Interdisciplinary strategies to enable data-driven plant breeding in a changing climate
暂无分享,去创建一个
Lizhi Wang | Baskar Ganapathysubramanian | Patrick S. Schnable | Aaron Kusmec | Guiping Hu | Sotirios Archontoulis | Zihao Zheng | Jianming Yu | P. Schnable | B. Ganapathysubramanian | Lizhi Wang | Jianming Yu | Guiping Hu | S. Archontoulis | Jianming Yu | Aaron Kusmec | Zihao Zheng
[1] Edward S. Buckler,et al. TASSEL: software for association mapping of complex traits in diverse samples , 2007, Bioinform..
[2] Anne D. Bjorkman,et al. Increasing homogeneity in global food supplies and the implications for food security , 2014, Proceedings of the National Academy of Sciences.
[3] Sanzhen Liu,et al. tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci , 2017, Nucleic acids research.
[4] Jacob D. Washburn,et al. Predictive breeding for maize: Making use of molecular phenotypes, machine learning, and physiological crop models , 2019 .
[5] Peter J. Bradbury,et al. The genetic architecture of teosinte catalyzed and constrained maize domestication , 2019, Proceedings of the National Academy of Sciences.
[6] J. Woolliams,et al. Potential of promotion of alleles by genome editing to improve quantitative traits in livestock breeding programs , 2015, Genetics Selection Evolution.
[7] Daniel Gianola,et al. Kernel-based whole-genome prediction of complex traits: a review , 2014, Front. Genet..
[8] Senthold Asseng,et al. An overview of APSIM, a model designed for farming systems simulation , 2003 .
[9] David B. Lobell,et al. Why are agricultural impacts of climate change so uncertain? The importance of temperature relative to precipitation , 2008, Environmental Research Letters.
[10] Meng Li,et al. Genetics and population analysis Advance Access publication July 13, 2012 , 2012 .
[11] Ashutosh Kumar Singh,et al. Deep Learning for Plant Stress Phenotyping: Trends and Future Perspectives. , 2018, Trends in plant science.
[12] James W. Jones,et al. Modeling the Effects of Genotypic and Environmental Variation on Maize Phenology: The Phenology Subroutine of the AgMaize Crop Model , 2018, Agronomy Monographs.
[13] Tara F Deubel,et al. Persistent Hunger: Perspectives on Vulnerability, Famine, and Food Security in , 2006 .
[14] Luis Perez,et al. The Effectiveness of Data Augmentation in Image Classification using Deep Learning , 2017, ArXiv.
[15] Lizhi Wang,et al. Crop Yield Prediction Using Deep Neural Networks , 2019, Front. Plant Sci..
[16] Peter J. Bradbury,et al. Dysregulation of expression correlates with rare-allele burden and fitness loss in maize , 2018, Nature.
[17] José Crossa,et al. A data-driven simulation platform to predict cultivars’ performances under uncertain weather conditions , 2020, Nature Communications.
[18] Vernon W. Ruttan,et al. Agricultural Research Policy , 1982 .
[19] W. Beavis,et al. Systematic design for trait introgression projects , 2017, Theoretical and Applied Genetics.
[20] J. Weiner. Looking in the Wrong Direction for Higher-Yielding Crop Genotypes. , 2019, Trends in plant science.
[21] Pjotr Prins,et al. Private Genomes and Public SNPs: Homomorphic encryption of genotypes and phenotypes for shared quantitative genetics , 2020, bioRxiv.
[22] S. Chapman,et al. Breeder friendly phenotyping. , 2020, Plant science : an international journal of experimental plant biology.
[23] Jun Wang,et al. Analytical and Decision Support Tools for Genomics-Assisted Breeding. , 2016, Trends in plant science.
[24] Sanzhen Liu,et al. Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS , 2017, Genome Biology.
[25] Shafi Goldwasser,et al. Secure large-scale genome-wide association studies using homomorphic encryption , 2020, Proceedings of the National Academy of Sciences.
[26] D. Easterling,et al. Observations: Atmosphere and surface , 2013 .
[27] Francois Tardieu,et al. Modelling strategies for assessing and increasing the effectiveness of new phenotyping techniques in plant breeding. , 2019, Plant science : an international journal of experimental plant biology.
[28] B. Walsh,et al. Models for navigating biological complexity in breeding improved crop plants. , 2006, Trends in plant science.
[29] R. Horton,et al. Net benefits to US soy and maize yields from intensifying hourly rainfall , 2020, Nature Climate Change.
