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Mangal V, Verma LK, Singh SK, Saxena K, Roy A, Karn A, Rohit R, Kashyap S, Bhatt A, Sood S. Triumphs of genomic-assisted breeding in crop improvement. Heliyon 2024; 10:e35513. [PMID: 39170454 PMCID: PMC11336775 DOI: 10.1016/j.heliyon.2024.e35513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 07/23/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024] Open
Abstract
Conventional breeding approaches have played a significant role in meeting the food demand remarkably well until now. However, the increasing population, yield plateaus in certain crops, and limited recombination necessitate using genomic resources for genomics-assisted crop improvement programs. As a result of advancements in the next-generation sequence technology, GABs have developed dramatically to characterize allelic variants and facilitate their rapid and efficient incorporation in crop improvement programs. Genomics-assisted breeding (GAB) has played an important role in harnessing the potential of modern genomic tools, exploiting allelic variation from genetic resources and developing cultivars over the past decade. The availability of pangenomes for major crops has been a significant development, albeit with varying degrees of completeness. Even though adopting these technologies is essentially determined on economic grounds and cost-effective assays, which create a wealth of information that can be successfully used to exploit the latent potential of crops. GAB has been instrumental in harnessing the potential of modern genomic resources and exploiting allelic variation for genetic enhancement and cultivar development. GAB strategies will be indispensable for designing future crops and are expected to play a crucial role in breeding climate-smart crop cultivars with higher nutritional value.
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Affiliation(s)
- Vikas Mangal
- ICAR-Central Potato Research Institute (CPRI), Shimla, Himachal Pradesh, 171001, India
| | | | - Sandeep Kumar Singh
- Department of Genetics and Plant Breeding, Faculty of Agricultural Sciences, Siksha ‘O’ Anusandhan University, Bhubaneswar, Odisha, 751030, India
| | - Kanak Saxena
- Department of Genetics and Plant Breeding, Rabindranath Tagore University, Raisen, Madhya Pradesh, India
| | - Anirban Roy
- Division of Genetics and Plant Breeding, Ramakrishna Mission Vivekananda Educational and Research Institute (RKMVERI), Narendrapur, Kolkata, 700103, India
| | - Anandi Karn
- Plant Breeding & Graduate Program, IFAS - University of Florida, Gainesville, USA
| | - Rohit Rohit
- Department of Genetics and Plant Breeding, GBPUA&T, Pantnagar, Uttarakhand, 263145, India
| | - Shruti Kashyap
- Department of Genetics and Plant Breeding, GBPUA&T, Pantnagar, Uttarakhand, 263145, India
| | - Ashish Bhatt
- Department of Genetics and Plant Breeding, GBPUA&T, Pantnagar, Uttarakhand, 263145, India
| | - Salej Sood
- ICAR-Central Potato Research Institute (CPRI), Shimla, Himachal Pradesh, 171001, India
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Panigrahi S, Kumar U, Swami S, Singh Y, Balyan P, Singh KP, Dhankher OP, Varshney RK, Roorkiwal M, Amiri KM, Mir RR. Meta QTL analysis for dissecting abiotic stress tolerance in chickpea. BMC Genomics 2024; 25:439. [PMID: 38698307 PMCID: PMC11067088 DOI: 10.1186/s12864-024-10336-9] [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: 02/12/2023] [Accepted: 04/23/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Chickpea is prone to many abiotic stresses such as heat, drought, salinity, etc. which cause severe loss in yield. Tolerance towards these stresses is quantitative in nature and many studies have been done to map the loci influencing these traits in different populations using different markers. This study is an attempt to meta-analyse those reported loci projected over a high-density consensus map to provide a more accurate information on the regions influencing heat, drought, cold and salinity tolerance in chickpea. RESULTS A meta-analysis of QTL reported to be responsible for tolerance to drought, heat, cold and salinity stress tolerance in chickpeas was done. A total of 1512 QTL responsible for the concerned abiotic stress tolerance were collected from literature, of which 1189 were projected on a chickpea consensus genetic map. The QTL meta-analysis predicted 59 MQTL spread over all 8 chromosomes, responsible for these 4 kinds of abiotic stress tolerance in chickpea. The physical locations of 23 MQTL were validated by various marker-trait associations and genome-wide association studies. Out of these reported MQTL, CaMQAST1.1, CaMQAST4.1, CaMQAST4.4, CaMQAST7.8, and CaMQAST8.2 were suggested to be useful for different breeding approaches as they were responsible for high per cent variance explained (PVE), had small intervals and encompassed a large number of originally reported QTL. Many putative candidate genes that might be responsible for directly or indirectly conferring abiotic stress tolerance were identified in the region covered by 4 major MQTL- CaMQAST1.1, CaMQAST4.4, CaMQAST7.7, and CaMQAST6.4, such as heat shock proteins, auxin and gibberellin response factors, etc. CONCLUSION: The results of this study should be useful for the breeders and researchers to develop new chickpea varieties which are tolerant to drought, heat, cold, and salinity stresses.
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Affiliation(s)
- Sourav Panigrahi
- Department of Molecular Biology & Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Upendra Kumar
- Department of Molecular Biology & Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004, India.
- Department of Plant Science, Mahatma Jyotiba Phule Rohilkhand University, Bareilly, 243001, India.
| | - Sonu Swami
- Department of Molecular Biology & Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004, India
- Department of Botany & Plant Physiology, College of Basic Sciences & Humanities, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Yogita Singh
- Department of Molecular Biology & Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Priyanka Balyan
- Department of Botany, Deva Nagri P.G. College, CCS University, Meerut, 245206, India
| | - Krishna Pal Singh
- Biophysics Unit, College of Basic Sciences & Humanities, GB Pant University of Agriculture & Technology, Pantnagar, 263145, India
- Vice-Chancellor's Secretariat, Mahatma Jyotiba Phule Rohilkhand University, Bareilly, 243001, India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, USA
| | - Rajeev K Varshney
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Manish Roorkiwal
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates.
| | - Khaled Ma Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-Kashmir), Srinagar, J&K, India.
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Nair RM, Chaudhari S, Devi N, Shivanna A, Gowda A, Boddepalli VN, Pradhan H, Schafleitner R, Jegadeesan S, Somta P. Genetics, genomics, and breeding of black gram [ Vigna mungo (L.) Hepper]. FRONTIERS IN PLANT SCIENCE 2024; 14:1273363. [PMID: 38288416 PMCID: PMC10822891 DOI: 10.3389/fpls.2023.1273363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 12/18/2023] [Indexed: 01/31/2024]
Abstract
Black gram [Vigna mungo (L.) Hepper] is a highly nutritious grain legume crop, mainly grown in South and Southeast Asia, with the largest area in India, where the crop is challenged by several biotic and abiotic stresses leading to significant yield losses. Improving genetic gains to increase on-farm yields is the primary goal of black gram breeding programs. This could be achieved by developing varieties resistant to major diseases like mungbean yellow mosaic disease, urdbean leaf crinkle virus, Cercospora leaf spot, anthracnose, powdery mildew, and insect pests such as whitefly, cowpea aphids, thrips, stem flies, and bruchids. Along with increasing on-farm yields, incorporating market-preferred traits ensures the adoption of improved varieties. Black gram breeding programs rely upon a limited number of parental lines, leading to a narrow genetic base of the developed varieties. For accelerating genetic gain, there is an urgent need to include more diverse genetic material for improving traits for better adaptability and stress resistance in breeding populations. The present review summarizes the importance of black gram, the major biotic and abiotic stresses, available genetic and genomic resources, major traits for potential crop improvement, their inheritance, and the breeding approaches being used in black gram for the development of new varieties.
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Suraninpong P, Thongkhao K, Azzeme AM, Suksa-Ard P. Monitoring Drought Tolerance in Oil Palm: Choline Monooxygenase as a Novel Molecular Marker. PLANTS (BASEL, SWITZERLAND) 2023; 12:3089. [PMID: 37687336 PMCID: PMC10490023 DOI: 10.3390/plants12173089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023]
Abstract
Water scarcity negatively impacts oil palm production, necessitating the development of drought-tolerant varieties. This study aimed to develop molecular markers for oil palm breeding programs focused on drought tolerance. Genes associated with drought tolerance were selected, and single nucleotide polymorphism (SNP)-based markers were developed. Genomic DNA was successfully extracted from 17 oil palm varieties, and 20 primers out of 44 were effectively amplified. Screening with single-strand conformation polymorphism (SSCP) revealed an informative SNP marker from the choline monooxygenase (CMO) gene, exhibiting CC, CT, and TT genotypes. Notably, the oil palm variety La Mé showed the CT genotype, while Surat Thani 2 (Deli × La Mé) exhibited the CT and CC genotypes in a 1:1 ratio. Gene expression analysis confirmed the association of the CMO gene with drought tolerance in commercial oil palm varieties. The full-length CMO gene was 1308 bp long and shared sequence similarities with other plant species. However, amino acid sequence variations were observed compared with existing databases. These findings highlight the potential utility of the CMO marker for drought tolerance selection, specifically within the La Mé parent of oil palm Surat Thani 2 varieties, and strongly confirm the La Mé S5 population and Surat Thani 2 as drought-tolerant varieties.
