Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large‐scale soybean dataset
Abstract The surge in high‐throughput technologies has empowered the acquisition of vast genomic datasets, prompting the search for genetic markers and biomarkers relevant to complex traits. However, grappling with the inherent complexities of high dimensionality and sparsity within these datasets p...
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| Format: | Article |
| Language: | English |
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Wiley
2025-03-01
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| Series: | The Plant Genome |
| Online Access: | https://doi.org/10.1002/tpg2.20503 |
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| author | Hawlader A. Al‐Mamun Monica F. Danilevicz Jacob I. Marsh Cedric Gondro David Edwards |
| author_facet | Hawlader A. Al‐Mamun Monica F. Danilevicz Jacob I. Marsh Cedric Gondro David Edwards |
| author_sort | Hawlader A. Al‐Mamun |
| collection | DOAJ |
| description | Abstract The surge in high‐throughput technologies has empowered the acquisition of vast genomic datasets, prompting the search for genetic markers and biomarkers relevant to complex traits. However, grappling with the inherent complexities of high dimensionality and sparsity within these datasets poses formidable hurdles. The immense number of features and their potential redundancy demand efficient strategies for extracting pertinent information and identifying significant markers. Feature selection is important in large genomic data as it helps in enhancing interpretability and computational efficiency. This study focuses on addressing these challenges through a comprehensive investigation into genomic feature selection methodologies, employing a rich soybean (Glycine max L. Merr.) dataset comprising 966 lines with over 5.5 million single nucleotide polymorphisms. Emphasizing the “small n large p” dilemma prevalent in contemporary genomic studies, we compared the efficacy of traditional genome‐wide association studies (GWAS) with two prominent machine learning tools, random forest and extreme gradient boosting, in pinpointing predictive features. Utilizing the expansive soybean dataset, we assessed the performance of these methodologies in selecting features that optimize predictive modeling for various phenotypes. By constructing predictive models based on the selected features, we ascertain the comparative prediction accuracies, thereby illuminating the strengths and limitations of these feature selection methodologies in the realm of genomic data analysis. |
| format | Article |
| id | doaj-art-a8d44b03c3ed4b8bbadd22d129596bdd |
| institution | OA Journals |
| issn | 1940-3372 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Plant Genome |
| spelling | doaj-art-a8d44b03c3ed4b8bbadd22d129596bdd2025-08-20T01:50:06ZengWileyThe Plant Genome1940-33722025-03-01181n/an/a10.1002/tpg2.20503Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large‐scale soybean datasetHawlader A. Al‐Mamun0Monica F. Danilevicz1Jacob I. Marsh2Cedric Gondro3David Edwards4Centre for Applied Bioinformatics and School of Biological Sciences University of Western Australia Perth Western Australia AustraliaCentre for Applied Bioinformatics and School of Biological Sciences University of Western Australia Perth Western Australia AustraliaDepartment of Biology University of North Carolina Chapel Hill North Carolina USADepartment of Animal Science Michigan State University East Lansing Michigan USACentre for Applied Bioinformatics and School of Biological Sciences University of Western Australia Perth Western Australia AustraliaAbstract The surge in high‐throughput technologies has empowered the acquisition of vast genomic datasets, prompting the search for genetic markers and biomarkers relevant to complex traits. However, grappling with the inherent complexities of high dimensionality and sparsity within these datasets poses formidable hurdles. The immense number of features and their potential redundancy demand efficient strategies for extracting pertinent information and identifying significant markers. Feature selection is important in large genomic data as it helps in enhancing interpretability and computational efficiency. This study focuses on addressing these challenges through a comprehensive investigation into genomic feature selection methodologies, employing a rich soybean (Glycine max L. Merr.) dataset comprising 966 lines with over 5.5 million single nucleotide polymorphisms. Emphasizing the “small n large p” dilemma prevalent in contemporary genomic studies, we compared the efficacy of traditional genome‐wide association studies (GWAS) with two prominent machine learning tools, random forest and extreme gradient boosting, in pinpointing predictive features. Utilizing the expansive soybean dataset, we assessed the performance of these methodologies in selecting features that optimize predictive modeling for various phenotypes. By constructing predictive models based on the selected features, we ascertain the comparative prediction accuracies, thereby illuminating the strengths and limitations of these feature selection methodologies in the realm of genomic data analysis.https://doi.org/10.1002/tpg2.20503 |
| spellingShingle | Hawlader A. Al‐Mamun Monica F. Danilevicz Jacob I. Marsh Cedric Gondro David Edwards Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large‐scale soybean dataset The Plant Genome |
| title | Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large‐scale soybean dataset |
| title_full | Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large‐scale soybean dataset |
| title_fullStr | Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large‐scale soybean dataset |
| title_full_unstemmed | Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large‐scale soybean dataset |
| title_short | Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large‐scale soybean dataset |
| title_sort | exploring genomic feature selection a comparative analysis of gwas and machine learning algorithms in a large scale soybean dataset |
| url | https://doi.org/10.1002/tpg2.20503 |
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