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Wild AJ, Steiner FA, Kiene M, Tyborski N, Tung SY, Koehler T, Carminati A, Eder B, Groth J, Vahl WK, Wolfrum S, Lueders T, Laforsch C, Mueller CW, Vidal A, Pausch J. Unraveling root and rhizosphere traits in temperate maize landraces and modern cultivars: Implications for soil resource acquisition and drought adaptation. PLANT, CELL & ENVIRONMENT 2024; 47:2526-2541. [PMID: 38515431 DOI: 10.1111/pce.14898] [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: 11/24/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/23/2024]
Abstract
A holistic understanding of plant strategies to acquire soil resources is pivotal in achieving sustainable food security. However, we lack knowledge about variety-specific root and rhizosphere traits for resource acquisition, their plasticity and adaptation to drought. We conducted a greenhouse experiment to phenotype root and rhizosphere traits (mean root diameter [Root D], specific root length [SRL], root tissue density, root nitrogen content, specific rhizosheath mass [SRM], arbuscular mycorrhizal fungi [AMF] colonization) of 16 landraces and 22 modern cultivars of temperate maize (Zea mays L.). Our results demonstrate that landraces and modern cultivars diverge in their root and rhizosphere traits. Although landraces follow a 'do-it-yourself' strategy with high SRLs, modern cultivars exhibit an 'outsourcing' strategy with increased mean Root Ds and a tendency towards increased root colonization by AMF. We further identified that SRM indicates an 'outsourcing' strategy. Additionally, landraces were more drought-responsive compared to modern cultivars based on multitrait response indices. We suggest that breeding leads to distinct resource acquisition strategies between temperate maize varieties. Future breeding efforts should increasingly target root and rhizosphere economics, with SRM serving as a valuable proxy for identifying varieties employing an outsourcing resource acquisition strategy.
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Affiliation(s)
- Andreas J Wild
- Agroecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Franziska A Steiner
- Soil Science, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Marvin Kiene
- Animal Ecology I, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Nicolas Tyborski
- Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Shu-Yin Tung
- Institute for Agroecology and Organic Farming, Bavarian State Research Center for Agriculture, Freising, Germany
- School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Tina Koehler
- Soil Physics, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
- Physics of Soils and Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Andrea Carminati
- Physics of Soils and Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Barbara Eder
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture (LfL), Freising, Germany
| | - Jennifer Groth
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture (LfL), Freising, Germany
| | - Wouter K Vahl
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture (LfL), Freising, Germany
| | - Sebastian Wolfrum
- Institute for Agroecology and Organic Farming, Bavarian State Research Center for Agriculture, Freising, Germany
| | - Tillmann Lueders
- Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Christian Laforsch
- Animal Ecology I, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Carsten W Mueller
- Chair of Soil Science, Institute of Ecology, Technische Universitaet Berlin, Berlin, Germany
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Alix Vidal
- Soil Biology Group, Wageningen University, Wageningen, The Netherlands
| | - Johanna Pausch
- Agroecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
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2
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Neysanian M, Iranbakhsh A, Ahmadvand R, Ardebili ZO, Ebadi M. Selenium nanoparticles conferred drought tolerance in tomato plants by altering the transcription pattern of microRNA-172 (miR-172), bZIP, and CRTISO genes, upregulating the antioxidant system, and stimulating secondary metabolism. PROTOPLASMA 2024; 261:735-747. [PMID: 38291258 DOI: 10.1007/s00709-024-01929-y] [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: 09/20/2023] [Accepted: 01/20/2024] [Indexed: 02/01/2024]
Abstract
Drought stress is one of the major limiting factors for the production of tomato in Iran. In this study, the efficiency of selenate and Se nanoparticle (SeNP) foliar application on tomato plants was assessed to vestigate mitigating the risk associated with water-deficit conditions. Tomato plants were treated with SeNPs at the concentrations of 0 and 4 mg L-1; after the third sprays, the plants were exposed to water-deficit conditions. The foliar spraying with SeNPs not only improved growth, yield, and developmental switch to the flowering phase but also noticeably mitigated the detrimental risk associated with the water-deficit conditions. Gene expression experiments showed a slight increase in expression of microRNA-172 (miR-172) in the SeNP-treated plants in normal irrigation, whereas miR-172 displayed a downregulation trend in response to drought stress. The bZIP transcription factor and CRTISO genes were upregulated following the SeNP and drought treatments. Drought stress significantly increased the H2O2 accumulation that is mitigated with SeNPs. The foliar spraying with Se or SeNPs shared a similar trend to alleviate the negative effect of drought stress on the membrane integrity. The applied supplements also conferred drought tolerance through noticeable improvements in the non-enzymatic (ascorbate and glutathione) and enzymatic (catalase and peroxidase) antioxidants. The SeNP-mediated improvement in drought stress tolerance correlated significantly with increases in the activity of phenylalanine ammonia-lyase, proline, non-protein thiols, and flavonoid concentrations. SeNPs also improved the fruit quality regarding K, Mg, Fe, and Se concentrations. It was concluded that foliar spraying with SeNPs could mitigate the detrimental risk associated with the water-deficit conditions.
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Affiliation(s)
- Maryam Neysanian
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Alireza Iranbakhsh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Rahim Ahmadvand
- Department of Vegetables Research, Seed and Plant Improvement Institute, Agricultural Research, Education & Extension Organization, Karaj, Iran
| | | | - Mostafa Ebadi
- Department of Biology, Damghan Branch, Islamic Azad University, Damghan, Iran
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3
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Cha JK, Park H, Kwon Y, Lee SM, Jang SG, Kwon SW, Lee JH. Synergizing breeding strategies via combining speed breeding, phenotypic selection, and marker-assisted backcrossing for the introgression of Glu-B1i in wheat. FRONTIERS IN PLANT SCIENCE 2024; 15:1402709. [PMID: 38863547 PMCID: PMC11165042 DOI: 10.3389/fpls.2024.1402709] [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: 03/18/2024] [Accepted: 05/16/2024] [Indexed: 06/13/2024]
Abstract
Wheat is a major food crop that plays a crucial role in the human diet. Various breeding technologies have been developed and refined to meet the increasing global wheat demand. Several studies have suggested breeding strategies that combine generation acceleration systems and molecular breeding methods to maximize breeding efficiency. However, real-world examples demonstrating the effective utilization of these strategies in breeding programs are lacking. In this study, we designed and demonstrated a synergized breeding strategy (SBS) that combines rapid and efficient breeding techniques, including speed breeding, speed vernalization, phenotypic selection, backcrossing, and marker-assisted selection. These breeding techniques were tailored to the specific characteristics of the breeding materials and objectives. Using the SBS approach, from artificial crossing to the initial observed yield trial under field conditions only took 3.5 years, resulting in a 53% reduction in the time required to develop a BC2 near-isogenic line (NIL) and achieving a higher recurrent genome recovery of 91.5% compared to traditional field conditions. We developed a new wheat NIL derived from cv. Jokyoung, a leading cultivar in Korea. Milyang56 exhibited improved protein content, sodium dodecyl sulfate-sedimentation value, and loaf volume compared to Jokyoung, which were attributed to introgression of the Glu-B1i allele from the donor parent, cv. Garnet. SBS represents a flexible breeding model that can be applied by breeders for developing breeding materials and mapping populations, as well as analyzing the environmental effects of specific genes or loci and for trait stacking.
