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Montesinos-López A, Crespo-Herrera L, Dreisigacker S, Gerard G, Vitale P, Saint Pierre C, Govindan V, Tarekegn ZT, Flores MC, Pérez-Rodríguez P, Ramos-Pulido S, Lillemo M, Li H, Montesinos-López OA, Crossa J. Deep learning methods improve genomic prediction of wheat breeding. Front Plant Sci 2024; 15:1324090. [PMID: 38504889 PMCID: PMC10949530 DOI: 10.3389/fpls.2024.1324090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024]
Abstract
In the field of plant breeding, various machine learning models have been developed and studied to evaluate the genomic prediction (GP) accuracy of unseen phenotypes. Deep learning has shown promise. However, most studies on deep learning in plant breeding have been limited to small datasets, and only a few have explored its application in moderate-sized datasets. In this study, we aimed to address this limitation by utilizing a moderately large dataset. We examined the performance of a deep learning (DL) model and compared it with the widely used and powerful best linear unbiased prediction (GBLUP) model. The goal was to assess the GP accuracy in the context of a five-fold cross-validation strategy and when predicting complete environments using the DL model. The results revealed the DL model outperformed the GBLUP model in terms of GP accuracy for two out of the five included traits in the five-fold cross-validation strategy, with similar results in the other traits. This indicates the superiority of the DL model in predicting these specific traits. Furthermore, when predicting complete environments using the leave-one-environment-out (LOEO) approach, the DL model demonstrated competitive performance. It is worth noting that the DL model employed in this study extends a previously proposed multi-modal DL model, which had been primarily applied to image data but with small datasets. By utilizing a moderately large dataset, we were able to evaluate the performance and potential of the DL model in a context with more information and challenging scenario in plant breeding.
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Affiliation(s)
- Abelardo Montesinos-López
- Departamento de Matemáticas, Centro Universitario de Ciencias Exactas e Ingenierías (CUCEI), Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Leonardo Crespo-Herrera
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Estado. de México, Mexico
| | - Susanna Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Estado. de México, Mexico
| | - Guillermo Gerard
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Estado. de México, Mexico
| | - Paolo Vitale
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Estado. de México, Mexico
| | - Carolina Saint Pierre
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Estado. de México, Mexico
| | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Estado. de México, Mexico
| | | | - Moisés Chavira Flores
- Instituto de Investigaciones en Matemáticas Aplicadas y Sistemas (IIMAS), Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Ciudad de México, Mexico
| | - Paulino Pérez-Rodríguez
- Estudios del Desarrollo Rural, Economía, Estadística y Cómputo Aplicado, Colegio de Postgraduados, Texcoco, Estado de México, Mexico
| | - Sofía Ramos-Pulido
- Departamento de Matemáticas, Centro Universitario de Ciencias Exactas e Ingenierías (CUCEI), Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Morten Lillemo
- Department of Plant Science, Norwegian University of Life Science (NMBU), Ås, Norway
| | - Huihui Li
- 6State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences and CIMMYT China Office, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | | | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Estado. de México, Mexico
- Estudios del Desarrollo Rural, Economía, Estadística y Cómputo Aplicado, Colegio de Postgraduados, Texcoco, Estado de México, Mexico
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2
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Togninalli M, Wang X, Kucera T, Shrestha S, Juliana P, Mondal S, Pinto F, Govindan V, Crespo-Herrera L, Huerta-Espino J, Singh RP, Borgwardt K, Poland J. Multi-modal deep learning improves grain yield prediction in wheat breeding by fusing genomics and phenomics. Bioinformatics 2023:7176366. [PMID: 37220903 DOI: 10.1093/bioinformatics/btad336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/15/2023] [Accepted: 05/22/2023] [Indexed: 05/25/2023] Open
Abstract
MOTIVATION Developing new crop varieties with superior performance is highly important to ensure robust and sustainable global food security. The speed of variety development is limited by long field cycles and advanced generation selections in plant breeding programs. While methods to predict yield from genotype or phenotype data have been proposed, improved performance and integrated models are needed. RESULTS We propose a machine learning model that leverages both genotype and phenotype measurements by fusing genetic variants with multiple data sources collected by unmanned aerial systems. We use a deep multiple instance learning framework with an attention mechanism that sheds light on the importance given to each input during prediction, enhancing interpretability. Our model reaches 0.754 ± 0.024 Pearson correlation coefficient when predicting yield in similar environmental conditions; a 34.8% improvement over the genotype-only linear baseline (0.559 ± 0.050). We further predict yield on new lines in an unseen environment using only genotypes, obtaining a prediction accuracy of 0.386 ± 0.010, a 13.5% improvement over the linear baseline. Our multi-modal deep learning architecture efficiently accounts for plant health and environment, distilling the genetic contribution and providing excellent predictions. Yield prediction algorithms leveraging phenotypic observations during training therefore promise to improve breeding programs, ultimately speeding up delivery of improved varieties. AVAILABILITY AND IMPLEMENTATION Available at https://github.com/BorgwardtLab/PheGeMIL (code) and https://doi.org/doi:10.5061/dryad.kprr4xh5p (data).
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Affiliation(s)
- Matteo Togninalli
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Visium, Lausanne, Switzerland
| | - Xu Wang
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas USA
- Department of Agricultural and Biological Engineering, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, Florida USA
| | - Tim Kucera
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Machine Learning and Systems Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sandesh Shrestha
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas USA
| | - Philomin Juliana
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, Mexico
| | - Suchismita Mondal
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, Mexico
| | - Francisco Pinto
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, Mexico
| | - Velu Govindan
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, Mexico
| | | | - Julio Huerta-Espino
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, Mexico
- Campo Experimental Valle de Mexico-INIFAP, Texcoco, Estado de Mexico Mexico
| | - Ravi P Singh
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, Mexico
| | - Karsten Borgwardt
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Machine Learning and Systems Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas USA
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Rathan ND, Krishnappa G, Singh AM, Govindan V. Mapping QTL for Phenological and Grain-Related Traits in a Mapping Population Derived from High-Zinc-Biofortified Wheat. Plants (Basel) 2023; 12:220. [PMID: 36616350 PMCID: PMC9823887 DOI: 10.3390/plants12010220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Genomic regions governing days to heading (DH), days to maturity (DM), plant height (PH), thousand-kernel weight (TKW), and test weight (TW) were investigated in a set of 190 RILs derived from a cross between a widely cultivated wheat-variety, Kachu (DPW-621-50), and a high-zinc variety, Zinc-Shakti. The RIL population was genotyped using 909 DArTseq markers and phenotyped in three environments. The constructed genetic map had a total genetic length of 4665 cM, with an average marker density of 5.13 cM. A total of thirty-seven novel quantitative trait loci (QTL), including twelve for PH, six for DH, five for DM, eight for TKW and six for TW were identified. A set of 20 stable QTLs associated with the expression of DH, DM, PH, TKW, and TW were identified in two or more environments. Three novel pleiotropic genomic-regions harboring co-localized QTLs governing two or more traits were also identified. In silico analysis revealed that the DArTseq markers were located on important putative candidate genes such as MLO-like protein, Phytochrome, Zinc finger and RING-type, Cytochrome P450 and pentatricopeptide repeat, involved in the regulation of pollen maturity, the photoperiodic modulation of flowering-time, abiotic-stress tolerance, grain-filling duration, thousand-kernel weight, seed morphology, and plant growth and development. The identified novel QTLs, particularly stable and co-localized QTLs, will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection (MAS).
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Affiliation(s)
| | | | | | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco 56237, Mexico
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4
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Kamble U, Mishra CN, Govindan V, Sharma AK, Pawar S, Kumar S, Krishnappa G, Gupta OP, Singh GP, Singh G. Ensuring Nutritional Security in India through Wheat Biofortification: A Review. Genes (Basel) 2022; 13:genes13122298. [PMID: 36553565 PMCID: PMC9778289 DOI: 10.3390/genes13122298] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Undernourishment of nutrients, also known as hidden hunger, affects over 2 billion populace globally. Even though stunting among children below five years of age has decreased in India in the last ten years, India is home to roughly thirty percent of the world's population of stunted pre-schoolers. A significant improvement has been witnessed in the targeted development and deployment of biofortified crops; approximately 20 million farm households from developing counties benefit from cultivating and consuming biofortified crops. There is ample scope for including biofortified varieties in the seed chain, ensuring nutritional security. Wheat is a dietary staple in India, typically consumed as wholemeal flour in the form of flatbreads such as chapatti and roti. Wheat contributes to nearly one fifth of global energy requirements and can also provide better amounts of iron (Fe) and zinc (Zn). As a result, biofortified wheat can serve as a medium for delivery of essential micronutrients such as Fe and Zn to end users. This review discusses wheat biofortification components such as Fe and Zn dynamics, its uptake and movement in plants, the genetics of their buildup, and the inclusion of biofortified wheat varieties in the seed multiplication chain concerning India.
