Many computational tools exist to extract coarse-grained features from 3D root images, such as total volume, root number and total root length. However, methods that can accurately and efficiently compute fine-grained root traits, such as root number and geometry at each hierarchy level, are still lacking. These traits would allow biologists to gain deeper insights into the root system architecture. RESULTS We present TopoRoot, a high-throughput computational method that computes fine-grained architectural traits from 3D images of maize root crowns or root systems. These traits include the number, length, thickness, angle, tortuosity, and number of children for the roots at each level of the hierarchy. TopoRoot combines state-of-the-art algorithms in computer graphics, such as topological simplification and geometric skeletonization, with customized heuristics for robustly obtaining the branching structure and hierarchical information. TopoRoot is validated on both CT scans of excavated field-grown root crowns and simulated images of root systems, and in both cases, it was shown to improve the accuracy of traits over existing methods. TopoRoot runs within a few minutes on a desktop workstation for images at the resolution range of 400^3, with minimal need for human intervention in the form of setting three intensity thresholds per image. CONCLUSIONS TopoRoot improves the state-of-the-art methods in obtaining more accurate and comprehensive fine-grained traits of maize roots from 3D imaging. The automation and efficiency make TopoRoot suitable for batch processing on large numbers of root images. Our method is thus useful for phenomic studies aimed at finding the genetic basis behind root system architecture and the subsequent development of more productive crops.
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Affiliation(s)
- Dan Zeng
- Department of Computer Science and Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA.
| | - Mao Li
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
| | - Ni Jiang
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
| | - Yiwen Ju
- Department of Computer Science and Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Hannah Schreiber
- Department of Computer Science, Saint Louis University, Saint Louis, MO, 63103, USA
| | - Erin Chambers
- Department of Computer Science, Saint Louis University, Saint Louis, MO, 63103, USA
| | - David Letscher
- Department of Computer Science, Saint Louis University, Saint Louis, MO, 63103, USA
| | - Tao Ju
- Department of Computer Science and Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
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Siddiqui MN, Teferi TJ, Ambaw AM, Gabi MT, Koua P, Léon J, Ballvora A. New drought-adaptive loci underlying candidate genes on wheat chromosome 4B with improved photosynthesis and yield responses. PHYSIOLOGIA PLANTARUM 2021; 173:2166-2180. [PMID: 34549429 DOI: 10.1111/ppl.13566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Flag leaf serves as an essential source of assimilates during grain filling, thereby contributing to grain yield up to 48%. Thus, high-throughput phenotyping of flag leaves is crucial to determine their physiological and genetic basis of yield formation and drought adaptation. Here, we utilized 200 wheat cultivars to identify drought-adaptive loci underlying candidate genes associated with flag leaf biomass and photosynthesis-related traits using a genome-wide association study (GWAS). GWAS revealed 21 significant marker-trait associations for key photosynthetic traits in response to drought stress. Analysis of linkage disequilibrium (LD) in these SNPs intervals discovered 103 significant SNPs that established distinct LD blocks containing a total of 382 candidate genes putatively involved in physiological processes, including photosynthesis and water responses. Further, in silico transcript analysis identified two candidate genes in locus AX-580365925 on chromosome 4B, those were found to be highly expressed under drought and associated with proton-transporting ATP synthase activity and stress response pathways. Accordingly, we identified significant allelic haplotype differences on this same locus. The tolerant haplotype (higher chlorophyll content under drought) representing major allele was more abundant and stably increased photosynthetic efficiency and yield under drought scenarios. Collectively, this study offers new adaptive loci and beneficial alleles to reshape the flag leaf physiological and associated photosynthetic components for better yield and sustainability to water-deficit stress.
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Affiliation(s)
- Md Nurealam Siddiqui
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Tesfaye J Teferi
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Abebaw M Ambaw
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Melesech T Gabi
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Patrice Koua
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
- Field Lab Campus Klein-Altendorf, University of Bonn, Rheinbach, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation (INRES)-Plant Breeding and Biotechnology, University of Bonn, Bonn, Germany
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Karlova R, Boer D, Hayes S, Testerink C. Root plasticity under abiotic stress. PLANT PHYSIOLOGY 2021; 187:1057-1070. [PMID: 34734279 PMCID: PMC8566202 DOI: 10.1093/plphys/kiab392] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/25/2021] [Indexed: 05/08/2023]
Abstract
Abiotic stresses increasingly threaten existing ecological and agricultural systems across the globe. Plant roots perceive these stresses in the soil and adapt their architecture accordingly. This review provides insights into recent discoveries showing the importance of root system architecture (RSA) and plasticity for the survival and development of plants under heat, cold, drought, salt, and flooding stress. In addition, we review the molecular regulation and hormonal pathways involved in controlling RSA plasticity, main root growth, branching and lateral root growth, root hair development, and formation of adventitious roots. Several stresses affect root anatomy by causing aerenchyma formation, lignin and suberin deposition, and Casparian strip modulation. Roots can also actively grow toward favorable soil conditions and avoid environments detrimental to their development. Recent advances in understanding the cellular mechanisms behind these different root tropisms are discussed. Understanding root plasticity will be instrumental for the development of crops that are resilient in the face of abiotic stress.