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Affiliation(s)
- Potjamarn Suraninpong
- School of Agricultural Technology and Food Industry, Walailak University, Nakhon Si Thammarat 80161, Thailand;
- Biomass and Oil Palm Center of Excellence, Walailak University, Nakhon Si Thammarat 80161, Thailand
| | - Kannika Thongkhao
- School of Languages and General Education, Walailak University, Nakhon Si Thammarat 80161, Thailand;
| | - Azzreena Mohamad Azzeme
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Padungsak Suksa-Ard
- School of Agricultural Technology and Food Industry, Walailak University, Nakhon Si Thammarat 80161, Thailand;
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Bhattacharya J, Srinivas Reddy D, Prasad K, Nitnavare RB, Bhatnagar-Mathur P, Sudhakar Reddy P. Ectopic expression of pigeonpea Orf147 gene imparts partial sterility in Cicer arietinum. Gene 2023; 868:147372. [PMID: 36933813 DOI: 10.1016/j.gene.2023.147372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023]
Abstract
Orf147, a cytotoxic peptide, has been found to cause cytoplasmic male sterility (CMS) in Cajanus cajanifolius (pigeonpea). In our study, Orf147 was introduced into self-pollinating Cicer arietinum (chickpea) using Agrobacterium-mediated transformation for induction of CMS. The stable integration and expression of the transgene has been assessed through PCR and qRT-PCR analysis. In addition, phenotypic sterility analysis has been performed, considering developmental parameters like flower development, pod formation and flower drop. Transgene inheritance analysis demonstrates that out of the five PCR positive events in the T0 generation, two events have segregated according to the Mendelian segregation ratio (3:1) in the T2 generation. Further, pollen viability test using microscopic analysis confirms the induction of partial CMS in transgenic chickpea. The study holds significant value regarding the heterosis of self-pollinating legumes like chickpea. As a part of the prospect, exploring inducible promoters of species-specific or related legumes would be the next step to developing a two-line hybrid system.
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Affiliation(s)
- Joorie Bhattacharya
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Hyderabad, 502324 Telangana, India; Department of Genetics, Osmania University, Hyderabad, Telangana, India
| | - Dumbala Srinivas Reddy
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Hyderabad, 502324 Telangana, India; ATGC Biotech Private Limited, ICCI Knowledge Park (IKP), Genome Valley, Hyderabad, 500078 Telangana, India
| | - Kalyani Prasad
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Hyderabad, 502324 Telangana, India
| | - Rahul B Nitnavare
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom; Plant Science Department, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | - Pooja Bhatnagar-Mathur
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz 16 Km. 45, El Batán, Texcoco C.P. 56237, Mexico.
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Hyderabad, 502324 Telangana, India.
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Kumar B, Singh AK, Bahuguna RN, Pareek A, Singla‐Pareek SL. Orphan crops: A genetic treasure trove for hunting stress tolerance genes. Food Energy Secur 2022. [DOI: 10.1002/fes3.436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Brijesh Kumar
- Plant Stress Biology Group International Centre for Genetic Engineering and Biotechnology New Delhi India
| | - Anil Kumar Singh
- ICAR‐National Institute for Plant Biotechnology LBS Centre New Delhi India
| | - Rajeev Nayan Bahuguna
- Center for Advanced Studies on Climate Change Dr. Rajendra Prasad Central Agricultural University Bihar Pusa, Samastipur India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences Jawaharlal Nehru University New Delhi India
| | - Sneh L. Singla‐Pareek
- Plant Stress Biology Group International Centre for Genetic Engineering and Biotechnology New Delhi India
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7
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Salgotra RK, Stewart CN. Genetic Augmentation of Legume Crops Using Genomic Resources and Genotyping Platforms for Nutritional Food Security. PLANTS (BASEL, SWITZERLAND) 2022; 11:1866. [PMID: 35890499 PMCID: PMC9325189 DOI: 10.3390/plants11141866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
Abstract
Recent advances in next generation sequencing (NGS) technologies have led the surge of genomic resources for the improvement legume crops. Advances in high throughput genotyping (HTG) and high throughput phenotyping (HTP) enable legume breeders to improve legume crops more precisely and efficiently. Now, the legume breeder can reshuffle the natural gene combinations of their choice to enhance the genetic potential of crops. These genomic resources are efficiently deployed through molecular breeding approaches for genetic augmentation of important legume crops, such as chickpea, cowpea, pigeonpea, groundnut, common bean, lentil, pea, as well as other underutilized legume crops. In the future, advances in NGS, HTG, and HTP technologies will help in the identification and assembly of superior haplotypes to tailor the legume crop varieties through haplotype-based breeding. This review article focuses on the recent development of genomic resource databases and their deployment in legume molecular breeding programmes to secure global food security.
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Affiliation(s)
- Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu 190008, India
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8
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Xiong R, Liu S, Considine MJ, Siddique KHM, Lam HM, Chen Y. Root system architecture, physiological and transcriptional traits of soybean (Glycine max L.) in response to water deficit: A review. PHYSIOLOGIA PLANTARUM 2021; 172:405-418. [PMID: 32880966 DOI: 10.1111/ppl.13201] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 05/24/2023]
Abstract
Drought stress is the main limiting factor for global soybean growth and production. Genetic improvement for water and nutrient uptake efficiency is critical to advance tolerance and enable more sustainable and resilient production, underpinning yield growth. The identification of quantitative traits and genes related to water and nutrient uptake will enhance our understanding of the mechanisms of drought tolerance in soybean. This review summarizes drought stress in the context of the physiological traits that enable effective acclimation, with a particular focus on roots. Genes controlling root system architecture play an important role in water and nutrient availability, and therefore important targets for breeding strategies to improve drought tolerance. This review highlights the candidate genes that have been identified as regulators of important root traits and responses to water stress. Progress in our understanding of the function of particular genes, including GmACX1, GmMS and GmPEPCK are discussed in the context of developing a system-based platform for genetic improvement of drought tolerance in soybean.
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Affiliation(s)
- Rentao Xiong
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, and Chinese Academy of Sciences, Yangling, Shaanxi, China
| | - Shuo Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, and Chinese Academy of Sciences, Yangling, Shaanxi, China
| | - Michael J Considine
- School of Molecular Sciences, The University of Western Australia, LB 5005, Perth, Western Australia, 6001, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, and UWA School of Agriculture and Environment, The University of Western Australia, LB 5005, Perth, Western Australia, 6001, Australia
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yinglong Chen
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, and Chinese Academy of Sciences, Yangling, Shaanxi, China
- The UWA Institute of Agriculture, and UWA School of Agriculture and Environment, The University of Western Australia, LB 5005, Perth, Western Australia, 6001, Australia
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9
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Bharadwaj C, Tripathi S, Soren KR, Thudi M, Singh RK, Sheoran S, Roorkiwal M, Patil BS, Chitikineni A, Palakurthi R, Vemula A, Rathore A, Kumar Y, Chaturvedi SK, Mondal B, Shanmugavadivel PS, Srivastava AK, Dixit GP, Singh NP, Varshney RK. Introgression of "QTL-hotspot" region enhances drought tolerance and grain yield in three elite chickpea cultivars. THE PLANT GENOME 2021; 14:e20076. [PMID: 33480153 DOI: 10.1002/tpg2.20076] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/10/2020] [Indexed: 05/27/2023]
Abstract
With an aim of enhancing drought tolerance using a marker-assisted backcrossing (MABC) approach, we introgressed the "QTL-hotspot" region from ICC 4958 accession that harbors quantitative trait loci (QTLs) for several drought-tolerance related traits into three elite Indian chickpea (Cicer arietinum L.) cultivars: Pusa 372, Pusa 362, and DCP 92-3. Of eight simple sequence repeat (SSR) markers in the QTL-hotspot region, two to three polymorphic markers were used for foreground selection with respective cross-combinations. A total of 47, 53, and 46 SSRs were used for background selection in case of introgression lines (ILs) developed in genetic backgrounds of Pusa 372, Pusa 362, and DCP 92-3, respectively. In total, 61 ILs (20 BC3 F3 in Pusa 372; 20 BC2 F3 in Pusa 362, and 21 BC3 F3 in DCP 92-3), with >90% recurrent parent genome recovery were developed. Six improved lines in different genetic backgrounds (e.g. BGM 10216 in Pusa 372; BG 3097 and BG 4005 in Pusa 362; IPC(L4-14), IPC(L4-16), and IPC(L19-1) in DCP 92-3) showed better performance than their respective recurrent parents. BGM 10216, with 16% yield gain over Pusa 372, has been released as Pusa Chickpea 10216 by the Central Sub-Committees on Crop Standards, Notification and Release of Varieties of Agricultural Crops, Ministry of Agriculture and Farmers Welfare, Government of India, for commercial cultivation in India. In summary, this study reports introgression of the QTL-hotspot for enhancing yield under rainfed conditions, development of several introgression lines, and release of Pusa Chickpea 10216 developed through molecular breeding in India.