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Affiliation(s)
- Umesh Kamble
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
| | - Chandra Nath Mishra
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
- Correspondence: ; Tel.: +91-946-8251-294
| | | | - Amit Kumar Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
| | - Sushma Pawar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
| | - Satish Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
| | | | - Om Prakash Gupta
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
| | | | - Gyanendra Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
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5
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Lopez-Cruz M, Dreisigacker S, Crespo-Herrera L, Bentley AR, Singh R, Poland J, Shrestha S, Huerta-Espino J, Govindan V, Juliana P, Mondal S, Pérez-Rodríguez P, Crossa J. Sparse kernel models provide optimization of training set design for genomic prediction in multiyear wheat breeding data. Plant Genome 2022; 15:e20254. [PMID: 36043341 DOI: 10.1002/tpg2.20254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
The success of genomic selection (GS) in breeding schemes relies on its ability to provide accurate predictions of unobserved lines at early stages. Multigeneration data provides opportunities to increase the training data size and thus, the likelihood of extracting useful information from ancestors to improve prediction accuracy. The genomic best linear unbiased predictions (GBLUPs) are performed by borrowing information through kinship relationships between individuals. Multigeneration data usually becomes heterogeneous with complex family relationship patterns that are increasingly entangled with each generation. Under these conditions, historical data may not be optimal for model training as the accuracy could be compromised. The sparse selection index (SSI) is a method for training set (TRN) optimization, in which training individuals provide predictions to some but not all predicted subjects. We added an additional trimming process to the original SSI (trimmed SSI) to remove less important training individuals for prediction. Using a large multigeneration (8 yr) wheat (Triticum aestivum L.) grain yield dataset (n = 68,836), we found increases in accuracy as more years are included in the TRN, with improvements of ∼0.05 in the GBLUP accuracy when using 5 yr of historical data relative to when using only 1 yr. The SSI method showed a small gain over the GBLUP accuracy but with an important reduction on the TRN size. These reduced TRNs were formed with a similar number of subjects from each training generation. Our results suggest that the SSI provides a more stable ranking of genotypes than the GBLUP as the TRN becomes larger.
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Affiliation(s)
- Marco Lopez-Cruz
- Dep. of Epidemiology and Biostatistics, Michigan State Univ., East Lansing, MI, USA
| | - Susanne Dreisigacker
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Leonardo Crespo-Herrera
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Alison R Bentley
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Ravi Singh
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jesse Poland
- Dep. of Agronomy, Kansas State Univ., Manhattan, KS, USA
| | | | - Julio Huerta-Espino
- Campo Experimental Valle de Mexico, Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias (INIFAP), Chapingo, Mexico
| | - Velu Govindan
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Philomin Juliana
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Suchismita Mondal
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Jose Crossa
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
- Colegio de Postgraduados, Montecillos, Mexico
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6
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Roy C, Kumar S, Ranjan RD, Kumhar SR, Govindan V. Genomic approaches for improving grain zinc and iron content in wheat. Front Genet 2022; 13:1045955. [PMID: 36437911 PMCID: PMC9683485 DOI: 10.3389/fgene.2022.1045955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/24/2022] [Indexed: 09/29/2023] Open
Abstract
More than three billion people worldwide suffer from iron deficiency associated anemia and an equal number people suffer from zinc deficiency. These conditions are more prevalent in Sub-Saharan Africa and South Asia. In developing countries, children under the age of five with stunted growth and pregnant or lactating women were found to be at high risk of zinc and iron deficiencies. Biofortification, defined as breeding to develop varieties of staple food crops whose grain contains higher levels of micronutrients such as iron and zinc, are one of the most promising, cost-effective and sustainable ways to improve the health in resource-poor households, particularly in rural areas where families consume some part of what they grow. Biofortification through conventional breeding in wheat, particularly for grain zinc and iron, have made significant contributions, transferring important genes and quantitative trait loci (QTLs) from wild and related species into cultivated wheat. Nonetheless, the quantitative, genetically complex nature of iron and zinc levels in wheat grain limits progress through conventional breeding, making it difficult to attain genetic gain both for yield and grain mineral concentrations. Wheat biofortification can be achieved by enhancing mineral uptake, source-to-sink translocation of minerals and their deposition into grains, and the bioavailability of the minerals. A number of QTLs with major and minor effects for those traits have been detected in wheat; introducing the most effective into breeding lines will increase grain zinc and iron concentrations. New approaches to achieve this include marker assisted selection and genomic selection. Faster breeding approaches need to be combined to simultaneously increase grain mineral content and yield in wheat breeding lines.
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Affiliation(s)
- Chandan Roy
- Department of Genetics and Plant Breeding, Agriculture University, Jodhpur, Rajasthan, India
| | - Sudhir Kumar
- Department of Plant Breeding and Genetics, Bihar Agricultural University, Bhagalpur, Bihar, India
| | - Rakesh Deo Ranjan
- Department of Plant Breeding and Genetics, Bihar Agricultural University, Bhagalpur, Bihar, India
| | - Sita Ram Kumhar
- Department of Genetics and Plant Breeding, Agriculture University, Jodhpur, Rajasthan, India
| | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
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7
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Navathe S, Pandey AK, Sharma S, Chand R, Mishra VK, Kumar D, Jaiswal S, Iquebal MA, Govindan V, Joshi AK, Singh PK. New Genomic Regions Identified for Resistance to Spot Blotch and Terminal Heat Stress in an Interspecific Population of Triticum aestivum and T. spelta. Plants (Basel) 2022; 11:2987. [PMID: 36365440 PMCID: PMC9657703 DOI: 10.3390/plants11212987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Wheat is one of the most widely grown and consumed food crops in the world. Spot blotch and terminal heat stress are the two significant constraints mainly in the Indo-Gangetic plains of South Asia. The study was undertaken using 185 recombinant lines (RILs) derived from the interspecific hybridization of 'Triticum aestivum (HUW234) × T. spelta (H+26)' to reveal genomic regions associated with tolerance to combined stress to spot blotch and terminal heat. Different physiological (NDVI, canopy temperature, leaf chlorophyll) and grain traits (TGW, grain size) were observed under stressed (spot blotch, terminal heat) and non-stressed environments. The mean maturity duration of RILs under combined stress was reduced by 12 days, whereas the normalized difference vegetation index (NDVI) was 46.03%. Similarly, the grain size was depleted under combined stress by 32.23% and thousand kernel weight (TKW) by 27.56% due to spot blotch and terminal heat stress, respectively. The genetic analysis using 6734 SNP markers identified 37 significant loci for the area under the disease progress curve (AUDPC) and NDVI. The genome-wide functional annotation of the SNP markers revealed gene functions such as plant chitinases, NB-ARC and NBS-LRR, and the peroxidase superfamily Cytochrome P450 have a positive role in the resistance through a hypersensitive response. Zinc finger domains, cysteine protease coding gene, F-box protein, ubiquitin, and associated proteins, play a substantial role in the combined stress of spot blotch and terminal heat in bread wheat, according to genomic domains ascribed to them. The study also highlights T. speltoides as a source of resistance to spot blotch and terminal heat tolerance.