[30] M. Olsen,et al. Enhancing genetic gain in the era of molecular breeding , 2017, Journal of experimental botany.
[31] Raziel A. Ordóñez,et al. Predicting crop yields and soil‐plant nitrogen dynamics in the US Corn Belt , 2020 .
[32] Enli Wang,et al. A generic approach to modelling, allocation and redistribution of biomass to and from plant organs , 2019, in silico Plants.
[33] David Tilman,et al. National food production stabilized by crop diversity , 2019, Nature.
[34] Eric Rodene,et al. Semantic Segmentation of Sorghum Using Hyperspectral Data Identifies Genetic Associations , 2020, Plant phenomics.
[35] E. Fischer,et al. Frequency of extreme precipitation increases extensively with event rareness under global warming , 2019, Scientific Reports.
[36] G. Hammer,et al. Crop science: A foundation for advancing predictive agriculture , 2020, Crop Science.
[37] R. W. Allard,et al. Implications of Genotype‐Environmental Interactions in Applied Plant Breeding1 , 1964 .
[38] Xiangfeng Wang,et al. Machine learning for Big Data analytics in plants. , 2014, Trends in plant science.
[39] D. W. Franzen,et al. Educational Needs of Precision Agriculture , 2002, Precision Agriculture.
[40] Kurt Hornik,et al. Universal approximation of an unknown mapping and its derivatives using multilayer feedforward networks , 1990, Neural Networks.
[41] Darwin A. Campbell,et al. Assessing plant performance in the Enviratron , 2019, Plant Methods.
[42] Daniel Wallach,et al. A new approach to crop model calibration: Phenotyping plus post‐processing , 2020 .
[43] Francois Tardieu,et al. On the dynamic determinants of reproductive failure under drought in maize , 2019, in silico Plants.
[44] Frank Technow,et al. Leveraging biological insight and environmental variation to improve phenotypic prediction: Integrating crop growth models (CGM) with whole genome prediction (WGP) , 2017, bioRxiv.
[45] Fred van Eeuwijk,et al. Intercontinental prediction of soybean phenology via hybrid ensemble of knowledge-based and data-driven models , 2020, bioRxiv.
[46] R. Richards,et al. Prognosis for genetic improvement of yield potential and water-limited yield of major grain crops. , 2013 .
[47] A. F. Troyer. Adaptedness and heterosis in corn and mule hybrids , 2006 .
[48] Jeffrey W. White,et al. Estimating parametric phenotypes that determine anthesis date in Zea mays: Challenges in combining ecophysiological models with genetics , 2018, PloS one.
[49] R. Bernardo. Prospective Targeted Recombination and Genetic Gains for Quantitative Traits in Maize , 2017, The plant genome.
[50] G. Hammer,et al. Characterizing drought stress and trait influence on maize yield under current and future conditions , 2014, Global change biology.
[51] G. Hammer,et al. Integrating genetic gain and gap analysis to predict improvements in crop productivity , 2020 .
[52] H. Piepho,et al. Enviromics in breeding: applications and perspectives on envirotypic-assisted selection , 2020, Theoretical and Applied Genetics.
[53] M. Sorrells,et al. Genomic Selection for Crop Improvement , 2009 .
[54] P. Schnable,et al. Genomic prediction contributing to a promising global strategy to turbocharge gene banks , 2016, Nature Plants.
[55] Han Liu,et al. Evolutionary and functional genomics of DNA methylation in maize domestication and improvement , 2020, bioRxiv.
[56] M. Edgerton,et al. Increasing Crop Productivity to Meet Global Needs for Feed, Food, and Fuel , 2009, Plant Physiology.
[57] William Stafford Noble,et al. Machine learning applications in genetics and genomics , 2015, Nature Reviews Genetics.
[58] Andrew J. Challinor,et al. Current warming will reduce yields unless maize breeding and seed systems adapt immediately , 2016 .
[59] Jason M. Beddow,et al. A Bounds Analysis of World Food Futures: Global Agriculture Through to 2050 , 2014 .
[60] Bruce Erickson,et al. Setting the Record Straight on Precision Agriculture Adoption , 2019, Agronomy Journal.
[61] Alain Charcosset,et al. Genomic prediction of maize yield across European environmental conditions , 2019, Nature Genetics.
[62] Joshua A. Udall,et al. Breeding for Quantitative Traits in Plants , 2003 .
[63] F. Tardieu,et al. The Physiological Basis of Drought Tolerance in Crop Plants: A Scenario-Dependent Probabilistic Approach. , 2018, Annual review of plant biology.