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Affiliation(s)
- Chellapilla Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, Delhi, 110012, India
| | - Shailesh Tripathi
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, Delhi, 110012, India
| | - Khela R Soren
- ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, Uttar Pradesh, 208024, India
| | - Mahendar Thudi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Rajesh K Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, Delhi, 110012, India
| | - Seema Sheoran
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, Delhi, 110012, India
- Present address: ICAR-Indian Institute of Maize Research (ICAR-IIMR), PAU campus, Ludhiana, Punjab, 141004, India
| | - Manish Roorkiwal
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | | | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Ramesh Palakurthi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Anilkumar Vemula
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Abhishek Rathore
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Yogesh Kumar
- ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, Uttar Pradesh, 208024, India
| | - Sushil K Chaturvedi
- ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, Uttar Pradesh, 208024, India
- Present address: Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, 284003, India
| | - Biswajit Mondal
- ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, Uttar Pradesh, 208024, India
| | | | - Avinash K Srivastava
- ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, Uttar Pradesh, 208024, India
| | - Girish P Dixit
- ICAR-All India Coordinated Research Project on Chickpea (AICRP-Chickpea), ICAR-IIPR, Kanpur, Uttar Pradesh, India
| | - Narendra P Singh
- ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, Uttar Pradesh, 208024, India
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
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10
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Fatiukha A, Deblieck M, Klymiuk V, Merchuk-Ovnat L, Peleg Z, Ordon F, Fahima T, Korol A, Saranga Y, Krugman T. Genomic Architecture of Phenotypic Plasticity in Response to Water Stress in Tetraploid Wheat. Int J Mol Sci 2021; 22:ijms22041723. [PMID: 33572141 PMCID: PMC7915520 DOI: 10.3390/ijms22041723] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 01/12/2023] Open
Abstract
Phenotypic plasticity is one of the main mechanisms of adaptation to abiotic stresses via changes in critical developmental stages. Altering flowering phenology is a key evolutionary strategy of plant adaptation to abiotic stresses, to achieve the maximum possible reproduction. The current study is the first to apply the linear regression residuals as drought plasticity scores while considering the variation in flowering phenology and traits under non-stress conditions. We characterized the genomic architecture of 17 complex traits and their drought plasticity scores for quantitative trait loci (QTL) mapping, using a mapping population derived from a cross between durum wheat (Triticum turgidum ssp. durum) and wild emmer wheat (T. turgidum ssp. dicoccoides). We identified 79 QTLs affected observed traits and their plasticity scores, of which 33 reflected plasticity in response to water stress and exhibited epistatic interactions and/or pleiotropy between the observed and plasticity traits. Vrn-B3 (TaTF1) residing within an interval of a major drought-escape QTL was proposed as a candidate gene. The favorable alleles for most of the plasticity QTLs were contributed by wild emmer wheat, demonstrating its high potential for wheat improvement. Our study presents a new approach for the quantification of plant adaptation to various stresses and provides new insights into the genetic basis of wheat complex traits under water-deficit stress.
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Affiliation(s)
- Andrii Fatiukha
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Mathieu Deblieck
- Julius Kühn-Institut (JKI) Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, 06484 Quedlinburg, Germany; (M.D.); (F.O.)
| | - Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Lianne Merchuk-Ovnat
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Zvi Peleg
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Frank Ordon
- Julius Kühn-Institut (JKI) Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, 06484 Quedlinburg, Germany; (M.D.); (F.O.)
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Yehoshua Saranga
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Correspondence: ; Tel.: +972-04-8240783
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11
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Vessal S, Arefian M, Siddique KHM. Proteomic responses to progressive dehydration stress in leaves of chickpea seedlings. BMC Genomics 2020; 21:523. [PMID: 32727351 PMCID: PMC7392671 DOI: 10.1186/s12864-020-06930-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/20/2020] [Indexed: 12/14/2022] Open
Abstract
Background Chickpea is an important food legume crop with high protein levels that is widely grown in rainfed areas prone to drought stress. Using an integrated approach, we describe the relative changes in some physiological parameters and the proteome of a drought-tolerant (MCC537, T) and drought-sensitive (MCC806, S) chickpea genotype. Results Under progressive dehydration stress, the T genotype relied on a higher relative leaf water content after 3 and 5 d (69.7 and 49.3%) than the S genotype (59.7 and 40.3%) to maintain photosynthetic activities and improve endurance under stress. This may have been facilitated by greater proline accumulation in the T genotype than the S genotype (14.3 and 11.1 μmol g− 1 FW at 5 d, respectively). Moreover, the T genotype had less electrolyte leakage and lower malondialdehyde contents than the S genotype under dehydration stress, indicating greater membrane stability and thus greater dehydration tolerance. The proteomic analysis further confirmed that, in response to dehydration, the T genotype activated more proteins related to photosynthesis, stress response, protein synthesis and degradation, and gene transcription and signaling than the S genotype. Of the time-point dependent proteins, the largest difference in protein abundance occurred at 5 d, with 29 spots increasing in the T genotype and 30 spots decreasing in the S genotype. Some of the identified proteins—including RuBisCo, ATP synthase, carbonic anhydrase, psbP domain-containing protein, L-ascorbate peroxidase, 6-phosphogluconate dehydrogenase, elongation factor Tu, zinc metalloprotease FTSH 2, ribonucleoproteins and auxin-binding protein—may play a functional role in drought tolerance in chickpea. Conclusions This study highlights the significance of genotype- and time-specific proteins associated with dehydration stress and identifies potential resources for molecular drought tolerance improvement in chickpea.
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Affiliation(s)
- Saeedreza Vessal
- Research Center for Plant Sciences, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Mohammad Arefian
- Plant Biotechnology and Breeding Department, College of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia
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Varshney RK, Ojiewo C, Monyo E. A decade of Tropical Legumes projects: Development and adoption of improved varieties, creation of market-demand to benefit smallholder farmers and empowerment of national programmes in sub-Saharan Africa and South Asia. PLANT BREEDING = ZEITSCHRIFT FUR PFLANZENZUCHTUNG 2019; 138:379-388. [PMID: 31762525 PMCID: PMC6853253 DOI: 10.1111/pbr.12744] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 05/17/2023]
Abstract
This article highlights 12 years (2007-2019) of research, achievements, lessons learned, challenges and gaps in discovery-to-delivery research in legumes emanating from three projects, collectively called Tropical Legumes (TL) with a total investment of about US$ 67 million funded by the Bill & Melinda Gates Foundation. These projects were implemented by three CGIAR centres (ICRISAT, CIAT and IITA) together with 15 national agricultural research system partners in sub-Saharan Africa and South Asia. The TL projects together with some of their precursors and complementary projects from other agencies, facilitated the development of 266 improved legume varieties and the production of about 497,901 tons of certified seeds of the target legume crops in the focus countries. The certified seeds have been planted on about 5.0 million ha by more than 25 million smallholder farmers in the 15 countries and beyond, producing about 6.1 million tons of grain worth US$ 3.2 billion. Furthermore, the projects also trained 52 next generation scientists that included 10 women, by supporting 34 Masters degrees and 18 PhD degrees.