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Affiliation(s)
- Sudhir Navathe
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
- Agharkar Research Institute, G.G. Agharkar Road, Pune 411004, India
| | - Ajeet Kumar Pandey
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Sandeep Sharma
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Ramesh Chand
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Vinod Kumar Mishra
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh 123031, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India
| | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Veracruz 56237, Mexico
| | - Arun Kumar Joshi
- Borlaug Institute for South Asia, NASC Complex, DPS Marg, New Delhi 110012, India
- International Maize and Wheat Improvement Center (CIMMYT), G-2, B-Block, NASC Complex, DPS Marg, New Delhi 110012, India
| | - Pawan Kumar Singh
- International Maize and Wheat Improvement Center (CIMMYT), Veracruz 56237, Mexico
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Ibba MI, Gupta OP, Govindan V, Johnson AAT, Brinch-Pedersen H, Nikolic M, Taleon V. Editorial: Wheat biofortification to alleviate global malnutrition. Front Nutr 2022; 9:1001443. [PMID: 36185675 PMCID: PMC9524417 DOI: 10.3389/fnut.2022.1001443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/26/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Maria Itria Ibba
- Wheat Chemistry and Quality Laboratory, International Center for the Improvement of Wheat and Maize (CIMMYT), Texcoco, Mexico
| | - Om Prakash Gupta
- Division of Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
- *Correspondence: Om Prakash Gupta
| | - Velu Govindan
- Global Wheat Breeding, International Center for the Improvement of Wheat and Maize (CIMMYT), Texcoco, Mexico
| | | | | | - Miroslav Nikolic
- Institute for Multidisciplinary Research, University of Belgrade, Belgrade, Serbia
| | - Victor Taleon
- International Food Policy Research Institute, Washington, DC, United States
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Bhati PK, Juliana P, Singh RP, Joshi AK, Vishwakarma MK, Poland J, Govindan V, Shrestha S, Crespo-Herrera L, Mondal S, Huerta-Espino J, Kumar U. Dissecting the Genetic Architecture of Phenology Affecting Adaptation of Spring Bread Wheat Genotypes to the Major Wheat-Producing Zones in India. Front Plant Sci 2022; 13:920682. [PMID: 35873987 PMCID: PMC9298574 DOI: 10.3389/fpls.2022.920682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Spring bread wheat adaptation to diverse environments is supported by various traits such as phenology and plant architecture. A large-scale genome-wide association study (GWAS) was designed to investigate and dissect the genetic architecture of phenology affecting adaptation. It used 48 datasets from 4,680 spring wheat lines. For 8 years (2014-2021), these lines were evaluated for days to heading (DH) and maturity (DM) at three sites: Jabalpur, Ludhiana, and Samastipur (Pusa), which represent the three major Indian wheat-producing zones: the Central Zone (CZ), North-Western Plain Zone (NWPZ), and North-Eastern Plain Zone (NEPZ), respectively. Ludhiana had the highest mean DH of 103.8 days and DM of 148.6 days, whereas Jabalpur had the lowest mean DH of 77.7 days and DM of 121.6 days. We identified 119 markers significantly associated with DH and DM on chromosomes 5B (76), 2B (18), 7D (10), 4D (8), 5A (1), 6B (4), 7B (1), and 3D (1). Our results clearly indicated the importance of the photoperiod-associated gene (Ppd-B1) for adaptation to the NWPZ and the Vrn-B1 gene for adaptation to the NEPZ and CZ. A maximum variation of 21.1 and 14% was explained by markers 2B_56134146 and 5B_574145576 linked to the Ppd-B1 and Vrn-B1 genes, respectively, indicating their significant role in regulating DH and DM. The results provide important insights into the genomic regions associated with the two phenological traits that influence adaptation to the major wheat-producing zones in India.
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Affiliation(s)
- Pradeep Kumar Bhati
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
- Borlaug Institute for South Asia (BISA), New Delhi, India
| | - Philomin Juliana
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
- Borlaug Institute for South Asia (BISA), New Delhi, India
| | - Ravi Prakash Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Arun Kumar Joshi
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
- Borlaug Institute for South Asia (BISA), New Delhi, India
| | - Manish Kumar Vishwakarma
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
- Borlaug Institute for South Asia (BISA), New Delhi, India
| | - Jesse Poland
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, United States
| | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Sandesh Shrestha
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, United States
| | | | - Suchismita Mondal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Julio Huerta-Espino
- Campo Experimental Valle de México-INIFAP, Carretera los Reyes-Texcoco, Texcoco, Mexico
| | - Uttam Kumar
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
- Borlaug Institute for South Asia (BISA), New Delhi, India
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Juliana P, Govindan V, Crespo-Herrera L, Mondal S, Huerta-Espino J, Shrestha S, Poland J, Singh RP. Genome-Wide Association Mapping Identifies Key Genomic Regions for Grain Zinc and Iron Biofortification in Bread Wheat. Front Plant Sci 2022; 13:903819. [PMID: 35845653 PMCID: PMC9280339 DOI: 10.3389/fpls.2022.903819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/19/2022] [Indexed: 05/02/2023]
Abstract
Accelerating breeding efforts for developing biofortified bread wheat varieties necessitates understanding the genetic control of grain zinc concentration (GZnC) and grain iron concentration (GFeC). Hence, the major objective of this study was to perform genome-wide association mapping to identify consistently significant genotyping-by-sequencing markers associated with GZnC and GFeC using a large panel of 5,585 breeding lines from the International Maize and Wheat Improvement Center. These lines were grown between 2018 and 2021 in an optimally irrigated environment at Obregon, Mexico, while some of them were also grown in a water-limiting drought-stressed environment and a space-limiting small plot environment and evaluated for GZnC and GFeC. The lines showed a large and continuous variation for GZnC ranging from 27 to 74.5 ppm and GFeC ranging from 27 to 53.4 ppm. We performed 742,113 marker-traits association tests in 73 datasets and identified 141 markers consistently associated with GZnC and GFeC in three or more datasets, which were located on all wheat chromosomes except 3A and 7D. Among them, 29 markers were associated with both GZnC and GFeC, indicating a shared genetic basis for these micronutrients and the possibility of simultaneously improving both. In addition, several significant GZnC and GFeC associated markers were common across the irrigated, water-limiting drought-stressed, and space-limiting small plots environments, thereby indicating the feasibility of indirect selection for these micronutrients in either of these environments. Moreover, the many significant markers identified had minor effects on GZnC and GFeC, suggesting a quantitative genetic control of these traits. Our findings provide important insights into the complex genetic basis of GZnC and GFeC in bread wheat while implying limited prospects for marker-assisted selection and the need for using genomic selection.
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Affiliation(s)
| | - Velu Govindan
- International Maize and Wheat Improvement Center, Texcoco, Mexico
| | | | | | - Julio Huerta-Espino
- Campo Experimental Valle de Mexico, Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Chapingo, Mexico
| | - Sandesh Shrestha
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, United States
| | - Jesse Poland
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, United States
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center, Texcoco, Mexico
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11
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Thapa DB, Subedi M, Yadav RP, Joshi BP, Adhikari BN, Shrestha KP, Magar PB, Pant KR, Gurung SB, Ghimire S, Gautam NR, Acharya NR, Sapkota M, Mishra VK, Joshi AK, Singh RP, Govindan V. Variation in Grain Zinc and Iron Concentrations, Grain Yield and Associated Traits of Biofortified Bread Wheat Genotypes in Nepal. Front Plant Sci 2022; 13:881965. [PMID: 35783930 PMCID: PMC9249123 DOI: 10.3389/fpls.2022.881965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Wheat (Triticum aestivum L.) is one of the major staples in Nepal providing the bulk of food calories and at least 30% of Fe and Zn intake and 20% of dietary energy and protein consumption; thus, it is essential to improve its nutritional quality. To select high-yielding genotypes with elevated grain zinc and iron concentration, the sixth, seventh, eighth, and ninth HarvestPlus Yield Trials (HPYTs) were conducted across diverse locations in Nepal for four consecutive years: 2015-16, 2016-17, 2017-18, and 2018-19, using 47 biofortified and 3 non-biofortified CIMMYT-bred, bread wheat genotypes: Baj#1, Kachu#1, and WK1204 (local check). Genotypic and spatial variations were found in agro-morphological traits; grain yield and its components; and the grain zinc and iron concentration of tested genotypes. Grain zinc concentration was highest in Khumaltar and lowest in Kabre. Likewise, grain iron concentration was highest in Doti and lowest in Surkhet. Most of the biofortified genotypes were superior for grain yield and for grain zinc and iron concentration to the non-biofortified checks. Combined analyses across environments showed moderate to high heritability for both Zn (0.48-0.81) and Fe (0.46-0.79) except a low heritability for Fe observed for 7th HPYT (0.15). Grain yield was positively correlated with the number of tillers per m2, while negatively correlated with days to heading and maturity, grain iron, grain weight per spike, and thousand grain weight. The grain zinc and iron concentration were positively correlated, suggesting that the simultaneous improvement of both micronutrients is possible through wheat breeding. Extensive testing of CIMMYT derived high Zn wheat lines in Nepal led to the release of five biofortified wheat varieties in 2020 with superior yield, better disease resistance, and 30-40% increased grain Zn and adaptable to a range of wheat growing regions in the country - from the hotter lowland, or Terai, regions to the dry mid- and high-elevation areas.
