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Khanna A, Anumalla M, Catolos M, Bhosale S, Jarquin D, Hussain W. Optimizing predictions in IRRI's rice drought breeding program by leveraging 17 years of historical data and pedigree information. Front Plant Sci 2022; 13:983818. [PMID: 36204059 PMCID: PMC9530897 DOI: 10.3389/fpls.2022.983818] [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: 07/01/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Prediction models based on pedigree and/or molecular marker information are now an inextricable part of the crop breeding programs and have led to increased genetic gains in many crops. Optimization of IRRI's rice drought breeding program is crucial for better implementation of selections based on predictions. Historical datasets with precise and robust pedigree information have been a great resource to help optimize the prediction models in the breeding programs. Here, we leveraged 17 years of historical drought data along with the pedigree information to predict the new lines or environments and dissect the G × E interactions. Seven models ranging from basic to proposed higher advanced models incorporating interactions, and genotypic specific effects were used. These models were tested with three cross-validation schemes (CV1, CV2, and CV0) to assess the predictive ability of tested and untested lines in already observed environments and tested lines in novel or new environments. In general, the highest prediction abilities were obtained when the model accounting interactions between pedigrees (additive) and environment were included. The CV0 scheme (predicting unobserved or novel environments) reveals very low predictive abilities among the three schemes. CV1 and CV2 schemes that borrow information from the target and correlated environments have much higher predictive abilities. Further, predictive ability was lower when predicting lines in non-stress conditions using drought data as training set and/or vice-versa. When predicting the lines using the data sets under the same conditions (stress or non-stress data sets), much better prediction accuracy was obtained. These results provide conclusive evidence that modeling G × E interactions are important in predictions. Thus, considering G × E interactions would help to build enhanced genomic or pedigree-based prediction models in the rice breeding program. Further, it is crucial to borrow the correlated information from other environments to improve prediction accuracy.
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Affiliation(s)
- Apurva Khanna
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Mahender Anumalla
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Margaret Catolos
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Sankalp Bhosale
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Diego Jarquin
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Waseem Hussain
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
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Rio S, Akdemir D, Carvalho T, Sánchez JIY. Assessment of genomic prediction reliability and optimization of experimental designs in multi-environment trials. Theor Appl Genet 2022; 135:405-419. [PMID: 34807267 PMCID: PMC8866390 DOI: 10.1007/s00122-021-03972-2] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
New forms of the coefficient of determination can help to forecast the accuracy of genomic prediction and optimize experimental designs in multi-environment trials with genotype-by-environment interactions. In multi-environment trials, the relative performance of genotypes may vary depending on the environmental conditions, and this phenomenon is commonly referred to as genotype-by-environment interaction (G[Formula: see text]E). With genomic prediction, G[Formula: see text]E can be accounted for by modeling the genetic covariance between trials, even when the overall experimental design is highly unbalanced between trials, thanks to the genomic relationship between genotypes. In this study, we propose new forms of the coefficient of determination (CD, i.e., the expected model-based square correlation between a genetic value and its corresponding prediction) that can be used to forecast the genomic prediction reliability of genotypes, both for their trial-specific performance and their mean performance. As the expected prediction reliability based on these new CD criteria is generally a good approximation of the observed reliability, we demonstrate that they can be used to optimize multi-environment trials in the presence of G[Formula: see text]E. In addition, this reliability may be highly variable between genotypes, especially in unbalanced designs with complex pedigree relationships between genotypes. Therefore, it can be useful for breeders to assess it before selecting genotypes based on their predicted genetic values. Using a wheat population evaluated both for simulated and phenology traits, and two maize populations evaluated for grain yield, we illustrate this approach and confirm the value of our new CD criteria.
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Affiliation(s)
- Simon Rio
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnologia Agraria y Alimentaria (INIA) Campus de Montegancedo-UPM, 28223 Pozuelo de Alarcón Madrid, Spain
| | - Deniz Akdemir
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN USA
| | - Tiago Carvalho
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnologia Agraria y Alimentaria (INIA) Campus de Montegancedo-UPM, 28223 Pozuelo de Alarcón Madrid, Spain
| | - Julio Isidro y Sánchez
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnologia Agraria y Alimentaria (INIA) Campus de Montegancedo-UPM, 28223 Pozuelo de Alarcón Madrid, Spain
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Montesinos-López OA, Montesinos-López A, Mosqueda-González BA, Bentley AR, Lillemo M, Varshney RK, Crossa J. A New Deep Learning Calibration Method Enhances Genome-Based Prediction of Continuous Crop Traits. Front Genet 2021; 12:798840. [PMID: 34976026 PMCID: PMC8718701 DOI: 10.3389/fgene.2021.798840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/18/2021] [Indexed: 11/13/2022] Open
Abstract
Genomic selection (GS) has the potential to revolutionize predictive plant breeding. A reference population is phenotyped and genotyped to train a statistical model that is used to perform genome-enabled predictions of new individuals that were only genotyped. In this vein, deep neural networks, are a type of machine learning model and have been widely adopted for use in GS studies, as they are not parametric methods, making them more adept at capturing nonlinear patterns. However, the training process for deep neural networks is very challenging due to the numerous hyper-parameters that need to be tuned, especially when imperfect tuning can result in biased predictions. In this paper we propose a simple method for calibrating (adjusting) the prediction of continuous response variables resulting from deep learning applications. We evaluated the proposed deep learning calibration method (DL_M2) using four crop breeding data sets and its performance was compared with the standard deep learning method (DL_M1), as well as the standard genomic Best Linear Unbiased Predictor (GBLUP). While the GBLUP was the most accurate model overall, the proposed deep learning calibration method (DL_M2) helped increase the genome-enabled prediction performance in all data sets when compared with the traditional DL method (DL_M1). Taken together, we provide evidence for extending the use of the proposed calibration method to evaluate its potential and consistency for predicting performance in the context of GS applied to plant breeding.
