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Garg V, Barmukh R, Chitikineni A, Roorkiwal M, Ojiewo C, Bohra A, Thudi M, Singh VK, Kudapa H, Saxena RK, Fountain J, Mir RR, Bharadwaj C, Chen X, Xin L, Pandey MK. Celebrating Professor Rajeev K. Varshney's transformative research odyssey from genomics to the field on his induction as Fellow of the Royal Society. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1504-1515. [PMID: 38206288 PMCID: PMC11123405 DOI: 10.1111/pbi.14282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/17/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024]
Abstract
Professor Rajeev K. Varshney's transformative impact on crop genomics, genetics, and agriculture is the result of his passion, dedication, and unyielding commitment to harnessing the potential of genomics to address the most pressing challenges faced by the global agricultural community. Starting from a small town in India and reaching the global stage, Professor Varshney's academic and professional trajectory has inspired many scientists active in research today. His ground-breaking work, especially his effort to list orphan tropical crops to genomic resource-rich entities, has been transformative. Beyond his scientific achievements, Professor Varshney is recognized by his colleagues as an exemplary mentor, fostering the growth of future researchers, building institutional capacity, and strengthening scientific capability. His focus on translational genomics and strengthening seed system in developing countries for the improvement of agriculture has made a tangible impact on farmers' lives. His skills have been best utilized in roles at leading research centres where he has applied his expertise to deliver a new vision for crop improvement. These efforts have now been recognized by the Royal Society with the award of the Fellowship (FRS). As we mark this significant milestone in his career, we not only celebrate Professor Varshney's accomplishments but also his wider contributions that continue to transform the agricultural landscape.
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Affiliation(s)
- Vanika Garg
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Rutwik Barmukh
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Annapurna Chitikineni
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Manish Roorkiwal
- Khalifa Center for Genetic Engineering and BiotechnologyUnited Arab Emirates UniversityAl AinUAE
| | - Chris Ojiewo
- International Maize and Wheat Improvement Center (CIMMYT)NairobiKenya
| | - Abhishek Bohra
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | | | - Vikas K. Singh
- International Rice Research Institute (IRRI)‐South‐Asia HubInternational Crops Research Institute for the Semi‐Arid TropicsHyderabadIndia
| | - Himabindu Kudapa
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | | | - Jake Fountain
- Department of Plant PathologyUniversity of GeorgiaGriffinGeorgiaUSA
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of AgricultureSKUAST‐KashmirWaduraIndia
| | | | - Xiaoping Chen
- Crops Research InstituteGuangdong Academy of Agricultural Sciences (GDAAS)GuangzhouChina
| | | | - Manish K. Pandey
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
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Istanbuli T, Nassar AE, Abd El-Maksoud MM, Tawkaz S, Alsamman AM, Hamwieh A. Genome-wide association study reveals SNP markers controlling drought tolerance and related agronomic traits in chickpea across multiple environments. FRONTIERS IN PLANT SCIENCE 2024; 15:1260690. [PMID: 38525151 PMCID: PMC10957531 DOI: 10.3389/fpls.2024.1260690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/06/2024] [Indexed: 03/26/2024]
Abstract
Chickpea, renowned for its exceptional nutritional value, stands as a crucial crop, serving as a dietary staple in various parts of the world. However, its productivity faces a significant challenge in the form of drought stress. This challenge highlights the urgent need to find genetic markers linked to drought tolerance for effective breeding programs. The primary objective of this study is to identify genetic markers associated with drought tolerance to facilitate effective breeding programs. To address this, we cultivated 185 chickpea accessions in two distinct locations in Lebanon over a two-year period, subjecting them to both irrigated and rain-fed environments. We assessed 11 drought-linked traits, including morphology, growth, yield, and tolerance score. SNP genotyping revealed 1344 variable SNP markers distributed across the chickpea genome. Genetic diversity across populations originating from diverse geographic locations was unveiled by the PCA, clustering, and structure analysis indicating that these genotypes have descend from five or four distinct ancestors. A genome-wide association study (GWAS) revealed several marker trait associations (MTAs) associated with the traits evaluated. Within the rainfed conditions, 11 significant markers were identified, each associated with distinct chickpea traits. Another set of 11 markers exhibited associations in both rainfed and irrigated environments, reflecting shared genetic determinants across these conditions for the same trait. The analysis of linkage disequilibrium (LD) highlighted two genomic regions with notably strong LD, suggesting significant interconnections among several investigated traits. This was further investigated by the correlation between major markers associated with these traits. Gene annotation of the identified markers has unveiled insights into 28 potential genes that play a role in influencing various chickpea drought-linked traits. These traits encompass crucial aspects such as blooming organ development, plant growth, seed weight, starch metabolism, drought regulation, and height index. Among the identified genes are CPN60-2, hsp70, GDSL(GELP), AHL16, NAT3, FAB1B, bZIP, and GL21. These genes collectively contribute to the multifaceted response of chickpea plants to drought stress. Our identified genetic factors exert their influence in both irrigated and rainfed environments, emphasizing their importance in shaping chickpea characteristics.
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Affiliation(s)
- Tawffiq Istanbuli
- Biotechnology Department, International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol, Lebanon
| | - Ahmed E. Nassar
- Biotechnology Department, International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | | | - Sawsan Tawkaz
- Biotechnology Department, International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Alsamman M. Alsamman
- Biotechnology Department, International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Aladdin Hamwieh
- Biotechnology Department, International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
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Thudi M, Samineni S, Li W, Boer MP, Roorkiwal M, Yang Z, Ladejobi F, Zheng C, Chitikineni A, Nayak S, He Z, Valluri V, Bajaj P, Khan AW, Gaur PM, van Eeuwijk F, Mott R, Xin L, Varshney RK. Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea. THE PLANT GENOME 2024; 17:e20333. [PMID: 37122200 DOI: 10.1002/tpg2.20333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/17/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
Terminal drought is one of the major constraints to crop production in chickpea (Cicer arietinum L.). In order to map drought tolerance related traits at high resolution, we sequenced multi-parent advanced generation intercross (MAGIC) population using whole genome resequencing approach and phenotyped it under drought stress environments for two consecutive years (2013-14 and 2014-15). A total of 52.02 billion clean reads containing 4.67 TB clean data were generated on the 1136 MAGIC lines and eight parental lines. Alignment of clean data on to the reference genome enabled identification of a total, 932,172 of SNPs, 35,973 insertions, and 35,726 deletions among the parental lines. A high-density genetic map was constructed using 57,180 SNPs spanning a map distance of 1606.69 cM. Using compressed mixed linear model, genome-wide association study (GWAS) enabled us to identify 737 markers significantly associated with days to 50% flowering, days to maturity, plant height, 100 seed weight, biomass, and harvest index. In addition to the GWAS approach, an identity-by-descent (IBD)-based mixed model approach was used to map quantitative trait loci (QTLs). The IBD-based mixed model approach detected major QTLs that were comparable to those from the GWAS analysis as well as some exclusive QTLs with smaller effects. The candidate genes like FRIGIDA and CaTIFY4b can be used for enhancing drought tolerance in chickpea. The genomic resources, genetic map, marker-trait associations, and QTLs identified in the study are valuable resources for the chickpea community for developing climate resilient chickpeas.
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Affiliation(s)
- Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Pusa, India
| | - Srinivasan Samineni
- Crop Improvement Program-Asia, ICRISAT, Patancheru, India
- International Center for Biosaline Agriculture, Dubai, United Arab Emirates
| | - Wenhao Li
- Wageningen University and Research, Wageningen, The Netherlands
| | - Martin P Boer
- Wageningen University and Research, Wageningen, The Netherlands
| | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), United Arab Emirates University, Al Ain, United Arab Emirates
| | | | - Funmi Ladejobi
- Department of Genetics, Evolution and Environment, Genetics Institute, University College London, London, UK
| | - Chaozhi Zheng
- Wageningen University and Research, Wageningen, The Netherlands
- BGI-Shenzhen, Shenzhen, China
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Sourav Nayak
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | | | - Vinod Valluri
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Prasad Bajaj
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Aamir W Khan
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Pooran M Gaur
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Pusa, India
- The UWA Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | | | - Richard Mott
- Department of Genetics, Evolution and Environment, Genetics Institute, University College London, London, UK
| | - Liu Xin
- BGI-Shenzhen, Shenzhen, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
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Zhang J, Wang J, Zhu C, Singh RP, Chen W. Chickpea: Its Origin, Distribution, Nutrition, Benefits, Breeding, and Symbiotic Relationship with Mesorhizobium Species. PLANTS (BASEL, SWITZERLAND) 2024; 13:429. [PMID: 38337962 PMCID: PMC10856887 DOI: 10.3390/plants13030429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/15/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
Chickpea (Cicer arietinum L.), encompassing the desi and kabuli varieties, is a beloved pulse crop globally. Its cultivation spans over fifty countries, from the Indian subcontinent and southern Europe to the Middle East, North Africa, the Americas, Australia, and China. With a rich composition of carbohydrates and protein, constituting 80% of its dry seed mass, chickpea is also touted for its numerous health benefits, earning it the title of a 'functional food'. In the past two decades, research has extensively explored the rhizobial diversity associated with chickpea and its breeding in various countries across Europe, Asia, and Oceania, aiming to understand its impact on the sustainable yield and quality of chickpea crops. To date, four notable species of Mesorhizobium-M. ciceri, M. mediterraneum, M. muleiense, and M. wenxiniae-have been reported, originally isolated from chickpea root nodules. Other species, such as M. amorphae, M. loti, M. tianshanense, M. oportunistum, M. abyssinicae, and M. shonense, have been identified as potential symbionts of chickpea, possibly acquiring symbiotic genes through lateral gene transfer. While M. ciceri and M. mediterraneum are widely distributed and studied across chickpea-growing regions, they remain absent in China, where M. muleiense and M. wenxiniae are the sole rhizobial species associated with chickpea. The geographic distribution of chickpea rhizobia is believed to be influenced by factors such as genetic characteristics, competitiveness, evolutionary adaptation to local soil conditions, and compatibility with native soil microbes. Inoculating chickpea with suitable rhizobial strains is crucial when introducing the crop to new regions lacking indigenous chickpea rhizobia. The introduction of a novel chickpea variety, coupled with the effective use of rhizobia for inoculation, offers the potential not only to boost the yield and seed quality of chickpeas, but also to enhance crop productivity within rotation and intercropped systems involving chickpea and other crops. Consequently, this advancement holds the promise to drive forward the cause of sustainable agriculture on a global scale.
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Affiliation(s)
- Junjie Zhang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China; (J.W.); (C.Z.)
- Collaborative Innovation Center for Food Production and Safety of Henan Province, Zhengzhou 450002, China
| | - Jingqi Wang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China; (J.W.); (C.Z.)
| | - Cancan Zhu
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China; (J.W.); (C.Z.)
| | - Raghvendra Pratap Singh
- Department of Research and Development, Biotechnology, Uttaranchal University, Dehradun 248007, India;
| | - Wenfeng Chen
- College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China
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Castro P, Caballo C, Carmona A, Millan T, Gil J, Die JV, Izquierdo I, Rubio J. Efficient Single Nucleotide Polymorphism Marker-Assisted Selection to Fusarium Wilt in Chickpea. PLANTS (BASEL, SWITZERLAND) 2024; 13:436. [PMID: 38337969 PMCID: PMC10856910 DOI: 10.3390/plants13030436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024]
Abstract
Fusarium wilt is one of the most destructive chickpea diseases worldwide. Race 5 (Foc5) is the most harmful in the Mediterranean basin. The primary objective of this study is to validate a block of six SNP markers previously mapped in Ca2 in a diverse panel of cultivars, advanced and inbred lines phenotyped for resistance to fusarium wilt. Additionally, we aim to assess the effectiveness of using these markers in the selection of resistant Foc5 lines in an ongoing breeding program. The results showed a 100% coincidence between phenotype and expected haplotype in plant material evaluated for Foc5. We also analyzed 67 inbred lines previously phenotyped by different authors for fusarium wilt reaction, though the specific race was not specified. In these accessions, 65.8% of the analyzed lines exhibited complete correspondence between the phenotype and haplotype. Our results suggest that in early generations it is possible to select resistant materials with reliability, leading to the removal of a significant number of lines, thereby reducing costs and facilitating the handling of materials for additional trait evaluations. Functional annotation of genes delimited by the SNP block revealed several genes in the "response to stimulus" category with potential roles in the resistance reaction.