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Affiliation(s)
| | - Mahesh Subedi
- Nepal Agricultural Research Council (NARC), Kathmandu, Nepal
| | | | | | | | | | | | - Khem Raj Pant
- Nepal Agricultural Research Council (NARC), Kathmandu, Nepal
| | | | - Sapana Ghimire
- Nepal Agricultural Research Council (NARC), Kathmandu, Nepal
| | | | - Nav Raj Acharya
- Nepal Agricultural Research Council (NARC), Kathmandu, Nepal
| | - Manoj Sapkota
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA, United States
| | - Vinod Kumar Mishra
- Department of Genetics and Plant Breeding, Banaras Hindu University (BHU), Varanasi, India
| | - Arun Kumar Joshi
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
| | - Ravi Prakash Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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12
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Wani SH, Gaikwad K, Razzaq A, Samantara K, Kumar M, Govindan V. Improving Zinc and Iron Biofortification in Wheat through Genomics Approaches. Mol Biol Rep 2022; 49:8007-8023. [PMID: 35661970 PMCID: PMC9165711 DOI: 10.1007/s11033-022-07326-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 02/09/2022] [Accepted: 03/02/2022] [Indexed: 11/27/2022]
Abstract
Globally, about 20% of calories (energy) come from wheat. In some countries, it is more than 70%. More than 2 billion people are at risk for zinc deficiency and even more, people are at risk of iron deficiency, nearly a quarter of all children underage group of 5 are physically and cognitively stunted, and lack of dietary zinc is a major contributing factor. Biofortified wheat with elevated levels of zinc and iron has several potential advantages as a delivery vehicle for micronutrients in the diets of resource-poor consumers who depend on cereal-based diets. The conventional breeding strategies have been successful in the introduction of novel alleles for grain Zn and Fe that led to the release of competitive Zn enriched wheat varieties in South Asia. The major challenge over the next few decades will be to maintain the rates of genetic gains for grain yield along with increased grain Zn/Fe concentration to meet the food and nutritional security challenges. Therefore, to remain competitive, the performance of Zn-enhanced lines/varieties must be equal or superior to that of current non-biofortified elite lines/varieties. Since both yield and Zn content are invisible and quantitatively inherited traits except few intermediate effect QTL regions identified for grain Zn, increased breeding efforts and new approaches are required to combine them at high frequency, ensuring that Zn levels are steadily increased to the required levels across the breeding pipelines. The current review article provides a comprehensive list of genomic regions for enhancing grain Zn and Fe concentrations in wheat including key candidate gene families such NAS, ZIP, VLT, ZIFL, and YSL. Implementing forward breeding by taking advantage of the rapid cycling trait pipeline approaches would simultaneously introgress high Zn and Fe QTL into the high Zn and normal elite lines, further increasing Zn and Fe concentrations.
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Affiliation(s)
- Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, 192102 Khudwani, J&K India
| | - Kiran Gaikwad
- ICAR-Indian Agricultural Research Institute, Pusa Campus, 110012 New Delhi, India
| | - Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, 38040 Faisalabad, Pakistan
| | - Kajal Samantara
- Department of Genetics and Plant Breeding, Centurion University of Technology and Management, 761211 Odisha, India
| | - Manjeet Kumar
- ICAR-Indian Agricultural Research Institute, Pusa Campus, 110012 New Delhi, India
| | - Velu Govindan
- Global Wheat Program International Maize and Wheat Improvement Center Texcoco Mexico, Texcoco, Mexico
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13
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Atanda SA, Govindan V, Singh R, Robbins KR, Crossa J, Bentley AR. Sparse testing using genomic prediction improves selection for breeding targets in elite spring wheat. Theor Appl Genet 2022; 135:1939-1950. [PMID: 35348821 PMCID: PMC9205816 DOI: 10.1007/s00122-022-04085-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/16/2022] [Indexed: 06/08/2023]
Abstract
Sparse testing using genomic prediction can be efficiently used to increase the number of testing environments while maintaining selection intensity in the early yield testing stage without increasing the breeding budget. Sparse testing using genomic prediction enables expanded use of selection environments in early-stage yield testing without increasing phenotyping cost. We evaluated different sparse testing strategies in the yield testing stage of a CIMMYT spring wheat breeding pipeline characterized by multiple populations each with small family sizes of 1-9 individuals. Our results indicated that a substantial overlap between lines across environments should be used to achieve optimal prediction accuracy. As sparse testing leverages information generated within and across environments, the genetic correlations between environments and genomic relationships of lines across environments were the main drivers of prediction accuracy in multi-environment yield trials. Including information from previous evaluation years did not consistently improve the prediction performance. Genomic best linear unbiased prediction was found to be the best predictor of true breeding value, and therefore, we propose that it should be used as a selection decision metric in the early yield testing stages. We also propose it as a proxy for assessing prediction performance to mirror breeder's advancement decisions in a breeding program so that it can be readily applied for advancement decisions by breeding programs.
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Affiliation(s)
| | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Ravi Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Kelly R Robbins
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
| | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Alison R Bentley
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
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14
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Wan Y, Stewart T, Amrahli M, Evans J, Sharp P, Govindan V, Hawkesford MJ, Shewry PR. Localisation of iron and zinc in grain of biofortified wheat. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2022.103470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Govindan V, Pappa N. Online learning based neural network adaptive controller for efficient power tracking of PWR type reactor with unknown internal dynamics. ANN NUCL ENERGY 2022. [DOI: 10.1016/j.anucene.2021.108866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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16
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Juliana P, He X, Poland J, Shrestha S, Joshi AK, Huerta-Espino J, Govindan V, Crespo-Herrera LA, Mondal S, Kumar U, Bhati PK, Vishwakarma M, Singh RP, Singh PK. Genome-Wide Association Mapping Indicates Quantitative Genetic Control of Spot Blotch Resistance in Bread Wheat and the Favorable Effects of Some Spot Blotch Loci on Grain Yield. Front Plant Sci 2022; 13:835095. [PMID: 35310648 PMCID: PMC8928540 DOI: 10.3389/fpls.2022.835095] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Spot blotch caused by the fungus Bipolaris sorokiniana poses a serious threat to bread wheat production in warm and humid wheat-growing regions of the world. Hence, the major objective of this study was to identify consistent genotyping-by-sequencing (GBS) markers associated with spot blotch resistance using genome-wide association mapping on a large set of 6,736 advanced bread wheat breeding lines from the International Maize and Wheat Improvement Center. These lines were phenotyped as seven panels at Agua Fria, Mexico between the 2013-2014 and 2019-2020 crop cycles. We identified 214 significant spot blotch associated GBS markers in all the panels, among which only 96 were significant in more than one panel, indicating a strong environmental effect on the trait and highlights the need for multiple phenotypic evaluations to identify lines with stable spot blotch resistance. The 96 consistent GBS markers were on chromosomes 1A, 1B, 1D, 2A, 3B, 4A, 5B, 5D, 6B, 7A, 7B, and 7D, including markers possibly linked to the Lr46, Sb1, Sb2 and Sb3 genes. We also report the association of the 2NS translocation from Aegilops ventricosa with spot blotch resistance in some environments. Moreover, the spot blotch favorable alleles at the 2NS translocation and two markers on chromosome 3BS (3B_2280114 and 3B_5601689) were associated with increased grain yield evaluated at several environments in Mexico and India, implying that selection for favorable alleles at these loci could enable simultaneous improvement for high grain yield and spot blotch resistance. Furthermore, a significant relationship between the percentage of favorable alleles in the lines and their spot blotch response was observed, which taken together with the multiple minor effect loci identified to be associated with spot blotch in this study, indicate quantitative genetic control of resistance. Overall, the results presented here have extended our knowledge on the genetic basis of spot blotch resistance in bread wheat and further efforts to improve genetic resistance to the disease are needed for reducing current and future losses under climate change.