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Affiliation(s)
- Rumyana Karlova
- Laboratory of Plant Physiology, Wageningen University, 6700 AA Wageningen, The Netherlands
| | - Damian Boer
- Laboratory of Plant Physiology, Wageningen University, 6700 AA Wageningen, The Netherlands
| | - Scott Hayes
- Laboratory of Plant Physiology, Wageningen University, 6700 AA Wageningen, The Netherlands
| | - Christa Testerink
- Laboratory of Plant Physiology, Wageningen University, 6700 AA Wageningen, The Netherlands
- Author for communication:
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Varshney RK, Barmukh R, Roorkiwal M, Qi Y, Kholova J, Tuberosa R, Reynolds MP, Tardieu F, Siddique KHM. Breeding custom-designed crops for improved drought adaptation. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:e202100017. [PMID: 36620433 PMCID: PMC9744523 DOI: 10.1002/ggn2.202100017] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 01/11/2023]
Abstract
The current pace of crop improvement is inadequate to feed the burgeoning human population by 2050. Higher, more stable, and sustainable crop production is required against a backdrop of drought stress, which causes significant losses in crop yields. Tailoring crops for drought adaptation may hold the key to address these challenges and provide resilient production systems for future harvests. Understanding the genetic and molecular landscape of the functionality of alleles associated with adaptive traits will make designer crop breeding the prospective approach for crop improvement. Here, we highlight the potential of genomics technologies combined with crop physiology for high-throughput identification of the genetic architecture of key drought-adaptive traits and explore innovative genomic breeding strategies for designing future crops.
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Affiliation(s)
- Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- State Agricultural Biotechnology Centre, Centre for Crop and Food InnovationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Rutwik Barmukh
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Manish Roorkiwal
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
| | - Jana Kholova
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Roberto Tuberosa
- Department of Agricultural and Food SciencesUniversity of BolognaBolognaItaly
| | | | - Francois Tardieu
- Université de Montpellier, INRAE, Laboratoire d'Ecophysiologie des Plantes sous Stress, EnvironnementauxMontpellierFrance
| | - Kadambot H. M. Siddique
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
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ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIF-containing protein that controls root growth angle in barley and wheat. Proc Natl Acad Sci U S A 2021; 118:2101526118. [PMID: 34446550 PMCID: PMC8536364 DOI: 10.1073/pnas.2101526118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
To date, the potential of utilizing root traits in plant breeding remains largely untapped. In this study, we cloned and characterized the ENHANCED GRAVITROPISM2 (EGT2) gene of barley that encodes a STERILE ALPHA MOTIF domain–containing protein. We demonstrated that EGT2 is a key gene of root growth angle regulation in response to gravity, which is conserved in barley and wheat and could be a promising target for crop improvement in cereals. The root growth angle defines how roots grow toward the gravity vector and is among the most important determinants of root system architecture. It controls water uptake capacity, nutrient use efficiency, stress resilience, and, as a consequence, yield of crop plants. We demonstrated that the egt2 (enhanced gravitropism 2) mutant of barley exhibits steeper root growth of seminal and lateral roots and an auxin-independent higher responsiveness to gravity compared to wild-type plants. We cloned the EGT2 gene by a combination of bulked-segregant analysis and whole genome sequencing. Subsequent validation experiments by an independent CRISPR/Cas9 mutant allele demonstrated that egt2 encodes a STERILE ALPHA MOTIF domain–containing protein. In situ hybridization experiments illustrated that EGT2 is expressed from the root cap to the elongation zone. We demonstrated the evolutionary conserved role of EGT2 in root growth angle control between barley and wheat by knocking out the EGT2 orthologs in the A and B genomes of tetraploid durum wheat. By combining laser capture microdissection with RNA sequencing, we observed that seven expansin genes were transcriptionally down-regulated in the elongation zone. This is consistent with a role of EGT2 in this region of the root where the effect of gravity sensing is executed by differential cell elongation. Our findings suggest that EGT2 is an evolutionary conserved regulator of root growth angle in barley and wheat that could be a valuable target for root-based crop improvement strategies in cereals.
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