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Affiliation(s)
- Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)PatancheruIndia
| | - Chris Ojiewo
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)NairobiKenya
| | - Emmanuel Monyo
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)NairobiKenya
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13
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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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14
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Das Bhowmik SS, Cheng AY, Long H, Tan GZH, Hoang TML, Karbaschi MR, Williams B, Higgins TJV, Mundree SG. Robust Genetic Transformation System to Obtain Non-chimeric Transgenic Chickpea. FRONTIERS IN PLANT SCIENCE 2019; 10:524. [PMID: 31105725 PMCID: PMC6498970 DOI: 10.3389/fpls.2019.00524] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 04/04/2019] [Indexed: 05/30/2023]
Abstract
Chickpea transformation is an important component for the genetic improvement of this crop, achieved through modern biotechnological approaches. However, recalcitrant tissue cultures and occasional chimerism, encountered during transformation, hinder the efficient generation of transgenic chickpeas. Two key parameters, namely micro-injury and light emitting diode (LED)-based lighting were used to increase transformation efficiency. Early PCR confirmation of positive in vitro transgenic shoots, together with efficient grafting and an extended acclimatization procedure contributed to the rapid generation of transgenic plants. High intensity LED light facilitate chickpea plants to complete their life cycle within 9 weeks thus enabling up to two generations of stable transgenic chickpea lines within 8 months. The method was validated with several genes from different sources, either as single or multi-gene cassettes. Stable transgenic chickpea lines containing GUS (uidA), stress tolerance (AtBAG4 and TlBAG), as well as Fe-biofortification (OsNAS2 and CaNAS2) genes have successfully been produced.
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Affiliation(s)
| | - Alam Yen Cheng
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Hao Long
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Grace Zi Hao Tan
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Thi My Linh Hoang
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Mohammad Reza Karbaschi
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Brett Williams
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Thomas Joseph V. Higgins
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Sagadevan G. Mundree
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
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15
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Gediya LN, Patel DA, Kumar S, Kumar D, Parmar DJ, Patel SS. Phenotypic variability, path analysis and molecular diversity analysis in chickpea (Cicer arietinum L.). ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s42535-019-00020-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Mousavi‐Derazmahalleh M, Bayer PE, Hane JK, Valliyodan B, Nguyen HT, Nelson MN, Erskine W, Varshney RK, Papa R, Edwards D. Adapting legume crops to climate change using genomic approaches. PLANT, CELL & ENVIRONMENT 2019; 42:6-19. [PMID: 29603775 PMCID: PMC6334278 DOI: 10.1111/pce.13203] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/10/2018] [Indexed: 05/05/2023]
Abstract
Our agricultural system and hence food security is threatened by combination of events, such as increasing population, the impacts of climate change, and the need to a more sustainable development. Evolutionary adaptation may help some species to overcome environmental changes through new selection pressures driven by climate change. However, success of evolutionary adaptation is dependent on various factors, one of which is the extent of genetic variation available within species. Genomic approaches provide an exceptional opportunity to identify genetic variation that can be employed in crop improvement programs. In this review, we illustrate some of the routinely used genomics-based methods as well as recent breakthroughs, which facilitate assessment of genetic variation and discovery of adaptive genes in legumes. Although additional information is needed, the current utility of selection tools indicate a robust ability to utilize existing variation among legumes to address the challenges of climate uncertainty.
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Affiliation(s)
- Mahsa Mousavi‐Derazmahalleh
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
| | - Philipp E. Bayer
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
| | - James K. Hane
- CCDM BioinformaticsCentre for Crop Disease Management, Curtin UniversityBentleyWestern Australia6102Australia
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean BiotechnologyUniversity of MissouriColumbiaMO65211USA
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean BiotechnologyUniversity of MissouriColumbiaMO65211USA
| | - Matthew N. Nelson
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- Natural Capital and Plant HealthRoyal Botanic Gardens Kew, Wakehurst PlaceArdinglyWest SussexRH17 6TNUK
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
| | - William Erskine
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- Centre for Plant Genetics and BreedingThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
| | - Rajeev K. Varshney
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)Patancheru502 324India
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental SciencesUniversità Politecnica delle Marche60131AnconaItaly
| | - David Edwards
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
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17
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Mannur DM, Babbar A, Thudi M, Sabbavarapu MM, Roorkiwal M, Yeri SB, Bansal VP, Jayalakshmi SK, Singh Yadav S, Rathore A, Chamarthi SK, Mallikarjuna BP, Gaur PM, Varshney RK. Super Annigeri 1 and improved JG 74: two Fusarium wilt-resistant introgression lines developed using marker-assisted backcrossing approach in chickpea ( Cicer arietinum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2018; 39:2. [PMID: 30631246 PMCID: PMC6308216 DOI: 10.1007/s11032-018-0908-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/27/2018] [Indexed: 05/19/2023]
Abstract
Annigeri 1 and JG 74 are elite high yielding desi cultivars of chickpea with medium maturity duration and extensively cultivated in Karnataka and Madhya Pradesh, respectively. Both cultivars, in recent years, have become susceptible to race 4 of Fusarium wilt (FW). To improve Annigeri 1 and JG 74, we introgressed a genomic region conferring resistance against FW race 4 (foc4) through marker-assisted backcrossing using WR 315 as the donor parent. For foreground selection, TA59, TA96, TR19 and TA27 markers were used at Agricultural Research Station, Kalaburagi, while GA16 and TA96 markers were used at Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur. Background selection using simple sequence repreats (SSRs) for the cross Annigeri 1 × WR 315 in BC1F1 and BC2F1 lines resulted in 76-87% and 90-95% recurrent parent genome recovery, respectively. On the other hand, 90-97% genome was recovered in BC3F1 lines in the case of cross JG 74 × WR 315. Multilocation evaluation of 10 BC2F5 lines derived from Annigeri 1 provided one superior line referred to as Super Annigeri 1 with 8% increase in yield and enhanced disease resistance over Annigeri 1. JG 74315-14, the superior line in JG 74 background, had a yield advantage of 53.5% and 25.6% over the location trial means in Pantnagar and Durgapura locations, respectively, under Initial Varietal Trial of All India Coordinated Research Project on Chickpea. These lines with enhanced resistance and high yield performance are demonstration of successful deployment of molecular breeding to develop superior lines for FW resistance in chickpea.
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Affiliation(s)
- D. M. Mannur
- Agricultural Research Station, University of Agricultural Sciences (UAS)-Raichur, Kalaburagi, Karnataka 585 101 India
| | - Anita Babbar
- Jawaharlal Nehru Krishi Vishwa Vidyalaya (JNKVV), Jabalpur, Madhya Pradesh 482 004 India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Murali Mohan Sabbavarapu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Sharanabasappa B. Yeri
- Agricultural Research Station, University of Agricultural Sciences (UAS)-Raichur, Kalaburagi, Karnataka 585 101 India
| | - Vijay Prakash Bansal
- Jawaharlal Nehru Krishi Vishwa Vidyalaya (JNKVV), Jabalpur, Madhya Pradesh 482 004 India
| | - S. K. Jayalakshmi
- Agricultural Research Station, University of Agricultural Sciences (UAS)-Raichur, Kalaburagi, Karnataka 585 101 India
| | - Shailendra Singh Yadav
- Jawaharlal Nehru Krishi Vishwa Vidyalaya (JNKVV), Jabalpur, Madhya Pradesh 482 004 India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Siva K. Chamarthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Bingi P. Mallikarjuna
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Pooran M. Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502 324 India
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18
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Abstract
Climate change, associated with global warming, extreme weather events, and increasing incidence of weeds, pests and pathogens, is strongly influencing major cropping systems. In this challenging scenario, miscellaneous strategies are needed to expedite the rate of genetic gains with the purpose of developing novel varieties. Large plant breeding populations, efficient high-throughput technologies, big data management tools, and downstream biotechnology and molecular techniques are the pillars on which next generation breeding is based. In this review, we describe the toolbox the breeder has to face the challenges imposed by climate change, remark on the key role bioinformatics plays in the analysis and interpretation of big “omics” data, and acknowledge all the benefits that have been introduced into breeding strategies with the biotechnological and digital revolution.