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Affiliation(s)
| | - Xinyao He
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jesse Poland
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, United States
| | - Sandesh Shrestha
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, United States
| | - Arun K. Joshi
- Borlaug Institute for South Asia (BISA), Ludhiana, India
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
| | - Julio Huerta-Espino
- Campo Experimental Valle de Mexico, Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias (INIFAP), Chapingo, Mexico
| | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Suchismita Mondal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | - Pradeep K. Bhati
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
| | - Manish Vishwakarma
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Pawan K. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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17
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Bari A, Geetha S, Shamanna V, Darmavaram S, Govindan V. Comparison of phenotypic and Whole Genome Sequencing (WGS)-derived antimicrobial resistance profiles of Salmonella typhi isolated from Blood cultures. Int J Infect Dis 2022. [DOI: 10.1016/j.ijid.2021.12.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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18
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Wen Z, Juliana P, Dhugga HS, Pacheco M, Martínez UI, Aguilar A, Ibba MI, Govindan V, Singh RP, Dhugga KS. Genome-Wide Association Study of Phytic Acid in Wheat Grain Unravels Markers for Improving Biofortification. Front Plant Sci 2022; 13:830147. [PMID: 35242157 PMCID: PMC8886111 DOI: 10.3389/fpls.2022.830147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/10/2022] [Indexed: 06/07/2023]
Abstract
Biofortification of cereal grains offers a lasting solution to combat micronutrient deficiency in developing countries where it poses developmental risks to children. Breeding efforts thus far have been directed toward increasing the grain concentrations of iron (Fe) and zinc (Zn) ions. Phytic acid (PA) chelates these metal ions, reducing their bioavailability in the digestive tract. We present a high-throughput assay for quantification of PA and its application in screening a breeding population. After extraction in 96-well megatiter plates, PA content was determined from the phosphate released after treatment with a commercially available phytase enzyme. In a set of 330 breeding lines of wheat grown in the field over 3 years as part of a HarvestPlus breeding program for high grain Fe and Zn, our assay unraveled variation for PA that ranged from 0.90 to 1.72% with a mean of 1.24%. PA content was not associated with grain yield. High yielding lines were further screened for low molar PA/Fe and PA/Zn ratios for increased metal ion bioavailability, demonstrating the utility of our assay. Genome-wide association study revealed 21 genetic associations, six of which were consistent across years. Five of these associations mapped to chromosomes 1A, 2A, 2D, 5A, and 7D. Additivity over four of these haplotypes accounted for an ∼10% reduction in PA. Our study demonstrates it is possible to scale up assays to directly select for low grain PA in forward breeding programs.
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19
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Chaturvedi P, Govindaraj M, Govindan V, Weckwerth W. Editorial: Sorghum and Pearl Millet as Climate Resilient Crops for Food and Nutrition Security. Front Plant Sci 2022; 13:851970. [PMID: 35360320 PMCID: PMC8963798 DOI: 10.3389/fpls.2022.851970] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/10/2022] [Indexed: 05/05/2023]
Affiliation(s)
- Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- *Correspondence: Palak Chaturvedi
| | - Mahalingam Govindaraj
- Department HarvestPlus Program, Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
- Wolfram Weckwerth
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20
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Singh S, Jighly A, Sehgal D, Burgueño J, Joukhadar R, Singh SK, Sharma A, Vikram P, Sansaloni CP, Govindan V, Bhavani S, Randhawa M, Solis-Moya E, Singh S, Pardo N, Arif MAR, Laghari KA, Basandrai D, Shokat S, Chaudhary HK, Saeed NA, Basandrai AK, Ledesma-Ramírez L, Sohu VS, Imtiaz M, Sial MA, Wenzl P, Singh GP, Bains NS. Direct introgression of untapped diversity into elite wheat lines. Nat Food 2021; 2:819-827. [PMID: 37117978 DOI: 10.1038/s43016-021-00380-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 08/27/2021] [Indexed: 04/30/2023]
Abstract
The effective utilization of natural variation has become essential in addressing the challenges that climate change and population growth pose to global food security. Currently adopted protracted approaches to introgress exotic alleles into elite cultivars need substantial transformation. Here, through a strategic three-way crossing scheme among diverse exotics and the best historical elites (exotic/elite1//elite2), 2,867 pre-breeding lines were developed, genotyped and screened for multiple agronomic traits in four mega-environments. A meta-genome-wide association study, selective sweeps and haplotype-block-based analyses unveiled selection footprints in the genomes of pre-breeding lines as well as exotic-specific associations with agronomic traits. A simulation with a neutrality assumption demonstrated that many pre-breeding lines had significant exotic contributions despite substantial selection bias towards elite genomes. National breeding programmes worldwide have adopted 95 lines for germplasm enhancement, and 7 additional lines are being advanced in varietal release trials. This study presents a great leap forwards in the mobilization of GenBank variation to the breeding pipelines.
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Affiliation(s)
- Sukhwinder Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
- Geneshifters, Pullman, WA, USA.
| | - A Jighly
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, Australia
| | - D Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - J Burgueño
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - R Joukhadar
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, Australia
| | - S K Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - A Sharma
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | - P Vikram
- International Center for Biosaline Agriculture, Dubai, United Arab Emirates
| | - C P Sansaloni
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - V Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - S Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - M Randhawa
- CIMMYT-World Agroforestry Centre (ICRAF), Nairobi, Kenya
| | - E Solis-Moya
- Carretera Celaya-San Miguel de Allende, Celaya, México
| | - S Singh
- ICAR-National Institute of Plant Biotechnology, New Delhi, India
| | - N Pardo
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - M A R Arif
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - K A Laghari
- Nuclear Institute of Agriculture, Tando Jam, Pakistan
| | - D Basandrai
- CSK Himachal Pradesh Agricultural University Palampur, Palampur, India
| | - S Shokat
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
- Department of Plant and Environmental Sciences, Crop Science, University of Copenhagen, Taastrup, Denmark
| | - H K Chaudhary
- CSK Himachal Pradesh Agricultural University Palampur, Palampur, India
| | - N A Saeed
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - A K Basandrai
- CSK Himachal Pradesh Agricultural University Palampur, Palampur, India
| | | | - V S Sohu
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | | | - M A Sial
- Nuclear Institute of Agriculture, Tando Jam, Pakistan
| | | | - G P Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - N S Bains
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
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21
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Rathan ND, Sehgal D, Thiyagarajan K, Singh R, Singh AM, Govindan V. Identification of Genetic Loci and Candidate Genes Related to Grain Zinc and Iron Concentration Using a Zinc-Enriched Wheat 'Zinc-Shakti'. Front Genet 2021; 12:652653. [PMID: 34194467 PMCID: PMC8237760 DOI: 10.3389/fgene.2021.652653] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/19/2021] [Indexed: 12/14/2022] Open
Abstract
The development of nutritionally enhanced wheat (Triticum aestivum L.) with higher levels of grain iron (Fe) and zinc (Zn) offers a sustainable solution to micronutrient deficiency among resource-poor wheat consumers. One hundred and ninety recombinant inbred lines (RILs) from 'Kachu' × 'Zinc-Shakti' cross were phenotyped for grain Fe and Zn concentrations and phenological and agronomically important traits at Ciudad Obregon, Mexico in the 2017-2018, 2018-2019, and 2019-2020 growing seasons and Diversity Arrays Technology (DArT) molecular marker data were used to determine genomic regions controlling grain micronutrients and agronomic traits. We identified seven new pleiotropic quantitative trait loci (QTL) for grain Zn and Fe on chromosomes 1B, 1D, 2B, 6A, and 7D. The stable pleiotropic QTL identified have expanded the diversity of QTL that could be used in breeding for wheat biofortification. Nine RILs with the best combination of pleiotropic QTL for Zn and Fe have been identified to be used in future crossing programs and to be screened in elite yield trials before releasing as biofortified varieties. In silico analysis revealed several candidate genes underlying QTL, including those belonging to the families of the transporters and kinases known to transport small peptides and minerals (thus assisting mineral uptake) and catalyzing phosphorylation processes, respectively.
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Affiliation(s)
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Ravi Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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22
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Juliana P, Singh RP, Poland J, Shrestha S, Huerta-Espino J, Govindan V, Mondal S, Crespo-Herrera LA, Kumar U, Joshi AK, Payne T, Bhati PK, Tomar V, Consolacion F, Campos Serna JA. Elucidating the genetics of grain yield and stress-resilience in bread wheat using a large-scale genome-wide association mapping study with 55,568 lines. Sci Rep 2021; 11:5254. [PMID: 33664297 PMCID: PMC7933281 DOI: 10.1038/s41598-021-84308-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/15/2021] [Indexed: 01/31/2023] Open
Abstract
Wheat grain yield (GY) improvement using genomic tools is important for achieving yield breakthroughs. To dissect the genetic architecture of wheat GY potential and stress-resilience, we have designed this large-scale genome-wide association study using 100 datasets, comprising 105,000 GY observations from 55,568 wheat lines evaluated between 2003 and 2019 by the International Maize and Wheat Improvement Center and national partners. We report 801 GY-associated genotyping-by-sequencing markers significant in more than one dataset and the highest number of them were on chromosomes 2A, 6B, 6A, 5B, 1B and 7B. We then used the linkage disequilibrium (LD) between the consistently significant markers to designate 214 GY-associated LD-blocks and observed that 84.5% of the 58 GY-associated LD-blocks in severe-drought, 100% of the 48 GY-associated LD-blocks in early-heat and 85.9% of the 71 GY-associated LD-blocks in late-heat, overlapped with the GY-associated LD-blocks in the irrigated-bed planting environment, substantiating that simultaneous improvement for GY potential and stress-resilience is feasible. Furthermore, we generated the GY-associated marker profiles and analyzed the GY favorable allele frequencies for a large panel of 73,142 wheat lines, resulting in 44.5 million datapoints. Overall, the extensive resources presented in this study provide great opportunities to accelerate breeding for high-yielding and stress-resilient wheat varieties.