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Affiliation(s)
- Jin-Kyung Cha
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Hyeonjin Park
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Youngho Kwon
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - So-Myeong Lee
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Seong-Gyu Jang
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Soon-Wook Kwon
- Department of Plant Bioscience, Pusan National University, Miryang, Republic of Korea
| | - Jong-Hee Lee
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
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Wang Y, Chen H, Pan Q, Wang J, Jiao X, Zhang Y. Development and evaluation of rapid and accurate one-tube RPA-CRISPR-Cas12b-based detection of mcr-1 and tet(X4). Appl Microbiol Biotechnol 2024; 108:345. [PMID: 38801527 PMCID: PMC11129972 DOI: 10.1007/s00253-024-13191-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024]
Abstract
The emergence and quick spread of the plasmid-mediated tigecycline resistance gene tet(X4) and colistin resistance gene mcr-1 have posed a great threat to public health and raised global concerns. It is imperative to develop rapid and accurate detection systems for the onsite surveillance of mcr-1 and tet(X4). In this study, we developed one-tube recombinase polymerase amplification (RPA) and CRISPR-Cas12b integrated mcr-1 and tet(X4) detection systems. We identified mcr-1- and tet(X4)-conserved and -specific protospacers through a comprehensive BLAST search based on the NCBI nt database and used them for assembling the detection systems. Our developed one-tube RPA-CRISPR-Cas12b-based detection systems enabled the specific detection of mcr-1 and tet(X4) with a sensitivity of 6.25 and 9 copies within a detection time of ~ 55 and ~ 40 min, respectively. The detection results using pork and associated environmental samples collected from retail markets demonstrated that our developed mcr-1 and tet(X4) detection systems could successfully monitor mcr-1 and tet(X4), respectively. Notably, mcr-1- and tet(X4)-positive strains were isolated from the positive samples, as revealed using the developed detection systems. Whole-genome sequencing of representative strains identified an mcr-1-carrying IncI2 plasmid and a tet(X4)-carrying IncFII plasmid, which are known as important vectors for mcr-1 and tet(X4) transmission, respectively. Taken together, our developed one-tube RPA-CRISPR-Cas12b-based mcr-1 and tet(X4) detection systems show promising potential for the onsite detection of mcr-1 and tet(X4). KEY POINTS: • One-tube RPA-CRISPR-Cas12b-based mcr-1 and tet(X4) detection systems were developed based on identified novel protospacers. • Both detection systems exhibited high sensitivity and specification with a sample-to-answer time of less than 1 h. • The detection systems show promising potential for onsite detection of mcr-1 and tet(X4).
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Affiliation(s)
- Yu Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Huan Chen
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Qingyun Pan
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Jing Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Xin'an Jiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China.
| | - Yunzeng Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China.
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5
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Cortés AJ. Abiotic Stress Tolerance Boosted by Genetic Diversity in Plants. Int J Mol Sci 2024; 25:5367. [PMID: 38791404 PMCID: PMC11121514 DOI: 10.3390/ijms25105367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 03/14/2024] [Indexed: 05/26/2024] Open
Abstract
Plant breeding [...].
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 vía Rionegro—Las Palmas, Rionegro 054048, Colombia;
- Facultad de Ciencias Agrarias—de Ciencias Forestales, Universidad Nacional de Colombia—Sede Medellín, Medellín 050034, Colombia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma 23436, Sweden
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6
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Bakala HS, Devi J, Singh G, Singh I. Drought and heat stress: insights into tolerance mechanisms and breeding strategies for pigeonpea improvement. PLANTA 2024; 259:123. [PMID: 38622376 DOI: 10.1007/s00425-024-04401-6] [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: 01/13/2024] [Accepted: 03/29/2024] [Indexed: 04/17/2024]
Abstract
MAIN CONCLUSION Pigeonpea has potential to foster sustainable agriculture and resilience in evolving climate change; understanding bio-physiological and molecular mechanisms of heat and drought stress tolerance is imperative to developing resilience cultivars. Pigeonpea is an important legume crop that has potential resilience in the face of evolving climate scenarios. However, compared to other legumes, there has been limited research on abiotic stress tolerance in pigeonpea, particularly towards drought stress (DS) and heat stress (HS). To address this gap, this review delves into the genetic, physiological, and molecular mechanisms that govern pigeonpea's response to DS and HS. It emphasizes the need to understand how this crop combats these stresses and exhibits different types of tolerance and adaptation mechanisms through component traits. The current article provides a comprehensive overview of the complex interplay of factors contributing to the resilience of pigeonpea under adverse environmental conditions. Furthermore, the review synthesizes information on major breeding techniques, encompassing both conventional methods and modern molecular omics-assisted tools and techniques. It highlights the potential of genomics and phenomics tools and their pivotal role in enhancing adaptability and resilience in pigeonpea. Despite the progress made in genomics, phenomics and big data analytics, the complexity of drought and heat tolerance in pigeonpea necessitate continuous exploration at multi-omic levels. High-throughput phenotyping (HTP) is crucial for gaining insights into perplexed interactions among genotype, environment, and management practices (GxExM). Thus, integration of advanced technologies in breeding programs is critical for developing pigeonpea varieties that can withstand the challenges posed by climate change. This review is expected to serve as a valuable resource for researchers, providing a deeper understanding of the mechanisms underlying abiotic stress tolerance in pigeonpea and offering insights into modern breeding strategies that can contribute to the development of resilient varieties suited for changing environmental conditions.
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Affiliation(s)
- Harmeet Singh Bakala
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Jomika Devi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
- Texas A&M University, AgriLife Research Center, Beaumont, TX, 77713, USA.
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
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Hafeez A, Ali S, Javed MA, Iqbal R, Khan MN, Çiğ F, Sabagh AE, Abujamel T, Harakeh S, Ercisli S, Ali B. Breeding for water-use efficiency in wheat: progress, challenges and prospects. Mol Biol Rep 2024; 51:429. [PMID: 38517566 DOI: 10.1007/s11033-024-09345-4] [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: 10/21/2023] [Accepted: 02/12/2024] [Indexed: 03/24/2024]
Abstract
Drought poses a significant challenge to wheat production globally, leading to substantial yield losses and affecting various agronomic and physiological traits. The genetic route offers potential solutions to improve water-use efficiency (WUE) in wheat and mitigate the negative impacts of drought stress. Breeding for drought tolerance involves selecting desirable plants such as efficient water usage, deep root systems, delayed senescence, and late wilting point. Biomarkers, automated and high-throughput techniques, and QTL genes are crucial in enhancing breeding strategies and developing wheat varieties with improved resilience to water scarcity. Moreover, the role of root system architecture (RSA) in water-use efficiency is vital, as roots play a key role in nutrient and water uptake. Genetic engineering techniques offer promising avenues to introduce desirable RSA traits in wheat to enhance drought tolerance. These technologies enable targeted modifications in DNA sequences, facilitating the development of drought-tolerant wheat germplasm. The article highlighted the techniques that could play a role in mitigating drought stress in wheat.
