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Jan N, Rather AMUD, John R, Chaturvedi P, Ghatak A, Weckwerth W, Zargar SM, Mir RA, Khan MA, Mir RR. Proteomics for abiotic stresses in legumes: present status and future directions. Crit Rev Biotechnol 2023; 43:171-190. [PMID: 35109728 DOI: 10.1080/07388551.2021.2025033] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Legumes are the most important crop plants in agriculture, contributing 27% of the world's primary food production. However, productivity and production of Legumes is reduced due to increasing environmental stress. Hence, there is a pressing need to understand the molecular mechanism involved in stress response and legumes adaptation. Proteomics provides an important molecular approach to investigate proteins involved in stress response. Both the gel-based and gel-free-based techniques have significantly contributed to understanding the proteome regulatory network in leguminous plants. In the present review, we have discussed the role of different proteomic approaches (2-DE, 2 D-DIGE, ICAT, iTRAQ, etc.) in the identification of various stress-responsive proteins in important leguminous crops, including soybean, chickpea, cowpea, pigeon pea, groundnut, and common bean under variable abiotic stresses including heat, drought, salinity, waterlogging, frost, chilling and metal toxicity. The proteomic analysis has revealed that most of the identified differentially expressed proteins in legumes are involved in photosynthesis, carbohydrate metabolism, signal transduction, protein metabolism, defense, and stress adaptation. The proteomic approaches provide insights in understanding the molecular mechanism of stress tolerance in legumes and have resulted in the identification of candidate genes used for the genetic improvement of plants against various environmental stresses. Identifying novel proteins and determining their expression under different stress conditions provide the basis for effective engineering strategies to improve stress tolerance in crop plants through marker-assisted breeding.
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Affiliation(s)
- Nelofer Jan
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Kashmir, India
| | | | - Riffat John
- Plant Molecular Biology Laboratory, Department of Botany, University of Kashmir, Srinagar, India
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Sajad Majeed Zargar
- Division of Plant Biotechnology, Faculty of Horticulture, SKUAST-Kashmir, Srinagar, India
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Jammu, India
| | - Mohd Anwar Khan
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Kashmir, India
| | - Reyazul Rouf Mir
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Kashmir, India
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Asati R, Tripathi MK, Tiwari S, Yadav RK, Tripathi N. Molecular Breeding and Drought Tolerance in Chickpea. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111846. [PMID: 36430981 PMCID: PMC9698494 DOI: 10.3390/life12111846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
Cicer arietinum L. is the third greatest widely planted imperative pulse crop worldwide, and it belongs to the Leguminosae family. Drought is the utmost common abiotic factor on plants, distressing their water status and limiting their growth and development. Chickpea genotypes have the natural ability to fight drought stress using certain strategies viz., escape, avoidance and tolerance. Assorted breeding methods, including hybridization, mutation, and marker-aided breeding, genome sequencing along with omics approaches, could be used to improve the chickpea germplasm lines(s) against drought stress. Root features, for instance depth and root biomass, have been recognized as the greatest beneficial morphological factors for managing terminal drought tolerance in the chickpea. Marker-aided selection, for example, is a genomics-assisted breeding (GAB) strategy that can considerably increase crop breeding accuracy and competence. These breeding technologies, notably marker-assisted breeding, omics, and plant physiology knowledge, underlined the importance of chickpea breeding and can be used in future crop improvement programmes to generate drought-tolerant cultivars(s).
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Affiliation(s)
- Ruchi Asati
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Manoj Kumar Tripathi
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Correspondence: (M.K.T.); (N.T.)
| | - Sushma Tiwari
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Rakesh Kumar Yadav
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Agricultural University, Jabalpur 482004, India
- Correspondence: (M.K.T.); (N.T.)