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Affiliation(s)
- Philomin Juliana
- grid.433436.50000 0001 2289 885XInternational Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Ravi Prakash Singh
- grid.433436.50000 0001 2289 885XInternational Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jesse Poland
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS USA
| | - Sandesh Shrestha
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS USA
| | - Julio Huerta-Espino
- grid.473273.60000 0001 2170 5278Campo Experimental Valle de Mexico, Instituto Nacional de Investigaciones Forestales, Agricolas Y Pecuarias (INIFAP), Chapingo, Mexico
| | - Velu Govindan
- grid.433436.50000 0001 2289 885XInternational Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Suchismita Mondal
- grid.433436.50000 0001 2289 885XInternational Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Uttam Kumar
- CIMMYT, NASC Complex, New Delhi, India ,grid.505936.cBorlaug Institute for South Asia (BISA), New Delhi, India
| | - Arun Kumar Joshi
- CIMMYT, NASC Complex, New Delhi, India ,grid.505936.cBorlaug Institute for South Asia (BISA), New Delhi, India
| | - Thomas Payne
- grid.433436.50000 0001 2289 885XInternational Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Pradeep Kumar Bhati
- CIMMYT, NASC Complex, New Delhi, India ,grid.505936.cBorlaug Institute for South Asia (BISA), New Delhi, India
| | - Vipin Tomar
- grid.505936.cBorlaug Institute for South Asia (BISA), New Delhi, India ,Institute of Advanced Research, Gandhinagar, Gujarat India
| | - Franjel Consolacion
- grid.433436.50000 0001 2289 885XInternational Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jaime Amador Campos Serna
- grid.433436.50000 0001 2289 885XInternational Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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Rathan ND, Mahendru-Singh A, Govindan V, Ibba MI. Impact of High and Low-Molecular-Weight Glutenins on the Processing Quality of a Set of Biofortified Common Wheat (Triticum aestivum L.) Lines. Front Sustain Food Syst 2020. [DOI: 10.3389/fsufs.2020.583367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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Juliana P, Singh RP, Braun HJ, Huerta-Espino J, Crespo-Herrera L, Govindan V, Mondal S, Poland J, Shrestha S. Genomic Selection for Grain Yield in the CIMMYT Wheat Breeding Program-Status and Perspectives. Front Plant Sci 2020; 11:564183. [PMID: 33042185 PMCID: PMC7522222 DOI: 10.3389/fpls.2020.564183] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Genomic breeding technologies offer new opportunities for grain yield (GY) improvement in common wheat. In this study, we have evaluated the potential of genomic selection (GS) in breeding for GY in wheat by modeling a large dataset of 48,562 GY observations from the International Maize and Wheat Improvement Center (CIMMYT), including 36 yield trials evaluated between 2012 and 2019 in Obregón, Sonora, Mexico. Our key objective was to determine the value that GS can add to the current three-stage yield testing strategy at CIMMYT, and we draw inferences from predictive modeling of GY using 420 different populations, environments, cycles, and model combinations. First, we evaluated the potential of genomic predictions for minimizing the number of replications and lines tested within a site and year and obtained mean prediction accuracies (PAs) of 0.56, 0.5, and 0.42 in Stages 1, 2, and 3 of yield testing, respectively. However, these PAs were similar to the mean pedigree-based PAs indicating that genomic relationships added no value to pedigree relationships in the yield testing stages, characterized by small family-sizes. Second, we evaluated genomic predictions for minimizing GY testing across stages/years in Obregón and observed mean PAs of 0.41, 0.31, and 0.37, respectively when GY in the full irrigation bed planting (FI BP), drought stress (DS), and late-sown heat stress environments were predicted across years using genotype × environment (G × E) interaction models. Third, we evaluated genomic predictions for minimizing the number of yield testing environments and observed that in Stage 2, the FI BP, full irrigation flat planting and early-sown heat stress environments (mean PA of 0.37 ± 0.12) and the reduced irrigation and DS environments (mean PA of 0.45 ± 0.07) had moderate predictabilities among them. However, in both predictions across years and environments, the PAs were inconsistent across years and the G × E models had no advantage over the baseline model with environment and line effects. Overall, our results provide excellent insights into the predictability of a quantitative trait like GY and will have important implications on the future design of GS for GY in wheat breeding programs globally.
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Affiliation(s)
- Philomin Juliana
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Ravi Prakash Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Hans-Joachim Braun
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Julio Huerta-Espino
- Campo Experimental Valle de Mexico, Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias (INIFAP), Chapingo, Mexico
| | | | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Suchismita Mondal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jesse Poland
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Sandesh Shrestha
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
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Mottaleb KA, Govindan V, Singh PK, Sonder K, He X, Singh RP, Joshi AK, Barma NC, Kruseman G, Erenstein O. Economic benefits of blast-resistant biofortified wheat in Bangladesh: The case of BARI Gom 33. Crop Prot 2019; 123:45-58. [PMID: 31481821 PMCID: PMC6686726 DOI: 10.1016/j.cropro.2019.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 05/29/2023]
Abstract
The first occurrence of wheat blast in 2016 threatened Bangladesh's already precarious food security situation. The Bangladesh Agricultural Research Institute (BARI), together with the International Maize and Wheat Improvement Center (CIMMYT) developed and released the wheat variety BARI Gom 33 that is resistant to wheat blast and other common diseases. The new variety provides a 5-8% yield gain over the available popular varieties, as well as being zinc enriched. This study examines the potential economic benefits of BARI Gom 33 in Bangladesh. First, applying a climate analogue model, this study identified that more than 55% of the total wheat-growing area in Bangladesh (across 45 districts) is vulnerable to wheat blast. Second, applying an ex-ante impact assessment framework, this study shows that with an assumed cumulative adoption starting from 2019-20 and increasing to 30% by 2027-28, the potential economic benefits of the newly developed wheat variety far exceeds its dissemination cost by 2029-30. Even if dissemination of the new wheat variety is limited to only the ten currently blast-affected districts, the yearly average net benefits could amount to USD 0.23-1.6 million. Based on the findings, international funder agencies are urged to support the national system in scaling out the new wheat variety and wheat research in general to ensure overall food security in Bangladesh and South Asia.
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Affiliation(s)
- Khondoker A. Mottaleb
- Socioeconomics Program, CIMMYT (International Maize and Wheat Improvement Center), Carretera México-Veracruz Km. 45, El Batán, Texcoco, Mexico, C.P. 56237
| | | | | | - Kai Sonder
- Geographical Information System Unit, CIMMYT Mexico
| | - Xinyao He
- Geographical Information System Unit, CIMMYT Mexico
| | - Ravi P. Singh
- Bread Wheat Improvement, Global Wheat Program, CIMMYT, Mexico
| | - Arun K. Joshi
- CIMMYT- Borlaug Institute for South Asia (BISA), NASC Complex, New Delhi, India
| | | | - Gideon Kruseman
- Ex ante and Foresight Specialist, Socioeconomics Program, CIMMYT, Mexico
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Juliana P, Montesinos-López OA, Crossa J, Mondal S, González Pérez L, Poland J, Huerta-Espino J, Crespo-Herrera L, Govindan V, Dreisigacker S, Shrestha S, Pérez-Rodríguez P, Pinto Espinosa F, Singh RP. Integrating genomic-enabled prediction and high-throughput phenotyping in breeding for climate-resilient bread wheat. Theor Appl Genet 2019; 132:177-194. [PMID: 30341493 PMCID: PMC6320358 DOI: 10.1007/s00122-018-3206-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 10/09/2018] [Indexed: 05/18/2023]
Abstract
Genomic selection and high-throughput phenotyping (HTP) are promising tools to accelerate breeding gains for high-yielding and climate-resilient wheat varieties. Hence, our objective was to evaluate them for predicting grain yield (GY) in drought-stressed (DS) and late-sown heat-stressed (HS) environments of the International maize and wheat improvement center's elite yield trial nurseries. We observed that the average genomic prediction accuracies using fivefold cross-validations were 0.50 and 0.51 in the DS and HS environments, respectively. However, when a different nursery/year was used to predict another nursery/year, the average genomic prediction accuracies in the DS and HS environments decreased to 0.18 and 0.23, respectively. While genomic predictions clearly outperformed pedigree-based predictions across nurseries, they were similar to pedigree-based predictions within nurseries due to small family sizes. In populations with some full-sibs in the training population, the genomic and pedigree-based prediction accuracies were on average 0.27 and 0.35 higher than the accuracies in populations with only one progeny per cross, indicating the importance of genetic relatedness between the training and validation populations for good predictions. We also evaluated the item-based collaborative filtering approach for multivariate prediction of GY using the green normalized difference vegetation index from HTP. This approach proved to be the best strategy for across-nursery predictions, with average accuracies of 0.56 and 0.62 in the DS and HS environments, respectively. We conclude that GY is a challenging trait for across-year predictions, but GS and HTP can be integrated in increasing the size of populations screened and evaluating unphenotyped large nurseries for stress-resilience within years.