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19
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Dwivedi SL, Siddique KHM, Farooq M, Thornton PK, Ortiz R. Using Biotechnology-Led Approaches to Uplift Cereal and Food Legume Yields in Dryland Environments. FRONTIERS IN PLANT SCIENCE 2018; 9:1249. [PMID: 30210519 PMCID: PMC6120061 DOI: 10.3389/fpls.2018.01249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/06/2018] [Indexed: 05/29/2023]
Abstract
Drought and heat in dryland agriculture challenge the enhancement of crop productivity and threaten global food security. This review is centered on harnessing genetic variation through biotechnology-led approaches to select for increased productivity and stress tolerance that will enhance crop adaptation in dryland environments. Peer-reviewed literature, mostly from the last decade and involving experiments with at least two seasons' data, form the basis of this review. It begins by highlighting the adverse impact of the increasing intensity and duration of drought and heat stress due to global warming on crop productivity and its impact on food and nutritional security in dryland environments. This is followed by (1) an overview of the physiological and molecular basis of plant adaptation to elevated CO2 (eCO2), drought, and heat stress; (2) the critical role of high-throughput phenotyping platforms to study phenomes and genomes to increase breeding efficiency; (3) opportunities to enhance stress tolerance and productivity in food crops (cereals and grain legumes) by deploying biotechnology-led approaches [pyramiding quantitative trait loci (QTL), genomic selection, marker-assisted recurrent selection, epigenetic variation, genome editing, and transgene) and inducing flowering independent of environmental clues to match the length of growing season; (4) opportunities to increase productivity in C3 crops by harnessing novel variations (genes and network) in crops' (C3, C4) germplasm pools associated with increased photosynthesis; and (5) the adoption, impact, risk assessment, and enabling policy environments to scale up the adoption of seed-technology to enhance food and nutritional security. This synthesis of technological innovations and insights in seed-based technology offers crop genetic enhancers further opportunities to increase crop productivity in dryland environments.
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Affiliation(s)
| | | | - Muhammad Farooq
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoud, Oman
- University of Agriculture, Faisalabad, Pakistan
| | - Philip K. Thornton
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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20
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Abstract
Global climate change has caused severe crop yield losses worldwide and is endangering food security in the future. The impact of climate change on food production is high in Australia and globally. Climate change is projected to have a negative impact on crop production. Chickpea is a cool season legume crop mostly grown on residual soil moisture. High temperature and terminal drought are common in different regions of chickpea production with varying intensities and frequencies. Therefore, stable chickpea production will depend on the release of new cultivars with improved adaptation to major events such as drought and high temperature. Recent progress in chickpea breeding has increased the efficiency of assessing genetic diversity in germplasm collections. This review provides an overview of the integration of new approaches and tools into breeding programs and their impact on the development of stress tolerance in chickpea.
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21
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Jha UC. Current advances in chickpea genomics: applications and future perspectives. PLANT CELL REPORTS 2018; 37:947-965. [PMID: 29860584 DOI: 10.1007/s00299-018-2305-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/23/2018] [Indexed: 05/27/2023]
Abstract
Chickpea genomics promises to illuminate our understanding of genome organization, structural variations, evolutionary and domestication-related insights and fundamental biology of legume crops. Unprecedented advancements of next generation sequencing (NGS) technologies have enabled in decoding of multiple chickpea genome sequences and generating huge genomic resources in chickpea both at functional and structural level. This review is aimed to update the current progress of chickpea genomics ranging from high density linkage map development, genome-wide association studies (GWAS), functional genomics resources for various traits, emerging role of abiotic stress responsive coding and non-coding RNAs after the completion of draft chickpea genome sequences. Additionally, the current efforts of whole genome re-sequencing (WGRS) approach of global chickpea germplasm to capture the global genetic diversity existing in the historically released varieties across the world and increasing the resolution of the previously identified candidate gene(s) of breeding importance have been discussed. Thus, the outcomes of these genomics resources will assist in genomics-assisted selection and facilitate breeding of climate-resilient chickpea cultivars for sustainable agriculture.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
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22
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Mahdavi Mashaki K, Garg V, Nasrollahnezhad Ghomi AA, Kudapa H, Chitikineni A, Zaynali Nezhad K, Yamchi A, Soltanloo H, Varshney RK, Thudi M. RNA-Seq analysis revealed genes associated with drought stress response in kabuli chickpea (Cicer arietinum L.). PLoS One 2018; 13:e0199774. [PMID: 29953498 PMCID: PMC6023194 DOI: 10.1371/journal.pone.0199774] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/13/2018] [Indexed: 11/24/2022] Open
Abstract
Drought is the most important constraint that effects chickpea production globally. RNA-Seq has great potential to dissect the molecular mechanisms of tolerance to environmental stresses. Transcriptome profiles in roots and shoots of two contrasting Iranian kabuli chickpea genotypes (Bivanij and Hashem) were investigated under water-limited conditions at early flowering stage using RNA-Seq approach. A total of 4,572 differentially expressed genes (DEGs) were identified. Of these, 261 and 169 drought stress responsive genes were identified in the shoots and the roots, respectively, and 17 genes were common in the shoots and the roots. Gene Ontology (GO) analysis revealed several sub-categories related to the stress, including response to stress, defense response and response to stimulus in the tolerant genotype Bivanij as compared to the sensitive genotype Hashem under drought stress. In addition, several Transcription factors (TFs) were identified in major metabolic pathways such as, ABA, proline and flavonoid biosynthesis. Furthermore, a number of the DEGs were observed in "QTL-hotspot" regions which were reported earlier in chickpea. Drought tolerance dissection in the genotypes revealed that the genes and the pathways involved in shoots of Bivanij were the most important factor to make a difference between the genotypes for drought tolerance. The identified TFs in the experiment, particularly those which were up-regulated in shoots of Bivanij during drought stress, were potential candidates for enhancing tolerance to drought.
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Affiliation(s)
- Keyvan Mahdavi Mashaki
- Department of Plant Breeding and Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Vanika Garg
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | | | - Himabindu Kudapa
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Khalil Zaynali Nezhad
- Department of Plant Breeding and Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Ahad Yamchi
- Department of Plant Breeding and Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Hasan Soltanloo
- Department of Plant Breeding and Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Rajeev Kumar Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
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23
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Sivasakthi K, Thudi M, Tharanya M, Kale SM, Kholová J, Halime MH, Jaganathan D, Baddam R, Thirunalasundari T, Gaur PM, Varshney RK, Vadez V. Plant vigour QTLs co-map with an earlier reported QTL hotspot for drought tolerance while water saving QTLs map in other regions of the chickpea genome. BMC PLANT BIOLOGY 2018; 18:29. [PMID: 29409451 PMCID: PMC5801699 DOI: 10.1186/s12870-018-1245-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 01/21/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Terminal drought stress leads to substantial annual yield losses in chickpea (Cicer arietinum L.). Adaptation to water limitation is a matter of matching water supply to water demand by the crop. Therefore, harnessing the genetics of traits contributing to plant water use, i.e. transpiration rate and canopy development dynamics, is important to design crop ideotypes suited to a varying range of water limited environments. With an aim of identifying genomic regions for plant vigour (growth and canopy size) and canopy conductance traits, 232 recombinant inbred lines derived from a cross between ICC 4958 and ICC 1882, were phenotyped at vegetative stage under well-watered conditions using a high throughput phenotyping platform (LeasyScan). RESULTS Twenty one major quantitative trait loci (M-QTLs) were identified for plant vigour and canopy conductance traits using an ultra-high density bin map. Plant vigour traits had 13 M-QTLs on CaLG04, with favourable alleles from high vigour parent ICC 4958. Most of them co-mapped with a previously fine mapped major drought tolerance "QTL-hotspot" region on CaLG04. One M-QTL was found for canopy conductance on CaLG03 with the ultra-high density bin map. Comparative analysis of the QTLs found across different density genetic maps revealed that QTL size reduced considerably and % of phenotypic variation increased as marker density increased. CONCLUSION Earlier reported drought tolerance hotspot is a vigour locus. The fact that canopy conductance traits, i.e. the other important determinant of plant water use, mapped on CaLG03 provides an opportunity to manipulate these loci to tailor recombinants having low/high transpiration rate and plant vigour, fitted to specific drought stress scenarios in chickpea.
