Fused Graphical Lasso Recovers Flowering Time Mutation Genes in <i>Arabidopsis thaliana</i>
Conventional breeding approaches that focus on yield under highly favorable nutrient conditions have resulted in reduced genetic and trait diversity in crops. Under the growing threat from climate change, the mining of novel genes in more resilient varieties can help dramatically improve trait impro...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-07-01
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| Series: | Inventions |
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| Online Access: | https://www.mdpi.com/2411-5134/6/3/52 |
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| author | Rajan Kapoor Aniruddha Datta Michael Thomson |
| author_facet | Rajan Kapoor Aniruddha Datta Michael Thomson |
| author_sort | Rajan Kapoor |
| collection | DOAJ |
| description | Conventional breeding approaches that focus on yield under highly favorable nutrient conditions have resulted in reduced genetic and trait diversity in crops. Under the growing threat from climate change, the mining of novel genes in more resilient varieties can help dramatically improve trait improvement efforts. In this work, we propose the use of the joint graphical lasso for discovering genes responsible for desired phenotypic traits. We prove its efficiency by using gene expression data for wild type and delayed flowering mutants for the model plant. <i>Arabidopsis thaliana</i> shows that it recovers the mutation causing genes <i>LNK1</i> and <i>LNK2</i>. Some novel interactions of these genes were also predicted. Observing the network level changes between two phenotypes can also help develop meaningful biological hypotheses regarding the novel functions of these genes. Now that this data analysis strategy has been validated in a model plant, it can be extended to crop plants to help identify the key genes for beneficial traits for crop improvement. |
| first_indexed | 2024-03-10T07:34:00Z |
| format | Article |
| id | doaj.art-90c87590edc14a8a8e2f4ac64d9c7e9d |
| institution | Directory Open Access Journal |
| issn | 2411-5134 |
| language | English |
| last_indexed | 2024-03-10T07:34:00Z |
| publishDate | 2021-07-01 |
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| record_format | Article |
| series | Inventions |
| spelling | doaj.art-90c87590edc14a8a8e2f4ac64d9c7e9d2023-11-22T13:37:39ZengMDPI AGInventions2411-51342021-07-01635210.3390/inventions6030052Fused Graphical Lasso Recovers Flowering Time Mutation Genes in <i>Arabidopsis thaliana</i>Rajan Kapoor0Aniruddha Datta1Michael Thomson2Department of Electrical and Computer Engineering, Texas A&M University, 188 Bizzell St., College Station, TX 77843, USADepartment of Electrical and Computer Engineering, Texas A&M University, 188 Bizzell St., College Station, TX 77843, USADepartment of Soil and Crop Sciences, Texas A&M University, 370 Olsen Blvd., College Station, TX 77843, USAConventional breeding approaches that focus on yield under highly favorable nutrient conditions have resulted in reduced genetic and trait diversity in crops. Under the growing threat from climate change, the mining of novel genes in more resilient varieties can help dramatically improve trait improvement efforts. In this work, we propose the use of the joint graphical lasso for discovering genes responsible for desired phenotypic traits. We prove its efficiency by using gene expression data for wild type and delayed flowering mutants for the model plant. <i>Arabidopsis thaliana</i> shows that it recovers the mutation causing genes <i>LNK1</i> and <i>LNK2</i>. Some novel interactions of these genes were also predicted. Observing the network level changes between two phenotypes can also help develop meaningful biological hypotheses regarding the novel functions of these genes. Now that this data analysis strategy has been validated in a model plant, it can be extended to crop plants to help identify the key genes for beneficial traits for crop improvement.https://www.mdpi.com/2411-5134/6/3/52Gaussian graphical modelsflowering timejoint graphical lassofused lasso penalty<i>Arabidopsis thaliana</i> |
| spellingShingle | Rajan Kapoor Aniruddha Datta Michael Thomson Fused Graphical Lasso Recovers Flowering Time Mutation Genes in <i>Arabidopsis thaliana</i> Inventions Gaussian graphical models flowering time joint graphical lasso fused lasso penalty <i>Arabidopsis thaliana</i> |
| title | Fused Graphical Lasso Recovers Flowering Time Mutation Genes in <i>Arabidopsis thaliana</i> |
| title_full | Fused Graphical Lasso Recovers Flowering Time Mutation Genes in <i>Arabidopsis thaliana</i> |
| title_fullStr | Fused Graphical Lasso Recovers Flowering Time Mutation Genes in <i>Arabidopsis thaliana</i> |
| title_full_unstemmed | Fused Graphical Lasso Recovers Flowering Time Mutation Genes in <i>Arabidopsis thaliana</i> |
| title_short | Fused Graphical Lasso Recovers Flowering Time Mutation Genes in <i>Arabidopsis thaliana</i> |
| title_sort | fused graphical lasso recovers flowering time mutation genes in i arabidopsis thaliana i |
| topic | Gaussian graphical models flowering time joint graphical lasso fused lasso penalty <i>Arabidopsis thaliana</i> |
| url | https://www.mdpi.com/2411-5134/6/3/52 |
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