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Affiliation(s)
| | - Abelardo Montesinos-López
- Centro Universitario de Ciencias Exactas e Ingenierías (CUCEI), Universidad de Guadalajara, Guadalajara, Mexico
- *Correspondence: Abelardo Montesinos-López, ; Rajeev K. Varshney, ; José Crossa,
| | - Brandon A. Mosqueda-González
- Centro de Investigación en Computación (CIC), Instituto Politécnico Nacional (IPN), Esq. Miguel Othón de Mendizábal, Mexico city, Mexico
| | - Alison R. Bentley
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Morten Lillemo
- Department of Plant Sciences, Norwegian University of Life Sciences, IHA/CIGENE, As, Norway
| | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Perth, WA, Australia
- *Correspondence: Abelardo Montesinos-López, ; Rajeev K. Varshney, ; José Crossa,
| | - José Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
- Colegio de Postgraduados, Montecillo, Mexico
- *Correspondence: Abelardo Montesinos-López, ; Rajeev K. Varshney, ; José Crossa,
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Saradadevi GP, Das D, Mangrauthia SK, Mohapatra S, Chikkaputtaiah C, Roorkiwal M, Solanki M, Sundaram RM, Chirravuri NN, Sakhare AS, Kota S, Varshney RK, Mohannath G. Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review. Biology (Basel) 2021; 10:biology10121255. [PMID: 34943170 PMCID: PMC8698797 DOI: 10.3390/biology10121255] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022]
Abstract
Simple Summary Globally, soil salinity, which refers to salt-affected soils, is increasing due to various environmental factors and human activities. Soil salinity poses one of the most serious challenges in the field of agriculture as it significantly reduces the growth and yield of crop plants, both quantitatively and qualitatively. Over the last few decades, several studies have been carried out to understand plant biology in response to soil salinity stress with a major emphasis on genetic and other hereditary components. Based on the outcome of these studies, several approaches are being followed to enhance plants’ ability to tolerate salt stress while still maintaining reasonable levels of crop yields. In this manuscript, we comprehensively list and discuss various biological approaches being followed and, based on the recent advances in the field of molecular biology, we propose some new approaches to improve salinity tolerance of crop plants. The global scientific community can make use of this information for the betterment of crop plants. This review also highlights the importance of maintaining global soil health to prevent several crop plant losses. Abstract Globally, soil salinity has been on the rise owing to various factors that are both human and environmental. The abiotic stress caused by soil salinity has become one of the most damaging abiotic stresses faced by crop plants, resulting in significant yield losses. Salt stress induces physiological and morphological modifications in plants as a result of significant changes in gene expression patterns and signal transduction cascades. In this comprehensive review, with a major focus on recent advances in the field of plant molecular biology, we discuss several approaches to enhance salinity tolerance in plants comprising various classical and advanced genetic and genetic engineering approaches, genomics and genome editing technologies, and plant growth-promoting rhizobacteria (PGPR)-based approaches. Furthermore, based on recent advances in the field of epigenetics, we propose novel approaches to create and exploit heritable genome-wide epigenetic variation in crop plants to enhance salinity tolerance. Specifically, we describe the concepts and the underlying principles of epigenetic recombinant inbred lines (epiRILs) and other epigenetic variants and methods to generate them. The proposed epigenetic approaches also have the potential to create additional genetic variation by modulating meiotic crossover frequency.
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Affiliation(s)
- Gargi Prasad Saradadevi
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
| | - Debajit Das
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, India; (D.D.); (C.C.)
| | - Satendra K. Mangrauthia
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Sridev Mohapatra
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, India; (D.D.); (C.C.)
| | - Manish Roorkiwal
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India;
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
| | - Manish Solanki
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Raman Meenakshi Sundaram
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Neeraja N. Chirravuri
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Akshay S. Sakhare
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
| | - Suneetha Kota
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (S.K.M.); (M.S.); (R.M.S.); (N.N.C.); (A.S.S.)
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India;
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
| | - Gireesha Mohannath
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad 500078, India; (G.P.S.); (S.M.)
- Correspondence: (S.K.); (R.K.V.); (G.M.); Tel.: +91-40-245-91268 (S.K.); +91-84-556-83305 (R.K.V.); +91-40-66303697 (G.M.)
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