Identification of Key Genes Related to Dormancy Control in <em>Prunus</em> Species by Meta-Analysis of RNAseq Data
Bud dormancy is a genotype-dependent mechanism observed in <i>Prunus</i> species in which bud growth is inhibited, and the accumulation of a specific amount of chilling (endodormancy) and heat (ecodormancy) is necessary to resume growth and reach flowering. We analyzed publicly available...
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MDPI AG
2022-09-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/11/19/2469 |
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| author | Alejandro Calle Christopher Saski Ana Wünsch Jérôme Grimplet Ksenija Gasic |
| author_facet | Alejandro Calle Christopher Saski Ana Wünsch Jérôme Grimplet Ksenija Gasic |
| author_sort | Alejandro Calle |
| collection | DOAJ |
| description | Bud dormancy is a genotype-dependent mechanism observed in <i>Prunus</i> species in which bud growth is inhibited, and the accumulation of a specific amount of chilling (endodormancy) and heat (ecodormancy) is necessary to resume growth and reach flowering. We analyzed publicly available transcriptome data from fifteen cultivars of four <i>Prunus</i> species (almond, apricot, peach, and sweet cherry) sampled at endo- and ecodormancy points to identify conserved genes and pathways associated with dormancy control in the genus. A total of 13,018 genes were differentially expressed during dormancy transitions, of which 139 and 223 were of interest because their expression profiles correlated with endo- and ecodormancy, respectively, in at least one cultivar of each species. The endodormancy-related genes comprised transcripts mainly overexpressed during chilling accumulation and were associated with abiotic stresses, cell wall modifications, and hormone regulation. The ecodormancy-related genes, upregulated after chilling fulfillment, were primarily involved in the genetic control of carbohydrate regulation, hormone biosynthesis, and pollen development. Additionally, the integrated co-expression network of differentially expressed genes in the four species showed clusters of co-expressed genes correlated to dormancy stages and genes of breeding interest overlapping with quantitative trait loci for bloom time and chilling and heat requirements. |
| first_indexed | 2024-03-09T21:18:14Z |
| format | Article |
| id | doaj.art-d00552b26ebb47c6a8f03a6282792d73 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T21:18:14Z |
| publishDate | 2022-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-d00552b26ebb47c6a8f03a6282792d732023-11-23T21:28:00ZengMDPI AGPlants2223-77472022-09-011119246910.3390/plants11192469Identification of Key Genes Related to Dormancy Control in <em>Prunus</em> Species by Meta-Analysis of RNAseq DataAlejandro Calle0Christopher Saski1Ana Wünsch2Jérôme Grimplet3Ksenija Gasic4Department of Plant and Environmental Sciences, Clemson University, 105 Collings St., Clemson, SC 29634, USADepartment of Plant and Environmental Sciences, Clemson University, 105 Collings St., Clemson, SC 29634, USADepartamento de Ciencia Vegetal, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Avda. Montanaña 930, 50059 Zaragoza, SpainDepartamento de Ciencia Vegetal, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Avda. Montanaña 930, 50059 Zaragoza, SpainDepartment of Plant and Environmental Sciences, Clemson University, 105 Collings St., Clemson, SC 29634, USABud dormancy is a genotype-dependent mechanism observed in <i>Prunus</i> species in which bud growth is inhibited, and the accumulation of a specific amount of chilling (endodormancy) and heat (ecodormancy) is necessary to resume growth and reach flowering. We analyzed publicly available transcriptome data from fifteen cultivars of four <i>Prunus</i> species (almond, apricot, peach, and sweet cherry) sampled at endo- and ecodormancy points to identify conserved genes and pathways associated with dormancy control in the genus. A total of 13,018 genes were differentially expressed during dormancy transitions, of which 139 and 223 were of interest because their expression profiles correlated with endo- and ecodormancy, respectively, in at least one cultivar of each species. The endodormancy-related genes comprised transcripts mainly overexpressed during chilling accumulation and were associated with abiotic stresses, cell wall modifications, and hormone regulation. The ecodormancy-related genes, upregulated after chilling fulfillment, were primarily involved in the genetic control of carbohydrate regulation, hormone biosynthesis, and pollen development. Additionally, the integrated co-expression network of differentially expressed genes in the four species showed clusters of co-expressed genes correlated to dormancy stages and genes of breeding interest overlapping with quantitative trait loci for bloom time and chilling and heat requirements.https://www.mdpi.com/2223-7747/11/19/2469breedingchilling and heat requirementscandidate genesco-expression network |
| spellingShingle | Alejandro Calle Christopher Saski Ana Wünsch Jérôme Grimplet Ksenija Gasic Identification of Key Genes Related to Dormancy Control in <em>Prunus</em> Species by Meta-Analysis of RNAseq Data Plants breeding chilling and heat requirements candidate genes co-expression network |
| title | Identification of Key Genes Related to Dormancy Control in <em>Prunus</em> Species by Meta-Analysis of RNAseq Data |
| title_full | Identification of Key Genes Related to Dormancy Control in <em>Prunus</em> Species by Meta-Analysis of RNAseq Data |
| title_fullStr | Identification of Key Genes Related to Dormancy Control in <em>Prunus</em> Species by Meta-Analysis of RNAseq Data |
| title_full_unstemmed | Identification of Key Genes Related to Dormancy Control in <em>Prunus</em> Species by Meta-Analysis of RNAseq Data |
| title_short | Identification of Key Genes Related to Dormancy Control in <em>Prunus</em> Species by Meta-Analysis of RNAseq Data |
| title_sort | identification of key genes related to dormancy control in em prunus em species by meta analysis of rnaseq data |
| topic | breeding chilling and heat requirements candidate genes co-expression network |
| url | https://www.mdpi.com/2223-7747/11/19/2469 |
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