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Affiliation(s)
- Philomin Juliana
- International Maize and Wheat Improvement Center (CIMMYT), Postal 6-641, 06600, Mexico, D.F., Mexico.
| | | | - José Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Postal 6-641, 06600, Mexico, D.F., Mexico
| | - Suchismita Mondal
- International Maize and Wheat Improvement Center (CIMMYT), Postal 6-641, 06600, Mexico, D.F., Mexico
| | - Lorena González Pérez
- International Maize and Wheat Improvement Center (CIMMYT), Postal 6-641, 06600, Mexico, D.F., Mexico
| | - Jesse Poland
- Department of Plant Pathology and Agronomy, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, 66506, USA
| | - Julio Huerta-Espino
- Campo Experimental Valle de México INIFAP, Chapingo, Edo. de México, 56230, Mexico
| | - Leonardo Crespo-Herrera
- International Maize and Wheat Improvement Center (CIMMYT), Postal 6-641, 06600, Mexico, D.F., Mexico
| | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Postal 6-641, 06600, Mexico, D.F., Mexico
| | - Susanne Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), Postal 6-641, 06600, Mexico, D.F., Mexico
| | - Sandesh Shrestha
- Department of Plant Pathology and Agronomy, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Francisco Pinto Espinosa
- International Maize and Wheat Improvement Center (CIMMYT), Postal 6-641, 06600, Mexico, D.F., Mexico
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), Postal 6-641, 06600, Mexico, D.F., Mexico.
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27
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Juliana P, Singh RP, Poland J, Mondal S, Crossa J, Montesinos-López OA, Dreisigacker S, Pérez-Rodríguez P, Huerta-Espino J, Crespo-Herrera L, Govindan V. Prospects and Challenges of Applied Genomic Selection-A New Paradigm in Breeding for Grain Yield in Bread Wheat. Plant Genome 2018; 11:10.3835/plantgenome2018.03.0017. [PMID: 30512048 PMCID: PMC7822054 DOI: 10.3835/plantgenome2018.03.0017] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Genomic selection (GS) has been promising for increasing genetic gains in several species. Therefore, we evaluated the potential integration of GS for grain yield (GY) in bread wheat ( L.) in CIMMYT's elite yield trial nurseries. We observed that the genomic prediction accuracies within nurseries (0.44 and 0.35) were substantially higher than across-nursery accuracies (0.15 and 0.05) for GY evaluated in the bed and flat planting systems, respectively. The accuracies from using only a subset of 251 genotyping-by-sequencing markers were comparable to the accuracies using all 2038 markers. We also used the item-based collaborative filtering approach for incorporating other related traits in predicting GY and observed that it outperformed genomic predictions across nurseries, but was less predictive when trait correlations with GY were low. Furthermore, we compared GS and phenotypic selections (PS) and observed that at a selection intensity of 0.5, GS could select a maximum of 70.9 and 61.5% of the top lines and discard 71.5 and 60.5% of the poor lines selected or discarded by PS within and across nurseries, respectively. Comparisons of GS and pedigree-based predictions revealed that the advantage of GS over the pedigree was moderate in populations without full-sibs. However, GS was less advantageous for within-family selections in elite families with few full-sibs and minimal Mendelian sampling variance. Overall, our results demonstrate the importance of applying GS for GY at the appropriate stage of the breeding cycle, and we speculate that gains can be maximized if it is implemented in early-generation within-family selections.
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Affiliation(s)
- Philomin Juliana
- CIMMYT, Apdo, Postal 6-641, 06600 Mexico, D.F., Mexico
- Corresponding authors (, )
| | - Ravi P. Singh
- CIMMYT, Apdo, Postal 6-641, 06600 Mexico, D.F., Mexico
- Corresponding authors (, )
| | - Jesse Poland
- Wheat Genetics Resource Center, Dep. of Plant Pathology, Kansas State Univ., Manhattan, KS 66506; J. Poland, Dep. of Agronomy, Kansas State Univ., Manhattan, KS 66506
| | | | - José Crossa
- CIMMYT, Apdo, Postal 6-641, 06600 Mexico, D.F., Mexico
| | | | | | | | - Julio Huerta-Espino
- Campo experimental Valle de México Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, 56230, Chapingo, Edo. de México, México
| | | | - Velu Govindan
- CIMMYT, Apdo, Postal 6-641, 06600 Mexico, D.F., Mexico
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28
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Singh S, Vikram P, Sehgal D, Burgueño J, Sharma A, Singh SK, Sansaloni CP, Joynson R, Brabbs T, Ortiz C, Solis-Moya E, Govindan V, Gupta N, Sidhu HS, Basandrai AK, Basandrai D, Ledesma-Ramires L, Suaste-Franco MP, Fuentes-Dávila G, Moreno JI, Sonder K, Singh VK, Singh S, Shokat S, Arif MAR, Laghari KA, Srivastava P, Bhavani S, Kumar S, Pal D, Jaiswal JP, Kumar U, Chaudhary HK, Crossa J, Payne TS, Imtiaz M, Sohu VS, Singh GP, Bains NS, Hall A, Pixley KV. Harnessing genetic potential of wheat germplasm banks through impact-oriented-prebreeding for future food and nutritional security. Sci Rep 2018; 8:12527. [PMID: 30131572 PMCID: PMC6104032 DOI: 10.1038/s41598-018-30667-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/02/2018] [Indexed: 12/03/2022] Open
Abstract
The value of exotic wheat genetic resources for accelerating grain yield gains is largely unproven and unrealized. We used next-generation sequencing, together with multi-environment phenotyping, to study the contribution of exotic genomes to 984 three-way-cross-derived (exotic/elite1//elite2) pre-breeding lines (PBLs). Genomic characterization of these lines with haplotype map-based and SNP marker approaches revealed exotic specific imprints of 16.1 to 25.1%, which compares to theoretical expectation of 25%. A rare and favorable haplotype (GT) with 0.4% frequency in gene bank identified on chromosome 6D minimized grain yield (GY) loss under heat stress without GY penalty under irrigated conditions. More specifically, the ‘T’ allele of the haplotype GT originated in Aegilops tauschii and was absent in all elite lines used in study. In silico analysis of the SNP showed hits with a candidate gene coding for isoflavone reductase IRL-like protein in Ae. tauschii. Rare haplotypes were also identified on chromosomes 1A, 6A and 2B effective against abiotic/biotic stresses. Results demonstrate positive contributions of exotic germplasm to PBLs derived from crosses of exotics with CIMMYT’s best elite lines. This is a major impact-oriented pre-breeding effort at CIMMYT, resulting in large-scale development of PBLs for deployment in breeding programs addressing food security under climate change scenarios.
