Abstract
BackgroundThe objective of this study was to increase understanding about genetic mechanisms affecting calyx persistence in Korla fragrant pear (Pyrus brestschneideri Rehd). Flowers were collected at early bloom, full bloom, and late bloom. The RNA was extracted from the flowers and then combined according to calyx type. Transcriptome and digital gene expression (DGE) profiles of flowers, ovaries, and sepals with persistent calyx (SC_hua, SC_ep, and SC_zf, respectively) were compared with those of flowers, ovaries, and sepals with deciduous calyx (TL_hua, TL_ep, and TL_zf, respectively). Temporal changes in the expression of selected genes in floral organs with either persistent or deciduous calyx were compared using real-time quantitative PCR (qRT-PCR).ResultsComparison of the transcriptome sequences for SC_hua and TL_hua indicated 26 differentially expressed genes (DEGs) with known relationship to abscission and 10 DEGs with unknown function. We identified 98 MYB and 21 SPL genes from the assembled unigenes. From SC_zf vs TL_zf, we identified 21 DEGs with known relationship to abscission and 18 DEGs with unknown function. From SC_ep vs TL_ep, 12 DEGs with known relationship to abscission were identified along with 11 DEGs with unknown function. Ten DEGs were identified by both transcriptome sequencing and DGE sequencing.ConclusionsMore than 50 DEGs were observed that were related to calyx persistence in Korla fragrant pear. Some of the genes were related to cell wall degradation, plant hormone signal transduction, and stress response. Other DEGs were identified as zinc finger protein genes and lipid transfer protein genes. Further analysis showed that calyx persistence in Korla fragment pear was a metabolic process regulated by many genes related to cell wall degradation and plant hormones.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2470-3) contains supplementary material, which is available to authorized users.
Highlights
The objective of this study was to increase understanding about genetic mechanisms affecting calyx persistence in Korla fragrant pear (Pyrus brestschneideri Rehd)
Sequence annotation The unigenes were aligned with seven public databases [i.e., NCBI nonredundant protein sequences (NR) (NCBI non-redundant protein sequences), NT (NCBI nucleotide sequences), KEGG (Kyoto Encyclopedia of Genes and Genomes), SwissProt (A manually annotated and reviewed protein sequence database), PFAM (Protein family), GO (Gene Ontology) and KOG/COG (Clusters of Orthologous Groups of proteins)] (Table 2)
The results showed that 18605 unigenes (38.05 %) had significant matches in the NR database, 16700 unigenes (34.15 %) had significant matches in the NT database, and 17326 unigenes (35.43 %) had significant matches in the SwissProt database
Summary
The objective of this study was to increase understanding about genetic mechanisms affecting calyx persistence in Korla fragrant pear (Pyrus brestschneideri Rehd). Previous studies about Korla fragrant pear have examined the relationship between calyx persistence and cultivation practice [2], tree vigor [2], pollen source [3,4,5], growth regulators [6,7,8], and plant nutrition [9]. High-throughput sequencing has contributed greatly to the study of gene function in non-model plants. High-throughput sequencing makes it possible to understand the genome and the transcriptome of a species more comprehensively [13,14,15]. High-throughput sequencing of RNA (RNA-Seq) has been successfully applied in Malus domestica [16, 17], Myrica rubra [18, 19], Vaccinium section Cyanococcus [20], Litchi chinensis Sonn [21], Pyrus bretschneideri Rehd [22], Vitis vinifera
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