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Affiliation(s)
- Patricia Castro
- ETSIAM-Dpto. Genética, Universidad de Córdoba, Campus de Rabanales, 14071 Córdoba, Spain; (A.C.); (T.M.); (J.V.D.)
| | - Cristina Caballo
- Área de Mejora Vegetal y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA), 14080 Córdoba, Spain (J.R.)
| | - Alejandro Carmona
- ETSIAM-Dpto. Genética, Universidad de Córdoba, Campus de Rabanales, 14071 Córdoba, Spain; (A.C.); (T.M.); (J.V.D.)
| | - Teresa Millan
- ETSIAM-Dpto. Genética, Universidad de Córdoba, Campus de Rabanales, 14071 Córdoba, Spain; (A.C.); (T.M.); (J.V.D.)
| | - Juan Gil
- ETSIAM-Dpto. Genética, Universidad de Córdoba, Campus de Rabanales, 14071 Córdoba, Spain; (A.C.); (T.M.); (J.V.D.)
| | - José V. Die
- ETSIAM-Dpto. Genética, Universidad de Córdoba, Campus de Rabanales, 14071 Córdoba, Spain; (A.C.); (T.M.); (J.V.D.)
| | | | - Josefa Rubio
- Área de Mejora Vegetal y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA), 14080 Córdoba, Spain (J.R.)
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Shah LR, Ahmed N, Hussain K, Mansoor S, Khan T, Khan I, Narayan S, Afroza B, Murtaza I, Shikari AB, Bhat B, Masoodi KZ. Mapping phenotypic performance and novel SNPs for cold tolerance in tomato (Solanum lycopersicum) genotypes through GWAS and population genetics. BMC Genom Data 2024; 25:9. [PMID: 38281048 PMCID: PMC10822167 DOI: 10.1186/s12863-024-01190-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/01/2024] [Indexed: 01/29/2024] Open
Abstract
The cold stress susceptibility of tomato (Solanum lycopersicum) curtails its cultivation, with significant impact in temperate regions and on cropping seasons. To unravel genomic regions responsible for cold stress resilience, a diverse set of fifty genotypes encompassing cultivated, wild species, and landraces were genotyped using genotyping-by-sequencing. Over two years and six trials employing both early and late sowing, these lines were evaluated. Illumina-based next-generation sequencing produced up to 3 million reads per sample from individually sequenced library pools. The Tassel pipeline yielded 10,802 variants, subsequently filtered to 3,854 SNPs for genome-wide association analysis (GWAS). Employing clustering methods (population structure) via TASSEL, SNPhylo, and Kinship matrix, the fifty genotypes clustered into four distinct gene pools. The GWAS for cold tolerance in tomato integrated key traits including yield. Using six independent phenotypic datasets representing various environments, the study identified 4,517 significant marker-trait associations for cold tolerance traits. Notably, pivotal variations (> 10%) in cold stress tolerance, particularly proline content, were linked to marker-trait associations. Additionally, 5,727 significant marker-trait associations for yield and yield-related traits were unveiled, shedding light on fruit yield and directly associated attributes. The investigation pinpointed 685 candidate genes across all examined traits, including 60 genes associated with biological processes within these genomic regions. Remarkably, 7 out of the 60 genes were directly linked to abiotic stress tolerance, functioning as stress-responsive genes either directly or indirectly. The identified genes, particularly those associated with stress response, could hold the key to enhancing cold tolerance and overall crop productivity in tomato cultivation.
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Affiliation(s)
- Labiba Riyaz Shah
- Division of Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Nazeer Ahmed
- Division of Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Khursheed Hussain
- Division of Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Sheikh Mansoor
- Transcriptomics Lab (K-Lab), Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India.
- Department of Plant Resources and Environment, Jeju National University, Jeju, 63243, Republic of Korea.
| | - Tamana Khan
- Division of Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Imran Khan
- Division of Statistics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Sumati Narayan
- Division of Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Baseerat Afroza
- Division of Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Imtiyaz Murtaza
- Division of Basic Sciences and Humanities, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Asif Bashir Shikari
- Division of Genetics and Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu and Kashmir, Wadoora, Sopore, 193201, India
| | - Basharat Bhat
- NAHEP, IDP, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, J&K, 190025, India
| | - Khalid Z Masoodi
- Transcriptomics Lab (K-Lab), Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India.
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Kumar R, Sharma VK, Rangari SK, Jha UC, Sahu A, Paul PJ, Gupta S, Gangurde SS, Kudapa H, Mir RR, Gaur PM, Varshney RK, Elango D, Thudi M. High confidence QTLs and key genes identified using Meta-QTL analysis for enhancing heat tolerance in chickpea ( Cicer arietinum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1274759. [PMID: 37929162 PMCID: PMC10623133 DOI: 10.3389/fpls.2023.1274759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 09/25/2023] [Indexed: 11/07/2023]
Abstract
The rising global temperatures seriously threaten sustainable crop production, particularly the productivity and production of heat-sensitive crops like chickpeas. Multiple QTLs have been identified to enhance the heat stress tolerance in chickpeas, but their successful use in breeding programs remains limited. Towards this direction, we constructed a high-density genetic map spanning 2233.5 cM with 1069 markers. Using 138 QTLs reported earlier, we identified six Meta-QTL regions for heat tolerance whose confidence interval was reduced by 2.7-folds compared to the reported QTLs. Meta-QTLs identified on CaLG01 and CaLG06 harbor QTLs for important traits, including days to 50% flowering, days to maturity, days to flower initiation, days to pod initiation, number of filled pods, visual score, seed yield per plant, biological yield per plant, chlorophyll content, and harvest index. In addition, key genes identified in Meta-QTL regions like Pollen receptor-like kinase 3 (CaPRK3), Flowering-promoting factor 1 (CaFPF1), Flowering Locus C (CaFLC), Heat stress transcription factor A-5 (CaHsfsA5), and Pollen-specific leucine-rich repeat extensins (CaLRXs) play an important role in regulating the flowering time, pollen germination, and growth. The consensus genomic regions, and the key genes reported in this study can be used in genomics-assisted breeding for enhancing heat tolerance and developing heat-resilient chickpea cultivars.
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Affiliation(s)
- Raj Kumar
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Pusa, Bihar, India
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | - Vinay Kumar Sharma
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Pusa, Bihar, India
| | - Sagar Krushnaji Rangari
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Pusa, Bihar, India
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | - Uday Chand Jha
- Indian Council for Agricultural Research (ICAR)- Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | - Aakash Sahu
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Pusa, Bihar, India
| | - Pronob J Paul
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
- Rice Breeding Innovations, International Rice Research Institute (IRRI), South Asia-Hub, Patancheru, Telangana, India
| | - Shreshth Gupta
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Pusa, Bihar, India
| | - Sunil S Gangurde
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Himabindu Kudapa
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | - Reyazul Rouf Mir
- Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST), Sopore, India
| | - Pooran M Gaur
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | - Rajeev K Varshney
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Dinakaran Elango
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Mahendar Thudi
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Pusa, Bihar, India
- Center for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
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Basu U, Parida SK. Restructuring plant types for developing tailor-made crops. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1106-1122. [PMID: 34260135 DOI: 10.1111/pbi.13666] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 05/27/2023]
Abstract
Plants have adapted to different environmental niches by fine-tuning the developmental factors working together to regulate traits. Variations in the developmental factors result in a wide range of quantitative variations in these traits that helped plants survive better. The major developmental pathways affecting plant architecture are also under the control of such pathways. Most notable are the CLAVATA-WUSCHEL pathway regulating shoot apical meristem fate, GID1-DELLA module influencing plant height and tillering, LAZY1-TAC1 module controlling branch/tiller angle and the TFL1-FT determining the floral fate in plants. Allelic variants of these key regulators selected during domestication shaped the crops the way we know them today. There is immense yield potential in the 'ideal plant architecture' of a crop. With the available genome-editing techniques, possibilities are not restricted to naturally occurring variations. Using a transient reprogramming system, one can screen the effect of several developmental gene expressions in novel ecosystems to identify the best targets. We can use the plant's fine-tuning mechanism for customizing crops to specific environments. The process of crop domestication can be accelerated with a proper understanding of these developmental pathways. It is time to step forward towards the next-generation molecular breeding for restructuring plant types in crops ensuring yield stability.
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Affiliation(s)
- Udita Basu
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Swarup K Parida
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
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Samal I, Bhoi TK, Raj MN, Majhi PK, Murmu S, Pradhan AK, Kumar D, Paschapur AU, Joshi DC, Guru PN. Underutilized legumes: nutrient status and advanced breeding approaches for qualitative and quantitative enhancement. Front Nutr 2023; 10:1110750. [PMID: 37275642 PMCID: PMC10232757 DOI: 10.3389/fnut.2023.1110750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Underutilized/orphan legumes provide food and nutritional security to resource-poor rural populations during periods of drought and extreme hunger, thus, saving millions of lives. The Leguminaceae, which is the third largest flowering plant family, has approximately 650 genera and 20,000 species and are distributed globally. There are various protein-rich accessible and edible legumes, such as soybean, cowpea, and others; nevertheless, their consumption rate is far higher than production, owing to ever-increasing demand. The growing global urge to switch from an animal-based protein diet to a vegetarian-based protein diet has also accelerated their demand. In this context, underutilized legumes offer significant potential for food security, nutritional requirements, and agricultural development. Many of the known legumes like Mucuna spp., Canavalia spp., Sesbania spp., Phaseolus spp., and others are reported to contain comparable amounts of protein, essential amino acids, polyunsaturated fatty acids (PUFAs), dietary fiber, essential minerals and vitamins along with other bioactive compounds. Keeping this in mind, the current review focuses on the potential of discovering underutilized legumes as a source of food, feed and pharmaceutically valuable chemicals, in order to provide baseline data for addressing malnutrition-related problems and sustaining pulse needs across the globe. There is a scarcity of information about underutilized legumes and is restricted to specific geographical zones with local or traditional significance. Around 700 genera and 20,000 species remain for domestication, improvement, and mainstreaming. Significant efforts in research, breeding, and development are required to transform existing local landraces of carefully selected, promising crops into types with broad adaptability and economic viability. Different breeding efforts and the use of biotechnological methods such as micro-propagation, molecular markers research and genetic transformation for the development of underutilized crops are offered to popularize lesser-known legume crops and help farmers diversify their agricultural systems and boost their profitability.
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Affiliation(s)
- Ipsita Samal
- Department of Entomology, Faculty of Agriculture, Sri Sri University, Cuttack, Odisha, India
| | - Tanmaya Kumar Bhoi
- Forest Protection Division, ICFRE-Arid Forest Research Institute, Jodhpur, India
| | - M. Nikhil Raj
- Division of Entomology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Prasanta Kumar Majhi
- Regional Research and Technology Transfer Station, Odisha University of Agriculture and Technology, Keonjhar, Odisha, India
| | - Sneha Murmu
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Dilip Kumar
- ICAR-National Institute of Agricultural Economics and Policy Research, New Delhi, India
| | | | | | - P. N. Guru
- ICAR-Central Institute of Post-Harvest Engineering and Technology, Ludhiana, India
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Yadav RK, Tripathi MK, Tiwari S, Tripathi N, Asati R, Patel V, Sikarwar RS, Payasi DK. Breeding and Genomic Approaches towards Development of Fusarium Wilt Resistance in Chickpea. Life (Basel) 2023; 13:life13040988. [PMID: 37109518 PMCID: PMC10144025 DOI: 10.3390/life13040988] [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: 03/07/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/29/2023] Open
Abstract
Chickpea is an important leguminous crop with potential to provide dietary proteins to both humans and animals. It also ameliorates soil nitrogen through biological nitrogen fixation. The crop is affected by an array of biotic and abiotic factors. Among different biotic stresses, a major fungal disease called Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceris (FOC), is responsible for low productivity in chickpea. To date, eight pathogenic races of FOC (race 0, 1A, and 1B/C, 2-6) have been reported worldwide. The development of resistant cultivars using different conventional breeding methods is very time consuming and depends upon the environment. Modern technologies can improve conventional methods to solve these major constraints. Understanding the molecular response of chickpea to Fusarium wilt can help to provide effective management strategies. The identification of molecular markers closely linked to genes/QTLs has provided great potential for chickpea improvement programs. Moreover, omics approaches, including transcriptomics, metabolomics, and proteomics give scientists a vast viewpoint of functional genomics. In this review, we will discuss the integration of all available strategies and provide comprehensive knowledge about chickpea plant defense against Fusarium wilt.