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Ambika, Aski MS, Gayacharan, Hamwieh A, Talukdar A, Kumar Gupta S, Sharma BB, Joshi R, Upadhyaya HD, Singh K, Kumar R. Unraveling Origin, History, Genetics, and Strategies for Accelerated Domestication and Diversification of Food Legumes. Front Genet 2022; 13:932430. [PMID: 35979429 PMCID: PMC9376740 DOI: 10.3389/fgene.2022.932430] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/15/2022] [Indexed: 11/24/2022] Open
Abstract
Domestication is a dynamic and ongoing process of transforming wild species into cultivated species by selecting desirable agricultural plant features to meet human needs such as taste, yield, storage, and cultivation practices. Human plant domestication began in the Fertile Crescent around 12,000 years ago and spread throughout the world, including China, Mesoamerica, the Andes and Near Oceania, Sub-Saharan Africa, and eastern North America. Indus valley civilizations have played a great role in the domestication of grain legumes. Crops, such as pigeon pea, black gram, green gram, lablab bean, moth bean, and horse gram, originated in the Indian subcontinent, and Neolithic archaeological records indicate that these crops were first domesticated by early civilizations in the region. The domestication and evolution of wild ancestors into today’s elite cultivars are important contributors to global food supply and agricultural crop improvement. In addition, food legumes contribute to food security by protecting human health and minimize climate change impacts. During the domestication process, legume crop species have undergone a severe genetic diversity loss, and only a very narrow range of variability is retained in the cultivars. Further reduction in genetic diversity occurred during seed dispersal and movement across the continents. In general, only a few traits, such as shattering resistance, seed dormancy loss, stem growth behavior, flowering–maturity period, and yield traits, have prominence in the domestication process across the species. Thus, identification and knowledge of domestication responsive loci were often useful in accelerating new species’ domestication. The genes and metabolic pathways responsible for the significant alterations that occurred as an outcome of domestication might aid in the quick domestication of novel crops. Further, recent advances in “omics” sciences, gene-editing technologies, and functional analysis will accelerate the domestication and crop improvement of new crop species without losing much genetic diversity. In this review, we have discussed about the origin, center of diversity, and seed movement of major food legumes, which will be useful in the exploration and utilization of genetic diversity in crop improvement. Further, we have discussed about the major genes/QTLs associated with the domestication syndrome in pulse crops and the future strategies to improve the food legume crops.
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Rajkumar MS, Jain M, Garg R. Discovery of DNA polymorphisms via whole genome resequencing and their functional relevance in salinity stress response in chickpea. PHYSIOLOGIA PLANTARUM 2021; 173:1573-1586. [PMID: 34287918 DOI: 10.1111/ppl.13507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/07/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Salinity stress is one of the major constraints for plant growth and yield. The salinity stress response of different genotypes of crop plants may largely be governed by DNA polymorphisms. To determine the molecular genetic factors involved in salinity stress tolerance in chickpea, we performed a whole genome resequencing data analysis of three each of salinity-sensitive and salinity-tolerant genotypes. A total of 6173 single nucleotide polymorphisms and 920 insertions and deletions differentiating the chickpea genotypes with contrasting salinity stress responses were identified. Gene ontology analysis revealed the enrichment of functional terms related to stress response and development among the genes harboring DNA polymorphisms in their promoter and/or coding regions. DNA polymorphisms located within the cis-regulatory motifs of the quantitative trait loci (QTL)-associated and abiotic stress related genes were identified, which may influence salinity stress response via modulating binding affinity of the transcription factors. Several genes including QTL-associated and abiotic stress response related genes harboring DNA polymorphisms exhibited differential expression in response to salinity stress especially at the reproductive stage of development in the salinity-tolerant genotype. Furthermore, effects of non-synonymous DNA polymorphisms on mutational sensitivity and structural integrity of the encoded proteins by the candidate QTL-associated and abiotic stress response related genes were revealed. The results suggest that DNA polymorphisms may determine salinity stress response via influencing differential gene expression in genotype and/or stage-dependent manner. Altogether, we provide a high-quality set of DNA polymorphisms and candidate genes that may govern salinity stress tolerance in chickpea.