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Affiliation(s)
- Aqsa Hafeez
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Shehzad Ali
- Department of Environmental Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Ammar Javed
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Rashid Iqbal
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63000, Pakistan
| | - Muhammad Nauman Khan
- Department of Botany, Islamia College Peshawar, Peshawar, 25120, Pakistan
- Biology Laboratory, University Public School, University of Peshawar, Peshawar, 25120, Pakistan
| | - Fatih Çiğ
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt, 56100, Turkey
| | - Ayman El Sabagh
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt, 56100, Turkey
| | - Turki Abujamel
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Yousef Abdullatif Jameel Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Sezai Ercisli
- Department of Horticulture, Agricultural Faculty, Ataturk University, Erzurum, 25240, Türkiye
- HGF Agro, Ata Teknokent, Erzurum, 25240, Türkiye
| | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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Raza A, Chen H, Zhang C, Zhuang Y, Sharif Y, Cai T, Yang Q, Soni P, Pandey MK, Varshney RK, Zhuang W. Designing future peanut: the power of genomics-assisted breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:66. [PMID: 38438591 DOI: 10.1007/s00122-024-04575-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 02/03/2024] [Indexed: 03/06/2024]
Abstract
KEY MESSAGE Integrating GAB methods with high-throughput phenotyping, genome editing, and speed breeding hold great potential in designing future smart peanut cultivars to meet market and food supply demands. Cultivated peanut (Arachis hypogaea L.), a legume crop greatly valued for its nourishing food, cooking oil, and fodder, is extensively grown worldwide. Despite decades of classical breeding efforts, the actual on-farm yield of peanut remains below its potential productivity due to the complicated interplay of genotype, environment, and management factors, as well as their intricate interactions. Integrating modern genomics tools into crop breeding is necessary to fast-track breeding efficiency and rapid progress. When combined with speed breeding methods, this integration can substantially accelerate the breeding process, leading to faster access of improved varieties to farmers. Availability of high-quality reference genomes for wild diploid progenitors and cultivated peanuts has accelerated the process of gene/quantitative locus discovery, developing markers and genotyping assays as well as a few molecular breeding products with improved resistance and oil quality. The use of new breeding tools, e.g., genomic selection, haplotype-based breeding, speed breeding, high-throughput phenotyping, and genome editing, is probable to boost genetic gains in peanut. Moreover, renewed attention to efficient selection and exploitation of targeted genetic resources is also needed to design high-quality and high-yielding peanut cultivars with main adaptation attributes. In this context, the combination of genomics-assisted breeding (GAB), genome editing, and speed breeding hold great potential in designing future improved peanut cultivars to meet market and food supply demands.
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Affiliation(s)
- Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Yuhui Zhuang
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Yasir Sharif
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Tiecheng Cai
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Qiang Yang
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Pooja Soni
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Manish K Pandey
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China.
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9
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Kudapa H, Ghatak A, Barmukh R, Chaturvedi P, Khan A, Kale S, Fragner L, Chitikineni A, Weckwerth W, Varshney RK. Integrated multi-omics analysis reveals drought stress response mechanism in chickpea (Cicer arietinum L.). THE PLANT GENOME 2024; 17:e20337. [PMID: 37165696 DOI: 10.1002/tpg2.20337] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/04/2023] [Accepted: 03/09/2023] [Indexed: 05/12/2023]
Abstract
Drought is one of the major constraints limiting chickpea productivity. To unravel complex mechanisms regulating drought response in chickpea, we generated transcriptomics, proteomics, and metabolomics datasets from root tissues of four contrasting drought-responsive chickpea genotypes: ICC 4958, JG 11, and JG 11+ (drought-tolerant), and ICC 1882 (drought-sensitive) under control and drought stress conditions. Integration of transcriptomics and proteomics data identified enriched hub proteins encoding isoflavone 4'-O-methyltransferase, UDP-d-glucose/UDP-d-galactose 4-epimerase, and delta-1-pyrroline-5-carboxylate synthetase. These proteins highlighted the involvement of pathways such as antibiotic biosynthesis, galactose metabolism, and isoflavonoid biosynthesis in activating drought stress response mechanisms. Subsequently, the integration of metabolomics data identified six metabolites (fructose, galactose, glucose, myoinositol, galactinol, and raffinose) that showed a significant correlation with galactose metabolism. Integration of root-omics data also revealed some key candidate genes underlying the drought-responsive "QTL-hotspot" region. These results provided key insights into complex molecular mechanisms underlying drought stress response in chickpea.
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Affiliation(s)
- Himabindu Kudapa
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Rutwik Barmukh
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Aamir Khan
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sandip Kale
- The Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Lena Fragner
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Centre (VIME), University of Vienna, Vienna, Austria
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
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10
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Jan S, Rustgi S, Barmukh R, Shikari AB, Leske B, Bekuma A, Sharma D, Ma W, Kumar U, Kumar U, Bohra A, Varshney RK, Mir RR. Advances and opportunities in unraveling cold-tolerance mechanisms in the world's primary staple food crops. THE PLANT GENOME 2024; 17:e20402. [PMID: 37957947 DOI: 10.1002/tpg2.20402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 11/15/2023]
Abstract
Temperatures below or above optimal growth conditions are among the major stressors affecting productivity, end-use quality, and distribution of key staple crops including rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays L.). Among temperature stresses, cold stress induces cellular changes that cause oxidative stress and slowdown metabolism, limit growth, and ultimately reduce crop productivity. Perception of cold stress by plant cells leads to the activation of cold-responsive transcription factors and downstream genes, which ultimately impart cold tolerance. The response triggered in crops to cold stress includes gene expression/suppression, the accumulation of sugars upon chilling, and signaling molecules, among others. Much of the information on the effects of cold stress on perception, signal transduction, gene expression, and plant metabolism are available in the model plant Arabidopsis but somewhat lacking in major crops. Hence, a complete understanding of the molecular mechanisms by which staple crops respond to cold stress remain largely unknown. Here, we make an effort to elaborate on the molecular mechanisms employed in response to low-temperature stress. We summarize the effects of cold stress on the growth and development of these crops, the mechanism of cold perception, and the role of various sensors and transducers in cold signaling. We discuss the progress in cold tolerance research at the genome, transcriptome, proteome, and metabolome levels and highlight how these findings provide opportunities for designing cold-tolerant crops for the future.