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Affiliation(s)
- Rakesh Kumar Yadav
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Manoj Kumar Tripathi
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Sushma Tiwari
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur 482004, India
| | - Ruchi Asati
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Vinod Patel
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - R S Sikarwar
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
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Gupta A, Sharma T, Singh SP, Bhardwaj A, Srivastava D, Kumar R. Prospects of microgreens as budding living functional food: Breeding and biofortification through OMICS and other approaches for nutritional security. Front Genet 2023; 14:1053810. [PMID: 36760994 PMCID: PMC9905132 DOI: 10.3389/fgene.2023.1053810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/05/2023] [Indexed: 01/26/2023] Open
Abstract
Nutrient deficiency has resulted in impaired growth and development of the population globally. Microgreens are considered immature greens (required light for photosynthesis and growing medium) and developed from the seeds of vegetables, legumes, herbs, and cereals. These are considered "living superfood/functional food" due to the presence of chlorophyll, beta carotene, lutein, and minerals like magnesium (Mg), Potassium (K), Phosphorus (P), and Calcium (Ca). Microgreens are rich at the nutritional level and contain several phytoactive compounds (carotenoids, phenols, glucosinolates, polysterols) that are helpful for human health on Earth and in space due to their anti-microbial, anti-inflammatory, antioxidant, and anti-carcinogenic properties. Microgreens can be used as plant-based nutritive vegetarian foods that will be fruitful as a nourishing constituent in the food industryfor garnish purposes, complement flavor, texture, and color to salads, soups, flat-breads, pizzas, and sandwiches (substitute to lettuce in tacos, sandwich, burger). Good handling practices may enhance microgreens'stability, storage, and shelf-life under appropriate conditions, including light, temperature, nutrients, humidity, and substrate. Moreover, the substrate may be a nutritive liquid solution (hydroponic system) or solid medium (coco peat, coconut fiber, coir dust and husks, sand, vermicompost, sugarcane filter cake, etc.) based on a variety of microgreens. However integrated multiomics approaches alongwith nutriomics and foodomics may be explored and utilized to identify and breed most potential microgreen genotypes, biofortify including increasing the nutritional content (macro-elements:K, Ca and Mg; oligo-elements: Fe and Zn and antioxidant activity) and microgreens related other traits viz., fast growth, good nutritional values, high germination percentage, and appropriate shelf-life through the implementation of integrated approaches includes genomics, transcriptomics, sequencing-based approaches, molecular breeding, machine learning, nanoparticles, and seed priming strategiesetc.
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Affiliation(s)
- Astha Gupta
- Sharda School of Agricultural Sciences, Sharda University, Greater Noida, India,*Correspondence: Astha Gupta, ; Rajendra Kumar,
| | - Tripti Sharma
- Sharda School of Agricultural Sciences, Sharda University, Greater Noida, India
| | - Surendra Pratap Singh
- Plant Molecular Biology Laboratory, Department of Botany, Dayanand Anglo-Vedic (PG) College, Chhatrapati Shahu Ji Maharaj University,, Kanpur, India
| | - Archana Bhardwaj
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, India
| | - Deepti Srivastava
- Department of Agriculture, Integral Institute of Agricultural Science and Technology, Integral University, Lucknow, Uttar Pradesh, India
| | - Rajendra Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India,*Correspondence: Astha Gupta, ; Rajendra Kumar,
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12
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Gayacharan, Parida SK, Mondal N, Yadav R, Vishwakarma H, Rana JC. Mining legume germplasm for genetic gains: An Indian perspective. Front Genet 2023; 14:996828. [PMID: 36816034 PMCID: PMC9933516 DOI: 10.3389/fgene.2023.996828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/05/2023] [Indexed: 01/24/2023] Open
Abstract
Legumes play a significant role in food and nutritional security and contribute to environmental sustainability. Although legumes are highly beneficial crops, it has not yet been possible to enhance their yield and production to a satisfactory level. Amid a rising population and low yield levels, per capita average legume consumption in India has fallen by 71% over the last 50 years, and this has led to protein-related malnutrition in a large segment of the Indian population, especially women and children. Several factors have hindered attempts to achieve yield enhancement in grain legumes, including biotic and abiotic pressures, a lack of good ideotypes, less amenability to mechanization, poorer responsiveness to fertilizer input, and a poor genetic base. Therefore, there is a need to mine the approximately 0.4 million ex situ collections of legumes that are being conserved in gene banks globally for identification of ideal donors for various traits. The Indian National Gene Bank conserves over 63,000 accessions of legumes belonging to 61 species. Recent initiatives have been undertaken in consortia mode with the aim of unlocking the genetic potential of ex situ collections and conducting large-scale germplasm characterization and evaluation analyses. We assume that large-scale phenotyping integrated with omics-based science will aid the identification of target traits and their use to enhance genetic gains. Additionally, in cases where the genetic base of major legumes is narrow, wild relatives have been evaluated, and these are being exploited through pre-breeding. Thus far, >200 accessions of various legumes have been registered as unique donors for various traits of interest.
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Affiliation(s)
- Gayacharan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Swarup K. Parida
- DBT-National Institute of Plant Genome Research, New Delhi, India
| | - Nupur Mondal
- Shivaji College, University of Delhi, New Delhi, India
| | - Rashmi Yadav
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Jai C. Rana
- Alliance of Bioversity International and CIAT, India Office, National Agricultural Science Complex, New Delhi, India
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13
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Barmukh R, Roorkiwal M, Dixit GP, Bajaj P, Kholova J, Smith MR, Chitikineni A, Bharadwaj C, Sreeman SM, Rathore A, Tripathi S, Yasin M, Vijayakumar AG, Rao Sagurthi S, Siddique KHM, Varshney RK. Characterization of 'QTL-hotspot' introgression lines reveals physiological mechanisms and candidate genes associated with drought adaptation in chickpea. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7255-7272. [PMID: 36006832 PMCID: PMC9730794 DOI: 10.1093/jxb/erac348] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/24/2022] [Indexed: 05/16/2023]
Abstract
'QTL-hotspot' is a genomic region on linkage group 04 (CaLG04) in chickpea (Cicer arietinum) that harbours major-effect quantitative trait loci (QTLs) for multiple drought-adaptive traits, and it therefore represents a promising target for improving drought adaptation. To investigate the mechanisms underpinning the positive effects of 'QTL-hotspot' on seed yield under drought, we introgressed this region from the ICC 4958 genotype into five elite chickpea cultivars. The resulting introgression lines (ILs) and their parents were evaluated in multi-location field trials and semi-controlled conditions. The results showed that the 'QTL-hotspot' region improved seed yield under rainfed conditions by increasing seed weight, reducing the time to flowering, regulating traits related to canopy growth and early vigour, and enhancing transpiration efficiency. Whole-genome sequencing data analysis of the ILs and parents revealed four genes underlying the 'QTL-hotspot' region associated with drought adaptation. We validated diagnostic KASP markers closely linked to these genes using the ILs and their parents for future deployment in chickpea breeding programs. The CaTIFY4b-H2 haplotype of a potential candidate gene CaTIFY4b was identified as the superior haplotype for 100-seed weight. The candidate genes and superior haplotypes identified in this study have the potential to serve as direct targets for genetic manipulation and selection for chickpea improvement.
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Affiliation(s)
- Rutwik Barmukh
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | | | - Girish P Dixit
- ICAR - Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Prasad Bajaj
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Jana Kholova
- Crops Physiology & Modeling, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Information Technologies, Faculty of Economics and Management, Czech University of Life Sciences Prague, Kamýcká 129, Prague, Czech Republic
| | - Millicent R Smith
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Australia
| | - Annapurna Chitikineni
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Chellapilla Bharadwaj
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
- ICAR - Indian Agricultural Research Institute (IARI), Delhi, India
| | - Sheshshayee M Sreeman
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | - Abhishek Rathore
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Mohammad Yasin
- RAK College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, India
| | | | | | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
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14
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Asati R, Tripathi MK, Tiwari S, Yadav RK, Tripathi N. Molecular Breeding and Drought Tolerance in Chickpea. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111846. [PMID: 36430981 PMCID: PMC9698494 DOI: 10.3390/life12111846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
Cicer arietinum L. is the third greatest widely planted imperative pulse crop worldwide, and it belongs to the Leguminosae family. Drought is the utmost common abiotic factor on plants, distressing their water status and limiting their growth and development. Chickpea genotypes have the natural ability to fight drought stress using certain strategies viz., escape, avoidance and tolerance. Assorted breeding methods, including hybridization, mutation, and marker-aided breeding, genome sequencing along with omics approaches, could be used to improve the chickpea germplasm lines(s) against drought stress. Root features, for instance depth and root biomass, have been recognized as the greatest beneficial morphological factors for managing terminal drought tolerance in the chickpea. Marker-aided selection, for example, is a genomics-assisted breeding (GAB) strategy that can considerably increase crop breeding accuracy and competence. These breeding technologies, notably marker-assisted breeding, omics, and plant physiology knowledge, underlined the importance of chickpea breeding and can be used in future crop improvement programmes to generate drought-tolerant cultivars(s).
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Affiliation(s)
- Ruchi Asati
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Manoj Kumar Tripathi
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Correspondence: (M.K.T.); (N.T.)
| | - Sushma Tiwari
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Rakesh Kumar Yadav
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Agricultural University, Jabalpur 482004, India
- Correspondence: (M.K.T.); (N.T.)
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15
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Koul B, Sharma K, Sehgal V, Yadav D, Mishra M, Bharadwaj C. Chickpea ( Cicer arietinum L.) Biology and Biotechnology: From Domestication to Biofortification and Biopharming. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212926. [PMID: 36365379 PMCID: PMC9654780 DOI: 10.3390/plants11212926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/13/2022] [Accepted: 10/25/2022] [Indexed: 05/13/2023]
Abstract
Chickpea (Cicer arietinum L.), the world's second most consumed legume crop, is cultivated in more than 50 countries around the world. It is a boon for diabetics and is an excellent source of important nutrients such as vitamins A, C, E, K, B1-B3, B5, B6, B9 and minerals (Fe, Zn, Mg and Ca) which all have beneficial effects on human health. By 2050, the world population can cross 9 billion, and in order to feed the teaming millions, chickpea production should also be increased, as it is a healthy alternative to wheat flour and a boon for diabetics. Moreover, it is an important legume that is crucial for food, nutrition, and health security and the livelihood of the small-scale farmers with poor resources, in developing countries. Although marvelous improvement has been made in the development of biotic and abiotic stress-resistant varieties, still there are many lacunae, and to fulfill that, the incorporation of genomic technologies in chickpea breeding (genomics-assisted breeding, high-throughput and precise-phenotyping and implementation of novel breeding strategies) will facilitate the researchers in developing high yielding, climate resilient, water use efficient, salt-tolerant, insect/pathogen resistant varieties, acceptable to farmers, consumers, and industries. This review focuses on the origin and distribution, nutritional profile, genomic studies, and recent updates on crop improvement strategies for combating abiotic and biotic stresses in chickpea.
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Affiliation(s)
- Bhupendra Koul
- Department of Biotechnology, Lovely Professional University, Phagwara 144411, India
- Correspondence: (B.K.); (D.Y.); (M.M.)
| | - Komal Sharma
- Department of Biotechnology, Lovely Professional University, Phagwara 144411, India
| | - Vrinda Sehgal
- Department of Biotechnology, Lovely Professional University, Phagwara 144411, India
| | - Dhananjay Yadav
- Department of Life Science, Yeungnam University, Gyeongsan 38541, Korea
- Correspondence: (B.K.); (D.Y.); (M.M.)
| | - Meerambika Mishra
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, FL 32611, USA
- Correspondence: (B.K.); (D.Y.); (M.M.)
| | - Chellapilla Bharadwaj
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa, New Delhi 110012, India
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Istanbuli T, Abu Assar A, Tawkaz S, Kumar T, Alsamman AM, Hamwieh A. The interaction between drought stress and nodule formation under multiple environments in chickpea. PLoS One 2022; 17:e0276732. [PMID: 36301853 PMCID: PMC9612560 DOI: 10.1371/journal.pone.0276732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental stresses, particularly drought, limit symbiotic nitrogen fixation in legumes, resulting in decreased yielding capacity. Drought is one of the most important constraints limiting yield potential in crops and it is the major abiotic stress that can cause more than 70% yield loss in chickpea. In this study, a total of two hundred four chickpea (Cicer arietinum L.) genotypes were selected to study the interaction between drought stress and nodule formation. This interaction was assessed by using morphological, yield and yield components. The field experiments were laid out in two locations (Terbol and Kfardan stations, Bekaa valley, Lebanon) using Alpha lattice design with two replications and two watering treatments (irrigation and rainfed) during 2016 and 2017 seasons. Parameters that were measured include days to 50% flowering (DFL), day to maturity (DM), plant height (PLH), nodule biomass (NB), nodule fresh weight (NFW), nodule dry weight (NDW), grain yield (GY), Biological yield (BY), 100 seed weight (100SW) and drought tolerance stress (DTS). The results indicated a significant variation between genotypes, environments and other morphological, yield and yield components traits. Drought stress reduced significantly the yield and the nodule's characteristics, biological and grain yield. The genotypes with the highest levels of drought tolerance, such as IG70399, IG8256, IG71832, IG70270, and IG70272, showed a minimal decrease in yield and nodule biomass. Nodule observations significantly and positively correlated with GY (0.36-0.38) under drought stress treatment. The correlation values for nodule characteristics with DFL and DM were higher under drought stress compared to irrigated conditions. This is a comparative study between drought stress and nodule formation traits associated with morphological, yield and yield components traits.