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Affiliation(s)
- Mohan Singh Rajkumar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, India
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Kumari P, Singh S, Yadav S, Tran LSP. Influence of different types of explants in chickpea regeneration using thidiazuron seed-priming. JOURNAL OF PLANT RESEARCH 2021; 134:1149-1154. [PMID: 33991285 DOI: 10.1007/s10265-021-01312-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
A comparative regeneration of three types of explants prepared from axillary meristems, plumular apices and hypocotyls of chickpea (Cicer arietinum) was carried out using four thidiazuron (TDZ) treatment methods. The first and third ones included the short-term 20 μM TDZ pre-treatment for all three explant types followed by non-supplementation or supplementation of TDZ (4 μM) into the shoot induction medium (SIM), while the second and fourth ones lacked TDZ pre-treatment followed by non-addition or addition of 4 μM TDZ in the SIM. Axillary meristem explants produced the best results with seed pre-treatment using 20 μM TDZ without TDZ in SIM and showed the highest rate of regeneration efficiency (71.33 ± 1.5%) after 20 days. Concurrently, plumular apex explants from TDZ-primed seeds was ranked second, exhibiting a regeneration percentage of 54.33 ± 2.3% in SIM without supplementation of TDZ, whereas explants from hypocotyls generated from seeds subjected to any of the TDZ treatments were not regenerated on any SIMs after 20 days.
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Affiliation(s)
- Pragati Kumari
- Department of Life Sciences, Singhania University, Jhunjhunu, Rajasthan, 333515, India
| | - Sumer Singh
- Department of Life Sciences, Singhania University, Jhunjhunu, Rajasthan, 333515, India
| | - Saurabh Yadav
- Department of Biotechnology, Hemvati Nandan Bahuguna Garhwal (Central) University, Srinagar Garhwal, Uttarakhand, 246174, India.
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, Vietnam.
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
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Wang X, Hu H, Li F, Yang B, Komatsu S, Zhou S. Quantitative proteomics reveals dual effects of calcium on radicle protrusion in soybean. J Proteomics 2021; 230:103999. [PMID: 33017647 DOI: 10.1016/j.jprot.2020.103999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/20/2020] [Accepted: 09/29/2020] [Indexed: 11/18/2022]
Abstract
To reveal calcium-mediated germination in soybean, a gel-free/label-free proteomics was performed in radicle of seed imbibed with CaCl2. Morphological analysis presented promoting and suppressing performance of seed growth under 5 and 50 mM CaCl2, respectively. A total of 106 and 581 proteins were identified in response to 5 and 50 mM CaCl2, respectively. Among 33 proteins, which were simultaneously affected by 5 and 50 mM CaCl2 imbibition, proteins related to protein metabolism, cell, development, and stress showed reversed abundance in response to CaCl2 on dose-dependent manner. Notably, protein abundance of late embryogenesis abundant (LEA) 4-5, LEA4, and dehydrin decreased and increased by 5 and 50 mM CaCl2, respectively, consistent with the transcript level. Moreover, inhibited biosynthesis of gibberellic acid repressed growth of 5 mM CaCl2-imbibed soybean, while inhibition of abscisic acid biosynthesis released the suppressing effects of 50 mM CaCl2. Taken together, these results suggest that decreased or increased protein abundance of LEA4-5, LEA4, and dehydrin might determine promoting or suppressing effects of low or high level of calcium on soybean through enhancing seed sensitivity to gibberellic acid or abscisic acid during radicle protrusion. SIGNIFICANCE: Calcium serves as a versatile signal in plant growth; however, calcium-mediated germination on dose-dependent manner remains elusive. In this study, dual effects of calcium on radicle protrusion in soybean were investigated using proteomic approach. Radicle growth of germinating seed was improved by 5 mM CaCl2; however, it was retarded by 50 mM CaCl2. Late embryogenesis abundant (LEA) 4-5, LEA4, and dehydrin displayed converse profiles in response to low and high concentrations of CaCl2 at both protein abundance and gene expression level. Inhibited biosynthesis of gibberellic acid (GA) significantly impeded radicle protrusion in presence of low concentration of CaCl2, while inhibiting of abscisic acid (ABA) biosynthesis released suppression induced by high concentration of CaCl2. These findings suggest that LEA proteins are associated with calcium-mediated radicle protrusion on dose-dependent manner, and seed sensitivity to GA and ABA might determine promoting and suppressing effects of calcium on radicle protrusion in soybean.
