Blooming date is an important trait in fruit tree species. Although several quantitative trait loci confirming blooming date were identified in Prunus spp., the molecular mechanism underlying it remains unclear. Arising from this, the transcriptomes of normal blooming and late-blooming Siberian apricot (P. sibirica L.) flower buds were analyzed using RNA-seq technology. A total of 68,855 unigenes were de novo assembled, among which 1204 were differentially expressed between normal and late blooming. Gene ontology enrichment analysis revealed that biological processes were enriched with metabolic processes. The catalytic-related gene transcripts between the two types of blooming were significantly changed in the molecular function. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that 156 genes were successfully annotated and 75 pathways enriched. Genes for gibberellin biosynthesis were up-regulated in normal blooming, whereas abscisic acid degradation-related genes were also up-regulated in normal blooming. Moreover, circadian rhythms related genes including EARLY FLOWERING 4, LATE ELONGATED HYPOCOTYL and CIRCANDIAN CLOCK ASSOCIATED1 were all up-regulated in normal blooming, indicating that circadian rhythms have a very important role in controlling blooming date. Furthermore, zinc finger protein CONSTANS-LIKE 12 was blasted onto the quantitative trait loci region on linkage group 4 in peach. However, changes in the abundance of key flowering genes such as SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1, FLOWERING LOCU T, LEAFY and FLOWERING LOCUS C were not significantly different, indicating that further investigation should explore the function of these genes on blooming date. The outcomes of this study will provide a valuable platform for further research on the molecular mechanism of blooming date in Prunus.
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