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Affiliation(s)
- Tawffiq Istanbuli
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
- * E-mail: (TI); (AH)
| | - Ahmed Abu Assar
- Department of Oil Crops, Agriculture Research Center (ARC), Wad Madani, Sudan
| | - Sawsan Tawkaz
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
| | - Tapan Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Amlaha, India
| | - Alsamman M. Alsamman
- Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza, Egypt
| | - Aladdin Hamwieh
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
- * E-mail: (TI); (AH)
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Proteometabolomic Analysis Reveals Molecular Features Associated with Grain Size and Antioxidant Properties amongst Chickpea (Cicer arietinum L.) Seeds Genotypes. Antioxidants (Basel) 2022; 11:antiox11101850. [DOI: 10.3390/antiox11101850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Legumes are an essential source of nutrients that complement energy and protein requirements in the human diet. They also contribute to the intake of bioactive compounds such as polyphenols, whose content can vary depending on cultivars and genotypes. We conducted a comparative proteomics and metabolomics study to determine if there were significant variations in relevant nutraceutical compounds in the five genotypes of Kabuli-type chickpea grains. We performed an isobaric tandem mass tag (TMT) couple to synchronous precursor selection (SPS)-MS3 method along with a targeted and untargeted metabolomics approach based on accurate mass spectrometry. We observed an association between the overproduction of proteins involved in starch, lipid, and amino acid metabolism with gibberellin accumulation in large grains. In contrast, we visualized the over-accumulation of proteins associated with water deprivation in small grains. It was possible to visualize in small grains the over-accumulation of some phenolics such as vanillin, salicylic acid, protocatechuic acid, 4-coumaric acid, 4-hydroxybenzoic acid, vanillic acid, ferulic acid, and kaempferol 3-O-glucoside as well as the amino acid l-phenylalanine. The activated phenolic pathway was associated with the higher antioxidant capacity of small grains. Small grains consumption could be advantageous due to their nutraceutical properties.
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Barmukh R, Roorkiwal M, Garg V, Khan AW, German L, Jaganathan D, Chitikineni A, Kholova J, Kudapa H, Sivasakthi K, Samineni S, Kale SM, Gaur PM, Sagurthi SR, Benitez‐Alfonso Y, Varshney RK. Genetic variation in CaTIFY4b contributes to drought adaptation in chickpea. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1701-1715. [PMID: 35534989 PMCID: PMC9398337 DOI: 10.1111/pbi.13840] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/28/2022] [Indexed: 05/26/2023]
Abstract
Chickpea production is vulnerable to drought stress. Identifying the genetic components underlying drought adaptation is crucial for enhancing chickpea productivity. Here, we present the fine mapping and characterization of 'QTL-hotspot', a genomic region controlling chickpea growth with positive consequences on crop production under drought. We report that a non-synonymous substitution in the transcription factor CaTIFY4b regulates seed weight and organ size in chickpea. Ectopic expression of CaTIFY4b in Medicago truncatula enhances root growth under water deficit. Our results suggest that allelic variation in 'QTL-hotspot' improves pre-anthesis water use, transpiration efficiency, root architecture and canopy development, enabling high-yield performance under terminal drought conditions. Gene expression analysis indicated that CaTIFY4b may regulate organ size under water deficit by modulating the expression of GRF-INTERACTING FACTOR1 (GIF1), a transcriptional co-activator of Growth-Regulating Factors. Taken together, our study offers new insights into the role of CaTIFY4b and on diverse physiological and molecular mechanisms underpinning chickpea growth and production under specific drought scenarios.
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Affiliation(s)
- Rutwik Barmukh
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Department of GeneticsOsmania UniversityHyderabadIndia
| | - Manish Roorkiwal
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Khalifa Center for Genetic Engineering and BiotechnologyUnited Arab Emirates UniversityAl‐AinUnited Arab Emirates
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Vanika Garg
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Aamir W. Khan
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Liam German
- Centre for Plant ScienceSchool of BiologyUniversity of LeedsLeedsUK
| | - Deepa Jaganathan
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Annapurna Chitikineni
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Jana Kholova
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Himabindu Kudapa
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Kaliamoorthy Sivasakthi
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Srinivasan Samineni
- Crop BreedingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Sandip M. Kale
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Pooran M. Gaur
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
- Crop BreedingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | | | | | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
- Murdoch’s Centre for Crop & Food InnovationState Agricultural Biotechnology CentreFood Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
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19
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Roorkiwal M, Bhandari A, Barmukh R, Bajaj P, Valluri VK, Chitikineni A, Pandey S, Chellapilla B, Siddique KHM, Varshney RK. Genome-wide association mapping of nutritional traits for designing superior chickpea varieties. FRONTIERS IN PLANT SCIENCE 2022; 13:843911. [PMID: 36082300 PMCID: PMC9445663 DOI: 10.3389/fpls.2022.843911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Micronutrient malnutrition is a serious concern in many parts of the world; therefore, enhancing crop nutrient content is an important challenge. Chickpea (Cicer arietinum L.), a major food legume crop worldwide, is a vital source of protein and minerals in the vegetarian diet. This study evaluated a diverse set of 258 chickpea germplasm accessions for 12 key nutritional traits. A significant variation was observed for several nutritional traits, including crude protein (16.56-24.64/100 g), β-Carotene (0.003-0.104 mg/100 g), calcium (60.69-176.55 mg/100 g), and folate (0.413-6.537 mg/kg). These data, combined with the available whole-genome sequencing data for 318,644 SNPs, were used in genome-wide association studies comprising single-locus and multi-locus models. We also explored the effect of varying the minor allele frequency (MAF) levels and heterozygosity. We identified 62 significant marker-trait associations (MTAs) explaining up to 28.63% of the phenotypic variance (PV), of which nine were localized within genes regulating G protein-coupled receptor signaling pathway, proteasome assembly, intracellular signal transduction, and oxidation-reduction process, among others. The significant effect MTAs were located primarily on Ca1, Ca3, Ca4, and Ca6. Importantly, varying the level of heterozygosity was found to significantly affect the detection of associations contributing to traits of interest. We further identified seven promising accessions (ICC10399, ICC1392, ICC1710, ICC2263, ICC1431, ICC4182, and ICC16915) with superior agronomic performance and high nutritional content as potential donors for developing nutrient-rich, high-yielding chickpea varieties. Validation of the significant MTAs with higher PV could identify factors controlling the nutrient acquisition and facilitate the design of biofortified chickpeas for the future.
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Affiliation(s)
- Manish Roorkiwal
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Aditi Bhandari
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rutwik Barmukh
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prasad Bajaj
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vinod Kumar Valluri
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sarita Pandey
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Bharadwaj Chellapilla
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- ICAR- Indian Agricultural Research Institute (IARI), New Delhi, India
| | | | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
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20
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Kushwah A, Bhatia D, Barmukh R, Singh I, Singh G, Bindra S, Vij S, Chellapilla B, Pratap A, Roorkiwal M, Kumar S, Varshney RK, Singh S. Genetic mapping of QTLs for drought tolerance in chickpea ( Cicer arietinum L.). Front Genet 2022; 13:953898. [PMID: 36061197 PMCID: PMC9437436 DOI: 10.3389/fgene.2022.953898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/05/2022] [Indexed: 01/24/2023] Open
Abstract
Chickpea yield is severely affected by drought stress, which is a complex quantitative trait regulated by multiple small-effect genes. Identifying genomic regions associated with drought tolerance component traits may increase our understanding of drought tolerance mechanisms and assist in the development of drought-tolerant varieties. Here, a total of 187 F8 recombinant inbred lines (RILs) developed from an interspecific cross between drought-tolerant genotype GPF 2 (Cicer arietinum) and drought-sensitive accession ILWC 292 (C. reticulatum) were evaluated to identify quantitative trait loci (QTLs) associated with drought tolerance component traits. A total of 21 traits, including 12 morpho-physiological traits and nine root-related traits, were studied under rainfed and irrigated conditions. Composite interval mapping identified 31 QTLs at Ludhiana and 23 QTLs at Faridkot locations for morphological and physiological traits, and seven QTLs were identified for root-related traits. QTL analysis identified eight consensus QTLs for six traits and five QTL clusters containing QTLs for multiple traits on linkage groups CaLG04 and CaLG06. The identified major QTLs and genomic regions associated with drought tolerance component traits can be introgressed into elite cultivars using genomics-assisted breeding to enhance drought tolerance in chickpea.
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Affiliation(s)
- Ashutosh Kushwah
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Rutwik Barmukh
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Gurpreet Singh
- Regional Research Station, Punjab Agricultural University, Faridkot, India
| | - Shayla Bindra
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Suruchi Vij
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | | | - Aditya Pratap
- Crop Improvement Division, ICAR- Indian Institute of Pulses Research, Kanpur, India
| | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Office, Rabat, Morocco
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Murdoch’s Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Sarvjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
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21
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Srungarapu R, Mahendrakar MD, Mohammad LA, Chand U, Jagarlamudi VR, Kondamudi KP, Kudapa H, Samineni S. Genome-Wide Association Analysis Reveals Trait-Linked Markers for Grain Nutrient and Agronomic Traits in Diverse Set of Chickpea Germplasm. Cells 2022; 11:cells11152457. [PMID: 35954301 PMCID: PMC9367858 DOI: 10.3390/cells11152457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/22/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Chickpea is an inexpensive source of protein, minerals, and vitamins to the poor people living in arid and semi-arid regions of Southern Asia and Sub-Saharan Africa. New chickpea cultivars with enhanced levels of protein, Fe and Zn content are a medium-term strategy for supplying essential nutrients for human health and reducing malnutrition. In the current study, a chickpea reference set of 280 accessions, including landraces, breeding lines, and advanced cultivars, was evaluated for grain protein, Fe, Zn content and agronomic traits over two seasons. Using a mid-density 5k SNP array, 4603 highly informative SNPs distributed across the chickpea genome were used for GWAS analysis. Population structure analysis revealed three subpopulations (K = 3). Linkage disequilibrium (LD) was extensive, and LD decay was relatively low. A total of 20 and 46 marker-trait associations (MTAs) were identified for grain nutrient and agronomic traits, respectively, using FarmCPU and BLINK models. Of which seven SNPs for grain protein, twelve for Fe, and one for Zn content were distributed on chromosomes 1, 4, 6, and 7. The marker S4_4477846 on chr4 was found to be co-associated with grain protein over seasons. The markers S1_11613376 and S1_2772537 co-associated with grain Fe content under NSII and pooled seasons and S7_9379786 marker under NSI and pooled seasons. The markers S4_31996956 co-associated with grain Fe and days to maturity. SNP annotation of associated markers were found to be related to gene functions of metal ion binding, transporters, protein kinases, transcription factors, and many more functions involved in plant metabolism along with Fe and protein homeostasis. The identified significant MTAs has potential use in marker-assisted selection for developing nutrient-rich chickpea cultivars after validation in the breeding populations.
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Affiliation(s)
- Rajasekhar Srungarapu
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
- Department of Molecular Biology and Biotechnology, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Mahesh Damodhar Mahendrakar
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
| | - Lal Ahamed Mohammad
- Department of Genetics and Plant Breeding, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Uttam Chand
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
| | - Venkata Ramana Jagarlamudi
- Department of Genetics and Plant Breeding, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Kiran Prakash Kondamudi
- Department of Statistics and Computer Applications, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Himabindu Kudapa
- Genomics, Pre-Breeding and Bioinformatics, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
| | - Srinivasan Samineni
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
- Correspondence:
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22
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Singh RK, Singh C, Chandana BS, Mahto RK, Patial R, Gupta A, Gahlaut V, Hamwieh A, Upadhyaya HD, Kumar R. Exploring Chickpea Germplasm Diversity for Broadening the Genetic Base Utilizing Genomic Resourses. Front Genet 2022; 13:905771. [PMID: 36035111 PMCID: PMC9416867 DOI: 10.3389/fgene.2022.905771] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/24/2022] [Indexed: 12/01/2022] Open
Abstract
Legume crops provide significant nutrition to humans as a source of protein, omega-3 fatty acids as well as specific macro and micronutrients. Additionally, legumes improve the cropping environment by replenishing the soil nitrogen content. Chickpeas are the second most significant staple legume food crop worldwide behind dry bean which contains 17%–24% protein, 41%–51% carbohydrate, and other important essential minerals, vitamins, dietary fiber, folate, β-carotene, anti-oxidants, micronutrients (phosphorus, calcium, magnesium, iron, and zinc) as well as linoleic and oleic unsaturated fatty acids. Despite these advantages, legumes are far behind cereals in terms of genetic improvement mainly due to far less effort, the bottlenecks of the narrow genetic base, and several biotic and abiotic factors in the scenario of changing climatic conditions. Measures are now called for beyond conventional breeding practices to strategically broadening of narrow genetic base utilizing chickpea wild relatives and improvement of cultivars through advanced breeding approaches with a focus on high yield productivity, biotic and abiotic stresses including climate resilience, and enhanced nutritional values. Desirable donors having such multiple traits have been identified using core and mini core collections from the cultivated gene pool and wild relatives of Chickpea. Several methods have been developed to address cross-species fertilization obstacles and to aid in inter-specific hybridization and introgression of the target gene sequences from wild Cicer species. Additionally, recent advances in “Omics” sciences along with high-throughput and precise phenotyping tools have made it easier to identify genes that regulate traits of interest. Next-generation sequencing technologies, whole-genome sequencing, transcriptomics, and differential genes expression profiling along with a plethora of novel techniques like single nucleotide polymorphism exploiting high-density genotyping by sequencing assays, simple sequence repeat markers, diversity array technology platform, and whole-genome re-sequencing technique led to the identification and development of QTLs and high-density trait mapping of the global chickpea germplasm. These altogether have helped in broadening the narrow genetic base of chickpeas.
