IP4GS: Bringing genomic selection analysis to breeders
Genomic selection (GS), a strategy to use genotypes to predict phenotypes via statistical or machine learning models, has become a routine practice in plant breeding programs. GS can speed up the genetic gain by reducing phenotyping costs and/or shortening the breeding cycles. GS analysis is complic...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1131493/full |
| _version_ | 1811159545427263488 |
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| author | Tong Li Shan Jiang Ran Fu Xiangfeng Wang Qian Cheng Shuqin Jiang |
| author_facet | Tong Li Shan Jiang Ran Fu Xiangfeng Wang Qian Cheng Shuqin Jiang |
| author_sort | Tong Li |
| collection | DOAJ |
| description | Genomic selection (GS), a strategy to use genotypes to predict phenotypes via statistical or machine learning models, has become a routine practice in plant breeding programs. GS can speed up the genetic gain by reducing phenotyping costs and/or shortening the breeding cycles. GS analysis is complicated involving data clean up and formatting, training and test population analysis, model selection and evaluation, and parameter optimization. In addition, GS analysis also requires some programming skills and knowledge of statistical modeling. Thus, we need a more practical GS tools for breeders. To alleviate this difficulty, we developed the web-based platform IP4GS (https://ngdc.cncb.ac.cn/ip4gs/), which offers a user-friendly interface to perform GS analysis simply through point-and-click actions. IP4GS currently includes seven commonly used models, eleven evaluation metrics, and visualization modules, offering great convenience for plant breeders with limited bioinformatics knowledge to apply GS analysis. |
| first_indexed | 2024-04-10T05:43:00Z |
| format | Article |
| id | doaj.art-3f2504e777be44ccb034b8760e4f1d12 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-10T05:43:00Z |
| publishDate | 2023-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-3f2504e777be44ccb034b8760e4f1d122023-03-06T06:43:09ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-03-011410.3389/fpls.2023.11314931131493IP4GS: Bringing genomic selection analysis to breedersTong LiShan JiangRan FuXiangfeng WangQian ChengShuqin JiangGenomic selection (GS), a strategy to use genotypes to predict phenotypes via statistical or machine learning models, has become a routine practice in plant breeding programs. GS can speed up the genetic gain by reducing phenotyping costs and/or shortening the breeding cycles. GS analysis is complicated involving data clean up and formatting, training and test population analysis, model selection and evaluation, and parameter optimization. In addition, GS analysis also requires some programming skills and knowledge of statistical modeling. Thus, we need a more practical GS tools for breeders. To alleviate this difficulty, we developed the web-based platform IP4GS (https://ngdc.cncb.ac.cn/ip4gs/), which offers a user-friendly interface to perform GS analysis simply through point-and-click actions. IP4GS currently includes seven commonly used models, eleven evaluation metrics, and visualization modules, offering great convenience for plant breeders with limited bioinformatics knowledge to apply GS analysis.https://www.frontiersin.org/articles/10.3389/fpls.2023.1131493/fullbioinformaticsgenomic selectiongenotype-to-phenotype predictionweb-based platformR shiny |
| spellingShingle | Tong Li Shan Jiang Ran Fu Xiangfeng Wang Qian Cheng Shuqin Jiang IP4GS: Bringing genomic selection analysis to breeders Frontiers in Plant Science bioinformatics genomic selection genotype-to-phenotype prediction web-based platform R shiny |
| title | IP4GS: Bringing genomic selection analysis to breeders |
| title_full | IP4GS: Bringing genomic selection analysis to breeders |
| title_fullStr | IP4GS: Bringing genomic selection analysis to breeders |
| title_full_unstemmed | IP4GS: Bringing genomic selection analysis to breeders |
| title_short | IP4GS: Bringing genomic selection analysis to breeders |
| title_sort | ip4gs bringing genomic selection analysis to breeders |
| topic | bioinformatics genomic selection genotype-to-phenotype prediction web-based platform R shiny |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1131493/full |
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