[64] D. Duvick. Genetic progress in yield of United States maize (Zea mays L.) , 2005 .
[65] R. Elmore,et al. Soybean Seed Yield and Composition Response to Stand Reduction at Vegetative and Reproductive Stages , 2008 .
[66] J. Batley,et al. Speed breeding: a powerful tool to accelerate crop research and breeding , 2017, bioRxiv.
[67] Juraj Balkovic,et al. Consistent negative response of US crops to high temperatures in observations and crop models , 2017, Nature Communications.
[68] J. Jannink,et al. Improving Genomic Prediction in Cassava Field Experiments by Accounting for Interplot Competition , 2018, G3: Genes, Genomes, Genetics.
[69] David Foster,et al. Advanced Analytics for Agricultural Product Development , 2016, Interfaces.
[70] José Crossa,et al. A reaction norm model for genomic selection using high-dimensional genomic and environmental data , 2013, Theoretical and Applied Genetics.
[71] D. Byerlee,et al. Crop yields and global food security: will yield increase continue to feed the world? , 2014 .
[72] B. Craig,et al. Walking through the statistical black boxes of plant breeding , 2016, Theoretical and Applied Genetics.
[73] James W. Jones,et al. Efficient crop model parameter estimation and site characterization using large breeding trial data sets , 2017 .
[74] H. Piepho,et al. Heritability in Plant Breeding on a Genotype-Difference Basis , 2019, Genetics.
[75] Athanasios Petsakos,et al. CGIAR modeling approaches for resource‐constrained scenarios: II. Models for analyzing socioeconomic factors to improve policy recommendations , 2020 .
[76] L. Totir,et al. Predicting the future of plant breeding: complementing empirical evaluation with genetic prediction , 2014, Crop and Pasture Science.
[77] R. A. Fischer,et al. Breeding and Cereal Yield Progress , 2010 .
[78] Graeme L. Hammer,et al. Evaluating Plant Breeding Strategies by Simulating Gene Action and Dryland Environment Effects , 2003, Agronomy Journal.
[79] James W. Jones,et al. Potential benefits of climate forecasting to agriculture , 2000 .
[80] Changying Li,et al. Convolutional Neural Networks for Image-Based High-Throughput Plant Phenotyping: A Review , 2020, Plant phenomics.
[81] P. Schnable,et al. Multi-trait Genomic Selection Methods for Crop Improvement , 2020, Genetics.
[82] J. Jannink. Dynamics of long-term genomic selection , 2010, Genetics Selection Evolution.
[83] Joseph L. Gage,et al. Comparing Genome-Wide Association Study Results from Different Measurements of an Underlying Phenotype , 2018, G3: Genes, Genomes, Genetics.
[84] G. Hammer,et al. Designing crops for adaptation to the drought and high‐temperature risks anticipated in future climates , 2020 .
[85] S. Huet,et al. Whole-genome prediction of reaction norms to environmental stress in bread wheat (Triticum aestivum L.) by genomic random regression , 2018 .
[86] Monia Santini,et al. An overview of available crop growth and yield models for studies and assessments in agriculture. , 2016, Journal of the science of food and agriculture.
[87] S. Hearne,et al. Initiating maize pre-breeding programs using genomic selection to harness polygenic variation from landrace populations , 2016, BMC Genomics.
[88] B. Muller,et al. Plant and crop simulation models: powerful tools to link physiology, genetics, and phenomics. , 2019, Journal of experimental botany.
[89] John M. Antle,et al. Brief history of agricultural systems modeling , 2017, Agricultural systems.
[90] G. de los Campos,et al. Genomic Selection in Plant Breeding: Methods, Models, and Perspectives. , 2017, Trends in plant science.
[91] James Taylor,et al. Next-generation sequencing data interpretation: enhancing reproducibility and accessibility , 2012, Nature Reviews Genetics.
[92] Yufeng Ge,et al. Conventional and hyperspectral time-series imaging of maize lines widely used in field trials , 2017, bioRxiv.
[93] Carson M. Andorf,et al. Technological advances in maize breeding: past, present and future , 2019, Theoretical and Applied Genetics.
[94] Deniz Akdemir,et al. Integrating environmental covariates and crop modeling into the genomic selection framework to predict genotype by environment interactions , 2013, Theoretical and Applied Genetics.
[95] Jacob D. Washburn,et al. Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence , 2019, Proceedings of the National Academy of Sciences.