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Affiliation(s)
| | - Charul Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - B S Chandana
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Rohit K Mahto
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Ranjana Patial
- Department of Agricultural Sciences, Chandigarh University, Mohali, India
| | - Astha Gupta
- School of Agricultural Sciences, Sharda University, Greater Noida, India
| | - Vijay Gahlaut
- Institute of Himalayan Bioresource Technology (CSIR), Pālampur, India
| | - Aladdin Hamwieh
- International Center for Agriculture Research in the Dry Areas (ICARDA), Giza, Egypt
| | - H D Upadhyaya
- Department of Entomology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Rajendra Kumar
- Indian Agricultural Research Institute (ICAR), New Delhi, India
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23
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Arriagada O, Cacciuttolo F, Cabeza RA, Carrasco B, Schwember AR. A Comprehensive Review on Chickpea ( Cicer arietinum L.) Breeding for Abiotic Stress Tolerance and Climate Change Resilience. Int J Mol Sci 2022; 23:ijms23126794. [PMID: 35743237 PMCID: PMC9223724 DOI: 10.3390/ijms23126794] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 02/05/2023] Open
Abstract
Chickpea is one of the most important pulse crops worldwide, being an excellent source of protein. It is grown under rain-fed conditions averaging yields of 1 t/ha, far from its potential of 6 t/ha under optimum conditions. The combined effects of heat, cold, drought, and salinity affect species productivity. In this regard, several physiological, biochemical, and molecular mechanisms are reviewed to confer tolerance to abiotic stress. A large collection of nearly 100,000 chickpea accessions is the basis of breeding programs, and important advances have been achieved through conventional breeding, such as germplasm introduction, gene/allele introgression, and mutagenesis. In parallel, advances in molecular biology and high-throughput sequencing have allowed the development of specific molecular markers for the genus Cicer, facilitating marker-assisted selection for yield components and abiotic tolerance. Further, transcriptomics, proteomics, and metabolomics have permitted the identification of specific genes, proteins, and metabolites associated with tolerance to abiotic stress of chickpea. Furthermore, some promising results have been obtained in studies with transgenic plants and with the use of gene editing to obtain drought-tolerant chickpea. Finally, we propose some future lines of research that may be useful to obtain chickpea genotypes tolerant to abiotic stress in a scenario of climate change.
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Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (F.C.)
| | - Felipe Cacciuttolo
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (F.C.)
| | - Ricardo A. Cabeza
- Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile;
| | - Basilio Carrasco
- Centro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, Chile;
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (F.C.)
- Correspondence:
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24
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Li Y, Kaur S, Pembleton LW, Valipour-Kahrood H, Rosewarne GM, Daetwyler HD. Strategies of preserving genetic diversity while maximizing genetic response from implementing genomic selection in pulse breeding programs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1813-1828. [PMID: 35316351 PMCID: PMC9205836 DOI: 10.1007/s00122-022-04071-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
Genomic selection maximizes genetic gain by recycling parents to germplasm pool earlier and preserves genetic diversity by restricting the number of fixed alleles and the relationship in pulse breeding programs. Using a stochastic computer simulation, we investigated the benefit of optimization strategies in the context of genomic selection (GS) for pulse breeding programs. We simulated GS for moderately complex to highly complex traits such as disease resistance, grain weight and grain yield in multiple environments with a high level of genotype-by-environment interaction for grain yield. GS led to higher genetic gain per unit of time and higher genetic diversity loss than phenotypic selection by shortening the breeding cycle time. The genetic gain obtained from selecting the segregating parents early in the breeding cycle (at F1 or F2 stages) was substantially higher than selecting at later stages even though prediction accuracy was moderate. Increasing the number of F1 intercross (F1i) families and keeping the total number of progeny of F1i families constant, we observed a decrease in genetic gain and increase in genetic diversity, whereas increasing the number of progeny per F1i family while keeping a constant number of F1i families increased the rate of genetic gain and had higher genetic diversity loss per unit of time. Adding 50 F2 family phenotypes to the training population increased the accuracy of genomic breeding values (GEBVs) and genetic gain per year and decreased the rate of genetic diversity loss. Genetic diversity could be preserved by applying a strategy that restricted both the percentage of alleles fixed and the average relationship of the group of selected parents to preserve long-term genetic improvement in the pulse breeding program.
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Affiliation(s)
- Yongjun Li
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, 3083, Australia.
| | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, 3083, Australia
| | - Luke W Pembleton
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, 3083, Australia
| | | | - Garry M Rosewarne
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, 3400, Australia
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
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25
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Chapman MA, He Y, Zhou M. Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security. THE NEW PHYTOLOGIST 2022; 234:1583-1597. [PMID: 35318683 PMCID: PMC9994440 DOI: 10.1111/nph.18021] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/22/2022] [Indexed: 04/14/2023]
Abstract
Underutilized crops are, by definition, under-researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress-tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Tansley Review, we show how this is only the very first step. We advocate that going 'beyond a reference genome' should be a priority, as it is only at this stage one can identify the specific genes and the adaptive alleles that underpin the valuable traits. We sum up how population genomic and pangenomic approaches have led to the identification of stress- and disease-tolerant alleles in staple crops and compare this to the small number of examples from underutilized crops. We also demonstrate how previously underutilized crops have benefitted from genomic advances and that many breeding targets in underutilized crops are often well studied in staple crops. This cross-crop population-level resequencing could lead to an understanding of the genetic basis of adaptive traits in underutilized crops. This level of investment may be crucial for fully understanding the value of these crops before they are lost.
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Affiliation(s)
- Mark A. Chapman
- Biological SciencesUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUK
| | - Yuqi He
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
| | - Meiliang Zhou
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
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26
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Rocchetti L, Gioia T, Logozzo G, Brezeanu C, Pereira LG, la Rosa LD, Marzario S, Pieri A, Fernie AR, Alseekh S, Susek K, Cook DR, Varshney RK, Agrawal SK, Hamwieh A, Bitocchi E, Papa R. Towards the Development, Maintenance and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Chickpea. Curr Protoc 2022; 2:e371. [PMID: 35179832 DOI: 10.1002/cpz1.371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Here we present the approach used to develop the INCREASE "Intelligent Chickpea" Collections, from analysis of the information on the life history and population structure of chickpea germplasm, the availability of genomic and genetic resources, the identification of key phenotypic traits and methodologies to characterize chickpea. We present two phenotypic protocols within H2O20 Project INCREASE to characterize, develop, and maintain chickpea single-seed-descent (SSD) line collections. Such protocols and related genetic resource data from the project will be available for the legume community to apply the standardized approaches to develop Chickpea Intelligent Collections further or for multiplication/seed-increase purposes. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Characterization of chickpea seeds for seed-trait descriptors Basic Protocol 2: Characterization of chickpea lines for plant-trait descriptors specific for primary seed increase.
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Affiliation(s)
- Lorenzo Rocchetti
- Department of Agricultural, Food, and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Tania Gioia
- School of Agriculture, Forestry, Food, and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Giuseppina Logozzo
- School of Agriculture, Forestry, Food, and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Creola Brezeanu
- Staţiunea de Cercetare Dezvoltare Pentru Legumicultură, Bacău, Romania
| | - Luis Guasch Pereira
- Spanish Plant Genetic Resources National Center, National Institute for Agricultural and Food Research and Technology (CRF-INIA-CSIC), Alcalá de Henares, Madrid, Spain
| | - Lucía De la Rosa
- Spanish Plant Genetic Resources National Center, National Institute for Agricultural and Food Research and Technology (CRF-INIA-CSIC), Alcalá de Henares, Madrid, Spain
| | - Stefania Marzario
- School of Agriculture, Forestry, Food, and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Alice Pieri
- Department of Agricultural, Food, and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center for Plant Systems Biology, Plovdiv, Bulgaria
| | - Karolina Susek
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Douglas R Cook
- Department of Plant Pathology, University of California Davis, Davis, California
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India
| | - Shiv Kumar Agrawal
- Genetic Resources Section, International Center for Agricultural Research in Dry Areas (ICARDA), Agdal Rabat, Morocco
| | - Aladdin Hamwieh
- Genetic Resources Section, International Center for Agricultural Research in Dry Areas (ICARDA), Agdal Rabat, Morocco
| | - Elena Bitocchi
- Department of Agricultural, Food, and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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Raza A, Tabassum J, Zahid Z, Charagh S, Bashir S, Barmukh R, Khan RSA, Barbosa F, Zhang C, Chen H, Zhuang W, Varshney RK. Advances in "Omics" Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants. FRONTIERS IN PLANT SCIENCE 2022; 12:794373. [PMID: 35058954 PMCID: PMC8764127 DOI: 10.3389/fpls.2021.794373] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/22/2021] [Indexed: 05/17/2023]
Abstract
Food safety has emerged as a high-urgency matter for sustainable agricultural production. Toxic metal contamination of soil and water significantly affects agricultural productivity, which is further aggravated by extreme anthropogenic activities and modern agricultural practices, leaving food safety and human health at risk. In addition to reducing crop production, increased metals/metalloids toxicity also disturbs plants' demand and supply equilibrium. Counterbalancing toxic metals/metalloids toxicity demands a better understanding of the complex mechanisms at physiological, biochemical, molecular, cellular, and plant level that may result in increased crop productivity. Consequently, plants have established different internal defense mechanisms to cope with the adverse effects of toxic metals/metalloids. Nevertheless, these internal defense mechanisms are not adequate to overwhelm the metals/metalloids toxicity. Plants produce several secondary messengers to trigger cell signaling, activating the numerous transcriptional responses correlated with plant defense. Therefore, the recent advances in omics approaches such as genomics, transcriptomics, proteomics, metabolomics, ionomics, miRNAomics, and phenomics have enabled the characterization of molecular regulators associated with toxic metal tolerance, which can be deployed for developing toxic metal tolerant plants. This review highlights various response strategies adopted by plants to tolerate toxic metals/metalloids toxicity, including physiological, biochemical, and molecular responses. A seven-(omics)-based design is summarized with scientific clues to reveal the stress-responsive genes, proteins, metabolites, miRNAs, trace elements, stress-inducible phenotypes, and metabolic pathways that could potentially help plants to cope up with metals/metalloids toxicity in the face of fluctuating environmental conditions. Finally, some bottlenecks and future directions have also been highlighted, which could enable sustainable agricultural production.
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Affiliation(s)
- Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Javaria Tabassum
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Zainab Zahid
- School of Civil and Environmental Engineering (SCEE), Institute of Environmental Sciences and Engineering (IESE), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Sidra Charagh
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Shanza Bashir
- School of Civil and Environmental Engineering (SCEE), Institute of Environmental Sciences and Engineering (IESE), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Rutwik Barmukh
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rao Sohail Ahmad Khan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Fernando Barbosa
- Department of Clinical Analysis, Toxicology and Food Sciences, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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Tiwari M, Singh B, Min D, Jagadish SVK. Omics Path to Increasing Productivity in Less-Studied Crops Under Changing Climate-Lentil a Case Study. FRONTIERS IN PLANT SCIENCE 2022; 13:813985. [PMID: 35615121 PMCID: PMC9125188 DOI: 10.3389/fpls.2022.813985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/04/2022] [Indexed: 05/08/2023]
Abstract
Conventional breeding techniques for crop improvement have reached their full potential, and hence, alternative routes are required to ensure a sustained genetic gain in lentils. Although high-throughput omics technologies have been effectively employed in major crops, less-studied crops such as lentils have primarily relied on conventional breeding. Application of genomics and transcriptomics in lentils has resulted in linkage maps and identification of QTLs and candidate genes related to agronomically relevant traits and biotic and abiotic stress tolerance. Next-generation sequencing (NGS) complemented with high-throughput phenotyping (HTP) technologies is shown to provide new opportunities to identify genomic regions and marker-trait associations to increase lentil breeding efficiency. Recent introduction of image-based phenotyping has facilitated to discern lentil responses undergoing biotic and abiotic stresses. In lentil, proteomics has been performed using conventional methods such as 2-D gel electrophoresis, leading to the identification of seed-specific proteome. Metabolomic studies have led to identifying key metabolites that help differentiate genotypic responses to drought and salinity stresses. Independent analysis of differentially expressed genes from publicly available transcriptomic studies in lentils identified 329 common transcripts between heat and biotic stresses. Similarly, 19 metabolites were common across legumes, while 31 were common in genotypes exposed to drought and salinity stress. These common but differentially expressed genes/proteins/metabolites provide the starting point for developing high-yielding multi-stress-tolerant lentils. Finally, the review summarizes the current findings from omic studies in lentils and provides directions for integrating these findings into a systems approach to increase lentil productivity and enhance resilience to biotic and abiotic stresses under changing climate.