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Affiliation(s)
- Sofora Jan
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore Kashmir, India
| | - Sachin Rustgi
- Department of Plant and Environmental Sciences, Clemson University, Florence, South Carolina, USA
| | - Rutwik Barmukh
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Asif B Shikari
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore Kashmir, India
| | - Brenton Leske
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Amanuel Bekuma
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Darshan Sharma
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Wujun Ma
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
- College of Agronomy, Qingdao Agriculture University, Qingdao, China
| | - Upendra Kumar
- Department of Plant Science, Mahatma Jyotiba Phule Rohilkhand University, Bareilly, Uttar Pradesh, India
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, Punjab, India
| | - Abhishek Bohra
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Rajeev K Varshney
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Reyazul Rouf Mir
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore Kashmir, India
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11
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Varshney RK, Barmukh R, Bentley A, Nguyen HT. Exploring the genomics of abiotic stress tolerance and crop resilience to climate change. THE PLANT GENOME 2024; 17:e20445. [PMID: 38481118 DOI: 10.1002/tpg2.20445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 03/22/2024]
Affiliation(s)
- Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Rutwik Barmukh
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Alison Bentley
- ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Henry T Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, USA
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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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Benitez-Alfonso Y, Soanes BK, Zimba S, Sinanaj B, German L, Sharma V, Bohra A, Kolesnikova A, Dunn JA, Martin AC, Khashi U Rahman M, Saati-Santamaría Z, García-Fraile P, Ferreira EA, Frazão LA, Cowling WA, Siddique KHM, Pandey MK, Farooq M, Varshney RK, Chapman MA, Boesch C, Daszkowska-Golec A, Foyer CH. Enhancing climate change resilience in agricultural crops. Curr Biol 2023; 33:R1246-R1261. [PMID: 38052178 DOI: 10.1016/j.cub.2023.10.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Climate change threatens global food and nutritional security through negative effects on crop growth and agricultural productivity. Many countries have adopted ambitious climate change mitigation and adaptation targets that will exacerbate the problem, as they require significant changes in current agri-food systems. In this review, we provide a roadmap for improved crop production that encompasses the effective transfer of current knowledge into plant breeding and crop management strategies that will underpin sustainable agriculture intensification and climate resilience. We identify the main problem areas and highlight outstanding questions and potential solutions that can be applied to mitigate the impacts of climate change on crop growth and productivity. Although translation of scientific advances into crop production lags far behind current scientific knowledge and technology, we consider that a holistic approach, combining disciplines in collaborative efforts, can drive better connections between research, policy, and the needs of society.
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Affiliation(s)
| | - Beth K Soanes
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sibongile Zimba
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK; Horticulture Department, Lilongwe University of Agriculture and Natural Resources, P.O. Box 219, Lilongwe, Malawi
| | - Besiana Sinanaj
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Liam German
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Anastasia Kolesnikova
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton SO17 1BJ, UK
| | - Jessica A Dunn
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK; Institute for Sustainable Food, University of Sheffield, Sheffield S10 2TN, UK
| | - Azahara C Martin
- Institute for Sustainable Agriculture (IAS-CSIC), Córdoba 14004, Spain
| | - Muhammad Khashi U Rahman
- Microbiology and Genetics Department, Universidad de Salamanca, Salamanca 37007, Spain; Institute for Agribiotechnology Research (CIALE), University of Salamanca, Villamayor de la Armuña 37185, Spain
| | - Zaki Saati-Santamaría
- Microbiology and Genetics Department, Universidad de Salamanca, Salamanca 37007, Spain; Institute for Agribiotechnology Research (CIALE), University of Salamanca, Villamayor de la Armuña 37185, Spain; Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Prague, Czech Republic
| | - Paula García-Fraile
- Microbiology and Genetics Department, Universidad de Salamanca, Salamanca 37007, Spain; Institute for Agribiotechnology Research (CIALE), University of Salamanca, Villamayor de la Armuña 37185, Spain
| | - Evander A Ferreira
- Institute of Agrarian Sciences, Federal University of Minas Gerais, Avenida Universitária 1000, 39404547, Montes Claros, Minas Gerais, Brazil
| | - Leidivan A Frazão
- Institute of Agrarian Sciences, Federal University of Minas Gerais, Avenida Universitária 1000, 39404547, Montes Claros, Minas Gerais, Brazil
| | - Wallace A Cowling
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Muhammad Farooq
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia; Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud 123, Oman
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton SO17 1BJ, UK
| | - Christine Boesch
- School of Food Science and Nutrition, Faculty of Environment, University of Leeds, Leeds LS2 9JT, UK
| | - Agata Daszkowska-Golec
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland
| | - Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
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Anjitha KS, Sarath NG, Sameena PP, Janeeshma E, Shackira AM, Puthur JT. Plant response to heavy metal stress toxicity: the role of metabolomics and other omics tools. FUNCTIONAL PLANT BIOLOGY : FPB 2023; 50:965-982. [PMID: 37995340 DOI: 10.1071/fp23145] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023]
Abstract
Metabolomic investigations offers a significant foundation for improved comprehension of the adaptability of plants to reconfigure the key metabolic pathways and their response to changing climatic conditions. Their application to ecophysiology and ecotoxicology help to assess potential risks caused by the contaminants, their modes of action and the elucidation of metabolic pathways associated with stress responses. Heavy metal stress is one of the most significant environmental hazards affecting the physiological and biochemical processes in plants. Metabolomic tools have been widely utilised in the massive characterisation of the molecular structure of plants at various stages for understanding the diverse aspects of the cellular functioning underlying heavy metal stress-responsive mechanisms. This review emphasises on the recent progressions in metabolomics in plants subjected to heavy metal stresses. Also, it discusses the possibility of facilitating effective management strategies concerning metabolites for mitigating the negative impacts of heavy metal contaminants on the growth and productivity of plants.
