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Prediction of count phenotypes using high-resolution images and genomic data

Creator: Kismiantini
Creator: Montesinos-Lopez, O.A.
Creator: Crossa, J.
Creator: Setiawan, E.P.
Creator: Wutsqa, D.U.
Year: 2021
URI: https://hdl.handle.net/10883/21353
Format: pdf
Language: English
Publisher: Genetics Society of America
Type: Article
Place of Publication: Bethesda, MD (USA)
Issue: 2
Volume: 11
DOI: 10.1093/G3JOURNAL/JKAB035
Keywords: High-Resolution Images
Keywords: Genomic Data
Keywords: Generalized Poisson Regression
Keywords: Genomic Selection
Keywords: Count Data
Description: Genomic selection (GS) is revolutionizing plant breeding since the selection process is done with the help of statistical machine learning methods. A model is trained with a reference population and then it is used for predicting the candidate individuals available in the testing set. However, given that breeding phenotypic values are very noisy, new models must be able to integrate not only genotypic and environmental data but also high-resolution images that have been collected by breeders with advanced image technology. For this reason, this paper explores the use of generalized Poisson regression (GPR) for genome-enabled prediction of count phenotypes using genomic and hyperspectral images. The GPR model allows integrating input information of many sources like environments, genomic data, high resolution data, and interaction terms between these three sources. We found that the best prediction performance was obtained when the three sources of information were taken into account in the predictor, and those measures of high-resolution images close to the harvest day provided the best prediction performance.
Agrovoc: IMAGE ANALYSIS
Agrovoc: GENOMICS
Agrovoc: DATA
Agrovoc: PLANT BREEDING
Agrovoc: MARKER-ASSISTED SELECTION
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Related Datasets: https://doi.org/10.5281/zenodo.4478247
ISSN: 2160-1836
Journal: G3: Genes, Genomes, Genetics
Article number: jkab035


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  • Genetic Resources
    Genetic Resources including germplasm collections, wild relatives, genotyping, genomics, and IP

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