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Abdul Aziz M, Masmoudi K. Insights into the Transcriptomics of Crop Wild Relatives to Unravel the Salinity Stress Adaptive Mechanisms. Int J Mol Sci 2023; 24:9813. [PMID: 37372961 DOI: 10.3390/ijms24129813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/29/2023] Open
Abstract
The narrow genomic diversity of modern cultivars is a major bottleneck for enhancing the crop's salinity stress tolerance. The close relatives of modern cultivated plants, crop wild relatives (CWRs), can be a promising and sustainable resource to broaden the diversity of crops. Advances in transcriptomic technologies have revealed the untapped genetic diversity of CWRs that represents a practical gene pool for improving the plant's adaptability to salt stress. Thus, the present study emphasizes the transcriptomics of CWRs for salinity stress tolerance. In this review, the impacts of salt stress on the plant's physiological processes and development are overviewed, and the transcription factors (TFs) regulation of salinity stress tolerance is investigated. In addition to the molecular regulation, a brief discussion on the phytomorphological adaptation of plants under saline environments is provided. The study further highlights the availability and use of transcriptomic resources of CWR and their contribution to pangenome construction. Moreover, the utilization of CWRs' genetic resources in the molecular breeding of crops for salinity stress tolerance is explored. Several studies have shown that cytoplasmic components such as calcium and kinases, and ion transporter genes such as Salt Overly Sensitive 1 (SOS1) and High-affinity Potassium Transporters (HKTs) are involved in the signaling of salt stress, and in mediating the distribution of excess Na+ ions within the plant cells. Recent comparative analyses of transcriptomic profiling through RNA sequencing (RNA-Seq) between the crops and their wild relatives have unraveled several TFs, stress-responsive genes, and regulatory proteins for generating salinity stress tolerance. This review specifies that the use of CWRs transcriptomics in combination with modern breeding experimental approaches such as genomic editing, de novo domestication, and speed breeding can accelerate the CWRs utilization in the breeding programs for enhancing the crop's adaptability to saline conditions. The transcriptomic approaches optimize the crop genomes with the accumulation of favorable alleles that will be indispensable for designing salt-resilient crops.
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Affiliation(s)
- Mughair Abdul Aziz
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Khaled Masmoudi
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
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Tirnaz S, Zandberg J, Thomas WJW, Marsh J, Edwards D, Batley J. Application of crop wild relatives in modern breeding: An overview of resources, experimental and computational methodologies. Front Plant Sci 2022; 13:1008904. [PMID: 36466237 PMCID: PMC9712971 DOI: 10.3389/fpls.2022.1008904] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/25/2022] [Indexed: 06/01/2023]
Abstract
Global agricultural industries are under pressure to meet the future food demand; however, the existing crop genetic diversity might not be sufficient to meet this expectation. Advances in genome sequencing technologies and availability of reference genomes for over 300 plant species reveals the hidden genetic diversity in crop wild relatives (CWRs), which could have significant impacts in crop improvement. There are many ex-situ and in-situ resources around the world holding rare and valuable wild species, of which many carry agronomically important traits and it is crucial for users to be aware of their availability. Here we aim to explore the available ex-/in- situ resources such as genebanks, botanical gardens, national parks, conservation hotspots and inventories holding CWR accessions. In addition we highlight the advances in availability and use of CWR genomic resources, such as their contribution in pangenome construction and introducing novel genes into crops. We also discuss the potential and challenges of modern breeding experimental approaches (e.g. de novo domestication, genome editing and speed breeding) used in CWRs and the use of computational (e.g. machine learning) approaches that could speed up utilization of CWR species in breeding programs towards crop adaptability and yield improvement.
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Samantara K, Bohra A, Mohapatra SR, Prihatini R, Asibe F, Singh L, Reyes VP, Tiwari A, Maurya AK, Croser JS, Wani SH, Siddique KHM, Varshney RK. Breeding More Crops in Less Time: A Perspective on Speed Breeding. Biology (Basel) 2022; 11:biology11020275. [PMID: 35205141 PMCID: PMC8869642 DOI: 10.3390/biology11020275] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/25/2022] [Accepted: 02/04/2022] [Indexed: 11/28/2022]
Abstract
Simple Summary Feeding our growing population is one of the primary concerns of plant breeders. Plant breeding needs to deliver a steady stream of modern cultivars in a time- and resource-efficient manner. This review discusses the speed breeding (SB) techniques which allow breeders to advance the crop generation in a shorter period of time. In addition, we highlight the current SB applications in major crops and explore ways to integrate SB with new breeding techniques for efficient and faster production of stable lines for basic and applied research. Abstract Breeding crops in a conventional way demands considerable time, space, inputs for selection, and the subsequent crossing of desirable plants. The duration of the seed-to-seed cycle is one of the crucial bottlenecks in the progress of plant research and breeding. In this context, speed breeding (SB), relying mainly on photoperiod extension, temperature control, and early seed harvest, has the potential to accelerate the rate of plant improvement. Well demonstrated in the case of long-day plants, the SB protocols are being extended to short-day plants to reduce the generation interval time. Flexibility in SB protocols allows them to align and integrate with diverse research purposes including population development, genomic selection, phenotyping, and genomic editing. In this review, we discuss the different SB methodologies and their application to hasten future plant improvement. Though SB has been extensively used in plant phenotyping and the pyramiding of multiple traits for the development of new crop varieties, certain challenges and limitations hamper its widespread application across diverse crops. However, the existing constraints can be resolved by further optimization of the SB protocols for critical food crops and their efficient integration in plant breeding pipelines.