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Affiliation(s)
- Kaliamoorthy Sivasakthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
- Bharathidasan University, Tiruchirappalli, Tamil Nadu India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Murugesan Tharanya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
- Bharathidasan University, Tiruchirappalli, Tamil Nadu India
| | - Sandip M. Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Jana Kholová
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Mahamat Hissene Halime
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Deepa Jaganathan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Rekha Baddam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | | | - Pooran M. Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Telangana, India
- Institut de Recherche pour le Developpement (IRD), Université de Montpellier – UMR DIADE, 911 Avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
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Millán T, Madrid E, Castro P, Gil J, Rubio J. Genetic Mapping and Quantitative Trait Loci. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/978-3-319-66117-9_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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25
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Dwivedi SL, Lammerts van Bueren ET, Ceccarelli S, Grando S, Upadhyaya HD, Ortiz R. Diversifying Food Systems in the Pursuit of Sustainable Food Production and Healthy Diets. TRENDS IN PLANT SCIENCE 2017; 22:842-856. [PMID: 28716581 DOI: 10.1016/j.tplants.2017.06.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 06/09/2017] [Accepted: 06/13/2017] [Indexed: 05/19/2023]
Abstract
Increasing demand for nutritious, safe, and healthy food because of a growing population, and the pledge to maintain biodiversity and other resources, pose a major challenge to agriculture that is already threatened by a changing climate. Diverse and healthy diets, largely based on plant-derived food, may reduce diet-related illnesses. Investments in plant sciences will be necessary to design diverse cropping systems balancing productivity, sustainability, and nutritional quality. Cultivar diversity and nutritional quality are crucial. We call for better cooperation between food and medical scientists, food sector industries, breeders, and farmers to develop diversified and nutritious cultivars that reduce soil degradation and dependence on external inputs, such as fertilizers and pesticides, and to increase adaptation to climate change and resistance to emerging pests.
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Affiliation(s)
- Sangam L Dwivedi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Edith T Lammerts van Bueren
- Louis Bolk Institute, Hoofdstraat 24, 3972 LA Driebergen, The Netherlands; Wageningen University and Research, PO Box 386, 6700 AJ Wageningen, The Netherlands
| | | | - Stefania Grando
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Rodomiro Ortiz
- Swedish University of Agricultural Sciences, Department of Plant Breeding, Sundsvagen, 14 Box 101, 23053 Alnarp, Sweden.
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Dwivedi V, Parida SK, Chattopadhyay D. A repeat length variation in myo-inositol monophosphatase gene contributes to seed size trait in chickpea. Sci Rep 2017; 7:4764. [PMID: 28684754 PMCID: PMC5500587 DOI: 10.1038/s41598-017-05332-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 05/26/2017] [Indexed: 11/11/2022] Open
Abstract
Chickpea (Cicer arietinum L.) is the third most important food legume crop. Seed size is the most economically important trait for chickpea. To understand the genetic regulation of seed size in chickpea, the present study established a three-way association of CT repeat length variation of a simple sequence repeat (SSR) in myo-inositol monophosphatase gene (CaIMP) with seed weight and phytic acid content by large scale validation and genotyping in a set of genetically diverse germplasm accessions and two reciprocal intra-specific mapping populations. Germplasms and mapping individuals with CT repeat-length expansion in the 5' untranslated region of CaIMP exhibited a pronounced increase in CaIMP protein level, enzymatic activity, seed-phytate content and seed weight. A chickpea transient expression system demonstrated this repeat-length variation influenced the translation of CaIMP mRNA, apparently by facilitating translation initiation. Our analyses proposed that the SSR marker derived from 5' UTR of a CaIMP gene is a promising candidate for selection of seed size/weight for agronomic trait improvement of chickpea.
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Affiliation(s)
- Vikas Dwivedi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swarup Kumar Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Debasis Chattopadhyay
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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27
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Chen Y, Ghanem ME, Siddique KH. Characterising root trait variability in chickpea (Cicer arietinum L.) germplasm. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1987-1999. [PMID: 28338728 PMCID: PMC5429021 DOI: 10.1093/jxb/erw368] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Chickpea (Cicer arietinum L.) is an important grain legume crop but its sustainable production is challenged by predicted climate changes, which are likely to increase production limitations and uncertainty in yields. Characterising the variability in root architectural traits in a core collection of chickpea germplasm will provide the basis for breeding new germplasm with suitable root traits for the efficient acquisition of soil resources and adaptation to drought and other abiotic stresses. This study used a semi-hydroponic phenotyping system for assessing root trait variability across 270 chickpea genotypes. The genotypes exhibited large variation in rooting patterns and branching manner. Thirty root-related traits were characterised, 17 of which had coefficients of variation ≥0.3 among genotypes and were selected for further examination. The Pearson correlation matrix showed a strong correlation among most of the selected traits (P≤0.05). Principal component analysis revealed three principal components with eigenvalues >1 capturing 81.5% of the total variation. An agglomerative hierarchical clustering analysis, based on root trait variation, identified three genotype homogeneous groups (rescaled distance of 15) and 16 sub-groups (rescaled distance of 5). The chickpea genotypes characterised in this study with vastly different root properties could be used for further studies in glasshouses and field trials, and for molecular marker studies, gene mapping, and modelling simulations, ultimately aimed at breeding germplasm with root traits for improved adaptation to drought and other specific environments.
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Affiliation(s)
- Yinglong Chen
- The UWA Institute of Agriculture, The University of Western Australia, LB 5005, Perth WA 6001, Australia
- The State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, and Chinese Academy of Sciences, Yangling, Shaanxi 712100, China
| | - Michel Edmond Ghanem
- International Centre for Agricultural Research in the Dry Areas, North-Africa Platform, Rabat, Morocco
| | - Kadambot Hm Siddique
- The UWA Institute of Agriculture, The University of Western Australia, LB 5005, Perth WA 6001, Australia
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28
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Thudi M, Chitikineni A, Liu X, He W, Roorkiwal M, Yang W, Jian J, Doddamani D, Gaur PM, Rathore A, Samineni S, Saxena RK, Xu D, Singh NP, Chaturvedi SK, Zhang G, Wang J, Datta SK, Xu X, Varshney RK. Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.). Sci Rep 2016; 6:38636. [PMID: 27982107 PMCID: PMC5159902 DOI: 10.1038/srep38636] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/10/2016] [Indexed: 12/18/2022] Open
Abstract
In order to understand the impact of breeding on genetic diversity and gain insights into temporal trends in diversity in chickpea, a set of 100 chickpea varieties released in 14 countries between 1948 and 2012 were re-sequenced. For analysis, the re-sequencing data for 29 varieties available from an earlier study was also included. Copy number variations and presence absence variations identified in the present study have potential to drive phenotypic variations for trait improvement. Re-sequencing of a large number of varieties has provided opportunities to inspect the genetic and genomic changes reflecting the history of breeding, which we consider as breeding signatures and the selected loci may provide targets for crop improvement. Our study also reports enhanced diversity in both desi and kabuli varieties as a result of recent chickpea breeding efforts. The current study will aid the explicit efforts to breed for local adaptation in the context of anticipated climate changes.
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Affiliation(s)
- Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Xin Liu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | | | - Dadakhalandar Doddamani
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pooran M. Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Srinivasan Samineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Narendra P. Singh
- All India Coordinated Research Project (AICRP) on Chickpea, Indian Council of Agricultural Research (ICAR), New Delhi, India
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, India
| | - Sushil K. Chaturvedi
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, India
| | | | | | | | | | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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29
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Kam J, Puranik S, Yadav R, Manwaring HR, Pierre S, Srivastava RK, Yadav RS. Dietary Interventions for Type 2 Diabetes: How Millet Comes to Help. FRONTIERS IN PLANT SCIENCE 2016; 7:1454. [PMID: 27729921 PMCID: PMC5037128 DOI: 10.3389/fpls.2016.01454] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/12/2016] [Indexed: 05/04/2023]
Abstract
Diabetes has become a highly problematic and increasingly prevalent disease world-wide. It has contributed toward 1.5 million deaths in 2012. Management techniques for diabetes prevention in high-risk as well as in affected individuals, beside medication, are mainly through changes in lifestyle and dietary regulation. Particularly, diet can have a great influence on life quality for those that suffer from, as well as those at risk of, diabetes. As such, considerations on nutritional aspects are required to be made to include in dietary intervention. This review aims to give an overview on the general consensus of current dietary and nutritional recommendation for diabetics. In light of such recommendation, the use of plant breeding, conventional as well as more recently developed molecular marker-based breeding and biofortification, are discussed in designing crops with desired characteristics. While there are various recommendations available, dietary choices are restricted by availability due to geo-, political-, or economical- considerations. This particularly holds true for countries such as India, where 65 million people (up from 50 million in 2010) are currently diabetic and their numbers are rising at an alarming rate. Millets are one of the most abundant crops grown in India as well as in Africa, providing a staple food source for many poorest of the poor communities in these countries. The potentials of millets as a dietary component to combat the increasing prevalence of global diabetes are highlighted in this review.