[96] G. Hammer,et al. Simulating the Yield Impacts of Organ-Level Quantitative Trait Loci Associated With Drought Response in Maize: A “Gene-to-Phenotype” Modeling Approach , 2009, Genetics.
[97] D. Akdemir,et al. Efficient Breeding by Genomic Mating , 2016, bioRxiv.
[98] T. Shepherd. Atmospheric circulation as a source of uncertainty in climate change projections , 2014 .
[99] James W. Jones,et al. Putting mechanisms into crop production models. , 2013, Plant, cell & environment.
[100] M. E. Otegui,et al. Co-ordination between leaf initiation and leaf appearance in field-grown maize (Zea mays): genotypic differences in response of rates to temperature. , 2005, Annals of botany.
[101] Mohsen Shahhosseini,et al. Maize yield and nitrate loss prediction with machine learning algorithms , 2019, Environmental Research Letters.
[102] J. Araus,et al. Field high-throughput phenotyping: the new crop breeding frontier. , 2014, Trends in plant science.
[103] Neil I. Huth,et al. Enhancing APSIM to simulate excessive moisture effects on root growth , 2019, Field Crops Research.
[104] Jean-Luc Jannink,et al. Genomic selection in plant breeding: from theory to practice. , 2010, Briefings in functional genomics.
[105] M. Goddard,et al. Prediction of total genetic value using genome-wide dense marker maps. , 2001, Genetics.
[106] B. Haussmann,et al. A unified strategy for West African pearl millet hybrid and heterotic group development , 2020 .
[107] H. Piepho,et al. Heritability in Plant Breeding on a Genotype-Difference Basis. , 2019, Genetics.
[108] G. Spangenberg,et al. Selection on Optimal Haploid Value Increases Genetic Gain and Preserves More Genetic Diversity Relative to Genomic Selection , 2015, Genetics.
[109] Ashutosh Kumar Singh,et al. Machine Learning for High-Throughput Stress Phenotyping in Plants. , 2016, Trends in plant science.
[110] M. Zaman-Allah,et al. Translating High-Throughput Phenotyping into Genetic Gain , 2018, Trends in plant science.
[111] James Hansen,et al. Land allocation conditioned on El Niño-Southern Oscillation phases in the Pampas of Argentina☆ , 1999 .
[112] P. Schnable,et al. Improving Response in Genomic Selection with a Population-Based Selection Strategy: Optimal Population Value Selection , 2017, Genetics.
[113] G. Hammer,et al. Modelling the nitrogen dynamics of maize crops – Enhancing the APSIM maize model , 2018, European Journal of Agronomy.
[114] John M. Antle,et al. Toward a new generation of agricultural system data, models, and knowledge products: State of agricultural systems science , 2017, Agricultural systems.
[115] R. Bernardo,et al. Prospects for genomewide selection for quantitative traits in maize , 2007 .
[116] R. Bernardo. Breeding for Quantitative Traits in Plants , 2002 .
[117] Robert J. Elshire,et al. A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species , 2011, PloS one.
[118] Frank Technow,et al. Integrating Crop Growth Models with Whole Genome Prediction through Approximate Bayesian Computation , 2015, bioRxiv.
[119] P. Schnable,et al. Shared Genetic Control of Root System Architecture between Zea mays and Sorghum bicolor1[OPEN] , 2019, Plant Physiology.
[120] James C. Schnable,et al. Increased Power and Accuracy of Causal Locus Identification in Time Series Genome-wide Association in Sorghum1[OPEN] , 2020, Plant Physiology.
[121] Jochem Marotzke,et al. Quantifying the irreducible uncertainty in near‐term climate projections , 2018, WIREs Climate Change.
[122] M. Cooper,et al. Accelerating crop genetic gains with genomic selection , 2018, Theoretical and Applied Genetics.
[123] F. Checchi,et al. Viewpoint: Determining famine: Multi-dimensional analysis for the twenty-first century , 2020 .
[124] E. Hawkins,et al. The potential to narrow uncertainty in projections of regional precipitation change , 2011 .
[125] G. de los Campos,et al. Can Deep Learning Improve Genomic Prediction of Complex Human Traits? , 2018, Genetics.
[126] Peter J. Bradbury,et al. Recombination in diverse maize is stable, predictable, and associated with genetic load , 2015, Proceedings of the National Academy of Sciences.
[127] K. Cassman. Ecological intensification of cereal production systems: yield potential, soil quality, and precision agriculture. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[128] Jordan M. Eizenga,et al. Genome graphs and the evolution of genome inference , 2017, bioRxiv.