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. 2022 Sep 21;11(19):2469.
doi: 10.3390/plants11192469.

Identification of Key Genes Related to Dormancy Control in Prunus Species by Meta-Analysis of RNAseq Data

Alejandro Calle  1 , Christopher Saski  1 , Ana Wünsch  2   3 , Jérôme Grimplet  2   3 , Ksenija Gasic  1
Affiliations

Identification of Key Genes Related to Dormancy Control in Prunus Species by Meta-Analysis of RNAseq Data

Alejandro Calle et al. Plants (Basel). .

Abstract

Bud dormancy is a genotype-dependent mechanism observed in Prunus 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 Prunus 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.

Keywords: breeding; candidate genes; chilling and heat requirements; co-expression network.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Summary of endodormancy-related genes. (A) Number of differentially expressed genes (DEGs) in each cultivar. (B) Venn diagram of common DEGs in all apricot, almond, peach, and sweet cherry cultivars. (C) Venn diagram of common DEGs in at least one cultivar of each species. (D) Enrichments in gene ontology terms for biological process, molecular function, and cellular component of common DEGs in at least one cultivar of each species. (E) Heatmap of the 139 commonly DEGs in at least one cultivar of each species during dormancy.
Figure 2
Figure 2
Summary of ecodormancy-related genes. (A) Number of differentially expressed genes (DEGs) in each cultivar. (B) Venn diagram of common DEGs in all apricot, almond, peach, and sweet cherry cultivars. (C) Venn diagram of common DEGs in at least one cultivar of each species. (D) Enrichments in gene ontology terms for biological process, molecular function, and cellular component of common DEGs in at least one cultivar of each species. (E) Heatmap of the 223 common DEGs in at least one cultivar of each species during dormancy.
Figure 3
Figure 3
Co-expression networks constructed in almond, apricot, peach, and sweet cherry. (A) Dendrograms of gene clustering based on RNAseq data. (B) Number of genes in each module. (C) Correlation (p−values) between modules and dormancy stages (red and blue colorations indicate a negative and positive correlation, respectively).
Figure 4
Figure 4
Integrated co-expression networks constructed using almond, apricot, peach, and sweet cherry differentially expressed genes. (A) Dendrograms of gene clustering based on RNAseq data. (B) Number of genes in each module. (C) Correlations (p−values) between modules and dormancy stages (red and blue colorations indicate a negative and positive correlation, respectively).
Figure 5
Figure 5
Average z-scores per species for each module from the integrated co-expression network.
Figure 6
Figure 6
Mapping of candidate genes within major bloom time, chilling, and heat requirements QTLs on Prunus species [8,10,11,18,19,20,21,22,54,55,56]. Only differentially expressed genes during dormancy were considered for mapping in these QTL intervals. Genes highlighted in red show annotations related to dormancy control. Gene names were obtained from peach genome v2.0.a1 [57]. The scale represents the chromosomal position in megabase pair (Mbp).
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References

    1. Olsen J.E. Light and temperature sensing and signaling in induction of bud dormancy in woody plants. Plant Mol. Biol. 2010;73:37–47. doi: 10.1007/s11103-010-9620-9. - DOI - PubMed
    1. Lang G.A., Early J.D., Martin G.C., Darnell R.L. Endo-, para-and ecodormancy: Physiological terminology and classification for dormancy research. Hortic. Sci. 1987;22:271–277.
    1. Rohde A., Bhalerao R.P. Plant dormancy in the perennial context. Trends Plant Sci. 2007;12:217–223. doi: 10.1016/j.tplants.2007.03.012. - DOI - PubMed
    1. Fadón E., Herrero M., Rodrigo J. Advances in Plant Dormancy. Springer; Berlin/Heidelberg, Germany: 2015. Flower bud dormancy in Prunus species; pp. 123–135. - DOI
    1. Cooke J.E.K., Eriksson M.E., Junttila O. The dynamic nature of bud dormancy in trees: Environmental control and molecular mechanisms. Plant Cell Environ. 2012;35:1707–1728. doi: 10.1111/j.1365-3040.2012.02552.x. - DOI - PubMed

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