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Affiliation(s)
- Kajal Samantara
- Department of Genetics and Plant Breeding, Centurion University of Technology and Management, Parlakhemundi 761211, Odisha, India;
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur 208024, Uttar Pradesh, India; (A.B.); (A.T.); (A.K.M.)
| | - Sourav Ranjan Mohapatra
- Division of Genetics and Tree Improvement, Forest Research Institute, Dehradun 173230, Uttarakhand, India;
| | - Riry Prihatini
- Indonesian Tropical Fruit Research Institute, Solok 27301, West Sumatera, Indonesia;
| | - Flora Asibe
- International Institute of Tropical Agriculture, Ibadan 200001, Oyo State, Nigeria;
| | - Lokendra Singh
- Department of Genetics and Plant Breeding, Agriculture and Forestry University, Chitwan 44200, Nepal;
| | - Vincent P. Reyes
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Aichi, Japan;
| | - Abha Tiwari
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur 208024, Uttar Pradesh, India; (A.B.); (A.T.); (A.K.M.)
| | - Alok Kumar Maurya
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur 208024, Uttar Pradesh, India; (A.B.); (A.T.); (A.K.M.)
| | - Janine S. Croser
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia;
| | - Shabir Hussain Wani
- Mountain Research Center for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Anantnag Khudwani, Srinagar 192101, Jammu and Kashmir, India
- Correspondence: (S.H.W.); (K.H.M.S.); (R.K.V.)
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia;
- Correspondence: (S.H.W.); (K.H.M.S.); (R.K.V.)
| | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, Andhra Pradesh, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA 6150, Australia
- Correspondence: (S.H.W.); (K.H.M.S.); (R.K.V.)
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Ajithan C, Vasudevan V, Sathish D, Sathish S, Krishnan V, Manickavasagam M. The influential role of polyamines on the in vitro regeneration of pea (Pisum sativum L.) and genetic fidelity assessment by SCoT and RAPD markers. Plant Cell Tiss Organ Cult 2019; 139:547-561. [DOI: 10.1007/s11240-019-01699-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/14/2019] [Indexed: 06/16/2023]
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Fraternale D, Bruno M, Rocchi L, Amicucci A, Ceccarini C, Ricci D. In Vitro Culture for Ex Situ Conservation of “Roveja” and Nutritional Considerations on this Italian Rare Legume. Nat Prod Commun 2018. [DOI: 10.1177/1934578x1801300912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Roveja is a pea cultivar from the Sibillini Mountains (Umbria-Marche Apennine mountain range, Italy). Abandoned for long time, Roveja is nowadays cultivated only in few farms. The present work deals with the in vitro plant growth of this pea by tissue culture for shoots regeneration and ex situ conservation. Total polyphenols content evaluation, DPPH (2,2-diphenyl-1-picrylhydrazyl) antioxidant activity test and ORAC (Oxygen Radical Absorbance Capacity) assay were performed on the flour obtained from Roveja seeds and the results were compared to those collected by performing the same tests on the flour from two common green peas. The best shoots regeneration from embryonic axes was obtained in Murashige & Skoog (MS) media with combinations of 4.0 mg/L BA (6-Benzyladenine) plus 0.4 mg/L NAA (1-Naphthaleneacetic acid), and the best roots induction from the regenerated shoots was obtained in half strength MS media containing 1.0 mg/L IBA (3-Indolebutyric acid). The embryonic axes of Roveja seeds can be used as the starting material for in vitro regeneration of the plant; the antioxidant properties shown by this legume suggest further investigations to evaluate its nutritional/functional benefit.
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Affiliation(s)
- Daniele Fraternale
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, Via Saffi 2 - 61029 Urbino (PU) Italy
| | - Marco Bruno
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, Via Saffi 2 - 61029 Urbino (PU) Italy
| | - Luigi Rocchi
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, Via Saffi 2 - 61029 Urbino (PU) Italy
| | - Antonella Amicucci
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, Via Saffi 2 - 61029 Urbino (PU) Italy
| | - Chiara Ceccarini
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, Via Saffi 2 - 61029 Urbino (PU) Italy
| | - Donata Ricci
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, Via Saffi 2 - 61029 Urbino (PU) Italy
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