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Affiliation(s)
- Manish Tiwari
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
- *Correspondence: Manish Tiwari,
| | - Baljinder Singh
- National Institute of Plant Genome Research, New Delhi, India
| | - Doohong Min
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - S. V. Krishna Jagadish
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
- S. V. Krishna Jagadish,
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Gangurde SS, Xavier A, Naik YD, Jha UC, Rangari SK, Kumar R, Reddy MSS, Channale S, Elango D, Mir RR, Zwart R, Laxuman C, Sudini HK, Pandey MK, Punnuri S, Mendu V, Reddy UK, Guo B, Gangarao NVPR, Sharma VK, Wang X, Zhao C, Thudi M. Two decades of association mapping: Insights on disease resistance in major crops. FRONTIERS IN PLANT SCIENCE 2022; 13:1064059. [PMID: 37082513 PMCID: PMC10112529 DOI: 10.3389/fpls.2022.1064059] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/10/2022] [Indexed: 05/03/2023]
Abstract
Climate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been effectively used to identify candidate genes and map loci associated with different diseases in crop plants. In this review, we highlight successful examples for the discovery of resistance genes to many important diseases. In addition, major developments in association studies, statistical models and bioinformatic tools that improve the power, resolution and the efficiency of identifying marker-trait associations. Overall this review provides comprehensive insights into the two decades of advances in GWAS studies and discusses the challenges and opportunities this research area provides for breeding resistant varieties.
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Affiliation(s)
- Sunil S. Gangurde
- Crop Genetics and Breeding Research, United States Department of Agriculture (USDA) - Agriculture Research Service (ARS), Tifton, GA, United States
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Alencar Xavier
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | | | - Uday Chand Jha
- Indian Council of Agricultural Research (ICAR), Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | | | - Raj Kumar
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - M. S. Sai Reddy
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - Sonal Channale
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
| | - Dinakaran Elango
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Reyazul Rouf Mir
- Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST), Sopore, India
| | - Rebecca Zwart
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
| | - C. Laxuman
- Zonal Agricultural Research Station (ZARS), Kalaburagi, University of Agricultural Sciences, Raichur, Karnataka, India
| | - Hari Kishan Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Manish K. Pandey
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Somashekhar Punnuri
- College of Agriculture, Family Sciences and Technology, Dr. Fort Valley State University, Fort Valley, GA, United States
| | - Venugopal Mendu
- Department of Plant Science and Plant Pathology, Montana State University, Bozeman, MT, United States
| | - Umesh K. Reddy
- Department of Biology, West Virginia State University, West Virginia, WV, United States
| | - Baozhu Guo
- Crop Genetics and Breeding Research, United States Department of Agriculture (USDA) - Agriculture Research Service (ARS), Tifton, GA, United States
| | | | - Vinay K. Sharma
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - Xingjun Wang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
- *Correspondence: Mahendar Thudi, ; Chuanzhi Zhao,
| | - Mahendar Thudi
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
- *Correspondence: Mahendar Thudi, ; Chuanzhi Zhao,
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Pratap A, Kumar S, Polowick PL, Blair MW, Baum M. Editorial: Accelerating Genetic Gains in Pulses. FRONTIERS IN PLANT SCIENCE 2022; 13:879377. [PMID: 35463449 PMCID: PMC9025562 DOI: 10.3389/fpls.2022.879377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 03/07/2022] [Indexed: 05/06/2023]
Affiliation(s)
- Aditya Pratap
- Indian Institute of Pulses Research, Indian Council of Agricultural Research, Kanpur, India
- *Correspondence: Aditya Pratap ; orcid.org/0000-0001-7280-0953
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas, New Delhi, India
| | | | - Matthew W. Blair
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
| | - Michael Baum
- International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
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Genomics Associated Interventions for Heat Stress Tolerance in Cool Season Adapted Grain Legumes. Int J Mol Sci 2021; 23:ijms23010399. [PMID: 35008831 PMCID: PMC8745526 DOI: 10.3390/ijms23010399] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
Cool season grain legumes occupy an important place among the agricultural crops and essentially provide multiple benefits including food supply, nutrition security, soil fertility improvement and revenue for farmers all over the world. However, owing to climate change, the average temperature is steadily rising, which negatively affects crop performance and limits their yield. Terminal heat stress that mainly occurred during grain development phases severely harms grain quality and weight in legumes adapted to the cool season, such as lentils, faba beans, chickpeas, field peas, etc. Although, traditional breeding approaches with advanced screening procedures have been employed to identify heat tolerant legume cultivars. Unfortunately, traditional breeding pipelines alone are no longer enough to meet global demands. Genomics-assisted interventions including new-generation sequencing technologies and genotyping platforms have facilitated the development of high-resolution molecular maps, QTL/gene discovery and marker-assisted introgression, thereby improving the efficiency in legumes breeding to develop stress-resilient varieties. Based on the current scenario, we attempted to review the intervention of genomics to decipher different components of tolerance to heat stress and future possibilities of using newly developed genomics-based interventions in cool season adapted grain legumes.
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Palakurthi R, Jayalakshmi V, Kumar Y, Kulwal P, Yasin M, Kute NS, Laxuman C, Yeri S, Vemula A, Rathore A, Samineni S, Soren KR, Mondal B, Dixit GP, Bharadwaj C, Chaturvedi SK, Gaur PM, Roorkiwal M, Thudi M, Singh NP, Varshney RK. Translational Chickpea Genomics Consortium to Accelerate Genetic Gains in Chickpea (Cicer arietinum L.). PLANTS 2021; 10:plants10122583. [PMID: 34961053 PMCID: PMC8703834 DOI: 10.3390/plants10122583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/23/2021] [Accepted: 10/30/2021] [Indexed: 12/03/2022]
Abstract
The Translational Chickpea Genomics Consortium (TCGC) was set up to increase the production and productivity of chickpea (Cicer arietinum L.). It represents research institutes from six major chickpea growing states (Madhya Pradesh, Maharashtra, Andhra Pradesh, Telangana, Karnataka and Uttar Pradesh) of India. The TCGC team has been engaged in deploying modern genomics approaches in breeding and popularizing improved varieties in farmers’ fields across the states. Using marker-assisted backcrossing, introgression lines with enhanced drought tolerance and fusarium wilt resistance have been developed in the genetic background of 10 elite varieties of chickpea. Multi-location evaluation of 100 improved lines (70 desi and 30 kabuli) during 2016–2017 and 2018–2019 enabled the identification of top performing desi and kabuli lines. In total, 909 Farmer Participatory Varietal Selection trials were conducted in 158 villages in 16 districts of the five states, during 2017–2018, 2018–2019, and 2019–2020, involving 16 improved varieties. New molecular breeding lines developed in different genetic backgrounds are potential candidates for national trials under the ICAR-All India Coordinated Research Project on Chickpea. The comprehensive efforts of TCGC resulted in the development and adoption of high-yielding varieties that will increase chickpea productivity and the profitability of chickpea growing farmers.
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Affiliation(s)
- Ramesh Palakurthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India; (R.P.); (A.V.); (A.R.); (S.S.); (P.M.G.); (M.R.)
| | - Veera Jayalakshmi
- Regional Agricultural Research Station (RARS), Acharya N.G. Ranga Agricultural University (ANGRAU), Nandyal 518501, India;
| | - Yogesh Kumar
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur 208024, India; (Y.K.); (K.R.S.); (B.M.); (G.P.D.); (S.K.C.)
| | - Pawan Kulwal
- Department Agricultural Botany, Mahatma Phule Krishi Vidyapeeth (MPKV), Rahuri 413722, India; (P.K.); (N.S.K.)
| | - Mohammad Yasin
- RAK College of Agriculture (RAKCA), Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya (RVSKVV), Sehore 466001, India;
| | - Nandkumar Surendra Kute
- Department Agricultural Botany, Mahatma Phule Krishi Vidyapeeth (MPKV), Rahuri 413722, India; (P.K.); (N.S.K.)
| | - Chinchole Laxuman
- Agricultural Research Station (ARS), University of Agricultural Sciences (UAS), Raichur 584104, India; (C.L.); (S.Y.)
| | - Sharanabasappa Yeri
- Agricultural Research Station (ARS), University of Agricultural Sciences (UAS), Raichur 584104, India; (C.L.); (S.Y.)
| | - Anilkumar Vemula
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India; (R.P.); (A.V.); (A.R.); (S.S.); (P.M.G.); (M.R.)
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India; (R.P.); (A.V.); (A.R.); (S.S.); (P.M.G.); (M.R.)
| | - Srinivasan Samineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India; (R.P.); (A.V.); (A.R.); (S.S.); (P.M.G.); (M.R.)
| | - Khela Ram Soren
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur 208024, India; (Y.K.); (K.R.S.); (B.M.); (G.P.D.); (S.K.C.)
| | - Biswajit Mondal
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur 208024, India; (Y.K.); (K.R.S.); (B.M.); (G.P.D.); (S.K.C.)
| | - Girish Prasad Dixit
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur 208024, India; (Y.K.); (K.R.S.); (B.M.); (G.P.D.); (S.K.C.)
| | - Chellapilla Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Delhi 110012, India;
| | - Sushil K. Chaturvedi
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur 208024, India; (Y.K.); (K.R.S.); (B.M.); (G.P.D.); (S.K.C.)
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, India
| | - Pooran M. Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India; (R.P.); (A.V.); (A.R.); (S.S.); (P.M.G.); (M.R.)
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India; (R.P.); (A.V.); (A.R.); (S.S.); (P.M.G.); (M.R.)
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India; (R.P.); (A.V.); (A.R.); (S.S.); (P.M.G.); (M.R.)
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Pusa 848125, India
- Correspondence: (M.T.); (N.P.S.); (R.K.V.)
| | - Narendra P. Singh
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur 208024, India; (Y.K.); (K.R.S.); (B.M.); (G.P.D.); (S.K.C.)
- Correspondence: (M.T.); (N.P.S.); (R.K.V.)
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India; (R.P.); (A.V.); (A.R.); (S.S.); (P.M.G.); (M.R.)
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
- Correspondence: (M.T.); (N.P.S.); (R.K.V.)
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Rubiales D, Annicchiarico P, Vaz Patto MC, Julier B. Legume Breeding for the Agroecological Transition of Global Agri-Food Systems: A European Perspective. FRONTIERS IN PLANT SCIENCE 2021; 12:782574. [PMID: 34868184 PMCID: PMC8637196 DOI: 10.3389/fpls.2021.782574] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Wider and more profitable legume crop cultivation is an indispensable step for the agroecological transition of global agri-food systems but represents a challenge especially in Europe. Plant breeding is pivotal in this context. Research areas of key interest are represented by innovative phenotypic and genome-based selection procedures for crop yield, tolerance to abiotic and biotic stresses enhanced by the changing climate, intercropping, and emerging crop quality traits. We see outmost priority in the exploration of genomic selection (GS) opportunities and limitations, to ease genetic gains and to limit the costs of multi-trait selection. Reducing the profitability gap of legumes relative to major cereals will not be possible in Europe without public funding devoted to crop improvement research, pre-breeding, and, in various circumstances, public breeding. While most of these activities may profit of significant public-private partnerships, all of them can provide substantial benefits to seed companies. A favorable institutional context may comprise some changes to variety registration tests and procedures.
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Affiliation(s)
- Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
| | | | | | - Bernadette Julier
- Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), URP3F, Lusignan, France
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Transcriptome analysis reveals key genes associated with root-lesion nematode Pratylenchus thornei resistance in chickpea. Sci Rep 2021; 11:17491. [PMID: 34471168 PMCID: PMC8410808 DOI: 10.1038/s41598-021-96906-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/18/2021] [Indexed: 02/07/2023] Open
Abstract
The root-lesion nematode, Pratylenchus thornei, is one of the major plant-parasitic nematode species causing significant yield losses in chickpea (Cicer arietinum). In order to identify the underlying mechanisms of resistance to P. thornei, the transcriptomes of control and inoculated roots of three chickpea genotypes viz. D05253 > F3TMWR2AB001 (resistant advanced breeding line), PBA HatTrick (moderately resistant cultivar), and Kyabra (susceptible cultivar) were studied at 20 and 50 days post inoculation using the RNA-seq approach. On analyzing the 633.3 million reads generated, 962 differentially expressed genes (DEGs) were identified. Comparative analysis revealed that the majority of DEGs upregulated in the resistant genotype were downregulated in the moderately resistant and susceptible genotypes. Transcription factor families WRKY and bZIP were uniquely expressed in the resistant genotype. The genes Cysteine-rich receptor-like protein kinase 10, Protein lifeguard-like, Protein detoxification, Bidirectional sugar transporter Sugars Will Eventually be Exported Transporters1 (SWEET1), and Subtilisin-like protease were found to play cross-functional roles in the resistant chickpea genotype against P. thornei. The identified candidate genes for resistance to P. thornei in chickpea can be explored further to develop markers and accelerate the introgression of P. thornei resistance into elite chickpea cultivars.