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Affiliation(s)
- K S Anjitha
- Plant Physiology and Biochemistry Division, Department of Botany, University of Calicut, C. U. Campus P.O., Malappuram, Kerala 673635, India
| | - Nair G Sarath
- Department of Botany, Mar Athanasius College, Kothamangalam, Ernakulam, Kerala 686666, India
| | - P P Sameena
- Department of Botany, PSMO College, Tirurangadi, Malappuram, Kerala 676306, India
| | - Edappayil Janeeshma
- Department of Botany, MES KEVEEYAM College, Valanchery, Malappuram, Kerala 676552, India
| | - A M Shackira
- Department of Botany, Sir Syed College, Kannur University, Kannur, Kerala 670142, India
| | - Jos T Puthur
- Plant Physiology and Biochemistry Division, Department of Botany, University of Calicut, C. U. Campus P.O., Malappuram, Kerala 673635, India
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15
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Wang M, Wang L, Yu X, Zhao J, Tian Z, Liu X, Wang G, Zhang L, Guo X. Enhancing cold and drought tolerance in cotton: a protective role of SikCOR413PM1. BMC PLANT BIOLOGY 2023; 23:577. [PMID: 37978345 PMCID: PMC10656917 DOI: 10.1186/s12870-023-04572-6] [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: 05/18/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
Abstract
The present study explored the potential role of cold-regulated plasma membrane protein COR413PM1 isolated from Saussurea involucrata (Matsum. & Koidz)(SikCOR413PM1), in enhancing cotton (Gossypium hirsutum) tolerance to cold and drought stresses through transgenic methods. Under cold and drought stresses, the survival rate and the fresh and dry weights of the SikCOR413PM1-overexpressing lines were higher than those of the wild-type plants, and the degree of leaf withering was much lower. Besides, overexpressing SikCOR413PM1 overexpression increased the relative water content, reduced malondialdehyde content and relative conductivity, and elevated proline and soluble sugar levels in cotton seedlings. These findings suggest that SikCOR413PM1 minimizes cell membrane damage and boosts plant stability under challenging conditions. Additionally, overexpression of this gene upregulated antioxidant enzyme-related genes in cotton seedlings, resulting in enhanced antioxidant enzyme activity, lowered peroxide content, and reduced oxidative stress. SikCOR413PM1 overexpression also modulated the expression of stress-related genes (GhDREB1A, GhDREB1B, GhDREB1C, GhERF2, GhNAC3, and GhRD22). In field trials, the transgenic cotton plants overexpressing SikCOR413PM1 displayed high yields and increased environmental tolerance. Our study thus demonstrates the role of SikCOR413PM1 in regulating stress-related genes, osmotic adjustment factors, and peroxide content while preserving cell membrane stability and improving cold and drought tolerance in cotton.
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Affiliation(s)
- Mei Wang
- College of Life Science, Shihezi University, Shihezi, Xinjiang, 832000, People's Republic of China
| | - Lepeng Wang
- College of Life Science, Shihezi University, Shihezi, Xinjiang, 832000, People's Republic of China
| | - Xiangxue Yu
- College of Life Science, Shihezi University, Shihezi, Xinjiang, 832000, People's Republic of China
| | - Jingyi Zhao
- College of Life Science, Shihezi University, Shihezi, Xinjiang, 832000, People's Republic of China
| | - Zhijia Tian
- College of Life Science, Shihezi University, Shihezi, Xinjiang, 832000, People's Republic of China
| | - Xiaohong Liu
- Xinjiang Agricultural Development Group Crop Hospital Co. LTD, Tumushuke, Xinjiang, 844000, People's Republic of China
| | - Guoping Wang
- Agricultural Science Institute of the seventh division of Xinjiang Corps, Kuitun, Xinjiang, 833200, People's Republic of China
| | - Li Zhang
- Department of Preventive Medicine, School of Medicine, Shihezi University, Shihezi, Xinjiang, 832000, People's Republic of China
| | - Xinyong Guo
- College of Life Science, Shihezi University, Shihezi, Xinjiang, 832000, People's Republic of China.
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16
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Sankarapillai LV, Vijayaraghavareddy P, Nanaiah K, Arpitha GD, Chaitanya PM, Sathishraj R, Shindhe D, Vemanna RS, Yin X, Struik PC, Sreeman S. Phenotyping and metabolome analysis reveal the role of AdoMetDC and Di19 genes in determining acquired tolerance to drought in rice. PHYSIOLOGIA PLANTARUM 2023; 175:e13992. [PMID: 37882292 DOI: 10.1111/ppl.13992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/29/2023] [Accepted: 08/03/2023] [Indexed: 10/27/2023]
Abstract
Water-saving attempts for rice cultivation often reduce yields. Maintaining productivity under drought is possible when rice genotypes are bred with improved metabolism and spikelet fertility. Although attempts have been made to introgress water mining and water use efficiency traits, combining acquired tolerance traits (ATTs), that is, specific traits induced or upregulated to better tolerate severe stress, appears equally important. In our study, we screened 90 rice germplasm accessions that represented the molecular and phenotypic variations of 851 lines of the 3 K rice panel. Utilising phenomics, we identified markers linked to ATTs through association analysis of over 0.2 million SNPs derived from whole-genome sequences. Propensity to respond to 'induction' stress varied significantly among genotypes, reflecting differences in cellular protection against oxidative stress. Among the ATTs, the hydroxyl radical and proline contents exhibited the highest variability. Furthermore, these significant variations in ATTs were strongly correlated with spikelet fertility. The 43 significant markers associated with ATTs were further validated using a different subset of contrasting genotypes. Gene expression studies and metabolomic profiling of two well-known contrasting genotypes, APO (tolerant) and IR64 (sensitive), identified two ATT genes: AdoMetDC and Di19. Our study highlights the relevance of polyamine biosynthesis in modulating ATTs in rice. Genotypes with superior ATTs and the associated markers can be effectively employed in breeding rice varieties with sustained spikelet fertility and grain yield under drought.
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Affiliation(s)
| | - Preethi Vijayaraghavareddy
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University & Research, Wageningen, the Netherlands
| | - Karthik Nanaiah
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | | | | | - Rajendran Sathishraj
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Dhananjay Shindhe
- Department of Pathology and Microbiology, University of Nebraska Medical Centre, Omaha, Nebraska, USA
| | - Ramu S Vemanna
- Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Xinyou Yin
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University & Research, Wageningen, the Netherlands
| | - Paul C Struik
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University & Research, Wageningen, the Netherlands
| | - Sheshshayee Sreeman
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
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17
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Cortés AJ, Barnaby JY. Editorial: Harnessing genebanks: High-throughput phenotyping and genotyping of crop wild relatives and landraces. FRONTIERS IN PLANT SCIENCE 2023; 14:1149469. [PMID: 36968416 PMCID: PMC10036837 DOI: 10.3389/fpls.2023.1149469] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria – AGROSAVIA, C.I. La Selva, Rionegro, Colombia
| | - Jinyoung Y. Barnaby
- U.S. Department of Agriculture, U.S. National Arboretum, Floral and Nursery Plants Research Unit, Beltsville, MD, United States
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18
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Raza A, Mubarik MS, Sharif R, Habib M, Jabeen W, Zhang C, Chen H, Chen ZH, Siddique KHM, Zhuang W, Varshney RK. Developing drought-smart, ready-to-grow future crops. THE PLANT GENOME 2023; 16:e20279. [PMID: 36366733 DOI: 10.1002/tpg2.20279] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/02/2022] [Indexed: 05/10/2023]
Abstract
Breeding crop plants with increased yield potential and improved tolerance to stressful environments is critical for global food security. Drought stress (DS) adversely affects agricultural productivity worldwide and is expected to rise in the coming years. Therefore, it is vital to understand the physiological, biochemical, molecular, and ecological mechanisms associated with DS. This review examines recent advances in plant responses to DS to expand our understanding of DS-associated mechanisms. Suboptimal water sources adversely affect crop growth and yields through physical impairments, physiological disturbances, biochemical modifications, and molecular adjustments. To control the devastating effect of DS in crop plants, it is important to understand its consequences, mechanisms, and the agronomic and genetic basis of DS for sustainable production. In addition to plant responses, we highlight several mitigation options such as omics approaches, transgenics breeding, genome editing, and biochemical to mechanical methods (foliar treatments, seed priming, and conventional agronomic practices). Further, we have also presented the scope of conventional and speed breeding platforms in helping to develop the drought-smart future crops. In short, we recommend incorporating several approaches, such as multi-omics, genome editing, speed breeding, and traditional mechanical strategies, to develop drought-smart cultivars to achieve the 'zero hunger' goal.
