Incompletely fused carpels ovary development revealed by miRNAs and target genes analysis in maize. (smallRNA-Seq and degradome-Seq)

To identify miRNAs involved in carpels fusion development in maize, four independent small RNA libraries and two degradome libraries from WT and IFC ovaries were constructed at the carpels fusion deficiency just being observed. A total of 162 known miRNAs distributed in 33 faimilies were identified, of which 20 known miRNAs were differentially expressed. In addition, 19 novel miRNAs were shown difference in expression levels between IFC and WT ovaries. By degradome analysis, totals of 113 and 78 target genes were predicted for known and novel miRNAs, respectively. 24 (60%) target genes of the differentially expressed known miRNAs coded for transcription factors, among which target genes encoding auxin response factors (ARF), TB1-CYC-PCFs (TCP), APETALA2 (AP2), growth regulating factor (GRF), MYB, NAC and NF-YA were classified as Class I. These target genes showed opposite expression patterns with their corresponding miRNAs according to quantitative real-time PCR results. The results suggested that the incomplete carpels fusion may partly due to the differential expression of these miRNAs and their target genes Overall design: sample 1: Examination of small RNA in IFC ovaries at the carpels fusion deficiency just emergence; sample 2: Examination of small RNA in WT ovaries on the same ear with IFC ovaries at the same time of the IFC ovaries collecting.