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Affiliation(s)
- Jason Kam
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, AberystwythUK
| | - Swati Puranik
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, AberystwythUK
| | - Rama Yadav
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, AberystwythUK
| | - Hanna R. Manwaring
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, AberystwythUK
| | - Sandra Pierre
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, AberystwythUK
| | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, PatancheruIndia
| | - Rattan S. Yadav
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, AberystwythUK
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30
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Jadhav AA, Rayate SJ, Mhase LB, Thudi M, Chitikineni A, Harer PN, Jadhav AS, Varshney RK, Kulwal PL. Marker-trait association study for protein content in chickpea (Cicer arietinum L.). J Genet 2016; 94:279-86. [PMID: 26174675 DOI: 10.1007/s12041-015-0529-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Chickpea (Cicer arietinum L.) is the second most important cool season food legume cultivated in arid and semiarid regions of the world. The objective of the present study was to study variation for protein content in chickpea germplasm, and to find markers associated with it. A set of 187 genotypes comprising both international and exotic collections, and representing both desi and kabuli types with protein content ranging from 13.25% to 26.77% was used. Twenty-three SSR markers representing all eight linkage groups (LG) amplifying 153 loci were used for the analysis. Population structure analysis identified three subpopulations, and corresponding Q values of principal components were used to take care of population structure in the analysis which was performed using general linear and mixed linear models. Marker-trait association (MTA) analysis identified nine significant associations representing four QTLs in the entire population. Subpopulation analyses identified ten significant MTAs representing five QTLs, four of which were common with that of the entire population. Two most significant QTLs linked with markers TR26.205 and CaM1068.195 were present on LG3 and LG5. Gene ontology search identified 29 candidate genes in the region of significant MTAs on LG3. The present study will be helpful in concentrating on LG3 and LG5 for identification of closely linked markers for protein content in chickpea and for their use in molecular breeding programme for nutritional quality improvement.
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Affiliation(s)
- A A Jadhav
- State Level Biotechnology Centre, Mahatma Phule Agricultural University, Rahuri 413 722, India.
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31
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Tiwari S, Lata C, Chauhan PS, Nautiyal CS. Pseudomonas putida attunes morphophysiological, biochemical and molecular responses in Cicer arietinum L. during drought stress and recovery. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 99:108-17. [PMID: 26744996 DOI: 10.1016/j.plaphy.2015.11.001] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/16/2015] [Accepted: 11/01/2015] [Indexed: 05/18/2023]
Abstract
Drought is one of the most important abiotic stresses that adversely affect plant growth and yield potential. However, some drought resistant rhizosphere competent bacteria are known to improve plant health and promote growth during abiotic stresses. Present study showed the role of Pseudomonas putida MTCC5279 (RA) in ameliorating drought stress on cv. BG-362 (desi) and cv. BG-1003 (kabuli) chickpea cultivars under in vitro and green house conditions. Polyethylene glycol-induced drought stress severely affected seed germination in both cultivars which was considerably improved on RA-inoculation. Drought stress significantly affected various growth parameters, water status, membrane integrity, osmolyte accumulation, ROS scavenging ability and stress-responsive gene expressions, which were positively modulated upon application of RA in both chickpea cultivars. Quantitative real-time (qRT)-PCR analysis showed differential expression of genes involved in transcription activation (DREB1A and NAC1), stress response (LEA and DHN), ROS scavenging (CAT, APX, GST), ethylene biosynthesis (ACO and ACS), salicylic acid (PR1) and jasmonate (MYC2) signalling in both chickpea cultivars exposed to drought stress and recovery in the presence or absence of RA. The observations imply that RA confers drought tolerance in chickpea by altering various physical, physiological and biochemical parameters, as well as by modulating differential expression of at least 11 stress-responsive genes. To the best of our knowledge, this is the first report on detailed analysis of plant growth promotion and stress alleviation in one month old desi and kabuli chickpea subjected to drought stress for 0, 1, 3 and 7 days and recovery in the presence of a PGPR.
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Affiliation(s)
- Shalini Tiwari
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
| | - Charu Lata
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
| | - Puneet Singh Chauhan
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India
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Thudi M, Khan AW, Kumar V, Gaur PM, Katta K, Garg V, Roorkiwal M, Samineni S, Varshney RK. Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.). BMC PLANT BIOLOGY 2016; 16 Suppl 1:10. [PMID: 26822060 PMCID: PMC4895712 DOI: 10.1186/s12870-015-0690-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
BACKGROUND Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in South Asia and Sub-Saharan Africa. In order to harness the untapped genetic potential available for chickpea improvement, we re-sequenced 35 chickpea genotypes representing parental lines of 16 mapping populations segregating for abiotic (drought, heat, salinity), biotic stresses (Fusarium wilt, Ascochyta blight, Botrytis grey mould, Helicoverpa armigera) and nutritionally important (protein content) traits using whole genome re-sequencing approach. RESULTS A total of 192.19 Gb data, generated on 35 genotypes of chickpea, comprising 973.13 million reads, with an average sequencing depth of ~10 X for each line. On an average 92.18 % reads from each genotype were aligned to the chickpea reference genome with 82.17 % coverage. A total of 2,058,566 unique single nucleotide polymorphisms (SNPs) and 292,588 Indels were detected while comparing with the reference chickpea genome. Highest number of SNPs were identified on the Ca4 pseudomolecule. In addition, copy number variations (CNVs) such as gene deletions and duplications were identified across the chickpea parental genotypes, which were minimum in PI 489777 (1 gene deletion) and maximum in JG 74 (1,497). A total of 164,856 line specific variations (144,888 SNPs and 19,968 Indels) with the highest percentage were identified in coding regions in ICC 1496 (21 %) followed by ICCV 97105 (12 %). Of 539 miscellaneous variations, 339, 138 and 62 were inter-chromosomal variations (CTX), intra-chromosomal variations (ITX) and inversions (INV) respectively. CONCLUSION Genome-wide SNPs, Indels, CNVs, PAVs, and miscellaneous variations identified in different mapping populations are a valuable resource in genetic research and helpful in locating genes/genomic segments responsible for economically important traits. Further, the genome-wide variations identified in the present study can be used for developing high density SNP arrays for genetics and breeding applications.
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Affiliation(s)
- Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
| | - Aamir W Khan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vinay Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pooran M Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Krishnamohan Katta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Srinivasan Samineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- The University of Western Australia (UWA), Crawley, Western Australia, Australia.
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Varshney RK. Exciting journey of 10 years from genomes to fields and markets: Some success stories of genomics-assisted breeding in chickpea, pigeonpea and groundnut. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:98-107. [PMID: 26566828 DOI: 10.1016/j.plantsci.2015.09.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/04/2015] [Accepted: 09/07/2015] [Indexed: 05/20/2023]
Abstract
Legume crops such as chickpea, pigeonpea and groundnut, mostly grown in marginal environments, are the major source of nutrition and protein to the human population in Asia and Sub-Saharan Africa. These crops, however, have a low productivity, mainly due to their exposure to several biotic and abiotic stresses in the marginal environments. Until 2005, these crops had limited genomics resources and molecular breeding was very challenging. During the last decade (2005-2015), ICRISAT led demand-driven innovations in genome science and translated the massive genome information in breeding. For instance, large-scale genomic resources including draft genome assemblies, comprehensive genetic and physical maps, thousands of SSR markers, millions of SNPs, several high-throughput as well as low cost marker genotyping platforms have been developed in these crops. After mapping several breeding related traits, several success stories of translational genomics have become available in these legumes. These include development of superior lines with enhanced drought tolerance in chickpea, enhanced and pyramided resistance to Fusarium wilt and Ascochyta blight in chickpea, enhanced resistance to leaf rust in groundnut, improved oil quality in groundnut and utilization of markers for assessing purity of hybrids/parental lines in pigeonpea. Some of these stories together with future prospects have been discussed.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India.