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Affiliation(s)
- Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry Univ., Fuzhou, 350002, China
| | | | - Rahat Sharif
- Dep. of Horticulture, College of Horticulture and Plant Protection, Yangzhou Univ., Yangzhou, Jiangsu, 225009, China
| | - Madiha Habib
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Rd., Islamabad, 45500, Pakistan
| | - Warda Jabeen
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National Univ. of Sciences and Technology, Islamabad, 44000, Pakistan
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry Univ., Fuzhou, 350002, China
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry Univ., Fuzhou, 350002, China
| | - Zhong-Hua Chen
- School of Science, Hawkesbury Institute for the Environment, Western Sydney Univ., Penrith, NSW, 2751, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The Univ. of Western Australia, Crawley, Perth, 6009, Australia
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry Univ., Fuzhou, 350002, China
| | - Rajeev K Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry Univ., Fuzhou, 350002, China
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch Univ., Murdoch, WA, 6150, Australia
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19
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Marker assisted backcross to introgress late leaf spot and rust resistance in groundnut (Arachis hypogaea L.). Mol Biol Rep 2023; 50:2411-2419. [PMID: 36586081 DOI: 10.1007/s11033-022-08234-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 12/22/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND Groundnut is affected by a variety of abiotic and biotic stressors, including late leaf spot and rust, which cause significant economic loss. In this study, QTL for resistance to late leaf spot and rust from donor variety GPBD 4 were incorporated into a popular groundnut variety (ICGV 00350) through marker assisted backcross (MABC) breeding. METHODS Eight foreground SSR markers [AhXII (GM1009, GM1573 and Seq8D09) and AhXV (GM1536, GM2009, GM2079, GM2301 and IPAHM103)] linked with disease resistant QTLs were utilized in this study. A set of 217 SSR markers spanning the whole groundnut genome were employed for background analysis. Three backcrosses with recurrent parent and selfing were followed in the cross ICGV 00350 × GPBD 4. Background analysis was carried out in BC3F2; while, phenotypic confirmation for resistance was carried out in BC3F3 generation. CONCLUSION Five advanced backcross lines in BC3F2 were found, with more than 90% recurrent parent genome. The phenotyping of the eight ILs recorded disease scores ranging from 2.0 to 3.0 for LLS and from 1.0 to 3.0 for rust disease scores. All these lines had superior characteristics compared to the recurrent parent ICGV 00350 in terms of late leaf spot and rust resistance. The enhanced ILs will be evaluated further for commercial release.
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20
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Barmukh R, Roorkiwal M, Dixit GP, Bajaj P, Kholova J, Smith MR, Chitikineni A, Bharadwaj C, Sreeman SM, Rathore A, Tripathi S, Yasin M, Vijayakumar AG, Rao Sagurthi S, Siddique KHM, Varshney RK. Characterization of 'QTL-hotspot' introgression lines reveals physiological mechanisms and candidate genes associated with drought adaptation in chickpea. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7255-7272. [PMID: 36006832 PMCID: PMC9730794 DOI: 10.1093/jxb/erac348] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/24/2022] [Indexed: 05/16/2023]
Abstract
'QTL-hotspot' is a genomic region on linkage group 04 (CaLG04) in chickpea (Cicer arietinum) that harbours major-effect quantitative trait loci (QTLs) for multiple drought-adaptive traits, and it therefore represents a promising target for improving drought adaptation. To investigate the mechanisms underpinning the positive effects of 'QTL-hotspot' on seed yield under drought, we introgressed this region from the ICC 4958 genotype into five elite chickpea cultivars. The resulting introgression lines (ILs) and their parents were evaluated in multi-location field trials and semi-controlled conditions. The results showed that the 'QTL-hotspot' region improved seed yield under rainfed conditions by increasing seed weight, reducing the time to flowering, regulating traits related to canopy growth and early vigour, and enhancing transpiration efficiency. Whole-genome sequencing data analysis of the ILs and parents revealed four genes underlying the 'QTL-hotspot' region associated with drought adaptation. We validated diagnostic KASP markers closely linked to these genes using the ILs and their parents for future deployment in chickpea breeding programs. The CaTIFY4b-H2 haplotype of a potential candidate gene CaTIFY4b was identified as the superior haplotype for 100-seed weight. The candidate genes and superior haplotypes identified in this study have the potential to serve as direct targets for genetic manipulation and selection for chickpea improvement.
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Affiliation(s)
- Rutwik Barmukh
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | | | - Girish P Dixit
- ICAR - Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Prasad Bajaj
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Jana Kholova
- Crops Physiology & Modeling, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Information Technologies, Faculty of Economics and Management, Czech University of Life Sciences Prague, Kamýcká 129, Prague, Czech Republic
| | - Millicent R Smith
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Australia
| | - Annapurna Chitikineni
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Chellapilla Bharadwaj
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
- ICAR - Indian Agricultural Research Institute (IARI), Delhi, India
| | - Sheshshayee M Sreeman
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | - Abhishek Rathore
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Mohammad Yasin
- RAK College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, India
| | | | | | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
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21
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Borrell AK, Wong ACS, George-Jaeggli B, van Oosterom EJ, Mace ES, Godwin ID, Liu G, Mullet JE, Klein PE, Hammer GL, McLean G, Hunt C, Jordan DR. Genetic modification of PIN genes induces causal mechanisms of stay-green drought adaptation phenotype. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6711-6726. [PMID: 35961690 PMCID: PMC9629789 DOI: 10.1093/jxb/erac336] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 08/10/2022] [Indexed: 05/27/2023]
Abstract
The stay-green trait is recognized as a key drought adaptation mechanism in cereals worldwide. Stay-green sorghum plants exhibit delayed senescence of leaves and stems, leading to prolonged growth, a reduced risk of lodging, and higher grain yield under end-of-season drought stress. More than 45 quantitative trait loci (QTL) associated with stay-green have been identified, including two major QTL (Stg1 and Stg2). However, the contributing genes that regulate functional stay-green are not known. Here we show that the PIN FORMED family of auxin efflux carrier genes induce some of the causal mechanisms driving the stay-green phenotype in sorghum, with SbPIN4 and SbPIN2 located in Stg1 and Stg2, respectively. We found that nine of 11 sorghum PIN genes aligned with known stay-green QTL. In transgenic studies, we demonstrated that PIN genes located within the Stg1 (SbPIN4), Stg2 (SbPIN2), and Stg3b (SbPIN1) QTL regions acted pleiotropically to modulate canopy development, root architecture, and panicle growth in sorghum, with SbPIN1, SbPIN2, and SbPIN4 differentially expressed in various organs relative to the non-stay-green control. The emergent consequence of such modifications in canopy and root architecture is a stay-green phenotype. Crop simulation modelling shows that the SbPIN2 phenotype can increase grain yield under drought.
