Transcriptome Analysis of Seed Weight Plasticity in <i>Brassica napus</i>
A critical barrier to improving crop yield is the trade-off between seed weight (SW) and seed number (SN), which has been commonly reported in several crops, including <i>Brassica napus</i>. Despite the agronomic relevance of this issue, the molecular factors involved in the interaction...
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MDPI AG
2021-04-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/9/4449 |
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| author | Javier Canales José Verdejo Gabriela Carrasco-Puga Francisca M. Castillo Anita Arenas-M Daniel F. Calderini |
| author_facet | Javier Canales José Verdejo Gabriela Carrasco-Puga Francisca M. Castillo Anita Arenas-M Daniel F. Calderini |
| author_sort | Javier Canales |
| collection | DOAJ |
| description | A critical barrier to improving crop yield is the trade-off between seed weight (SW) and seed number (SN), which has been commonly reported in several crops, including <i>Brassica napus</i>. Despite the agronomic relevance of this issue, the molecular factors involved in the interaction between SW and SN are largely unknown in crops. In this work, we performed a detailed transcriptomic analysis of 48 seed samples obtained from two rapeseed spring genotypes subjected to different source–sink (S–S) ratios in order to examine the relationship between SW and SN under different field conditions. A multifactorial analysis of the RNA-seq data was used to identify a group of 1014 genes exclusively regulated by the S–S ratio. We found that a reduction in the S–S ratio during seed filling induces the expression of genes involved in sucrose transport, seed weight, and stress responses. Moreover, we identified five co-expression modules that are positively correlated with SW and negatively correlated with SN. Interestingly, one of these modules was significantly enriched in transcription factors (TFs). Furthermore, our network analysis predicted several NAC TFs as major hubs underlying SW and SN compensation. Taken together, our study provides novel insights into the molecular factors associated with the SW–SN relationship in rapeseed and identifies TFs as potential targets when improving crop yield. |
| first_indexed | 2024-03-10T12:01:24Z |
| format | Article |
| id | doaj.art-f6e9cfb5dcfc472eabe3707b4ebc765e |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T12:01:24Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-f6e9cfb5dcfc472eabe3707b4ebc765e2023-11-21T16:58:30ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-04-01229444910.3390/ijms22094449Transcriptome Analysis of Seed Weight Plasticity in <i>Brassica napus</i>Javier Canales0José Verdejo1Gabriela Carrasco-Puga2Francisca M. Castillo3Anita Arenas-M4Daniel F. Calderini5Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, 5110566 Valdivia, ChileGraduate School, Faculty of Agricultural Sciences, Universidad Austral de Chile, 5110566 Valdivia, ChilePlant Production and Plant Protection Institute, Faculty of Agricultural Sciences, Universidad Austral de Chile, 5110566 Valdivia, ChileInstitute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, 5110566 Valdivia, ChileInstitute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, 5110566 Valdivia, ChilePlant Production and Plant Protection Institute, Faculty of Agricultural Sciences, Universidad Austral de Chile, 5110566 Valdivia, ChileA critical barrier to improving crop yield is the trade-off between seed weight (SW) and seed number (SN), which has been commonly reported in several crops, including <i>Brassica napus</i>. Despite the agronomic relevance of this issue, the molecular factors involved in the interaction between SW and SN are largely unknown in crops. In this work, we performed a detailed transcriptomic analysis of 48 seed samples obtained from two rapeseed spring genotypes subjected to different source–sink (S–S) ratios in order to examine the relationship between SW and SN under different field conditions. A multifactorial analysis of the RNA-seq data was used to identify a group of 1014 genes exclusively regulated by the S–S ratio. We found that a reduction in the S–S ratio during seed filling induces the expression of genes involved in sucrose transport, seed weight, and stress responses. Moreover, we identified five co-expression modules that are positively correlated with SW and negatively correlated with SN. Interestingly, one of these modules was significantly enriched in transcription factors (TFs). Furthermore, our network analysis predicted several NAC TFs as major hubs underlying SW and SN compensation. Taken together, our study provides novel insights into the molecular factors associated with the SW–SN relationship in rapeseed and identifies TFs as potential targets when improving crop yield.https://www.mdpi.com/1422-0067/22/9/4449<i>Brassica napus</i>seed weightseed numbergene co-expressionnetwork analysistranscriptomics |
| spellingShingle | Javier Canales José Verdejo Gabriela Carrasco-Puga Francisca M. Castillo Anita Arenas-M Daniel F. Calderini Transcriptome Analysis of Seed Weight Plasticity in <i>Brassica napus</i> International Journal of Molecular Sciences <i>Brassica napus</i> seed weight seed number gene co-expression network analysis transcriptomics |
| title | Transcriptome Analysis of Seed Weight Plasticity in <i>Brassica napus</i> |
| title_full | Transcriptome Analysis of Seed Weight Plasticity in <i>Brassica napus</i> |
| title_fullStr | Transcriptome Analysis of Seed Weight Plasticity in <i>Brassica napus</i> |
| title_full_unstemmed | Transcriptome Analysis of Seed Weight Plasticity in <i>Brassica napus</i> |
| title_short | Transcriptome Analysis of Seed Weight Plasticity in <i>Brassica napus</i> |
| title_sort | transcriptome analysis of seed weight plasticity in i brassica napus i |
| topic | <i>Brassica napus</i> seed weight seed number gene co-expression network analysis transcriptomics |
| url | https://www.mdpi.com/1422-0067/22/9/4449 |
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