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Dadu RHR, Bar I, Ford R, Sambasivam P, Croser J, Ribalta F, Kaur S, Sudheesh S, Gupta D. Lens orientalis Contributes Quantitative Trait Loci and Candidate Genes Associated With Ascochyta Blight Resistance in Lentil. FRONTIERS IN PLANT SCIENCE 2021; 12:703283. [PMID: 34539696 PMCID: PMC8442733 DOI: 10.3389/fpls.2021.703283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/28/2021] [Indexed: 05/24/2023]
Abstract
Australian lentil production is affected by several major biotic constraints including Ascochyta blight (AB), caused by Ascochyta lentis, a devastating fungal disease. Cultivation of AB resistant cultivars, alongside agronomic management including fungicide application, is the current most economically viable control strategy. However, the breakdown of AB resistance in cultivars, such as Northfield and Nipper, suggests the need for introgression of new and diverse resistance genes. Successful introgression entails an understanding of the genetic basis of resistance. In this context, a biparental mapping population derived from a cross between a recently identified AB resistant accession ILWL 180 (Lens orientalis) and a susceptible cultivar ILL 6002 was produced. A genetic linkage map was constructed from single-nucleotide polymorphism markers generated using a genotyping-by-sequencing transcript approach. Genetic dissection of the mapping population revealed a major quantitative trait loci (QTL) region nested with three QTLs on linkage group 5 and explained 9.5-11.5 percent (%) of phenotypic variance for AB resistance. Another QTL was identified on LG2 with phenotypic variance of 9.6%. The identified QTL regions harbored putative candidate genes potentially associated with defense responses to A. lentis infection. The QTL analysis and the candidate gene information are expected to contribute to the development of diagnostic markers and enable marker-assisted resistance selection in lentil breeding programmes.
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Affiliation(s)
- Rama Harinath Reddy Dadu
- School of Agriculture and Food, Faculty of Veterinary and Agriculture Sciences, Dookie College, The University of Melbourne, Dookie, VIC, Australia
- Grains Innovation Park, Agriculture Victoria, DJPR, Horsham, VIC, Australia
| | - Ido Bar
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
| | - Rebecca Ford
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
| | - Prabhakaran Sambasivam
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
| | - Janine Croser
- Centre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Federico Ribalta
- Centre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for Agri Bioscience, Bundoora, VIC, Australia
| | - Shimna Sudheesh
- Agriculture Victoria, AgriBio, Centre for Agri Bioscience, Bundoora, VIC, Australia
| | - Dorin Gupta
- School of Agriculture and Food, Faculty of Veterinary and Agriculture Sciences, Dookie College, The University of Melbourne, Dookie, VIC, Australia
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Thudi M, Chen Y, Pang J, Kalavikatte D, Bajaj P, Roorkiwal M, Chitikineni A, Ryan MH, Lambers H, Siddique KHM, Varshney RK. Novel Genes and Genetic Loci Associated With Root Morphological Traits, Phosphorus-Acquisition Efficiency and Phosphorus-Use Efficiency in Chickpea. FRONTIERS IN PLANT SCIENCE 2021; 12:636973. [PMID: 34122467 PMCID: PMC8192852 DOI: 10.3389/fpls.2021.636973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 05/04/2021] [Indexed: 06/05/2023]
Abstract
Chickpea-the second most important grain legume worldwide-is cultivated mainly on marginal soils. Phosphorus (P) deficiency often restricts chickpea yields. Understanding the genetics of traits encoding P-acquisition efficiency and P-use efficiency will help develop strategies to reduce P-fertilizer application. A genome-wide association mapping approach was used to determine loci and genes associated with root architecture, root traits associated with P-acquisition efficiency and P-use efficiency, and any associated proxy traits. Using three statistical models-a generalized linear model (GLM), a mixed linear model (MLM), and a fixed and random model circulating probability unification (FarmCPU) -10, 51, and 40 marker-trait associations (MTAs), respectively were identified. A single nucleotide polymorphism (SNP) locus (Ca1_12310101) on Ca1 associated with three traits, i.e., physiological P-use efficiency, shoot dry weight, and shoot P content was identified. Genes related to shoot P concentration (NAD kinase 2, dynamin-related protein 1C), physiological P-use efficiency (fasciclin-like arabinogalactan protein), specific root length (4-coumarate-CoA ligase 1) and manganese concentration in mature leaves (ABC1 family protein) were identified. The MTAs and novel genes identified in this study can be used to improve P-use efficiency in chickpea.
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Affiliation(s)
- Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Yinglong Chen
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Jiayin Pang
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Danamma Kalavikatte
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prasad Bajaj
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Megan H Ryan
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Hans Lambers
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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Barmukh R, Soren KR, Madugula P, Gangwar P, Shanmugavadivel PS, Bharadwaj C, Konda AK, Chaturvedi SK, Bhandari A, Rajain K, Singh NP, Roorkiwal M, Varshney RK. Construction of a high-density genetic map and QTL analysis for yield, yield components and agronomic traits in chickpea (Cicer arietinum L.). PLoS One 2021; 16:e0251669. [PMID: 33989359 PMCID: PMC8121343 DOI: 10.1371/journal.pone.0251669] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/30/2021] [Indexed: 12/04/2022] Open
Abstract
Unravelling the genetic architecture underlying yield components and agronomic traits is important for enhancing crop productivity. Here, a recombinant inbred line (RIL) population, developed from ICC 4958 and DCP 92–3 cross, was used for constructing linkage map and QTL mapping analysis. The RIL population was genotyped using a high-throughput Axiom®CicerSNP array, which enabled the development of a high-density genetic map consisting of 3,818 SNP markers and spanning a distance of 1064.14 cM. Analysis of phenotyping data for yield, yield components and agronomic traits measured across three years together with genetic mapping data led to the identification of 10 major-effect QTLs and six minor-effect QTLs explaining up to 59.70% phenotypic variance. The major-effect QTLs identified for 100-seed weight, and plant height possessed key genes, such as C3HC4 RING finger protein, pentatricopeptide repeat (PPR) protein, sugar transporter, leucine zipper protein and NADH dehydrogenase, amongst others. The gene ontology studies highlighted the role of these genes in regulating seed weight and plant height in crop plants. The identified genomic regions for yield, yield components, and agronomic traits, and the closely linked markers will help advance genetics research and breeding programs in chickpea.
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Affiliation(s)
- Rutwik Barmukh
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | | | - Praveen Madugula
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | | | | | | | - Sushil K. Chaturvedi
- ICAR-Indian Institute of Pulses Research, Kanpur, UP, India
- Rani Lakshmi Bai Central Agricultural University, Jhansi, India
| | - Aditi Bhandari
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Kritika Rajain
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Narendra Pratap Singh
- ICAR-Indian Institute of Pulses Research, Kanpur, UP, India
- * E-mail: (RKV); (MR); (NPS)
| | - Manish Roorkiwal
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- * E-mail: (RKV); (MR); (NPS)
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- * E-mail: (RKV); (MR); (NPS)
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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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Ye CY, Fan L. Orphan Crops and their Wild Relatives in the Genomic Era. MOLECULAR PLANT 2021; 14:27-39. [PMID: 33346062 DOI: 10.1016/j.molp.2020.12.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/01/2020] [Accepted: 12/15/2020] [Indexed: 05/06/2023]
Abstract
More than half of the calories consumed by humans are provided by three major cereal crops (rice, maize, and wheat). Orphan crops are usually well adapted to low-input agricultural conditions, and they not only play vital roles in local areas but can also contribute to food and nutritional needs worldwide. Interestingly, many wild relatives of orphan crops are important weeds of major crops. Although orphan crops and their wild relatives have received little attentions from researchers for many years, genomic studies have recently been performed on these plants. Here, we provide an overview of genomic studies on orphan crops, with a focus on orphan cereals and their wild relatives. The genomes of at least 12 orphan cereals and/or their wild relatives have been sequenced. In addition to genomic benefits for orphan crop breeding, we discuss the potential ways for mutual utilization of genomic data from major crops, orphan crops, and their wild relatives (including weeds) and provide perspectives on genetic improvement of both orphan and major crops (including de novo domestication of orphan crops) in the coming genomic era.
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Affiliation(s)
- Chu-Yu Ye
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Longjiang Fan
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572024, China.
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40
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Manchikatla PK, Kalavikatte D, Mallikarjuna BP, Palakurthi R, Khan AW, Jha UC, Bajaj P, Singam P, Chitikineni A, Varshney RK, Thudi M. MutMap Approach Enables Rapid Identification of Candidate Genes and Development of Markers Associated With Early Flowering and Enhanced Seed Size in Chickpea ( Cicer arietinum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:688694. [PMID: 34326857 PMCID: PMC8313520 DOI: 10.3389/fpls.2021.688694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/02/2021] [Indexed: 05/16/2023]
Abstract
Globally terminal drought is one of the major constraints to chickpea (Cicer arietinum L.) production. Early flowering genotypes escape terminal drought, and the increase in seed size compensates for yield losses arising from terminal drought. A MutMap population for early flowering and large seed size was developed by crossing the mutant line ICC4958-M3-2828 with wild-type ICC 4958. Based on the phenotyping of MutMap population, extreme bulks for days to flowering and 100-seed weight were sequenced using Hi-Seq2500 at 10X coverage. On aligning 47.41 million filtered reads to the CDC Frontier reference genome, 31.41 million reads were mapped and 332,395 single nucleotide polymorphisms (SNPs) were called. A reference genome assembly for ICC 4958 was developed replacing these SNPs in particular positions of the CDC Frontier genome. SNPs specific for each mutant bulk ranged from 3,993 to 5,771. We report a single unique genomic region on Ca6 (between 9.76 and 12.96 Mb) harboring 31, 22, 17, and 32 SNPs with a peak of SNP index = 1 for low bulk for flowering time, high bulk for flowering time, high bulk for 100-seed weight, and low bulk for 100-seed weight, respectively. Among these, 22 SNPs are present in 20 candidate genes and had a moderate allelic impact on the genes. Two markers, Ca6EF10509893 for early flowering and Ca6HSDW10099486 for 100-seed weight, were developed and validated using the candidate SNPs. Thus, the associated genes, candidate SNPs, and markers developed in this study are useful for breeding chickpea varieties that mitigate yield losses under drought stress.
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Affiliation(s)
- Praveen Kumar Manchikatla
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Danamma Kalavikatte
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Bingi Pujari Mallikarjuna
- Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, Regional Research Centre, Dharwad, India
| | - Ramesh Palakurthi
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Aamir W. Khan
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Uday Chand Jha
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Prasad Bajaj
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prashant Singam
- Department of Genetics, Osmania University, Hyderabad, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
- *Correspondence: Rajeev K. Varshney, ;
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
- Mahendar Thudi,
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Jha UC, Nayyar H, Palakurthi R, Jha R, Valluri V, Bajaj P, Chitikineni A, Singh NP, Varshney RK, Thudi M. Major QTLs and Potential Candidate Genes for Heat Stress Tolerance Identified in Chickpea ( Cicer arietinum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:655103. [PMID: 34381469 PMCID: PMC8350164 DOI: 10.3389/fpls.2021.655103] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/31/2021] [Indexed: 05/15/2023]
Abstract
In the context of climate change, heat stress during the reproductive stages of chickpea (Cicer arietinum L.) leads to significant yield losses. In order to identify the genomic regions responsible for heat stress tolerance, a recombinant inbred line population derived from DCP 92-3 (heat sensitive) and ICCV 92944 (heat tolerant) was genotyped using the genotyping-by-sequencing approach and evaluated for two consecutive years (2017 and 2018) under normal and late sown or heat stress environments. A high-density genetic map comprising 788 single-nucleotide polymorphism markers spanning 1,125 cM was constructed. Using composite interval mapping, a total of 77 QTLs (37 major and 40 minor) were identified for 12 of 13 traits. A genomic region on CaLG07 harbors quantitative trait loci (QTLs) explaining >30% phenotypic variation for days to pod initiation, 100 seed weight, and for nitrogen balance index explaining >10% PVE. In addition, we also reported for the first time major QTLs for proxy traits (physiological traits such as chlorophyll content, nitrogen balance index, normalized difference vegetative index, and cell membrane stability). Furthermore, 32 candidate genes in the QTL regions that encode the heat shock protein genes, heat shock transcription factors, are involved in flowering time regulation as well as pollen-specific genes. The major QTLs reported in this study, after validation, may be useful in molecular breeding for developing heat-tolerant superior lines or varieties.