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Affiliation(s)
| | - Albert C S Wong
- University of Queensland, QAAFI, Brisbane, QLD 4072, Australia
| | - Barbara George-Jaeggli
- University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), Warwick, QLD 4370, Australia
- Agri-Science Queensland, Department of Agriculture & Fisheries, Warwick, QLD 4370, Australia
| | | | - Emma S Mace
- University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), Warwick, QLD 4370, Australia
- Agri-Science Queensland, Department of Agriculture & Fisheries, Warwick, QLD 4370, Australia
| | - Ian D Godwin
- University of Queensland, QAAFI, Brisbane, QLD 4072, Australia
| | - Guoquan Liu
- University of Queensland, QAAFI, Brisbane, QLD 4072, Australia
| | - John E Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Patricia E Klein
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Graeme L Hammer
- University of Queensland, QAAFI, Brisbane, QLD 4072, Australia
| | - Greg McLean
- University of Queensland, QAAFI, Brisbane, QLD 4072, Australia
| | - Colleen Hunt
- Agri-Science Queensland, Department of Agriculture & Fisheries, Warwick, QLD 4370, Australia
| | - David R Jordan
- University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), Warwick, QLD 4370, Australia
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22
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Wohor OZ, Rispail N, Ojiewo CO, Rubiales D. Pea Breeding for Resistance to Rhizospheric Pathogens. PLANTS (BASEL, SWITZERLAND) 2022; 11:2664. [PMID: 36235530 PMCID: PMC9572552 DOI: 10.3390/plants11192664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 09/30/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Pea (Pisum sativum L.) is a grain legume widely cultivated in temperate climates. It is important in the race for food security owing to its multipurpose low-input requirement and environmental promoting traits. Pea is key in nitrogen fixation, biodiversity preservation, and nutritional functions as food and feed. Unfortunately, like most crops, pea production is constrained by several pests and diseases, of which rhizosphere disease dwellers are the most critical due to their long-term persistence in the soil and difficulty to manage. Understanding the rhizosphere environment can improve host plant root microbial association to increase yield stability and facilitate improved crop performance through breeding. Thus, the use of various germplasm and genomic resources combined with scientific collaborative efforts has contributed to improving pea resistance/cultivation against rhizospheric diseases. This improvement has been achieved through robust phenotyping, genotyping, agronomic practices, and resistance breeding. Nonetheless, resistance to rhizospheric diseases is still limited, while biological and chemical-based control strategies are unrealistic and unfavourable to the environment, respectively. Hence, there is a need to consistently scout for host plant resistance to resolve these bottlenecks. Herein, in view of these challenges, we reflect on pea breeding for resistance to diseases caused by rhizospheric pathogens, including fusarium wilt, root rots, nematode complex, and parasitic broomrape. Here, we will attempt to appraise and harmonise historical and contemporary knowledge that contributes to pea resistance breeding for soilborne disease management and discuss the way forward.
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Affiliation(s)
- Osman Z. Wohor
- Instituto de Agricultura Sostenible, CSIC, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
- Savanna Agriculture Research Institute, CSIR, Nyankpala, Tamale Post TL52, Ghana
| | - Nicolas Rispail
- Instituto de Agricultura Sostenible, CSIC, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Chris O. Ojiewo
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue—Gigiri, Nairobi P.O. Box 1041-00621, Kenya
| | - Diego Rubiales
- Instituto de Agricultura Sostenible, CSIC, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
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23
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Barmukh R, Roorkiwal M, Garg V, Khan AW, German L, Jaganathan D, Chitikineni A, Kholova J, Kudapa H, Sivasakthi K, Samineni S, Kale SM, Gaur PM, Sagurthi SR, Benitez‐Alfonso Y, Varshney RK. Genetic variation in CaTIFY4b contributes to drought adaptation in chickpea. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1701-1715. [PMID: 35534989 PMCID: PMC9398337 DOI: 10.1111/pbi.13840] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/28/2022] [Indexed: 05/26/2023]
Abstract
Chickpea production is vulnerable to drought stress. Identifying the genetic components underlying drought adaptation is crucial for enhancing chickpea productivity. Here, we present the fine mapping and characterization of 'QTL-hotspot', a genomic region controlling chickpea growth with positive consequences on crop production under drought. We report that a non-synonymous substitution in the transcription factor CaTIFY4b regulates seed weight and organ size in chickpea. Ectopic expression of CaTIFY4b in Medicago truncatula enhances root growth under water deficit. Our results suggest that allelic variation in 'QTL-hotspot' improves pre-anthesis water use, transpiration efficiency, root architecture and canopy development, enabling high-yield performance under terminal drought conditions. Gene expression analysis indicated that CaTIFY4b may regulate organ size under water deficit by modulating the expression of GRF-INTERACTING FACTOR1 (GIF1), a transcriptional co-activator of Growth-Regulating Factors. Taken together, our study offers new insights into the role of CaTIFY4b and on diverse physiological and molecular mechanisms underpinning chickpea growth and production under specific drought scenarios.
