Identification of miRNAs involved in calyx persistence in Korla fragrant pear (Pyrus sinkiangensis Yu) by high-throughput sequencing

• Published in: Scientia horticulturae Vol. 240; pp. 344 - 353
• Main Authors: Zhou, Li, Li, Chenjing, Niu, Jianxin, Pei, Maosong, Cao, Fujun, Quan, Shaowen
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 20.10.2018
• Subjects: Deciduous calyx; High-throughput sequencing; Korla fragrant pear (Pyrus sinkiangensisYu); Persistent calyx; qRT-PCR; Korla fragrant pear (Pyrus sinkiangensisYu); Persistent calyx; High-throughput sequencing; Deciduous calyx; qRT-PCR
• ISSN: 0304-4238; 1879-1018
• DOI: 10.1016/j.scienta.2018.06.026

•MiRNAs related to calyx persistence in a native pear cultivar “Korla fragrant pear” (Pyrus sinkiangensis Yu) were identified by high-throughput sequencing.•The differentially expressed miRNAs were identified in “ovaries with persistent calyx” vs “ovaries with deciduous calyx” (S_z vs T_z) and “sepals with persistent calyx” vs “sepals with deciduous calyx” (S_e vs T_e).•There were 51 differentially expressed miRNAs in S_z vs T_z, 31 differentially expressed miRNAs in S_e vs T_e, and 11 of the miRNAs were common to the two groups.•Some differentially expressed miRNAs were involved in calyx persistence. The objective of this experiment was to learn more about the genetic mechanisms influencing calyx persistence in Korla fragrant pear (Pyrus sinkiangensis Yu). Flowers were collected from fragrant pear trees at three flowering stages. High-throughput small RNA sequencing profiles of sepals and ovaries with persistent calyx (S_e and S_z, respectively) were compared with those of sepals and ovaries with deciduous calyx (T_e and T_z, respectively). A total of 46 known miRNAs belonging to 33 families and 102 novel miRNAs were identified through high-throughput sequencing. There were 51 differentially expressed miRNAs in S_z vs T_z and 31 differentially expressed miRNAs in S_e vs T_e. Eleven miRNAs were differentially expressed in both comparisons. The expression patterns of eight miRNAs were validated by quantitative reverse transcription real-time PCR (qRT-PCR). A total of 263 target genes were predicted for the differentially expressed miRNAs. The target genes were correlated with various transcription factors (psi-miR156p/x－SPL, psi-miR172i－AP2/SAUR, psi-miR160a－ARF, psi-miR396a/b－GRF, psi-miR164a－NAC and psi-miR159c－MYB) and other related proteins. GO analysis showed that the differentially expressed miRNAs were involved in regulating various biological processes, plant hormone and auxin response, lignin metabolic process, DNA binding, intracellular membrane-bounded organelle and membrane-bounded organelle. KEGG pathway analysis showed that the differentially expressed miRNAs were mainly related to steroid biosynthesis, starch and sucrose metabolism, and galactose metabolism.