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Affiliation(s)
- Uday Chand Jha
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
| | - Ramesh Palakurthi
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rintu Jha
- Institute of Crop Science, Chinese Academy of Agricultural Science (CAAS), Beijing, China
| | - Vinod Valluri
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prasad Bajaj
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Narendra P. Singh
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- University of Southern Queensland, Toowoomba, QLD, Australia
- *Correspondence: Mahendar Thudi
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Roorkiwal M, Pandey S, Thavarajah D, Hemalatha R, Varshney RK. Molecular Mechanisms and Biochemical Pathways for Micronutrient Acquisition and Storage in Legumes to Support Biofortification for Nutritional Security. FRONTIERS IN PLANT SCIENCE 2021; 12:682842. [PMID: 34163513 PMCID: PMC8215609 DOI: 10.3389/fpls.2021.682842] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/06/2021] [Indexed: 05/10/2023]
Abstract
The world faces a grave situation of nutrient deficiency as a consequence of increased uptake of calorie-rich food that threaten nutritional security. More than half the world's population is affected by different forms of malnutrition. Unhealthy diets associated with poor nutrition carry a significant risk of developing non-communicable diseases, leading to a high mortality rate. Although considerable efforts have been made in agriculture to increase nutrient content in cereals, the successes are insufficient. The number of people affected by different forms of malnutrition has not decreased much in the recent past. While legumes are an integral part of the food system and widely grown in sub-Saharan Africa and South Asia, only limited efforts have been made to increase their nutrient content in these regions. Genetic variation for a majority of nutritional traits that ensure nutritional security in adverse conditions exists in the germplasm pool of legume crops. This diversity can be utilized by selective breeding for increased nutrients in seeds. The targeted identification of precise factors related to nutritional traits and their utilization in a breeding program can help mitigate malnutrition. The principal objective of this review is to present the molecular mechanisms of nutrient acquisition, transport and metabolism to support a biofortification strategy in legume crops to contribute to addressing malnutrition.
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Affiliation(s)
- Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Sarita Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Dil Thavarajah
- Plant and Environmental Sciences, Poole Agricultural Center, Clemson University, Clemson, SC, United States
| | - R. Hemalatha
- ICMR-National Institute of Nutrition (NIN), Hyderabad, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
- *Correspondence: Rajeev K. Varshney, ;
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Scott MF, Ladejobi O, Amer S, Bentley AR, Biernaskie J, Boden SA, Clark M, Dell'Acqua M, Dixon LE, Filippi CV, Fradgley N, Gardner KA, Mackay IJ, O'Sullivan D, Percival-Alwyn L, Roorkiwal M, Singh RK, Thudi M, Varshney RK, Venturini L, Whan A, Cockram J, Mott R. Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding. Heredity (Edinb) 2020; 125:396-416. [PMID: 32616877 PMCID: PMC7784848 DOI: 10.1038/s41437-020-0336-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 11/21/2022] Open
Abstract
Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm 'package' that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding.
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Affiliation(s)
| | | | - Samer Amer
- University of Reading, Reading, RG6 6AH, UK
- Faculty of Agriculture, Alexandria University, Alexandria, 23714, Egypt
| | - Alison R Bentley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Jay Biernaskie
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Scott A Boden
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | | | | | - Laura E Dixon
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Carla V Filippi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Nicolas Repetto y Los Reseros s/n, 1686, Hurlingham, Buenos Aires, Argentina
| | - Nick Fradgley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Keith A Gardner
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Ian J Mackay
- SRUC, West Mains Road, Kings Buildings, Edinburgh, EH9 3JG, UK
| | | | | | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rakesh Kumar Singh
- International Center for Biosaline Agriculture, Academic City, Dubai, United Arab Emirates
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev Kumar Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Alex Whan
- CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - James Cockram
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Richard Mott
- UCL Genetics Institute, Gower Street, London, WC1E 6BT, UK
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Barmukh R, Roorkiwal M, Jaba J, Chitikineni A, Mishra SP, Sagurthi SR, Munghate R, Sharma HC, Varshney RK. Development of a dense genetic map and QTL analysis for pod borer Helicoverpa armigera (Hübner) resistance component traits in chickpea (Cicer arietinum L.). THE PLANT GENOME 2020; 14:e20071. [PMID: 33289349 DOI: 10.1002/tpg2.20071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/15/2020] [Indexed: 06/12/2023]
Abstract
Genetic enhancement for resistance against the pod borer, Helicoverpa armigera is crucial for enhancing production and productivity of chickpea. Here we provide some novel insights into the genetic architecture of natural variation in H. armigera resistance in chickpea, an important legume, which plays a major role in food and nutritional security. An interspecific recombinant inbred line (RIL) population developed from a cross between H. armigera susceptible accession ICC 4958 (Cicer arietinum) and resistant accession PI 489777 (Cicer reticulatum) was evaluated for H. armigera resistance component traits using detached leaf assay and under field conditions. A high-throughput AxiomCicerSNP array was utilized to construct a dense linkage map comprising of 3,873 loci and spanning a distance of 949.27 cM. Comprehensive analyses of extensive genotyping and phenotyping data identified nine main-effect QTLs and 955 epistatic QTLs explaining up to 42.49% and 38.05% phenotypic variance, respectively, for H. armigera resistance component traits. The main-effect QTLs identified in this RIL population were linked with previously described genes, known to modulate resistance against lepidopteran insects in crop plants. One QTL cluster harbouring main-effect QTLs for three H. armigera resistance component traits and explaining up to 42.49% of the phenotypic variance, was identified on CaLG03. This genomic region, after validation, may be useful to improve H. armigera resistance component traits in elite chickpea cultivars.
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Affiliation(s)
- Rutwik Barmukh
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Manish Roorkiwal
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Jagdish Jaba
- Theme-Integrated Crop Management, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Suraj Prasad Mishra
- Theme-Integrated Crop Management, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Rajendra Munghate
- Theme-Integrated Crop Management, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - H C Sharma
- Theme-Integrated Crop Management, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Sab S, Lokesha R, Mannur DM, Somasekhar, Jadhav K, Mallikarjuna BP, C L, Yeri S, Valluri V, Bajaj P, Chitikineni A, Vemula A, Rathore A, Varshney RK, Shankergoud I, Thudi M. Genome-Wide SNP Discovery and Mapping QTLs for Seed Iron and Zinc Concentrations in Chickpea ( Cicer arietinum L.). Front Nutr 2020; 7:559120. [PMID: 33154975 PMCID: PMC7588353 DOI: 10.3389/fnut.2020.559120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/21/2020] [Indexed: 11/16/2022] Open
Abstract
Biofortification through plant breeding is a cost-effective and sustainable approach towards addressing micronutrient malnutrition prevailing across the globe. Screening cultivars for micronutrient content and identification of quantitative trait loci (QTLs)/genes and markers help in the development of biofortified varieties in chickpea (Cicer arietinum L.). With the aim of identifying the genomic regions controlling seed Fe and Zn concentrations, the F2:3 population derived from a cross between MNK-1 and Annigeri 1 was genotyped using genotyping by sequencing approach and evaluated for Fe and Zn concentration. An intraspecific genetic linkage map comprising 839 single nucleotide polymorphisms (SNPs) spanning a total distance of 1,088.04 cM with an average marker density of 1.30 cM was constructed. By integrating the linkage map data with the phenotypic data of the F2:3 population, a total of 11 QTLs were detected for seed Fe concentration on CaLG03, CaLG04, and CaLG05, with phenotypic variation explained ranging from 7.2% (CaqFe3.4) to 13.4% (CaqFe4.2). For seed Zn concentration, eight QTLs were identified on CaLG04, CaLG05, and CaLG08. The QTLs individually explained phenotypic variations ranging between 5.7% (CaqZn8.1) and 13.7% (CaqZn4.3). Three QTLs for seed Fe and Zn concentrations (CaqFe4.4, CaqFe4.5, and CaqZn4.1) were colocated in the "QTL-hotspot" region on CaLG04 that harbors several drought tolerance-related QTLs. We identified genes in the QTL regions that encode iron-sulfur metabolism and zinc-dependent alcohol dehydrogenase activity on CaLG03, iron ion binding oxidoreductase on CaLG04, and zinc-induced facilitator-like protein and ZIP zinc/iron transport family protein on CaLG05. These genomic regions and the associated markers can be used in marker-assisted selection to increase seed Fe and Zn concentrations in agronomically superior chickpea varieties.
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Affiliation(s)
- Syed Sab
- Department of Genetics and Plant Breeding, University of Agricultural Sciences - Raichur (UAS-R), Raichur, India
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ramappa Lokesha
- Department of Genetics and Plant Breeding, University of Agricultural Sciences - Raichur (UAS-R), Raichur, India
| | - D. M. Mannur
- Department of Genetics and Plant Breeding, University of Agricultural Sciences - Raichur (UAS-R), Raichur, India
| | - Somasekhar
- Department of Genetics and Plant Breeding, University of Agricultural Sciences - Raichur (UAS-R), Raichur, India
| | - Kisan Jadhav
- Department of Genetics and Plant Breeding, University of Agricultural Sciences - Raichur (UAS-R), Raichur, India
| | - Bingi Pujari Mallikarjuna
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Laxuman C
- Zonal Agricultural Research Station, University of Agricultural Sciences - Raichur, Kalaburagi, India
| | - Sharanbasappa Yeri
- Zonal Agricultural Research Station, University of Agricultural Sciences - Raichur, Kalaburagi, India
| | - Vinod Valluri
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prasad Bajaj
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - AnilKumar Vemula
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Abhishek Rathore
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev Kumar Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - I. Shankergoud
- Department of Genetics and Plant Breeding, University of Agricultural Sciences - Raichur (UAS-R), Raichur, India
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Singh RK, Prasad A, Muthamilarasan M, Parida SK, Prasad M. Breeding and biotechnological interventions for trait improvement: status and prospects. PLANTA 2020; 252:54. [PMID: 32948920 PMCID: PMC7500504 DOI: 10.1007/s00425-020-03465-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/12/2020] [Indexed: 05/06/2023]
Abstract
Present review describes the molecular tools and strategies deployed in the trait discovery and improvement of major crops. The prospects and challenges associated with these approaches are discussed. Crop improvement relies on modulating the genes and genomic regions underlying key traits, either directly or indirectly. Direct approaches include overexpression, RNA interference, genome editing, etc., while breeding majorly constitutes the indirect approach. With the advent of latest tools and technologies, these strategies could hasten the improvement of crop species. Next-generation sequencing, high-throughput genotyping, precision editing, use of space technology for accelerated growth, etc. had provided a new dimension to crop improvement programmes that work towards delivering better varieties to cope up with the challenges. Also, studies have widened from understanding the response of plants to single stress to combined stress, which provides insights into the molecular mechanisms regulating tolerance to more than one stress at a given point of time. Altogether, next-generation genetics and genomics had made tremendous progress in delivering improved varieties; however, the scope still exists to expand its horizon to other species that remain underutilized. In this context, the present review systematically analyses the different genomics approaches that are deployed for trait discovery and improvement in major species that could serve as a roadmap for executing similar strategies in other crop species. The application, pros, and cons, and scope for improvement of each approach have been discussed with examples, and altogether, the review provides comprehensive coverage on the advances in genomics to meet the ever-growing demands for agricultural produce.
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Affiliation(s)
- Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Swarup K Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom ®CicerSNP Array in Chickpea. Int J Mol Sci 2020; 21:ijms21145058. [PMID: 32709160 PMCID: PMC7404205 DOI: 10.3390/ijms21145058] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/10/2020] [Accepted: 07/14/2020] [Indexed: 01/22/2023] Open
Abstract
Globally, chickpea production is severely affected by salinity stress. Understanding the genetic basis for salinity tolerance is important to develop salinity tolerant chickpeas. A recombinant inbred line (RIL) population developed using parental lines ICCV 10 (salt-tolerant) and DCP 92-3 (salt-sensitive) was screened under field conditions to collect information on agronomy, yield components, and stress tolerance indices. Genotyping data generated using Axiom®CicerSNP array was used to construct a linkage map comprising 1856 SNP markers spanning a distance of 1106.3 cM across eight chickpea chromosomes. Extensive analysis of the phenotyping and genotyping data identified 28 quantitative trait loci (QTLs) explaining up to 28.40% of the phenotypic variance in the population. We identified QTL clusters on CaLG03 and CaLG06, each harboring major QTLs for yield and yield component traits under salinity stress. The main-effect QTLs identified in these two clusters were associated with key genes such as calcium-dependent protein kinases, histidine kinases, cation proton antiporter, and WRKY and MYB transcription factors, which are known to impart salinity stress tolerance in crop plants. Molecular markers/genes associated with these major QTLs, after validation, will be useful to undertake marker-assisted breeding for developing better varieties with salinity tolerance.
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Zhang Q, Xu M, Xia X, Komatsuda T, Varshney RK, Shi K. Crop genetics research in Asia: improving food security and nutrition. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1339-1344. [PMID: 32306095 DOI: 10.1007/s00122-020-03597-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Mingliang Xu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xianchun Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Takao Komatsuda
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India
| | - Kai Shi
- Department of Horticulture, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
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