Modeling multiple phenotypes in wheat using data-driven genomic exploratory factor analysis and Bayesian network learning
Inferring trait networks from a large volume of genetically correlated diverse phenotypes such as yield, architecture, and disease resistance can provide information on the manner in which complex phenotypes are interrelated. However, studies on statistical methods tailored to multidimensional pheno...
| Autores principales: | , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Wiley
2021
|
| Acceso en línea: | https://hdl.handle.net/10568/164356 |
| _version_ | 1855522306120482816 |
|---|---|
| author | Momen, Mehdi Bhatta, Madhav Hussain, Waseem Yu, Haipeng Morota, Gota |
| author_browse | Bhatta, Madhav Hussain, Waseem Momen, Mehdi Morota, Gota Yu, Haipeng |
| author_facet | Momen, Mehdi Bhatta, Madhav Hussain, Waseem Yu, Haipeng Morota, Gota |
| author_sort | Momen, Mehdi |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Inferring trait networks from a large volume of genetically correlated diverse phenotypes such as yield, architecture, and disease resistance can provide information on the manner in which complex phenotypes are interrelated. However, studies on statistical methods tailored to multidimensional phenotypes are limited, whereas numerous methods are available for evaluating the massive number of genetic markers. Factor analysis operates at the level of latent variables predicted to generate observed responses. The objectives of this study were to illustrate the manner in which data‐driven exploratory factor analysis can map observed phenotypes into a smaller number of latent variables and infer a genomic latent factor network using 45 agro‐morphological, disease, and grain mineral phenotypes measured in synthetic hexaploid wheat lines (Triticum aestivum L.). In total, eight latent factors including grain yield, architecture, flag leaf‐related traits, grain minerals, yellow rust, two types of stem rust, and leaf rust were identified as common sources of the observed phenotypes. The genetic component of the factor scores for each latent variable was fed into a Bayesian network to obtain a trait structure reflecting the genetic interdependency among traits. Three directed paths were consistently identified by two Bayesian network algorithms. Flag leaf‐related traits influenced leaf rust, and yellow rust and stem rust influenced grain yield. Additional paths that were identified included flag leaf‐related traits to minerals and minerals to architecture. This study shows that data‐driven exploratory factor analysis can reveal smaller dimensional common latent phenotypes that are likely to give rise to numerous observed field phenotypes without relying on prior biological knowledge. The inferred genomic latent factor structure from the Bayesian network provides insights for plant breeding to simultaneously improve multiple traits, as an intervention on one trait will affect the values of focal phenotypes in an interrelated complex trait system. |
| format | Journal Article |
| id | CGSpace164356 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace1643562025-08-21T15:39:31Z Modeling multiple phenotypes in wheat using data-driven genomic exploratory factor analysis and Bayesian network learning Momen, Mehdi Bhatta, Madhav Hussain, Waseem Yu, Haipeng Morota, Gota Inferring trait networks from a large volume of genetically correlated diverse phenotypes such as yield, architecture, and disease resistance can provide information on the manner in which complex phenotypes are interrelated. However, studies on statistical methods tailored to multidimensional phenotypes are limited, whereas numerous methods are available for evaluating the massive number of genetic markers. Factor analysis operates at the level of latent variables predicted to generate observed responses. The objectives of this study were to illustrate the manner in which data‐driven exploratory factor analysis can map observed phenotypes into a smaller number of latent variables and infer a genomic latent factor network using 45 agro‐morphological, disease, and grain mineral phenotypes measured in synthetic hexaploid wheat lines (Triticum aestivum L.). In total, eight latent factors including grain yield, architecture, flag leaf‐related traits, grain minerals, yellow rust, two types of stem rust, and leaf rust were identified as common sources of the observed phenotypes. The genetic component of the factor scores for each latent variable was fed into a Bayesian network to obtain a trait structure reflecting the genetic interdependency among traits. Three directed paths were consistently identified by two Bayesian network algorithms. Flag leaf‐related traits influenced leaf rust, and yellow rust and stem rust influenced grain yield. Additional paths that were identified included flag leaf‐related traits to minerals and minerals to architecture. This study shows that data‐driven exploratory factor analysis can reveal smaller dimensional common latent phenotypes that are likely to give rise to numerous observed field phenotypes without relying on prior biological knowledge. The inferred genomic latent factor structure from the Bayesian network provides insights for plant breeding to simultaneously improve multiple traits, as an intervention on one trait will affect the values of focal phenotypes in an interrelated complex trait system. 2021-01 2024-12-19T12:53:46Z 2024-12-19T12:53:46Z Journal Article https://hdl.handle.net/10568/164356 en Open Access Wiley Momen, Mehdi; Bhatta, Madhav; Hussain, Waseem; Yu, Haipeng and Morota, Gota. 2021. Modeling multiple phenotypes in wheat using data-driven genomic exploratory factor analysis and Bayesian network learning. Plant Direct, Volume 5, no. 1 |
| spellingShingle | Momen, Mehdi Bhatta, Madhav Hussain, Waseem Yu, Haipeng Morota, Gota Modeling multiple phenotypes in wheat using data-driven genomic exploratory factor analysis and Bayesian network learning |
| title | Modeling multiple phenotypes in wheat using data-driven genomic exploratory factor analysis and Bayesian network learning |
| title_full | Modeling multiple phenotypes in wheat using data-driven genomic exploratory factor analysis and Bayesian network learning |
| title_fullStr | Modeling multiple phenotypes in wheat using data-driven genomic exploratory factor analysis and Bayesian network learning |
| title_full_unstemmed | Modeling multiple phenotypes in wheat using data-driven genomic exploratory factor analysis and Bayesian network learning |
| title_short | Modeling multiple phenotypes in wheat using data-driven genomic exploratory factor analysis and Bayesian network learning |
| title_sort | modeling multiple phenotypes in wheat using data driven genomic exploratory factor analysis and bayesian network learning |
| url | https://hdl.handle.net/10568/164356 |
| work_keys_str_mv | AT momenmehdi modelingmultiplephenotypesinwheatusingdatadrivengenomicexploratoryfactoranalysisandbayesiannetworklearning AT bhattamadhav modelingmultiplephenotypesinwheatusingdatadrivengenomicexploratoryfactoranalysisandbayesiannetworklearning AT hussainwaseem modelingmultiplephenotypesinwheatusingdatadrivengenomicexploratoryfactoranalysisandbayesiannetworklearning AT yuhaipeng modelingmultiplephenotypesinwheatusingdatadrivengenomicexploratoryfactoranalysisandbayesiannetworklearning AT morotagota modelingmultiplephenotypesinwheatusingdatadrivengenomicexploratoryfactoranalysisandbayesiannetworklearning |