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Affiliation(s)
- Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Han Hu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Fang Li
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Bingxian Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Setsuko Komatsu
- Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Shunli Zhou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
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Sahruzaini NA, Rejab NA, Harikrishna JA, Khairul Ikram NK, Ismail I, Kugan HM, Cheng A. Pulse Crop Genetics for a Sustainable Future: Where We Are Now and Where We Should Be Heading. FRONTIERS IN PLANT SCIENCE 2020; 11:531. [PMID: 32431724 PMCID: PMC7212832 DOI: 10.3389/fpls.2020.00531] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/07/2020] [Indexed: 05/12/2023]
Abstract
The last decade has witnessed dramatic changes in global food consumption patterns mainly because of population growth and economic development. Food substitutions for healthier eating, such as swapping regular servings of meat for protein-rich crops, is an emerging diet trend that may shape the future of food systems and the environment worldwide. To meet the erratic consumer demand in a rapidly changing world where resources become increasingly scarce due largely to anthropogenic activity, the need to develop crops that benefit both human health and the environment has become urgent. Legumes are often considered to be affordable plant-based sources of dietary proteins. Growing legumes provides significant benefits to cropping systems and the environment because of their natural ability to perform symbiotic nitrogen fixation, which enhances both soil fertility and water-use efficiency. In recent years, the focus in legume research has seen a transition from merely improving economically important species such as soybeans to increasingly turning attention to some promising underutilized species whose genetic resources hold the potential to address global challenges such as food security and climate change. Pulse crops have gained in popularity as an affordable source of food or feed; in fact, the United Nations designated 2016 as the International Year of Pulses, proclaiming their critical role in enhancing global food security. Given that many studies have been conducted on numerous underutilized pulse crops across the world, we provide a systematic review of the related literature to identify gaps and opportunities in pulse crop genetics research. We then discuss plausible strategies for developing and using pulse crops to strengthen food and nutrition security in the face of climate and anthropogenic changes.
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Affiliation(s)
- Nurul Amylia Sahruzaini
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Nur Ardiyana Rejab
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Jennifer Ann Harikrishna
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Nur Kusaira Khairul Ikram
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Hazel Marie Kugan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Acga Cheng
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- *Correspondence: Acga Cheng,
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A comprehensive analysis of the B3 superfamily identifies tissue-specific and stress-responsive genes in chickpea ( Cicer arietinum L.). 3 Biotech 2019; 9:346. [PMID: 31497464 DOI: 10.1007/s13205-019-1875-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/14/2019] [Indexed: 12/31/2022] Open
Abstract
The aim of this study was to provide a comprehensive analysis of the plant-specific B3 domain-containing transcription factors (TFs) in chickpea. Scanning of the chickpea genome resulted in the identification of 51 B3 domain-containing TFs that were located on seven out of eight chickpea chromosomes. Based on the presence of additional domains other than the B3 domain, the candidates were classified into four subfamilies, i.e., ARF (24), REM (19), LAV (6) and RAV (2). Phylogenetic analysis classified them into four groups in which members of the same group had similar intron-exon organization and motif composition. Genome duplication analysis of the candidate B3 genes revealed an event of segmental duplication that was instrumental in the expansion of the B3 gene family. Ka/Ks analysis showed that the B3 gene family was under purifying selection. Further, chickpea B3 genes showed maximum orthology with Medicago followed by soybean and Arabidopsis. Promoter analyses of the B3 genes led to the identification of several tissue-specific and stress-responsive cis-regulatory elements. Expression profiling of the candidate B3 genes using publicly available RNA-seq data of several chickpea tissues indicated their putative role in plant development and abiotic stress response. These findings were further validated by real-time expression analysis. Overall, this study provides a comprehensive analysis of the B3 domain-containing proteins in chickpea that would aid in devising strategies for crop manipulation in chickpea.
