Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration
In this paper, we explore potential genetic factors in control of flax phenotypes associated with fiber by mining a collection of 306 flax accessions from the Federal Research Centre of the Bast Fiber Crops, Torzhok, Russia. In total, 11 traits were assessed in the course of 3 successive years. A ge...
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| Format: | Article |
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MDPI AG
2022-11-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/23/14536 |
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| author | Alexander Kanapin Tatyana Rozhmina Mikhail Bankin Svetlana Surkova Maria Duk Ekaterina Osyagina Maria Samsonova |
| author_facet | Alexander Kanapin Tatyana Rozhmina Mikhail Bankin Svetlana Surkova Maria Duk Ekaterina Osyagina Maria Samsonova |
| author_sort | Alexander Kanapin |
| collection | DOAJ |
| description | In this paper, we explore potential genetic factors in control of flax phenotypes associated with fiber by mining a collection of 306 flax accessions from the Federal Research Centre of the Bast Fiber Crops, Torzhok, Russia. In total, 11 traits were assessed in the course of 3 successive years. A genome-wide association study was performed for each phenotype independently using six different single-locus models implemented in the GAPIT3 R package. Moreover, we applied a multivariate linear mixed model implemented in the GEMMA package to account for trait correlations and potential pleiotropic effects of polymorphisms. The analyses revealed a number of genomic variants associated with different fiber traits, implying the complex and polygenic control. All stable variants demonstrate a statistically significant allelic effect across all 3 years of the experiment. We tested the validity of the predicted variants using gene expression data available for the flax fiber studies. The results shed new light on the processes and pathways associated with the complex fiber traits, while the pinpointed candidate genes may be further used for marker-assisted selection. |
| first_indexed | 2024-03-09T17:47:51Z |
| format | Article |
| id | doaj.art-d383fd96b579440fb42d8a68b9686d77 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T17:47:51Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-d383fd96b579440fb42d8a68b9686d772023-11-24T11:03:36ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-11-0123231453610.3390/ijms232314536Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data IntegrationAlexander Kanapin0Tatyana Rozhmina1Mikhail Bankin2Svetlana Surkova3Maria Duk4Ekaterina Osyagina5Maria Samsonova6Centre for Computational Biology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, RussiaLaboratory of Breeding Technologies, Federal Research Center for Bast Fiber Crops, 172002 Torzhok, RussiaMathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, RussiaMathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, RussiaMathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, RussiaMathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, RussiaMathematical Biology & Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, RussiaIn this paper, we explore potential genetic factors in control of flax phenotypes associated with fiber by mining a collection of 306 flax accessions from the Federal Research Centre of the Bast Fiber Crops, Torzhok, Russia. In total, 11 traits were assessed in the course of 3 successive years. A genome-wide association study was performed for each phenotype independently using six different single-locus models implemented in the GAPIT3 R package. Moreover, we applied a multivariate linear mixed model implemented in the GEMMA package to account for trait correlations and potential pleiotropic effects of polymorphisms. The analyses revealed a number of genomic variants associated with different fiber traits, implying the complex and polygenic control. All stable variants demonstrate a statistically significant allelic effect across all 3 years of the experiment. We tested the validity of the predicted variants using gene expression data available for the flax fiber studies. The results shed new light on the processes and pathways associated with the complex fiber traits, while the pinpointed candidate genes may be further used for marker-assisted selection.https://www.mdpi.com/1422-0067/23/23/14536flaxGWASfiberGEMMAgene expression |
| spellingShingle | Alexander Kanapin Tatyana Rozhmina Mikhail Bankin Svetlana Surkova Maria Duk Ekaterina Osyagina Maria Samsonova Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration International Journal of Molecular Sciences flax GWAS fiber GEMMA gene expression |
| title | Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration |
| title_full | Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration |
| title_fullStr | Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration |
| title_full_unstemmed | Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration |
| title_short | Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration |
| title_sort | genetic determinants of fiber associated traits in flax identified by omics data integration |
| topic | flax GWAS fiber GEMMA gene expression |
| url | https://www.mdpi.com/1422-0067/23/23/14536 |
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