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Affiliation(s)
- Sukhwinder Singh
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico.
| | - Prashant Vikram
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Juan Burgueño
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Achla Sharma
- Department Plant Breeding & Genetics, Punjab Agriculture University, Ludhiana, 141004, India
| | - Sanjay K Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Carolina P Sansaloni
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Ryan Joynson
- Earlham Institute, Norwich, Norfolk, NR4 7UG, UK
| | | | - Cynthia Ortiz
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Ernesto Solis-Moya
- Carretera Celaya-San Miguel de Allende, Km 0.6.5, C.P., 38110, Celaya, Guanajuato, Mexico
| | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Naveen Gupta
- Borlaug Institute for South Asia (BISA), CIMMYT, Ladhowal, Punjab, 141004, India
| | - Harminder S Sidhu
- Borlaug Institute for South Asia (BISA), CIMMYT, Ladhowal, Punjab, 141004, India
| | - Ashwani K Basandrai
- CSK Himachal Pradesh Agricultural University Palampur, Palampur, Himachal Pradesh, 176062, India
| | - Daisy Basandrai
- CSK Himachal Pradesh Agricultural University Palampur, Palampur, Himachal Pradesh, 176062, India
| | | | - Maria P Suaste-Franco
- Carretera Celaya-San Miguel de Allende, Km 0.6.5, C.P., 38110, Celaya, Guanajuato, Mexico
| | - Guillermo Fuentes-Dávila
- INIFAP-CIRNO, Campo Experimental Norman E. Borlaug, Apdo. Postal 155, Km 12 Norman E. Borlaug, Cd. Obregon, Sonora, C.P., 85000, Mexico
| | - Javier I Moreno
- INIFAP, Interior Parque Los Colomos S/N, Colonia Providencia, CP, 44660, Guadalajara, Jalisco, Mexico
| | - Kai Sonder
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Vaibhav K Singh
- ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110 012, India
| | - Sanjay Singh
- National Research Center for Plant Biotechnology, New Delhi, 110 012, India
| | - Sajid Shokat
- Nuclear Institute for Agriculture and Biology, Faislabad, 38000, Pakistan.,Department of Plant and Environmental Sciences, Crop Science, University of Copenhagen, Højbakkegård Allé 13, DK-2630, Taastrup, Denmark
| | - Mian A R Arif
- Nuclear Institute for Agriculture and Biology, Faislabad, 38000, Pakistan
| | - Khalil A Laghari
- Nuclear Institute of Agriculture, Tando Jam, Sindh, 70050, Pakistan
| | - Puja Srivastava
- Department Plant Breeding & Genetics, Punjab Agriculture University, Ludhiana, 141004, India
| | - Sridhar Bhavani
- CIMMYT - World Agroforestry Centre (ICRAF), United Nations Avenue, Gigiri. P.O. Box 1041-00621, Nairobi, Kenya
| | - Satish Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Dharam Pal
- ICAR-Indian Agricultural Research Institute, Regional Station, Shimla, 171004, India
| | - Jai P Jaiswal
- Department of Genetics and Plant Breeding, G.B. Pant University of Agriculture & Technology, Pantnagar, 263145, Uttarakhand, India
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), CIMMYT, Ladhowal, Punjab, 141004, India
| | - Harinder K Chaudhary
- CSK Himachal Pradesh Agricultural University Palampur, Palampur, Himachal Pradesh, 176062, India
| | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Thomas S Payne
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico
| | - Muhammad Imtiaz
- CIMMYT - Pakistan, NARC CSI Complex, Park Road, Islamabad, 44000, Pakistan
| | - Virinder S Sohu
- Department Plant Breeding & Genetics, Punjab Agriculture University, Ludhiana, 141004, India
| | - Gyanendra P Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Navtej S Bains
- Department Plant Breeding & Genetics, Punjab Agriculture University, Ludhiana, 141004, India
| | - Anthony Hall
- Earlham Institute, Norwich, Norfolk, NR4 7UG, UK.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Kevin V Pixley
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico.
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Crespo-Herrera LA, Govindan V, Stangoulis J, Hao Y, Singh RP. QTL Mapping of Grain Zn and Fe Concentrations in Two Hexaploid Wheat RIL Populations with Ample Transgressive Segregation. Front Plant Sci 2017; 8:1800. [PMID: 29093728 PMCID: PMC5651365 DOI: 10.3389/fpls.2017.01800] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/04/2017] [Indexed: 05/02/2023]
Abstract
More than 50% of undernourished children live in Asia and more than 25% live in Africa. Coupled with an inadequate food supply, mineral deficiencies are widespread in these populations; particularly zinc (Zn) and iron (Fe) deficiencies that lead to retarded growth, adverse effects on both the immune system and an individual's cognitive abilities. Biofortification is one solution aimed at reducing the incidence of these deficiencies. To efficiently breed a biofortified wheat variety, it is important to generate knowledge of the genomic regions associated with grain Zn (GZn) and Fe (GFe) concentration. This allows for the introgression of favorable alleles into elite germplasm. In this study we evaluated two bi-parental populations of 188 recombinant inbred lines (RILs) displaying a significant range of transgressive segregation for GZn and GFe during three crop cycles in CIMMYT, Mexico. Parents of the RILs were derived from Triticum spelta L. and synthetic hexaploid wheat crosses. QTL analysis identified a number of significant QTL with a region denominated as QGZn.cimmyt-7B_1P2 on chromosome 7B explaining the largest (32.7%) proportion of phenotypic variance (PVE) for GZn and leading to an average additive effect of -1.3. The QTL with the largest average additive effect for GFe (-0.161) was found on chromosome 4A (QGFe.cimmyt-4A_P2), with 21.14% of the PVE. The region QGZn.cimmyt-7B_1P2 co-localized closest to the region QGZn.cimmyt-7B_1P1 in a consensus map built from the linkage maps of both populations. Pleiotropic or tightly linked QTL were also found on chromosome 3B, however of minor effects and PVE between 4.3 and 10.9%. Further efforts are required to utilize the QTL information in marker assisted backcrossing schemes for wheat biofortification. A strategy to follow is to intercross the transgressive individuals from both populations and then utilize them as sources in biofortification breeding pipelines.
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Affiliation(s)
- Leonardo A. Crespo-Herrera
- Global Wheat Program, Centro Internacional de Mejoramiento de Maíz y Trigo, Texcoco, Mexico
- *Correspondence: Leonardo A. Crespo-Herrera
| | - Velu Govindan
- Global Wheat Program, Centro Internacional de Mejoramiento de Maíz y Trigo, Texcoco, Mexico
| | - James Stangoulis
- School of Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ravi P. Singh
- Global Wheat Program, Centro Internacional de Mejoramiento de Maíz y Trigo, Texcoco, Mexico
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Singh RP, Hodson DP, Huerta-Espino J, Jin Y, Bhavani S, Njau P, Herrera-Foessel S, Singh PK, Singh S, Govindan V. The emergence of Ug99 races of the stem rust fungus is a threat to world wheat production. Annu Rev Phytopathol 2011; 49:465-81. [PMID: 21568701 DOI: 10.1146/annurev-phyto-072910-095423] [Citation(s) in RCA: 307] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Race Ug99 of the fungus Puccinia graminis tritici that causes stem or black rust disease on wheat was first detected in Uganda in 1998. Seven races belonging to the Ug99 lineage are now known and have spread to various wheat-growing countries in the eastern African highlands, as well as Zimbabwe, South Africa, Sudan, Yemen, and Iran. Because of the susceptibility of 90% of the wheat varieties grown worldwide, the Ug99 group of races was recognized as a major threat to wheat production and food security. Its spread, either wind-mediated or human-aided, to other countries in Africa, Asia, and beyond is evident. Screening in Kenya and Ethiopia has identified a low frequency of resistant wheat varieties and breeding materials. Identification and transfer of new sources of race-specific resistance from various wheat relatives is underway to enhance the diversity of resistance. Although new Ug99-resistant varieties that yield more than current popular varieties are being released and promoted, major efforts are required to displace current Ug99 susceptible varieties with varieties that have diverse race-specific or durable resistance and mitigate the Ug99 threat.
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Affiliation(s)
- Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico.
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Govindan V, Blair S. Limitations on nonlinear pulse propagation in coupled-resonator slow-light waveguides. Opt Express 2007; 15:3922-3930. [PMID: 19532634 DOI: 10.1364/oe.15.003922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Under the constraint of fixed pulse distortion, we study the bandwidth-delay product and nonlinear phase shift performance of coupled-resonator slow-light waveguides with designs that produce maximally-flat transmission and maximally-flat group delay responses. Even though improvement in bandwidth-delay product can be obtained with increasing number of resonators, the nonlinear response fails to improve beyond a certain number of resonators due to the increased filter bandwidth necessary to maintain a fixed pulse distortion. However, as expected, the nonlinear response improves with resonator finesse and degrades with resonator loss.
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32
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D'Cruz IA, Pahlajani DB, Govindan V, Shah NK. Repetitive ectopic atrial tachyarrhythmia (syndrome of alternating tachycardia--bradycardia). Indian Heart J 1974; 26:90-6. [PMID: 4424765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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33
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Pahlajani DB, Govindan V, Buch VR, Gandhi MJ. V.C.G. diagnosis of inferior wall myocardial infarction. Indian Heart J 1973; 25:36-40. [PMID: 4268196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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