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Kumar J, Choudhary AK, Gupta DS, Kumar S. Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses. Int J Mol Sci 2019; 20:E2971. [PMID: 31216660 PMCID: PMC6627977 DOI: 10.3390/ijms20122971] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/18/2019] [Accepted: 05/28/2019] [Indexed: 12/20/2022] Open
Abstract
Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to various abiotic and biotic stresses, leading to significant yield losses. Furthermore, climate change due to global warming has increased their vulnerability to emerging new insect pests and abiotic stresses that can become even more serious in the coming years. The changing climate scenario has made it more challenging to breed and develop climate-resilient smart pulses. Although pulses are climate smart, as they simultaneously adapt to and mitigate the effects of climate change, their narrow genetic diversity has always been a major constraint to their improvement for adaptability. However, existing genetic diversity still provides opportunities to exploit novel attributes for developing climate-resilient cultivars. The mining and exploitation of adaptive traits imparting tolerance/resistance to climate-smart pulses can be accelerated further by using cutting-edge approaches of biotechnology such as transgenics, genome editing, and epigenetics. This review discusses various classical and molecular approaches and strategies to exploit adaptive traits for breeding climate-smart pulses.
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Affiliation(s)
- Jitendra Kumar
- Indian Institute of Pulses Research, Kalyanpur, Kanpur 208 024, Uttar Pradesh, India.
| | | | - Debjyoti Sen Gupta
- Indian Institute of Pulses Research, Kalyanpur, Kanpur 208 024, Uttar Pradesh, India.
| | - Shiv Kumar
- Biodiversity and Integrated Gene Management Program, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 6299, Rabat-Institute, Rabat, Morocco.
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Badhan S, Kole P, Ball A, Mantri N. RNA sequencing of leaf tissues from two contrasting chickpea genotypes reveals mechanisms for drought tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 129:295-304. [PMID: 29913357 DOI: 10.1016/j.plaphy.2018.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/07/2018] [Accepted: 06/07/2018] [Indexed: 05/02/2023]
Abstract
Chickpea (Cicer arietinum L.) is the second most important winter crop which is consumed globally due to its high nutritional value. Chickpea as one of the leguminous crop is important in crop rotation with cereal crops like wheat and barley. The main constraints for chickpea production are abiotic stresses such as drought, salinity, and heat. Among these, drought is a major cause of the decline in chickpea production in worldwide. Studies conducted so far have provided a limited insight into different genetic pathways associated with drought tolerance/response. In this study, the leaf tissue from shoots apical meristem stage of drought tolerant (ICC8261) and drought sensitive (ICC283) genotypes were analysed using RNA sequencing to identify genes/pathways associated with drought tolerance/sensitivity in both genotypes. It was observed that genes related to ethylene response, MYB-related protein, xyloglucan endotransglycosylase, alkane hydroxylase MAH-like, BON-1 associated, peroxidase 3, cysteine-rich and transmembrane domain, vignain and mitochondrial uncoupling were specifically up-regulated in the tolerant genotype whereas, same genes were down-regulated in sensitive genotype. The crosstalk between the different hormones and transcriptional factors involved in drought tolerance and sensitivity in both genotypes make them great candidates for future research.