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Pushpavalli R, Krishnamurthy L, Thudi M, Gaur PM, Rao MV, Siddique KHM, Colmer TD, Turner NC, Varshney RK, Vadez V. Two key genomic regions harbour QTLs for salinity tolerance in ICCV 2 × JG 11 derived chickpea (Cicer arietinum L.) recombinant inbred lines. BMC PLANT BIOLOGY 2015; 15:124. [PMID: 25994494 PMCID: PMC4440540 DOI: 10.1186/s12870-015-0491-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/09/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Although chickpea (Cicer arietinum L.), an important food legume crop, is sensitive to salinity, considerable variation for salinity tolerance exists in the germplasm. To improve any existing cultivar, it is important to understand the genetic and physiological mechanisms underlying this tolerance. RESULTS In the present study, 188 recombinant inbred lines (RILs) derived from the cross ICCV 2 × JG 11 were used to assess yield and related traits in a soil with 0 mM NaCl (control) and 80 mM NaCl (salinity) over two consecutive years. Salinity significantly (P < 0.05) affected almost all traits across years and yield reduction was in large part related to a reduction in seed number but also a reduction in above ground biomass. A genetic map was constructed using 56 polymorphic markers (28 simple sequence repeats; SSRs and 28 single nucleotide polymorphisms; SNPs). The QTL analysis revealed two key genomic regions on CaLG05 (28.6 cM) and on CaLG07 (19.4 cM), that harboured QTLs for six and five different salinity tolerance associated traits, respectively, and imparting either higher plant vigour (on CaLG05) or higher reproductive success (on CaLG07). Two major QTLs for yield in the salinity treatment (explaining 12 and 17% of the phenotypic variation) were identified within the two key genomic regions. Comparison with already published chickpea genetic maps showed that these regions conferred salinity tolerance across two other populations and the markers can be deployed for enhancing salinity tolerance in chickpea. Based on the gene ontology annotation, forty eight putative candidate genes responsive to salinity stress were found on CaLG05 (31 genes) and CaLG07 (17 genes) in a distance of 11.1 Mb and 8.2 Mb on chickpea reference genome. Most of the genes were known to be involved in achieving osmoregulation under stress conditions. CONCLUSION Identification of putative candidate genes further strengthens the idea of using CaLG05 and CaLG07 genomic regions for marker assisted breeding (MAB). Further fine mapping of these key genomic regions may lead to novel gene identification for salinity stress tolerance in chickpea.
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Affiliation(s)
- Raju Pushpavalli
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 234, Telangana State, India.
- Department of Plant Science, Bharathidasan University, 620024, Tiruchirappalli, Tamil Nadu, India.
| | - Laxmanan Krishnamurthy
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 234, Telangana State, India.
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 234, Telangana State, India.
| | - Pooran M Gaur
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 234, Telangana State, India.
| | - Mandali V Rao
- Department of Plant Science, Bharathidasan University, 620024, Tiruchirappalli, Tamil Nadu, India.
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, 6009, Crawley, WA, Australia.
| | - Timothy D Colmer
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, 6009, , Crawley, WA, Australia.
| | - Neil C Turner
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, 6009, Crawley, WA, Australia.
- Centre for Plant Genetics and Breeding, M080, The University of Western Australia, 35 Stirling Highway, 6009, Crawley, WA, Australia.
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 234, Telangana State, India.
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, 6009, , Crawley, WA, Australia.
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502 234, Telangana State, India.
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Tuberosa R, Turner NC, Cakir M. Preface: two decades of InterDrought conferences: are we bridging the genotype-to-phenotype gap? JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6137-6139. [PMID: 25544976 DOI: 10.1093/jxb/eru407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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Jaganathan D, Thudi M, Kale S, Azam S, Roorkiwal M, Gaur PM, Kishor PBK, Nguyen H, Sutton T, Varshney RK. Genotyping-by-sequencing based intra-specific genetic map refines a ''QTL-hotspot" region for drought tolerance in chickpea. Mol Genet Genomics 2014; 290:559-71. [PMID: 25344290 PMCID: PMC4361754 DOI: 10.1007/s00438-014-0932-3] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 09/23/2014] [Indexed: 11/27/2022]
Abstract
To enhance the marker density in the “QTL-hotspot” region, harboring several QTLs for drought tolerance-related traits identified on linkage group 04 (CaLG04) in chickpea recombinant inbred line (RIL) mapping population ICC 4958 × ICC 1882, a genotyping-by-sequencing approach was adopted. In total, 6.24 Gb data from ICC 4958, 5.65 Gb data from ICC 1882 and 59.03 Gb data from RILs were generated, which identified 828 novel single-nucleotide polymorphisms (SNPs) for genetic mapping. Together with these new markers, a high-density intra-specific genetic map was developed that comprised 1,007 marker loci spanning a distance of 727.29 cM. QTL analysis using the extended genetic map along with precise phenotyping data for 20 traits collected over one to seven seasons identified 49 SNP markers in the “QTL-hotspot” region. These efforts have refined the “QTL-hotspot” region to 14 cM. In total, 164 main-effect QTLs including 24 novel QTLs were identified. In addition, 49 SNPs integrated in the “QTL-hotspot” region were converted into cleaved amplified polymorphic sequence (CAPS) and derived CAPS (dCAPS) markers which can be used in marker-assisted breeding.
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Affiliation(s)
- Deepa Jaganathan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Vadez V, Palta J, Berger J. Developing drought tolerant crops: hopes and challenges in an exciting journey. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:v-vi. [PMID: 32481053 DOI: 10.1071/fpv41n11_fo] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Under increasing water scarcity, food production for an increasing population is a global challenge. Maintaining crop production under limiting water supply is a common problem in agriculture, which is best addressed by the coordinated efforts of geneticists, physiologists and agronomists. This special issue is a selection of oral and poster presentations at the InterDrought IV conference, held in Perth (2-6 September 2013). These papers provide a broad, multidisciplinary view on the way to develop improved cultivars in the face of water deficit, providing the conference highlight: an integration of views from different disciplinary angles, generating constructive debate that was not buried in disciplinary silos. More specifically, the topics covered deal with the challenge of adaptation implicit in genotype-by-environment interaction, bring new perspectives on root systems and water productivity, and review the challenges and opportunities provided by crop management, genomic and transgenic approaches to cultivar improvement.
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Affiliation(s)
- Vincent Vadez
- International Crops Research Institute for Semiarid Tropics, Crop Physiology Laboratory, Patancheru, 502 324 Telangana, India
| | - Jairo Palta
- CSIRO Agricultural Productivity Flagship, Floreat, WA 6014, Australia
| | - Jens Berger
- CSIRO Plant Industry, Private Bag No. 5, Wembley, WA 6913, Australia
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Turner NC, Blum A, Cakir M, Steduto P, Tuberosa R, Young N. Strategies to increase the yield and yield stability of crops under drought - are we making progress? FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:1199-1206. [PMID: 32481069 DOI: 10.1071/fp14057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 04/02/2014] [Indexed: 06/11/2023]
Abstract
The objective of the InterDrought conferences is to be a platform for debating key issues that are relevant for increasing the yield and yield stability of crops under drought via integrated approaches. InterDrought-IV, held in Perth, Australia, in September 2013, followed previous InterDrought conferences in bringing together researchers in agronomy, soil science, modelling, physiology, biochemistry, molecular biology, genetics and plant breeding. Key themes were (i) maximising water productivity; (ii) maximising dryland crop production; (iii) adaptation to water-limited environments; (iv) plant productivity under drought through effective water capture, improved transpiration efficiency, and growth and yield; and (v) breeding for water-limited environments through variety development, and trait-based genomics-assisted and transgenic approaches. This paper highlights some key issues and presents recommendations for future action. Improved agronomic interventions were recognised as being important contributors to improved dryland crop yields in water-limited environments, and new methods for exploring root architecture and water capture were highlighted. The increase in crop yields under drought through breeding and selection, the development of high-throughput phenotyping facilities for field-grown and pot-grown plants, and advances in understanding the molecular basis of plant responses and resistance to drought stress were recognised. Managed environment phenotyping facilities, a range of field environments, modelling, and genomic molecular tools are being used to select and release drought-resistant cultivars of all major crops. Delegates discussed how individuals and small teams can contribute to progress, and concluded that interdisciplinary research, linkages to international agricultural research centres, public-private partnerships and continuation of the InterDrought conferences will be instrumental for progress.
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Affiliation(s)
- Neil C Turner
- The University of Western Australia Institute of Agriculture and Centre for Plant Genetics and Breeding, M080, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | | | - Mehmet Cakir
- School of Biological Sciences and Biotechnology, Faculty of Sustainability, Environmental and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Pasquale Steduto
- Food and Agriculture Organisation of the United Nations, Viale delle Terme di Caracalla, 00153 Rome, Italy
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Neil Young
- Rural Mail Box 232, Kojonup, WA 6395, Australia
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