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Affiliation(s)
- Rutwik Barmukh
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Department of GeneticsOsmania UniversityHyderabadIndia
| | - Manish Roorkiwal
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Khalifa Center for Genetic Engineering and BiotechnologyUnited Arab Emirates UniversityAl‐AinUnited Arab Emirates
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Vanika Garg
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Aamir W. Khan
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Liam German
- Centre for Plant ScienceSchool of BiologyUniversity of LeedsLeedsUK
| | - Deepa Jaganathan
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Annapurna Chitikineni
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Jana Kholova
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Himabindu Kudapa
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Kaliamoorthy Sivasakthi
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Srinivasan Samineni
- Crop BreedingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Sandip M. Kale
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Pooran M. Gaur
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
- Crop BreedingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | | | | | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
- Murdoch’s Centre for Crop & Food InnovationState Agricultural Biotechnology CentreFood Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
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24
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Roorkiwal M, Bhandari A, Barmukh R, Bajaj P, Valluri VK, Chitikineni A, Pandey S, Chellapilla B, Siddique KHM, Varshney RK. Genome-wide association mapping of nutritional traits for designing superior chickpea varieties. FRONTIERS IN PLANT SCIENCE 2022; 13:843911. [PMID: 36082300 PMCID: PMC9445663 DOI: 10.3389/fpls.2022.843911] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Micronutrient malnutrition is a serious concern in many parts of the world; therefore, enhancing crop nutrient content is an important challenge. Chickpea (Cicer arietinum L.), a major food legume crop worldwide, is a vital source of protein and minerals in the vegetarian diet. This study evaluated a diverse set of 258 chickpea germplasm accessions for 12 key nutritional traits. A significant variation was observed for several nutritional traits, including crude protein (16.56-24.64/100 g), β-Carotene (0.003-0.104 mg/100 g), calcium (60.69-176.55 mg/100 g), and folate (0.413-6.537 mg/kg). These data, combined with the available whole-genome sequencing data for 318,644 SNPs, were used in genome-wide association studies comprising single-locus and multi-locus models. We also explored the effect of varying the minor allele frequency (MAF) levels and heterozygosity. We identified 62 significant marker-trait associations (MTAs) explaining up to 28.63% of the phenotypic variance (PV), of which nine were localized within genes regulating G protein-coupled receptor signaling pathway, proteasome assembly, intracellular signal transduction, and oxidation-reduction process, among others. The significant effect MTAs were located primarily on Ca1, Ca3, Ca4, and Ca6. Importantly, varying the level of heterozygosity was found to significantly affect the detection of associations contributing to traits of interest. We further identified seven promising accessions (ICC10399, ICC1392, ICC1710, ICC2263, ICC1431, ICC4182, and ICC16915) with superior agronomic performance and high nutritional content as potential donors for developing nutrient-rich, high-yielding chickpea varieties. Validation of the significant MTAs with higher PV could identify factors controlling the nutrient acquisition and facilitate the design of biofortified chickpeas for the future.
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Affiliation(s)
- Manish Roorkiwal
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Aditi Bhandari
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rutwik Barmukh
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prasad Bajaj
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vinod Kumar Valluri
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sarita Pandey
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Bharadwaj Chellapilla
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- ICAR- Indian Agricultural Research Institute (IARI), New Delhi, India
| | | | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
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25
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Kushwah A, Bhatia D, Barmukh R, Singh I, Singh G, Bindra S, Vij S, Chellapilla B, Pratap A, Roorkiwal M, Kumar S, Varshney RK, Singh S. Genetic mapping of QTLs for drought tolerance in chickpea ( Cicer arietinum L.). Front Genet 2022; 13:953898. [PMID: 36061197 PMCID: PMC9437436 DOI: 10.3389/fgene.2022.953898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/05/2022] [Indexed: 01/24/2023] Open
Abstract
Chickpea yield is severely affected by drought stress, which is a complex quantitative trait regulated by multiple small-effect genes. Identifying genomic regions associated with drought tolerance component traits may increase our understanding of drought tolerance mechanisms and assist in the development of drought-tolerant varieties. Here, a total of 187 F8 recombinant inbred lines (RILs) developed from an interspecific cross between drought-tolerant genotype GPF 2 (Cicer arietinum) and drought-sensitive accession ILWC 292 (C. reticulatum) were evaluated to identify quantitative trait loci (QTLs) associated with drought tolerance component traits. A total of 21 traits, including 12 morpho-physiological traits and nine root-related traits, were studied under rainfed and irrigated conditions. Composite interval mapping identified 31 QTLs at Ludhiana and 23 QTLs at Faridkot locations for morphological and physiological traits, and seven QTLs were identified for root-related traits. QTL analysis identified eight consensus QTLs for six traits and five QTL clusters containing QTLs for multiple traits on linkage groups CaLG04 and CaLG06. The identified major QTLs and genomic regions associated with drought tolerance component traits can be introgressed into elite cultivars using genomics-assisted breeding to enhance drought tolerance in chickpea.
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Affiliation(s)
- Ashutosh Kushwah
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Rutwik Barmukh
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Gurpreet Singh
- Regional Research Station, Punjab Agricultural University, Faridkot, India
| | - Shayla Bindra
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Suruchi Vij
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | | | - Aditya Pratap
- Crop Improvement Division, ICAR- Indian Institute of Pulses Research, Kanpur, India
| | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Office, Rabat, Morocco
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Murdoch’s Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Sarvjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
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26
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Lynch JP. Harnessing root architecture to address global challenges. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:415-431. [PMID: 34724260 PMCID: PMC9299910 DOI: 10.1111/tpj.15560] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 05/06/2023]
Abstract
Root architecture can be targeted in breeding programs to develop crops with better capture of water and nutrients. In rich nations, such crops would reduce production costs and environmental pollution and, in developing nations, they would improve food security and economic development. Crops with deeper roots would have better climate resilience while also sequestering atmospheric CO2 . Deeper rooting, which improves water and N capture, is facilitated by steeper root growth angles, fewer axial roots, reduced lateral branching, and anatomical phenotypes that reduce the metabolic cost of root tissue. Mechanical impedance, hypoxia, and Al toxicity are constraints to subsoil exploration. To improve topsoil foraging for P, K, and other shallow resources, shallower root growth angles, more axial roots, and greater lateral branching are beneficial, as are metabolically cheap roots. In high-input systems, parsimonious root phenotypes that focus on water capture may be advantageous. The growing prevalence of Conservation Agriculture is shifting the mechanical impedance characteristics of cultivated soils in ways that may favor plastic root phenotypes capable of exploiting low resistance pathways to the subsoil. Root ideotypes for many low-input systems would not be optimized for any one function, but would be resilient against an array of biotic and abiotic challenges. Root hairs, reduced metabolic cost, and developmental regulation of plasticity may be useful in all environments. The fitness landscape of integrated root phenotypes is large and complex, and hence will benefit from in silico tools. Understanding and harnessing root architecture for crop improvement is a transdisciplinary opportunity to address global challenges.
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Affiliation(s)
- Jonathan P. Lynch
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPA16802USA
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27
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Cortés AJ, Cornille A, Yockteng R. Evolutionary Genetics of Crop-Wild Complexes. Genes (Basel) 2021; 13:1. [PMID: 35052346 PMCID: PMC8774885 DOI: 10.3390/genes13010001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 12/07/2021] [Indexed: 12/12/2022] Open
Abstract
Since Darwin's time, the role of crop wild relatives (CWR), landraces, and cultivated genepools in shaping plant diversity and boosting food resources has been a major question [...].
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Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 vía Rionegro—Las Palmas, Rionegro 054048, Colombia
- Facultad de Ciencias Agrarias—Departamento de Ciencias Forestales, Universidad Nacional de Colombia—Sede Medellín, Medellín 050034, Colombia
| | - Amandine Cornille
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Gif-sur-Yvette, France; or
| | - Roxana Yockteng
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. Tibaitatá, Km 14 vía Mosquera, Cundinamarca 250047, Colombia;
- Institut de Systématique, Evolution, Biodiversité-UMR-CNRS 7205, National Museum of Natural History, 75005 Paris, France
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