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Affiliation(s)
- Sapna Badhan
- The Pangenomics Group, School of Science, RMIT University, Melbourne, Victoria, 3000, Australia.
| | - Pravas Kole
- The Pangenomics Group, School of Science, RMIT University, Melbourne, Victoria, 3000, Australia.
| | - Andrew Ball
- The Pangenomics Group, School of Science, RMIT University, Melbourne, Victoria, 3000, Australia.
| | - Nitin Mantri
- The Pangenomics Group, School of Science, RMIT University, Melbourne, Victoria, 3000, Australia.
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Singh J, Singh V, Sharma PC. Elucidating the role of osmotic, ionic and major salt responsive transcript components towards salinity tolerance in contrasting chickpea ( Cicer arietinum L.) genotypes. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:441-453. [PMID: 29692552 PMCID: PMC5911262 DOI: 10.1007/s12298-018-0517-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 01/23/2018] [Accepted: 01/31/2018] [Indexed: 05/25/2023]
Abstract
The growth of chickpea (Cicer arietinum L.) is extremely hampered by salt stress. Understanding of physio-biochemical and molecular attributes along with morphological traits contributing to the salinity tolerance is important for developing salt tolerant chickpea varieties. To explore these facts, two genotypes CSG8962 and HC5 with contrasting salt tolerance were evaluated in the salinity stress (Control and 120 mM NaCl) conditions. CSG8962 maintained lower Na/K ratio in root and shoot, trammeled Na translocation to the shoots from roots compared to HC5 which ascribed to better exclusion of salt from its roots and compartmentation in the shoot. In chickpea, salt stress specifically induced genes/sequences involved at several levels in the salt stress signaling pathway. Higher induction of trehalose 6 phosphate synthase and protein kinase genes pertaining to the osmotic and signaling modules, respectively, were evident in CSG8962 compared to HC5. Further transcripts of late embryogenesis abundant, non-specific lipid transfer protein, HI and 219 genes/sequences were also highly induced in CSG8962 compared to HC5 which emphasizes the better protection of cellular membranous network and membrane-bound macromolecules under salt stress. This further suppressed the stress enhanced electrolyte leakage, loss of turgidity, promoted the higher compatible solute accumulation and maintained better cellular ion homoeostasis in CSG8962 compared to HC5. Our study further adds to the importance of these genes in salt tolerance by comparing their behavior in contrasting chickpea genotypes.
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Affiliation(s)
- Jogendra Singh
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001 India
| | - Vijayata Singh
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001 India
| | - P. C. Sharma
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001 India
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Kaashyap M, Ford R, Bohra A, Kuvalekar A, Mantri N. Improving Salt Tolerance of Chickpea Using Modern Genomics Tools and Molecular Breeding. Curr Genomics 2017; 18:557-567. [PMID: 29204084 PMCID: PMC5684649 DOI: 10.2174/1389202918666170705155252] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/28/2016] [Accepted: 12/15/2016] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION The high protein value, essential minerals, dietary fibre and notable ability to fix atmospheric nitrogen make chickpea a highly remunerative crop, particularly in low-input food production systems. Of the variety of constraints challenging chickpea productivity worldwide, salinity remains of prime concern owing to the intrinsic sensitivity of the crop. In view of the projected expansion of chickpea into arable and salt-stressed land by 2050, increasing attention is being placed on improving the salt tolerance of this crop. Considerable effort is currently underway to address salinity stress and substantial breeding progress is being made despite the seemingly highly-complex and environment-dependent nature of the tolerance trait. CONCLUSION This review aims to provide a holistic view of recent advances in breeding chickpea for salt tolerance. Initially, we focus on the identification of novel genetic resources for salt tolerance via extensive germplasm screening. We then expand on the use of genome-wide and cost-effective techniques to gain new insights into the genetic control of salt tolerance, including the responsive genes/QTL(s), gene(s) networks/cross talk and intricate signalling cascades.
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Affiliation(s)
- Mayank Kaashyap
- School of Science, RMIT University, Melbourne, 3000, Victoria, Australia
| | - Rebecca Ford
- Environmental Futures Research Institute, School of Natural Sciences, Griffith University, Queensland 4111, Australia
| | - Abhishek Bohra
- Crop Improvement Division, Indian Institute of Pulses Research, Kanpur, India
| | - Aniket Kuvalekar
- Interactive Research School for Health Affairs, Bharati Vidyapeeth University, Pune-Satara Road, Pune, Maharashtra, 411043, India
| | - Nitin Mantri
- School of Science, RMIT University, Melbourne, 3000, Victoria, Australia
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Zamora-Briseño JA, de Jiménez ES. A LEA 4 protein up-regulated by ABA is involved in drought response in maize roots. Mol Biol Rep 2016; 43:221-8. [PMID: 26922182 DOI: 10.1007/s11033-016-3963-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 02/19/2016] [Indexed: 11/25/2022]
Abstract
Late embryogenesis abundant (LEA) proteins are hydrophilic proteins that accumulate to high concentrations during the late stages of seeds development, which are integral to desiccation tolerance. LEA proteins also play a protective role under other abiotic stresses. We analyzed in silico a maize protein predicted to be highly hydrophilic and intrinsically disordered. This prediction was experimentally corroborated by solubility assays under denaturing conditions. Based on its amino acid sequence, we propose that this protein belongs to group four of the LEA proteins. The accumulation pattern of this protein was similar to that of dehydrins during the desiccation process that takes place during seed development. This protein was induced by exogenous abscisic acid in immature embryos, but during imbibition was down-regulated by gibberellins. It was also induced in maize roots under osmotic stress. So far, this is the first member of the LEA proteins belonging to group four to be characterized in maize, and it plays a role in the response to osmotic stress.
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Affiliation(s)
- Jesús Alejandro Zamora-Briseño
- Laboratorio 103, Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, México, DF, Mexico.
| | - Estela Sánchez de Jiménez
- Laboratorio 103, Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, México, DF, Mexico.
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Reddy PS, Reddy GM, Pandey P, Chandrasekhar K, Reddy MK. Cloning and molecular characterization of a gene encoding late embryogenesis abundant protein from Pennisetum glaucum: protection against abiotic stresses. Mol Biol Rep 2012; 39:7163-74. [PMID: 22311039 DOI: 10.1007/s11033-012-1548-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 01/24/2012] [Indexed: 10/14/2022]
Abstract
Late embryogenesis abundant (LEA) protein family is a large protein family that protects other proteins from aggregation due to desiccation or osmotic stresses. A cDNA clone encoding a group 7 late embryogenesis abundant protein, termed PgLEA, was isolated from Pennisetum glaucum by screening a heat stress cDNA library. PgLEA cDNA encodes a 176 amino acid polypeptide with a predicted molecular mass of 19.21 kDa and an estimated isoelectric point of 7.77. PgLEA shares 70-74% sequence identity with other plant homologs. Phylogenetic analysis revealed that PgLEA is evolutionarily close to the LEA 7 group. Recombinant PgLEA protein expressed in Escherichia coli possessed in vitro chaperone activity and protected PgLEA-producing bacteria from damage caused by heat and salinity. Positive correlation existed between differentially up-regulated PgLEA transcript levels and the duration and intensity of different environmental stresses. In silico analysis of the promoter sequence of PgLEA revealed the presence of a distinct set of cis-elements and transcription factor binding sites. Transcript induction data, the presence of several putative stress-responsive transcription factor binding sites in the promoter region of PgLEA, the in vitro chaperone activity of this protein and its protective effect against heat and salt damage in E. coli suggest a role in conferring abiotic stress tolerance in plants.
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Affiliation(s)
- Palakolanu Sudhakar Reddy
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
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